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About the Authors

Jan Koolman (left) was born in Lübeck, Ger-

took his doctorate under the supervision of

many, and grew up with the sea wind blowing

Friedhelm Schneider, and his postdoctoral de-

off the Baltic. The high school he attended in

gree in 1980 was in the Department of Chem-

the Hanseatic city of Lübeck was one that

istry. He has been an Honorary Professor since

focused on providing a classical education,

1986. His research group is concerned with

which left its mark on him. From 1963 to

the structure and function of enzymes in-

1969, he studied biochemistry at the Univer-

volved in amino acid metabolism. He is mar-

sity of Tübingen. He then took his doctorate

ried to a biologist and has two children.

(in the discipline of chemistry) at the Univer-

Jürgen Wirth (center) studied in Berlin and at

sity of Marburg, under the supervision of bio-

the College of Design in Offenbach, Germany.

chemist Peter Karlson. In Marburg, he began

His studies focused on free graphics and illus-

to study the biochemistry of insects and other

tration, and his diploma topic was “The devel-

invertebrates. He took his postdoctoral de-

opment and function of scientific illustration.”

gree in 1977 in the field of human medicine,

From 1963 to 1977, Jürgen Wirth was involved

and was appointed Honorary Professor in

in designing the exhibition space in the

1984. His field of study today is biochemical

Senckenberg Museum of Natural History in

endocrinology. His other interests include ed-

Frankfurt am Main, while at the same time

ucational methods in biochemistry. He is cur-

working as a freelance associate with several

rently Dean of Studies in the Department of

publishing companies, providing illustrations

Medicine in Marburg; he is married to an art

for schoolbooks, non-fiction titles, and scien-

teacher.

tific publications. He has received several

Klaus-Heinrich Röhm

(right) comes from

awards for book illustration and design. In

Stuttgart, Germany. After graduating from

1978, he was appointed to a professorship at

the School of Protestant Theology in Urach

the College of Design in Schwäbisch Gmünd,

—another institution specializing in classical

Germany, and in 1986 he became Professor of

studies—and following a period working in

Design at the Academy of Design in Darm-

the field of physics, he took a diploma in bio-

stadt, Germany. His specialist fields include

chemistry at the University of Tübingen,

scientific graphics/information graphics and

where the two authors first met. Since 1970,

illustration methods. He is married and has

he has also worked in the Department of

three children.

Medicine at the University of Marburg. He

Preface

Biochemistry is a dynamic, rapidly growing

elements had to be found that make compli-

field, and the goal of this color atlas is to

cated phenomena appear tangible. The

illustrate this fact visually. The precise boun-

graphics were designed conservatively, the

daries between biochemistry and related

aim being to avoid illustrations that might

fields, such as cell biology, anatomy, physiol-

look too spectacular or exaggerated. Our

ogy, genetics, and pharmacology, are dif cult

goal was to achieve a visual and aesthetic

to define and, in many cases, arbitrary. This

way of representing scientific facts that would

overlap is not coincidental. The object being

be simple and at the same time effective for

studied is often the same—a nerve cell or a

teaching purposes. Use of graphics software

mitochondrion, for example—and only the

helped to maintain consistency in the use of

point of view differs.

shapes, colors, dimensions, and labels, in par-

For a considerable period of its history, bio-

ticular. Formulae and other repetitive ele-

chemistry was strongly influenced by chem-

ments and structures could be handled easily

istry and concentrated on investigating met-

and precisely with the assistance of the com-

abolic conversions and energy transfers. Ex-

puter.

plaining the composition, structure, and me-

Color-coding has been used throughout to aid

tabolism of biologically important molecules

the reader, and the key to this is given in two

has always been in the foreground. However,

special color plates on the front and rear in-

new aspects inherited from biochemistry’s

side covers. For example, in molecular models

other parent, the biological sciences, are

each of the more important atoms has a par-

now increasingly being added: the relation-

ticular color: gray for carbon, white for hydro-

ship between chemical structure and biolog-

gen, blue for nitrogen, red for oxygen, and so

ical function, the pathways of information

on. The different classes of biomolecules are

transfer, observance of the ways in which

also distinguished by color: proteins are al-

biomolecules are spatially and temporally dis-

ways shown in brown tones, carbohydrates in

tributed in cells and organisms, and an aware-

violet, lipids in yellow, DNA in blue, and RNA

ness of evolution as a biochemical process.

in green. In addition, specific symbols are

These new aspects of biochemistry are bound

used for the important coenzymes, such as

to become more and more important.

ATP and NAD⁺. The compartments in which

Owing to space limitations, we have concen-

biochemical processes take place are color-

trated here on the biochemistry of humans

coded as well. For example, the cytoplasm is

and mammals, although the biochemistry of

shown in yellow, while the extracellular space

other animals, plants, and microorganisms is

is shaded in blue. Arrows indicating a chem-

no less interesting. In selecting the material

ical reaction are always black and those rep-

for this book, we have put the emphasis on

resenting a transport process are gray.

subjects relevant to students of human med-

In terms of the visual clarity of its presenta-

icine. The main purpose of the atlas is to serve

tion, biochemistry has still to catch up with

as an overview and to provide visual informa-

anatomy and physiology. In this book, we

tion quickly and ef ciently. Referring to text-

sometimes use simplified ball-and-stick mod-

books can easily fill any gaps. For readers

els instead of the classical chemical formulae.

encountering biochemistry for the first time,

In addition, a number of compounds are rep-

some of the plates may look rather complex. It

resented by space-filling models. In these

must be emphasized, therefore, that the atlas

cases, we have tried to be as realistic as pos-

is not intended as a substitute for a compre-

sible. The models of small molecules are

hensive textbook of biochemistry.

based on conformations calculated by com-

As the subject matter is often dif cult to vis-

puter-based molecular modeling. In illustrat-

ualize, symbols, models, and other graphic

ing macromolecules, we used structural infor-

Preface

VII

mation obtained by X-ray crystallography

We are grateful to many readers for their

that is stored in the Protein Data Bank. In

comments and valuable criticisms during the

naming enzymes, we have followed the of -

preparation of this book. Of course, we would

cial nomenclature recommended by the

also welcome further comments and sugges-

IUBMB. For quick identification, EC numbers

tions from our readers.

(in italics) are included with enzyme names.

To help students assess the relevance of the

material (while preparing for an examination,

August 2004

for example), we have included symbols on

the text pages next to the section headings to

indicate how important each topic is. A filled

Jan Koolman,

circle stands for “basic knowledge,” a half-

Klaus-Heinrich Röhm

filled circle indicates “standard knowledge,”

Marburg

and an empty circle stands for

“in-depth

knowledge.” Of course, this classification

Jürgen Wirth

only reflects our subjective views.

Darmstadt

This second edition was carefully revised and

a significant number of new plates were

added to cover new developments.

VIII

Contents

Introduction

Structural proteins

Globular proteins

Basics

Protein folding

Molecular models: insulin

Chemistry

Isolation and analysis of proteins

Periodic table

Bonds

Nucleotides and Nucleic Acids

Molecular structure

Bases and nucleotides

Isomerism

RNA

Biomolecules I

DNA

Biomolecules II

Molecular models: DNA and RNA

Chemical reactions

Metabolism

Physical Chemistry

Enzymes

Energetics

Basics

Equilibriums

Enzyme catalysis

Enthalpy and entropy

Enzyme kinetics I

Reaction kinetics

Enzyme kinetics II

Catalysis

Inhibitors

Water as a solvent

Lactate dehydrogenase: structure

Hydrophobic interactions

Lactate dehydrogenase: mechanism . . .

100

Acids and bases

Enzymatic analysis

102

Redox processes

Coenzymes 1

104

Coenzymes 2

106

Biomolecules

Coenzymes 3

108

Carbohydrates

Activated metabolites

110

Overview

Metabolic Regulation

Chemistry of sugars

Intermediary metabolism

112

Monosaccharides and disaccharides . . .

Regulatory mechanisms

114

Polysaccharides: overview

Allosteric regulation

116

Plant polysaccharides

Transcription control

118

Glycosaminoglycans and glycoproteins .

Hormonal control

120

Lipids

Energy Metabolism

Overview

ATP

122

Fatty acids and fats

Energetic coupling

124

Phospholipids and glycolipids

Energy conservation at membranes

126

Isoprenoids

Photosynthesis: light reactions

128

Steroid structure

Photosynthesis: dark reactions

130

Steroids: overview

Molecular models: membrane proteins .

132

Amino Acids

Oxoacid dehydrogenases

134

Chemistry and properties

Tricarboxylic acid cycle: reactions

136

Proteinogenic amino acids

Tricarboxylic acid cycle: functions

138

Non-proteinogenic amino acids

Respiratory chain

140

Peptides and Proteins

ATP synthesis

142

Overview

Regulation

144

Peptide bonds

Respiration and fermentation

146

Secondary structures

Fermentations

148

Contents

Carbohydrate Metabolism

Endoplasmic Reticulum and Golgi Apparatus

Glycolysis

150

ER: structure and function

226

Pentose phosphate pathway

152

Protein sorting

228

Gluconeogenesis

154

Protein synthesis and maturation

230

Glycogen metabolism

156

Protein maturation

232

Regulation

158

Lysosomes

234

Diabetes mellitus

160

Lipid Metabolism

Molecular Genetics

Overview

162

Overview

236

Fatty acid degradation

164

Genome

238

Minor pathways of fatty acid

Replication

240

degradation

166

Transcription

242

Fatty acid synthesis

168

Transcriptional control

244

Biosynthesis of complex lipids

170

RNA maturation

246

Biosynthesis of cholesterol

172

Amino acid activation

248

Protein Metabolism

Translation I: initiation

250

Protein metabolism: overview

174

Translation II: elongation and

Proteolysis

176

termination

252

Transamination and deamination

178

Antibiotics

254

Amino acid degradation

180

Mutation and repair

256

Urea cycle

182

Genetic engineering

Amino acid biosynthesis

184

DNA cloning

258

Nucleotide Metabolism

DNA sequencing

260

Nucleotide degradation

186

PCR and protein expression

262

Purine and pyrimidine biosynthesis

188

Genetic engineering in medicine

264

Nucleotide biosynthesis

190

Tissues and organs

Porphyrin Metabolism

Heme biosynthesis

192

Digestion

Heme degradation

194

Overview

266

Digestive secretions

268

Organelles

Digestive processes

270

Resorption

272

Basics

Structure of cells

196

Blood

Cell fractionation

198

Composition and functions

274

Centrifugation

200

Plasma proteins

276

Cell components and cytoplasm

202

Lipoproteins

278

Hemoglobin

280

Cytoskeleton

Gas transport

282

Components

204

Erythrocyte metabolism

284

Structure and functions

206

Iron metabolism

286

Nucleus

208

Acid-base balance

288

Mitochondria

Blood clotting

290

Structure and functions

210

Fibrinolysis, blood groups

292

Transport systems

212

Immune system

Biological Membranes

Immune response

294

Structure and components

214

T-cell activation

296

Functions and composition

216

Complement system

298

Transport processes

218

Antibodies

300

Transport proteins

220

Antibody biosynthesis

302

Ion channels

222

Monoclonal antibodies, immunoassay .

304

Membrane receptors

224

Contents

Liver

Hydrophilic hormones

380

Functions

306

Metabolism of peptide hormones

382

Buffer function in organ metabolism

308

Mechanisms of action

384

Carbohydrate metabolism

310

Second messengers

386

Lipid metabolism

312

Signal cascades

388

Bile acids

314

Other signaling substances

Biotransformations

316

Eicosanoids

390

Cytochrome P450 systems

318

Cytokines

392

Ethanol metabolism

320

Kidney

Growth and development

Functions

322

Cell proliferation

Urine

324

Cell cycle

394

Functions in the acid-base balance

326

Apoptosis

396

Electrolyte and water recycling

328

Oncogenes

398

Renal hormones

330

Tumors

400

Muscle

Cytostatic drugs

402

Muscle contraction

332

Viruses

404

Control of muscle contraction

334

Metabolic charts

406

Muscle metabolism I

336

Calvin cycle

407

Muscle metabolism II

338

Carbohydrate metabolism

408

Connective tissue

Biosynthesis of fats and

Bone and teeth

340

membrane liquids

409

Calcium metabolism

342

Synthesis of ketone bodies and steroids

410

Collagens

344

Degradation of fats and phospholipids .

411

Extracellular matrix

346

Biosynthesis of the essential

Brain and Sensory Organs

amino acids

412

Signal transmission in the CNS

348

Biosynthesis of the non-essential

Resting potential and action potential. .

350

amino acids

413

Neurotransmitters

352

Amino acid degradation I

414

Receptors for neurotransmitters

354

Amino acid degradation II

415

Metabolism

356

Ammonia metabolism

416

Sight

358

Biosynthesis of purine nucleotides

417

Biosynthesis of the pyrimidine nucleotides

Nutrition

and C₁ metabolism

418

Nucleotide degradation

419

Nutrients

Organic substances

360

Annotated enzyme list

420

Minerals and trace elements

362

Abbreviations

431

Vitamins

Quantities and units

433

Lipid-soluble vitamins

364

Further reading

434

Water-soluble vitamins I

366

Water-soluble vitamins II

368

Source credits

435

Index

437

Hormones

Hormonal system

Basics

370

Key to color-coding:

Plasma levels and hormone hierarchy. .

372

see front and rear inside covers

Lipophilic hormones

374

Metabolism of steroid hormones

376

Mechanism of action

378

Chemistry

Introduction

This paperback atlas is intended for students

The next part presents the reactions

of medicine and the biological sciences. It

involved in the interconversion of these

provides an introduction to biochemistry,

compounds—the part of biochemistry that is

but with its modular structure it can also be

commonly referred to as metabolism

used as a reference book for more detailed

(pp. 88-195). The section starts with a dis-

information. The

216 color plates provide

cussion of the enzymes and coenzymes, and

knowledge in the field of biochemistry, ac-

discusses the mechanisms of metabolic regu-

companied by detailed information in the

lation and the so-called energy metabolism.

text on the facing page. The degree of dif -

After this, the central metabolic pathways

culty of the subject-matter is indicated by

are presented, once again arranged according

symbols in the text:

to the class of metabolite (pp. 150-195).

The second half of the book begins with a

stands for “basic biochemical knowledge”

discussion of the functional compartments

indicates

“standard biochemical knowl-

within the cell, the cellular organelles (pp.

edge”

196-235). This is followed on pp. 236-265

means “specialist biochemical knowledge.”

by the current field of molecular genetics

Some general rules used in the structure of

(molecular biology). A further extensive sec-

the illustrations are summed up in two ex-

tion is devoted to the biochemistry of

planatory plates inside the front and back

individual tissues and organs (pp. 266-359).

covers. Keywords, definitions, explanations

Here, it has only been possible to focus on the

of unfamiliar concepts and chemical formulas

most important organs and organ systems—

can be found using the index. The book starts

the digestive system, blood, liver, kidneys,

with a few basics in biochemistry (pp. 2-33).

muscles, connective and supportive tissues,

There is a brief explanation of the concepts

and the brain.

and principles of chemistry (pp. 2-15). These

Other topics include the biochemistry of

include the periodic table of the elements,

nutrition

(pp. 360-369), the structure and

chemical bonds, the general rules governing

function of important hormones

(pp.

molecular structure, and the structures of im-

370-393), and growth and development

portant classes of compounds. Several basic

(pp. 394-405).

concepts of physical chemistry are also essen-

The paperback atlas concludes with a series

tial for an understanding of biochemical

of schematic metabolic

“charts”

(pp.

processes. Pages 16-33 therefore discuss the

407-419). These plates, which are not accom-

various forms of energy and their intercon-

panied by explanatory text apart from a brief

version, reaction kinetics and catalysis, the

introduction on p. 406, show simplified ver-

properties of water, acids and bases, and re-

sions of the most important synthetic and

dox processes.

degradative pathways. The charts are mainly

These basic concepts are followed by a sec-

intended for reference, but they can also be

tion on the structure of the important biomo-

used to review previously learned material.

lecules (pp. 34-87). This part of the book is

The enzymes catalyzing the various reactions

arranged according to the different classes of

are only indicated by their EC numbers. Their

metabolites. It discusses carbohydrates, lipids,

names can be found in the systematically ar-

amino acids, peptides and proteins, nucleoti-

ranged and annotated enzyme list

(pp.

des, and nucleic acids.

420-430).

Basics

tailed discussions of the subject are available

Periodic table

in chemistry textbooks.

The possible states of electrons are called

A. Biologically important elements

orbitals. These are indicated by what is

There are 81 stable elements in nature. Fifteen

known as the principal quantum number

of these are present in all living things, and a

and by a letter—s, p, or d. The orbitals are

further 8-10 are only found in particular or-

filled one by one as the number of electrons

ganisms. The illustration shows the first half

increases. Each orbital can hold a maximum of

of the periodic table, containing all of the bio-

two electrons, which must have oppositely

logically important elements. In addition to

directed “spins.” Fig. A shows the distribution

physical and chemical data, it also provides

of the electrons among the orbitals for each of

information about the distribution of the ele-

the elements. For example, the six electrons of

ments in the living world and their abun-

carbon (B1) occupy the 1s orbital, the 2s orbi-

dance in the human body. The laws of atomic

tal, and two 2p orbitals. A filled 1s orbital has

structure underlying the periodic table are

the same electron configuration as the noble

discussed in chemistry textbooks.

gas helium (He). This region of the electron

More than 99% of the atoms in animals’

shell of carbon is therefore abbreviated as

bodies are accounted for by just four ele-

“He” in Fig. A. Below this, the numbers of

ments—hydrogen (H), oxygen (O), carbon (C)

electrons in each of the other filled orbitals

and nitrogen (N). Hydrogen and oxygen are

(2s and 2p in the case of carbon) are shown on

the constituents of water, which alone makes

the right margin. For example, the electron

up 60-70 % of cell mass (see p. 196). Together

shell of chlorine (B2) consists of that of neon

with carbon and nitrogen, hydrogen and oxy-

(Ne) and seven additional electrons in 3s and

gen are also the major constituents of the

3p orbitals. In iron (B3), a transition metal of

organic compounds on which most living

the first series, electrons occupy the 4s orbital

processes depend. Many biomolecules also

even though the 3d orbitals are still partly

contain sulfur

(S) or phosphorus

(P). The

empty. Many reactions of the transition met-

above macroelements are essential for all or-

als involve empty d orbitals—e. g., redox reac-

ganisms.

tions or the formation of complexes with

A second biologically important group of

bases.

elements, which together represent only

Particularly stable electron arrangements

about 0.5% of the body mass, are present al-

arise when the outermost shell is fully occu-

most exclusively in the form of inorganic ions.

pied with eight electrons (the “octet rule”).

This group includes the alkali metals sodium

This applies, for example, to the noble gases,

(Na) and potassium (K), and the alkaline earth

as well as to ions such as Cl^- (3s²3p⁶) and Na⁺

metals magnesium (Mg) and calcium (Ca). The

(2s²2p⁶). It is only in the cases of hydrogen

halogen chlorine (Cl) is also always ionized in

and helium that two electrons are already

the cell. All other elements important for life

suf cient to fill the outermost 1s orbital.

are present in such small quantities that they

are referred to as trace elements. These in-

clude transition metals such as iron (Fe), zinc

(Zn), copper (Cu), cobalt (Co) and manganese

(Mn). A few nonmetals, such as iodine (I) and

selenium (Se), can also be classed as essential

trace elements.

B. Electron configurations: examples

The chemical properties of atoms and the

types of bond they form with each other are

determined by their electron shells. The elec-

tron configurations of the elements are there-

fore also shown in Fig. A. Fig. B explains the

symbols and abbreviations used. More de-

Chemistry

A. Biologically important elements

Group

1.01

4.00

Alkaline

Boron

Nitrogen

earths

group

Halogens

6.94

9.01

10.81

12.01

14.01

16.00

19.00

20.18

9.5

1.4

25.5

22.99

24.31

26.98

28.09

30.97

32.07

35.45

39.95

0.03

0.01

0.22

0.05

0.03

39.10

40.08

69.72

72.61

74.92

78.96

79.90

83.80

0.06

0.31

126.9

Alkali

Carbon

Oxygen

Noble

metals

group

gases

Group

44.96

47.88

50.94

52.00

54.94

55.85

58.93

58.69

63.55

65.39

95.94

Macro element

Trace

element

Relative atomic

30.97

Electron

Essential for...

mass

configuration

Metal

all/most

Chemical symbol

organisms

Semi-metal

Percent (%) of

Atomic number

0.22

human body

for some

Non-metal

possibly

Noble gas

B. Electron configurations: examples

Helium

Neon

Argon

(He, Noble gas)

(Ne, Noble gas)

(Ar, Noble gas)

1s²

1s² 2s² 2p⁶

1s² 2s² 2p⁶ 3s² 3p⁶

1. Carbon (C)

[He] 2s² 2p

[Ar]

[Ne]

2. Chlorine (Cl)

3. Iron (Fe)

[He]

[Ne] 3s² 3p⁵

[Ar] 4s² 3d⁶

Basics

tatable, since rotation would distort the π-

Bonds

molecular orbital. This is why all of the atoms

lie in one plane (2c); in addition, cis-trans

A. Orbital hybridization and chemical

isomerism arises in such cases

(see p. 8).

bonding

Double bonds that are common in biomole-

Stable, covalent bonds between nonmetal

cules are C=C and C=O. C=N double bonds are

atoms are produced when orbitals (see p. 2)

found in aldimines (Schiff bases, see p. 178).

of the two atoms form molecular orbitals that

are occupied by one electron from each of the

B. Resonance

atoms. Thus, the four bonding electrons of the

carbon atom occupy 2s and 2p atomic orbitals

Many molecules that have several double

(1a). The 2s orbital is spherical in shape, while

bonds are much less reactive than might be

the three 2p orbitals are shaped like dumb-

expected. The reason for this is that the

bells arranged along the x, y, and z axes. It

double bonds in these structures cannot be

might therefore be assumed that carbon

localized unequivocally. Their π orbitals are

atoms should form at least two different types

not confined to the space between the dou-

of molecular orbital. However, this is not nor-

ble-bonded atoms, but form a shared,

mally the case. The reason is an effect known

extended S-molecular orbital. Structures

as orbital hybridization. Combination of the s

with this property are referred to as reso-

orbital and the three p orbitals of carbon gives

nance hybrids, because it is impossible to de-

rise to four equivalent, tetrahedrally arranged

scribe their actual bonding structure using

sp³ atomic orbitals (sp³ hybridization). When

standard formulas. One can either use what

these overlap with the 1s orbitals of H atoms,

are known as resonance structures—i. e.,

four equivalent σ-molecular orbitals (1b) are

idealized configurations in which π electrons

formed. For this reason, carbon is capable of

are assigned to specific atoms (cf. pp. 32 and

forming four bonds—i. e., it has a valency of

66, for example)—or one can use dashed lines

four. Single bonds between nonmetal atoms

as in Fig. B to suggest the extent of the delo-

arise in the same way as the four σ or single

calized orbitals.

(Details are discussed in

bonds in methane (CH₄). For example, the

chemistry textbooks.)

hydrogen phosphate ion (HPO_42-) and the

Resonance-stabilized systems include car-

ammonium ion (NH₄₊) are also tetrahedral

boxylate groups, as in formate; aliphatic hy-

in structure (1c).

drocarbons with conjugated double bonds,

A second common type of orbital hybrid-

such as 1,3-butadiene; and the systems known

ization involves the 2s orbital and only two of

as aromatic ring systems. The best-known

the three 2p orbitals (2a). This process is

aromatic compound is benzene, which has

therefore referred to as sp²

hybridization.

six delocalized π electrons in its ring. Ex-

The result is three equivalent sp² hybrid orbi-

tended resonance systems with 10 or more

tals lying in one plane at an angle of 120° to

π electrons absorb light within the visible

one another. The remaining 2p_x orbital is ori-

spectrum and are therefore colored. This

ented perpendicular to this plane. In contrast

group includes the aliphatic carotenoids (see

to their sp³

counterparts, sp²-hybridized

p. 132), for example, as well as the heme

atoms form two different types of bond

group, in which 18 π electrons occupy an ex-

when they combine into molecular orbitals

tended molecular orbital (see p. 106).

(2b). The three sp² orbitals enter into σ bonds,

as described above. In addition, the electrons

in the two 2p_x orbitals, known as S electrons,

combine to give an additional, elongated π

molecular orbital, which is located above

and below the plane of the σ bonds. Bonds

of this type are called double bonds. They

consist of a σ bond and a π bond, and arise

only when both of the atoms involved are

capable of sp² hybridization. In contrast to

single bonds, double bonds are not freely ro-

Basics

Molecular structure

B. Bond lengths and angles

The physical and chemical behavior of mole-

Atomic radii and distances are now usually

cules is largely determined by their constitu-

expressed in picometers

(pm;

1 pm =

tion (the type and number of the atoms they

10^-12 m). The old angstrom unit

(Å,

contain and their bonding). Structural formu-

Å = 100 pm) is now obsolete. The length of

las can therefore be used to predict not only

single bonds approximately corresponds to

the chemical reactivity of a molecule, but also

the sum of what are known as the covalent

its size and shape, and to some extent its

radii of the atoms involved (see inside front

conformation

(the spatial arrangement of

cover). Double bonds are around

10-20%

the atoms). Some data providing the basis

shorter than single bonds. In sp³-hybridized

for such predictions are summarized here

atoms, the angle between the individual

and on the facing page. In addition, L-dihy-

bonds is approx.

110°; in sp²-hybridized

droxyphenylalanine (L-dopa; see p. 352), is

atoms it is approx. 120°.

used as an example to show the way in which

molecules are illustrated in this book.

C. Bond polarity

A. Molecule illustrations

Depending on the position of the element in

the periodic table

(see p. 2), atoms have

In traditional two-dimensional structural

different electronegativity—i. e., a different

formulas (A1), atoms are represented as letter

tendency to take up extra electrons. The val-

symbols and electron pairs are shown as lines.

ues given in C2 are on a scale between 2 and 4.

Lines between two atomic symbols symbolize

The higher the value, the more electronega-

two bonding electrons (see p. 4), and all of the

tive the atom. When two atoms with very

other lines represent free electron pairs, such

different electronegativities are bound to

as those that occur in O and N atoms. Free

one another, the bonding electrons are drawn

electrons are usually not represented explic-

toward the more electronegative atom, and

itly (and this is the convention used in this

the bond is polarized. The atoms involved

book as well). Dashed or continuous circles or

then carry positive or negative partial

arcs are used to emphasize delocalized elec-

charges. In C1, the van der Waals surface is

trons.

colored according to the different charge con-

Ball-and-stick models (A2) are used to illus-

ditions (red = negative, blue = positive). Oxy-

trate the spatial structure of molecules. Atoms

gen is the most strongly electronegative of the

are represented as colored balls (for the color

biochemically important elements, with C=O

coding, see the inside front cover) and bonds

double bonds being especially highly polar.

(including multiple bonds) as gray cylinders.

Although the relative bond lengths and angles

correspond to actual conditions, the size at

D. Hydrogen bonds

which the atoms are represented is too small

to make the model more comprehensible.

The hydrogen bond, a special type of nonco-

Space-filling van der Waals models (A3) are

valent bond, is extremely important in bio-

useful for illustrating the actual shape and

chemistry. In this type of bond, hydrogen

size of molecules. These models represent

atoms of OH, NH, or SH groups (known as

atoms as truncated balls. Their effective ex-

hydrogen bond donors) interact with free

tent is determined by what is known as the

electrons of acceptor atoms (for example, O,

van der Waals radius. This is calculated from

N, or S). The bonding energies of hydrogen

the energetically most favorable distance be-

bonds

(10-40 kJ mol^-1) are much lower

tween atoms that are not chemically bonded

than those of covalent bonds

(approx.

to one another.

400 kJ mol^-1). However, as hydrogen bonds

can be very numerous in proteins and DNA,

they play a key role in the stabilization of

these molecules (see pp. 68, 84). The impor-

tance of hydrogen bonds for the properties of

water is discussed on p. 26.

Chemistry

A. Molecule illustrations

B. Bond lengths and angles

Chiral center

H H

140 pm

154 pm

110°

137 pm

C C C

120°

110°

108°

120°

110°

100 pm

110°

1. Formula illustration

C. Bond polarity

2. Ball- and-stick model

Positive

Neutral

Negative

1. Partial charges in L-dopa

0.9

2.1

2.5

3.0

3.5

4.0

Increasing electronegativity

3. Van der Waals model

2. Electronegativities

D. Hydrogen bonds

Dissociated Protonated

Acid

Base

Donor

Acceptor

acid

base

A H

H B

Initial state

Hydrogen bond

Complete reaction

1. Principle

290 pm

280 pm

C O

N H O

CH₃

H H

C C

R₁

HC R₂

H N

N H O C

N C

C N

290 pm

Water

Proteins

DNA

2. Examples

Basics

romolecules such as proteins or nucleic acids

Isomerism

usually have well-defined (“native”) confor-

Isomers are molecules with the same compo-

mations, which are stabilized by interactions

sition (i. e. the same molecular formula), but

in the molecule (see p. 74).

with different chemical and physical proper-

ties. If isomers differ in the way in which their

C. Optical isomers

atoms are bonded in the molecule, they are

described as structural isomers (cf. citric acid

Another type of isomerism arises when a mol-

and isocitric acid, D). Other forms of isomer-

ecule contains a chiral center or is chiral as a

ism are based on different arrangements of

whole. Chirality (from the Greek cheir, hand)

the substituents of bonds (A, B) or on the

leads to the appearance of structures that

presence of chiral centers in the molecule (C).

behave like image and mirror-image and

that cannot be superimposed (“mirror” iso-

mers). The most frequent cause of chiral be-

A. cis-trans isomers

havior is the presence of an asymmetric C

Double bonds are not freely rotatable (see

atom—i. e., an atom with four different sub-

p. 4). If double-bonded atoms have different

stituents. Then there are two forms (enan-

substituents, there are two possible orienta-

tiomers) with different configurations. Usu-

tions for these groups. In fumaric acid, an

ally, the two enantiomers of a molecule are

intermediate of the tricarboxylic acid cycle

designated as L and D forms. Clear classifica-

(see p. 136), the carboxy groups lie on different

tion of the configuration is made possible by

sides of the double bond (trans or E position).

the R/S system (see chemistry textbooks).

In its isomer maleic acid, which is not pro-

Enantiomers have very similar chemical

duced in metabolic processes, the carboxy

properties, but they rotate polarized light in

groups lie on the same side of the bond (cis

opposite directions

(optical activity, see

or Z position). Cis-trans isomers (geometric

pp. 36, 58). The same applies to the enantiom-

isomers) have different chemical and physical

ers of lactic acid. The dextrorotatory L-lactic

properties—e. g., their melting points

(Fp.)

acid occurs in animal muscle and blood, while

and pK_a values. They can only be intercon-

the D form produced by microorganisms is

verted by chemical reactions.

found in milk products, for example (see

In lipid metabolism, cis-trans isomerism is

p. 148). The Fischer projection is often used

particularly important. For example, double

to represent the formulas for chiral centers

bonds in natural fatty acids (see p. 48) usually

(cf. p. 58).

have a cis configuration. By contrast, unsatu-

rated intermediates of β oxidation have a

D. The aconitase reaction

trans configuration. This makes the break-

down of unsaturated fatty acids more compli-

Enzymes usually function stereospecifically. In

cated (see p. 166). Light-induced cis-trans iso-

chiral substrates, they only accept one of the

merization of retinal is of central importance

enantiomers, and the reaction products are

in the visual cycle (see p. 358).

usually also sterically uniform. Aconitate

hydratase (aconitase) catalyzes the conver-

sion of citric acid into the constitution isomer

B. Conformation

isocitric acid (see p. 136). Although citric acid

Molecular forms that arise as a result of rota-

is not chiral, aconitase only forms one of the

tion around freely rotatable bonds are known

four possible isomeric forms of isocitric acid

as conformers. Even small molecules can have

(2R,3S-isocitric acid). The intermediate of the

different conformations in solution. In the

reaction, the unsaturated tricarboxylic acid

two conformations of succinic acid illustrated

aconitate, only occurs in the cis form in the

opposite, the atoms are arranged in a similar

reaction. The trans form of aconitate is found

way to fumaric acid and maleic acid. Both

as a constituent of certain plants.

forms are possible, although conformation 1

is more favorable due to the greater distance

between the COOH groups and therefore oc-

curs more frequently. Biologically active mac-

Chemistry

A. cis-trans isomers

B. Conformers

Fumaric acid

Succinic acid

Fp. 287 °C

Conformation 1

pK_a 3.0, 4.5

Not rotatable

Freely rotatable

Maleic acid

Succinic

Fp. 130 °C

acid

pK_a 1.9, 6.5

Conformation 2

C. Optical isomers

Fischer projections

COO

CH₃

COO

OOC

L(S)

D(R)

CH₃

L-lactic acid

D-lactic acid

Fp.

53 °C

Fp.

pKa value

3.7

pKa value

Specific

+ 2.5˚

-2.5˚

Specific

rotation

In muscle, blood

In milk products

D. The aconitase reaction

COO

H₂O

COO

OOC

CH₂

COO

H₂C

COO

H₂C

COO

Citrate (prochiral)

cis-Aconitate (intermediate product)

(2R,3S)-Isocitrate

trans-Aconitate occurs in plants

Aconitase 4.2.1.3

Basics

acetals (see p. 36). The oxidation of hemiace-

Biomolecules I

tals produces carboxylic acid esters.

A. Important classes of compounds

Very important compounds are the carbox-

Most biomolecules are derivatives of simple

ylic acids and their derivatives, which can be

compounds of the non-metals oxygen (O),

formally obtained by exchanging the OH

hydrogen (H), nitrogen (N), sulfur (S), and

group for another group. In fact, derivatives

phosphorus (P). The biochemically important

of this type are formed by nucleophilic sub-

oxygen, nitrogen, and sulfur compounds can

stitutions of activated intermediate com-

be formally derived from their compounds

pounds and the release of water (see p. 14).

with hydrogen (i. e., H₂O, NH₃, and H₂S). In

Carboxylic acid esters (R-O-CO-R ) arise from

biological systems, phosphorus is found al-

carboxylic acids and alcohols. This group in-

most exclusively in derivatives of phosphoric

cludes the fats, for example (see p. 48). Sim-

acid, H₃PO₄.

ilarly, a carboxylic acid and a thiol yield a

thioester (R-S-CO-R ). Thioesters play an ex-

If one or more of the hydrogen atoms of a

tremely important role in carboxylic acid me-

non-metal hydride are replaced formally with

tabolism. The best-known compound of this

another group, R—e. g., alkyl residues—then

type is acetyl-coenzyme A (see p. 12).

derived compounds of the type R-XH_n-1,

R-XH_n-2-R, etc., are obtained. In this way,

Carboxylic acids and primary amines react

alcohols (R-OH) and ethers (R-O-R) are de-

to form carboxylic acid amides (R-NH-CO-R ).

rived from water (H₂O); primary amines (R-

The amino acid constituents of peptides and

NH₂), secondary amines (R-NH-R) and terti-

proteins are linked by carboxylic acid amide

ary amines (R-N-R R ) amines are obtained

bonds, which are therefore also known as

from ammonia (NH₃); and thiols (R-SH) and

peptide bonds (see p. 66).

thioethers (R-S-R ) arise from hydrogen sul-

fide (H₂S). Polar groups such as -OH and -NH₂

Phosphoric acid, H₃PO₄, is a tribasic (three-

are found as substituents in many organic

protic) acid—i. e., it contains three hydroxyl

compounds. As such groups are much more

groups able to donate H⁺ ions. At least one

reactive than the hydrocarbon structures to

of these three groups is fully dissociated

which they are attached, they are referred to

under normal physiological conditions, while

as functional groups.

the other two can react with alcohols. The

resulting products are phosphoric acid mono-

New functional groups can arise as a result

esters

(R-O-P(O)O-OH) and diesters

(R-O-

of oxidation of the compounds mentioned

P(O)O-O-R ). Phosphoric acid monoesters are

above. For example, the oxidation of a thiol

found in carbohydrate metabolism, for exam-

yields a disulfide (R-S-S-R). Double oxidation

ple

(see p. 36), whereas phosphoric acid

of a primary alcohol (R-CH₂-OH) gives rise

diester bonds occur in phospholipids

(see

initially to an aldehyde (R-C(O)-H), and then

p. 50) and nucleic acids (see p. 82 ).

to a carboxylic acid (R-C(O)-OH). In contrast,

the oxidation of a secondary alcohol yields a

Compounds of one acid with another are

ketone (R-C(O)-R). The carbonyl group (C=O)

referred to as acid anhydrides. A particularly

is characteristic of aldehydes and ketones.

large amount of energy is required for the

formation of an acid—anhydride bond. Phos-

The addition of an amine to the carbonyl

phoric anhydride bonds therefore play a cen-

group of an aldehyde yields—after removal of

tral role in the storage and release of chemical

water—an aldimine (not shown; see p. 178).

energy in the cell (see p. 122). Mixed anhy-

Aldimines are intermediates in amino acid

drides between carboxylic acids and phos-

metabolism (see p. 178) and serve to bond

phoric acid are also very important “energy-

aldehydes to amino groups in proteins (see

rich metabolites” in cellular metabolism.

p. 62, for example). The addition of an alcohol

to the carbonyl group of an aldehyde yields a

hemiacetal (R-O-C(H)OH-R). The cyclic forms

of sugars are well-known examples of hemi-

Chemistry

A. Important classes of compounds

Carbonyl group

Oxygen

Nitrogen

Water

Amino group

Secondary

Ketone

alcohol

Oxidation

Primary

Ammonia

amine

Primary

Oxidation

alcohol

R''

Aldehyde

Secondary

Tertiary

Ether

amine

Oxidation

O P O

Hemiacetal

Carboxylic acid amide

Carboxyl group

Phosphoric

acid ester

O R'

Carboxylic acid

O R'

Thioester

Carboxylic acid ester

Phosphorus

Sulfur

H H

Hydrogen sulfide

Mixed anhydride

Sulfhydryl

Thiol

group

Dihydrogen phosphate

Disulfide

Phosphoric acid anhydride

“energy-rich” bond

Basics

genic amine (see p. 62) formed by decarbox-

Biomolecules II

ylation of the amino acid cysteine.

Many biomolecules are made up of smaller

(2) The amino group of cysteamine is

units in a modular fashion, and they can be

bound to the carboxy group of another bio-

broken down into these units again. The con-

genic amine via an acid amide bond (-CO-

struction of these molecules usually takes

NH-). β-Alanine arises through decarboxyla-

place through condensation reactions involv-

tion of the amino acid aspartate, but it can

ing the removal of water. Conversely, their

also be formed by breakdown of pyrimidine

breakdown functions in a hydrolytic fash-

bases (see p. 186).

ion—i. e., as a result of water uptake. The

(3) Another acid amide bond (-CO-NH-)

page opposite illustrates this modular princi-

creates the compound for the next

ple using the example of an important coen-

constituent, pantoinate. This compound con-

zyme.

tains a chiral center and can therefore appear

in two enantiomeric forms (see p. 8). In natu-

ral coenzyme A, only one of the two forms is

A. Acetyl CoA

found, the (R)-pantoinate. Human metabo-

Coenzyme A (see also p. 106) is a nucleotide

lism is not capable of producing pantoinate

with a complex structure (see p. 80). It serves

itself, and it therefore has to take up a

to activate residues of carboxylic acids (acyl

compound of β-alanine and pantoinate—

residues). Bonding of the carboxy group of the

pantothenate

(“pantothenic acid”)—in the

carboxylic acid with the thiol group of the

form of a vitamin in food (see p. 366).

coenzyme creates a thioester bond (-S-CO-R;

(4) The hydroxy group at C-4 of pantoinate

see p. 10) in which the acyl residue has a high

is bound to a phosphate residue by an ester

chemical potential. It can therefore be trans-

bond.

ferred to other molecules in exergonic reac-

The section of the molecule discussed so

tions. This fact plays an important role in lipid

far represents a functional unit. In the cell, it is

metabolism in particular (see pp. 162ff.), as

produced from pantothenate. The molecule

well as in two reactions of the tricarboxylic

also occurs in a protein-bound form as 4 -

acid cycle (see p. 136).

phosphopantetheine in the enzyme fatty

As discussed on p.16, the group transfer

acid synthase (see p. 168). In coenzyme A,

potential can be expressed quantitatively as

however, it is bound to 3 ,5 -adenosine di-

the change in free enthalpy (∆G) during hy-

phosphate.

drolysis of the compound concerned. This is

(5) When two phosphate residues bond,

an arbitrary determination, but it provides

they do not form an ester, but an “energy-

important indications of the chemical energy

rich” phosphoric acid anhydride bond, as

stored in such a group. In the case of acetyl-

also occurs in other nucleoside phosphates.

CoA, the reaction to be considered is:

By contrast, (6) and (7) are ester bonds again.

(8) The base adenine is bound to C-1 of

Acetyl CoA + H₂O acetate + CoA

ribose by an N-glycosidic bond (see p. 36). In

addition to C-2 to C-4, C-1 of ribose also rep-

In standard conditions and at pH 7, the

resents a chiral center. The E-configuration is

change in the chemical potential G (∆G⁰, see

usually found in nucleotides.

p. 18) in this reaction amounts to -32 kJ

mol^-1 and it is therefore as high as the ∆G⁰

of ATP hydrolysis (see p. 18). In addition to the

“energy-rich” thioester bond, acetyl-CoA also

has seven other hydrolyzable bonds with dif-

ferent degrees of stability. These bonds, and

the fragments that arise when they are hydro-

lyzed, will be discussed here in sequence.

(1) The reactive thiol group of coenzyme A

is located in the part of the molecule that is

derived from cysteamine. Cysteamine is a bio-

Basics

hol (1b). The elimination of water from the

Chemical reactions

alcohol (2, dehydration) is also catalyzed by

Chemical reactions are processes in which

an acid and passes via the same intermediate

electrons or groups of atoms are taken up

as the addition reaction.

into molecules, exchanged between mole-

cules, or shifted within molecules. Illustrated

D. Nucleophilic substitutions

here are the most important types of reaction

in organic chemistry, using simple examples.

A reaction in which one functional group (see

Electron shifts are indicated by red arrows.

p. 10) is replaced by another is termed substi-

tution. Depending on the process involved, a

distinction is made between nucleophilic and

A. Redox reactions

electrophilic substitution reactions

(see

In redox reactions (see also p. 32), electrons

chemistry textbooks). Nucleophilic substitu-

are transferred from one molecule (the reduc-

tions start with the addition of one molecule

ing agent) to another (the oxidizing agent).

to another, followed by elimination of the so-

One or two protons are often also transferred

called leaving group.

in the process, but the decisive criterion for

The hydrolysis of an ester to alcohol and

the presence of a redox reaction is the elec-

acid (1) and the esterification of a carboxylic

tron transfer. The reducing agent is oxidized

acid with an alcohol (2) are shown here as an

during the reaction, and the oxidizing agent is

example of the S_N2 mechanism. Both reac-

reduced.

tions are made easier by the marked polarity

Fig. A shows the oxidation of an alcohol

of the C=O double bond. In the form of ester

into an aldehyde (1) and the reduction of

hydrolysis shown here, a proton is removed

the aldehyde to alcohol (2). In the process,

from a water molecule by the catalytic effect

one hydride ion is transferred (two electrons

of the base B. The resulting strongly nucleo-

and one proton; see p. 32), which moves to

philic OH^- ion attacks the positively charged

the oxidizing agent A in reaction 1. The super-

carbonyl C of the ester (1a), and an unstable

fluous proton is bound by the catalytic effect

sp³-hybridized transition state is produced.

of a base B. In the reduction of the aldehyde

From this, either water is eliminated (2b)

(2), A-H serves as the reducing agent and the

and the ester re-forms, or the alcohol ROH is

acid H-B is involved as the catalyst.

eliminated (1b) and the free acid results. In

esterification (2), the same steps take place in

reverse.

B. Acid-base reactions

In contrast to redox reactions, only proton

Further information

transfer takes place in acid-base reactions

(see also p. 30). When an acid dissociates (1),

In rearrangements

(isomerizations, not

water serves as a proton acceptor (i. e., as a

shown), groups are shifted within one and

base). Conversely, water has the function of

the same molecule. Examples of this in bio-

an acid in the protonation of a carboxylate

chemistry include the isomerization of sugar

anion (2).

phosphates (see p. 36) and of methylmalonyl-

CoA to succinyl CoA (see p. 166).

C. Additions/eliminations

A reaction in which atoms or molecules are

taken up by a multiple bond is described as

addition. The converse of addition—i. e., the

removal of groups with the formation of a

double bond, is termed elimination. When

water is added to an alkene (1a), a proton is

first transferred to the alkene. The unstable

carbenium cation that occurs as an intermedi-

ate initially takes up water (not shown), be-

fore the separation of a proton produces alco-

Chemistry

A. Redox reactions

B. Acid-base reactions

H HB

O H

R C

A B H B A

H H

R C

A B H B H

Alcohol

Aldehyde

Acid

R C

Anion

R C

H B

C. Additions/eliminations

H H

C C

R C

C C

BH B

Alkene

Carbonium ion

Alcohol

D. Nucleophilic substitutions

R C

O C

Alcohol

B R'

O C

R C

B R'

Ester

Transitional state

Carboxylic

H acid

Alcohol

H B

O H

R C O

R' O

Basics

the amount of matter reacting

(in mol).

Energetics

Although absolute values for free enthalpy G

To obtain a better understanding of the pro-

cannot be determined, ∆G can be calculated

cesses involved in energy storage and conver-

from the equilibrium constant of the reaction

sion in living cells, it may be useful first to

(see p. 18).

recall the physical basis for these processes.

B. Energetics and the course of processes

A. Forms of work

Everyday experience shows that water never

There is essentially no difference between

flows uphill spontaneously. Whether a partic-

work and energy. Both are measured in joule

ular process can occur spontaneously or not

(J = 1 N m). An outdated unit is the calorie

depends on whether the potential difference

(1 cal = 4.187 J). Energy is defined as the abil-

between the final and the initial state, ∆P =

ity of a system to perform work. There are

P₂ - P₁, is positive or negative. If P₂ is smaller

many different forms of energy—e. g., me-

than P₁, then ∆P will be negative, and the

chanical, chemical, and radiation energy.

process will take place and perform work.

A system is capable of performing work

Processes of this type are called exergonic

when matter is moving along a potential gra-

(B1). If there is no potential difference, then

dient. This abstract definition is best under-

the system is in equilibrium (B2). In the case of

stood by an example involving mechanical

endergonic processes,

∆P is positive

(B3).

work (A1). Due to the earth’s gravitational

Processes of this type do not proceed sponta-

pull, the mechanical potential energy of an

neously.

object is the greater the further the object is

Forcing endergonic processes to take place

away from the center of the earth. A potential

requires the use of the principle of energetic

difference

(∆P) therefore exists between a

coupling. This effect can be illustrated by a

higher location and a lower one. In a waterfall,

mechanical analogy (B4). When two masses

the water spontaneously follows this poten-

M₁ and M₂ are connected by a rope, M₁ will

tial gradient and, in doing so, is able to per-

move upward even though this part of the

form work—e. g., turning a mill.

process is endergonic. The sum of the two

Work and energy consist of two quantities:

potential differences

(∆P_eff = ∆P₁ + ∆P₂) is

an intensity factor, which is a measure of the

the determining factor in coupled processes.

potential difference—i. e., the “driving force”

When ∆P_eff is negative, the entire process can

of the process—(here it is the height differ-

proceed.

ence) and a capacity factor, which is a mea-

Energetic coupling makes it possible to

sure of the quantity of the substance being

convert different forms of work and energy

transported

(here it is the weight of the

into one another. For example, in a flashlight,

water). In the case of electrical work (A2),

an exergonic chemical reaction provides an

the intensity factor is the voltage—i. e., the

electrical voltage that can then be used for

electrical potential difference between the

the endergonic generation of light energy. In

source of the electrical current and the

the luminescent organs of various animals, it

“ground,” while the capacity factor is the

is a chemical reaction that produces the light.

amount of charge that is flowing.

In the musculature (see p. 336), chemical en-

Chemical work and chemical energy are

ergy is converted into mechanical work and

defined in an analogous way. The intensity

heat energy. A form of storage for chemical

factor here is the chemical potential of a mol-

energy that is used in all forms of life is aden-

ecule or combination of molecules. This is

osine triphosphate (ATP; see p. 122). Ender-

stated as free enthalpy G

(also known as

gonic processes are usually driven by cou-

“Gibbs free energy”). When molecules spon-

pling to the strongly exergonic breakdown

taneously react with one another, the result is

of ATP (see p. 122).

products at lower potential. The difference in

the chemical potentials of the educts and

products (the change in free enthalpy, 'G) is

a measure of the “driving force” of the reac-

tion. The capacity factor in chemical work is

Physical Chemistry

A. Forms of work

Elevated position

Voltage

Educts

source

Weight

Charge

Quantity

Lower position

Products

Ground

1. Mechanical work

2. Electrical work

3. Chemical work

J = Joule = N · m =1 kg · m² · s-2, 1 cal = 4.187 J

Form of work

Intensity factor

Unit

Capacity factor

Unit

Work =

Unit

Mechanical

Height

Weight

J · m ^-1

Height · Weight

V =

Electrical

Voltage

Charge

Voltage · Charge

J · C ^-1

Free-enthalpy

Chemical

J · mol ^-1

Quantity

mol

∆G · Quantity

change ∆G

B. Energetics and the course of processes

∆P < 0

∆P = 0

∆P > 0

∆Peff < 0

Process occurs

Process cannot

Coupled processes can

spontaneously

occur

occur spontaneously

Potential

∆P

∆P1

∆P

∆ P

eff

∆P2

1. Exergonic

2. Equilibrium

3. Endergonic

4. Energetically coupled

Basics

redox potential of a system is, the higher the

Equilibriums

chemical potential of the transferred elec-

trons. To describe reactions between two re-

A. Group transfer reactions

dox systems, ∆Ε —the difference between the

Every chemical reaction reaches after a time a

two systems’ redox potentials—is usually

state of equilibrium in which the forward and

used instead of ∆G. ∆G and ∆E have a simple

back reactions proceed at the same speed. The

relationship, but opposite signs (below). A

law of mass action describes the concentra-

redox reaction proceeds spontaneously

tions of the educts (A, B) and products (C, D) in

when ∆E > 0, i. e. ∆G < 0.

equilibrium. The equilibrium constant K is di-

The right side of the illustration shows the

rectly related to

∆G⁰, the change in free

way in which the redox potential E is depen-

enthalpy G involved in the reaction

(see

dent on the composition (the proportion of

p. 16) under standard conditions (∆G⁰ = - R

the reduced form as a %) in two biochemically

T ln K). For any given concentrations, the

important redox systems

(pyruvate/lactate

lower equation applies. At ∆G < 0, the reac-

and NAD⁺/NADH+H⁺; see pp. 98, 104). In the

tion proceeds spontaneously for as long as it

standard state (both systems reduced to 50%),

takes for equilibrium to be reached (i. e., until

electron transfer from lactate to NAD⁺ is not

∆G = 0). At ∆G > 0, a spontaneous reaction is

possible, because ∆E is negative (∆E = -0.13 V,

no longer possible

(endergonic case; see

red arrow). By contrast, transfer can proceed

p. 16). In biochemistry, ∆G is usually related

successfully if the pyruvate/lactate system is

to pH 7, and this is indicated by the “prime”

reduced to 98 % and NAD⁺/NADH is 98% oxi-

symbol (∆G⁰ or ∆G ).

dized (green arrow, ∆E = +0.08 V).

As examples, we can look at two group

transfer reactions (on the right). In ATP (see

C. Acid-base reactions

p. 122), the terminal phosphate residue is at a

high chemical potential. Its transfer to water

Pairs of conjugated acids and bases are always

(reaction a, below) is therefore strongly exer-

involved in proton exchange reactions (see

gonic. The equilibrium of the reaction

p. 30). The dissociation state of an acid-base

(∆G = 0; see p. 122) is only reached when

pair depends on the H⁺ concentration. Usu-

more than 99.9% of the originally available

ally, it is not this concentration itself that is

ATP has been hydrolyzed. ATP and similar

expressed, but its negative decadic logarithm,

compounds have a high group transfer

the pH value. The connection between the pH

potential for phosphate residues. Quantita-

value and the dissociation state is described

tively, this is expressed as the 'G of hydrolysis

by the Henderson-Hasselbalch equation (be-

(∆G⁰

= -32 kJ mol^-1; see p. 122).

low). As a measure of the proton transfer

In contrast, the endergonic transfer of am-

potential of an acid-base pair, its pK_a value

monia (NH₃) to glutamate (Glu, reaction b,

is used—the negative logarithm of the acid

∆G⁰ = +14 kJ mol^-1) reaches equilibrium so

constant K_a (where “a” stands for acid).

quickly that only minimal amounts of the

The stronger an acid is, the lower its pK_a

product glutamine (Gln) can be formed in

value. The acid of the pair with the lower pK_a

this way. The synthesis of glutamine from

value (the stronger acid—in this case acetic

these preliminary stages is only possible

acid, CH₃COOH) can protonate (green arrow)

through energetic coupling (see pp. 16, 124).

the base of the pair with the higher pK_a (in

this case NH₃), while ammonium acetate

(NH₄₊ and CH₃COO^-) only forms very little

B. Redox reactions

CH₃COOH and NH₃.

The course of electron transfer reactions (re-

dox reactions, see p. 14) also follows the law of

mass action. For a single redox system (see

p. 32), the Nernst equation applies (top). The

electron transfer potential of a redox system

(i. e., its tendency to give off or take up elec-

trons) is given by its redox potential E (in

standard conditions, E⁰ or E⁰ ). The lower the

Physical Chemistry

A. Group transfer reactions

Glu + NH₄

Gln + H₂O

Reaction

A + B

C + D

Only applies

Law of

[C] · [D]

in chemical

mass action

equilibrium

∆G°(b)

[A] · [B]

Equilibrium constant

Equi-

-10

librium

∆G°(a)

Relationship

∆G° = - R · T · ln K

-20

between

∆G⁰ and K

R = 8.314 J · mol -1 · K-1

-30

In any conditions

-40

[C] · [D]

ATP + H₂O

ADP + Pi

∆G = ∆G° + R · T · ln

-50

[A] · [B]

100

Measure of group transfer potential

% converted

B. Redox reactions

- 0.5

A_red

A_ox

For a redox

R · T

- 0.4

system

E = E° +

· ln[Aox]

n · F

[A_red]

NAD

/NADH+H

Measure of electron transfer potential

- 0.3

For any redox

∆E° (a)

R · T

reaction

∆E = ∆E° +

· ln[Box] ·[Ared]

n · F

[B_red] · [A_ox]

-0.2

- 0.1

∆Eº (b)

Definition

∆E = EAcceptor - E_Donor

and sizes

∆G = - n · F · ∆E

Pyruvate/lactate

0.0

n = No. of electrons transferred

F = Faraday constant

100

% reduced

C. Acid-base reactions

Standard

HA + H₂O

A + H₃O

reaction

CH₃

COOH/CH₃COO

pK_a(a)

Law of mass

] · [H₃O

]

action

K =

[HA] · [H₂O]

] · [H

]

pK_a(b)

Simplified

K_a=

[HA]

NH₄

/NH₃

Henderson-

]

Hasselbalch

pH = pKa + log

equation

[HA]

Measure of proton transfer potential

100

% dissociated

Basics

this is the normal state of affairs—∆S is pos-

Enthalpy and entropy

itive for this process. An increase in the order

The change in the free enthalpy of a chemical

in a system (∆S < 0) always requires an input

reaction (i. e., its ∆G) depends on a number of

of energy. Both of these statements are

factors—e. g., the concentrations of the reac-

consequences of an important natural law,

tants and the temperature (see p. 18). Two

the Second Law of Thermodynamics. The

further factors associated with molecular

connection between changes in enthalpy

changes occurring during the reaction are dis-

and entropy is described quantitatively by

cussed here.

the Gibbs-Helmholtz equation

(∆G = ∆H -

∆S). The following examples will help

explain these relationships.

A. Heat of reaction and calorimetry

In the knall-gas

(oxyhydrogen) reaction

All chemical reactions involve heat exchange.

(1), gaseous oxygen and gaseous hydrogen

Reactions that release heat are called

react to form liquid water. Like many redox

exothermic, and those that consume heat

reactions, this reaction is strongly exothermic

are called endothermic. Heat exchange is

(i. e.,

∆H < 0). However, during the reaction,

measured as the enthalpy change ∆H (the

the degree of order increases. The total num-

heat of reaction). This corresponds to the

ber of molecules is reduced by one-third, and

heat exchange at constant pressure. In exo-

a more highly ordered liquid is formed from

thermic reactions, the system loses heat, and

freely moving gas molecules. As a result of the

∆H is negative. When the reaction is endo-

increase in the degree of order (∆S < 0), the

thermic, the system gains heat, and ∆H be-

term -T

∆S becomes positive. However, this

comes positive.

is more than compensated for by the decrease

In many reactions, ∆H and ∆G are similar in

in enthalpy, and the reaction is still strongly

magnitude (see B1, for example). This fact is

exergonic (∆G < 0).

used to estimate the caloric content of foods.

The dissolution of salt in water (2) is endo-

In living organisms, nutrients are usually oxi-

thermic (∆H > 0)—i. e., the liquid cools. Never-

dized by oxygen to CO₂ and H₂O (see p. 112).

theless, the process still occurs spontane-

The maximum amount of chemical work sup-

ously, since the degree of order in the

plied by a particular foodstuff (i. e., the ∆G for

system decreases. The Na⁺ and Cl^- ions are

the oxidation of the utilizable constituents)

initially rigidly fixed in a crystal lattice. In

can be estimated by burning a weighed

solution, they move about independently

amount in a calorimeter in an oxygen atmo-

and in random directions through the fluid.

sphere. The heat of the reaction increases the

The decrease in order (∆S > 0) leads to a

water temperature in the calorimeter. The

negative

-T

∆S term, which compensates

reaction heat can then be calculated from

for the positive

∆H term and results in a

the temperature difference ∆T.

negative ∆G term overall. Processes of this

type are described as being entropy-driven.

The folding of proteins (see p. 74) and the

B. Enthalpy and entropy

formation of ordered lipid structures in water

The reaction enthalpy ∆H and the change in

(see p. 28) are also mainly entropy-driven.

free enthalpy ∆G are not always of the same

magnitude. There are even reactions that oc-

cur spontaneously (∆G < 0) even though they

are endothermic (∆H > 0). The reason for this

is that changes in the degree of order of the

system also strongly affect the progress of a

reaction. This change is measured as the en-

tropy change ('S).

Entropy is a physical value that describes

the degree of order of a system. The lower the

degree of order, the larger the entropy. Thus,

when a process leads to increase in disor-

der—and everyday experience shows that

Physical Chemistry

A. Heat of reaction and calorimetry

Thermometer

Ignition wire

to start the reaction

Temperature

insulation

Water

Combustion

heated

Pressurized

O₂

CO2

metal

container

An enthalpy of

H2O

1kJ warms 1 l of water

Sample

by 0.24 ºC

Stirrer

B. Enthalpy and entropy

∆H: change

∆S: change of

∆G =

∆H

- T ·

∆S

of enthalpy,

entropy, i.e.

heat exchange

degree of order

Gibbs-Helmholtz equation

1 mol H₂

1 mol NaCl

1/2 mol O₂

(crystalline)

Low degree

High degree

of order

System re-

System

leases heat,

absorbs

∆H <0

heat,

(exothermic)

∆H > 0

(endothermic)

1 mol H₂O

1 mol Na

(liquid)

1 mol Cl

Lower

Higher degree

degree

of order,

of order

∆S < 0

∆S > 0

∆H = - 287 kJ · mol -1

∆H = +3.8 kJ · mol -1

-T · ∆S = +49 kJ · mol -1

-T · ∆S = - 12.8 kJ · mol -1

∆G = - 238 kJ · mol -1

∆G = - 9.0 kJ · mol -1

-200

-100

+100

+200

-12

-8

-4

+12

Energy

1. “Knall-gas” reaction

2. Dissolution of NaCl in water

Basics

doubles with an increase in temperature of

Reaction kinetics

10 °C.

The change in free enthalpy ∆G in a reaction

indicates whether or not the reaction can take

B. Reaction rate

place spontaneously in given conditions and

how much work it can perform (see p. 18).

The velocity v of a chemical reaction is deter-

However, it does not tell us anything about

mined experimentally by observing the

the rate of the reaction—i. e., its kinetics.

change in the concentration of an educt or

product over time. In the example shown

(again a reaction of the A B type), 3 mmol

A. Activation energy

of the educt A is converted per second and

Most organic chemical reactions (with the

3 mmol of the product B is formed per second

exception of acid-base reactions) proceed

in one liter of the solution. This corresponds

only very slowly, regardless of the value

to a rate of

∆G. The reason for the slow reaction rate

is that the molecules that react—the

v = 3 mM s^-1 = 3

10^-3 mol L^-1 s^-1

educts—have to have a certain minimum en-

ergy before they can enter the reaction. This is

C. Reaction order

best understood with the help of an energy

diagram (1) of the simplest possible reaction

Reaction rates are influenced not only by the

A B. The educt A and the product B are each

activation energy and the temperature, but

at a specific chemical potential (G_e and G_p,

also by the concentrations of the reactants.

respectively). The change in the free enthalpy

When there is only one educt, A (1), v is

of the reaction, ∆G, corresponds to the differ-

proportional to the concentration [A] of this

ence between these two potentials. To be

substance, and a first-order reaction is in-

converted into B, A first has to overcome a

volved. When two educts, A and B, react

potential energy barrier, the peak of which,

with one another (2), it is a second order

Ga, lies well above Ge. The potential difference

reaction (shown on the right). In this case,

Ga -Ge is the activation energy Ea of the re-

the rate v is proportional to the product of

action (in kJ mol^-1).

the educt concentrations

(12 mM² at the

The fact that A can be converted into B at all

top, 24 mM² in the middle, and 36 mM² at

is because the potential G_e only represents

the bottom). The proportionality factors k and

the average potential of all the molecules.

k are the rate constants of the reaction. They

Individual molecules may occasionally reach

are not dependent on the reaction concentra-

much higher potentials—e. g., due to collisions

tions, but depend on the external conditions

with other molecules. When the increase in

for the reaction, such as temperature.

energy thus gained is greater than E_a, these

In B, only the kinetics of simple irreversible

molecules can overcome the barrier and be

reactions is shown. More complicated cases,

converted into B. The energy distribution for a

such as reaction with three or more reversible

group of molecules of this type, as calculated

steps, can usually be broken down into first-

from a simple model, is shown in (2) and (3).

order or second-order partial reactions and

∆n/n is the fraction of molecules that have

described using the corresponding equations

reached or exceeded energy E (in kJ per mol).

(for an example, see the Michaelis-Menten

At 27 °C, for example, approximately 10% of

reaction, p. 92).

the molecules have energies > 6 kJ mol^-1.

The typical activation energies of chemical

reactions are much higher. The course of

the energy function at energies of around

50 kJ mol^-1 is shown in (3). Statistically, at

27 °C only two out of 10⁹ molecules reach this

energy. At 37 °C, the figure is already four.

This is the basis for the long-familiar “Q₁₀

law”—a rule of thumb that states that the

speed of biological processes approximately

Physical Chemistry

A. Activation energy

Chemical

potential

Activation energy

Substrate A

³⁷˚^C

Ga - Ge

²⁷˚^C

∆G = G

Product B

p - Ge

0.0

0.5

1.0

∆n/n

∆n/n · 109

B. Reaction rate

[A]

= 32 mM

[A] = 29 mM

[A] = 23 mM

∆[A] = -3 mM

∆[A] = -9 mM

0 s

1 s

3 s

∆t = 1 s

∆t = 3 s

[B]

= 3 mM

[B] = 6 mM

[B] = 12 mM

∆[B] = 3 mM

∆[B] =

9 mM

mM =

mmol · l-1

= -∆ [A] / ∆t = ∆ [ B] / ∆t

( mol · l ^-1 · s ^-1 )

C. Reaction order

1 Liter

+ B

0 s

1 s

0 s

1 s

[A] (mM)

v (mM · s-1)

(mM)

v (mM · s-1)

[A]

= 12

[B]

= 1

[A]

= 6

[B]

= 4

[A]

= 3

[B]

= 12

v = k · [A]

k, k' : Rate constants

v = k' · [A] · [B]

First-order reaction

k = 1/5 s -1

Second-order reaction

k' = 1/12 l · mmol^-1· s -1

Basics

B. Catalysis of H₂O₂ - breakdown by iodide

Catalysis

As a simple example of a catalyzed reaction,

Catalysts are substances that accelerate

we can look at the disproportionation of hy-

chemical reactions without themselves being

drogen peroxide

(H₂O₂) into oxygen and

consumed in the process. Since catalysts

water. In the uncatalyzed reaction (at the

emerge from the catalyzed reaction without

top), an H₂O₂ molecule initially decays into

being changed, even small amounts are usu-

H₂O and atomic oxygen (O), which then reacts

ally suf cient to cause a powerful acceleration

with a second H₂O₂ molecule to form water

of the reaction. In the cell, enzymes (see p. 88)

and molecular oxygen (O₂). The activation

generally serve as catalysts. A few chemical

energy E_a required for this reaction is rela-

changes are catalyzed by special RNA mole-

tively high, at 75 kJ mol^-1. In the presence of

cules, known as ribozymes (see p. 246).

iodide (I^-) as a catalyst, the reaction takes a

different course (bottom). The intermediate

A. Catalysis: principle

arising in this case is hypoiodide (OI^-), which

also forms H₂O and O₂ with another H₂O₂

The reason for the slow rates of most reac-

molecule. In this step, the I^- ion is released

tions involving organic substances is the high

and can once again take part in the reaction.

activation energy (see p. 22) that the reacting

The lower activation energy of the reaction

molecules have to reach before they can react.

catalyzed by iodide

(E_a = 56 kJ mol^-1)

In aqueous solution, a large proportion of the

causes acceleration of the reaction by a factor

activation energy is required to remove the

of 2000, as the reaction rate depends expo-

hydration shells surrounding the educts. Dur-

nentially on E_a (v ~ e^{-Ea/R T}).

ing the course of a reaction, resonance-stabi-

Free metal ions such as iron (Fe) and plat-

lized structures (see p. 4) are often tempora-

inum (Pt) are also effective catalysts for the

rily suspended; this also requires energy. The

breakdown of H₂O₂. Catalase (see p. 284), an

highest point on the reaction coordinates cor-

enzyme that protects cells against the toxic

responds to an energetically unfavorable tran-

effects of hydrogen peroxide (see p. 284), is

sition state of this type (1).

much more catalytically effective still. In the

A catalyst creates a new pathway for the

enzyme-catalyzed disproportionation, H₂O₂

reaction (2). When all of the transition states

is bound to the enzyme’s heme group, where

arising have a lower activation energy than

it is quickly converted to atomic oxygen and

that of the uncatalyzed reaction, the reaction

water, supported by amino acid residues of

will proceed more rapidly along the alterna-

the enzyme protein. The oxygen atom is tem-

tive pathway, even when the number of in-

porarily bound to the central iron atom of the

termediates is greater. Since the starting

heme group, and then transferred from there

points and end points are the same in both

to the second H₂O₂ molecule. The activation

routes, the change in the enthalpy ∆G of the

energy of the enzyme-catalyzed reaction is

reaction is not influenced by the catalyst. Cat-

only 23 kJ mol^-1, which in comparison with

alysts—including enzymes—are in principle

the uncatalyzed reaction leads to acceleration

not capable of altering the equilibrium state

by a factor of 1.3

10⁹.

of the catalyzed reaction.

Catalase is one of the most ef cient en-

The often-heard statement that “a catalyst

zymes there are. A single molecule can con-

reduces the activation energy of a reaction” is

vert up to 10⁸ (a hundred million) H₂O₂ mol-

not strictly correct, since a completely different

ecules per second.

reaction takes place in the presence of a cata-

lyst than in uncatalyzed conditions. However,

its activation energy is lower than in the un-

catalyzed reaction.

Basics

of water clusters increases until the water

Water as a solvent

begins to crystallize. Under normal atmo-

Life as we know it evolved in water and is still

spheric pressure, this occurs at 0 °C. In ice,

absolutely dependent on it. The properties of

most of the water molecules are fixed in a

water are therefore of fundamental impor-

hexagonal lattice (3). Since the distance be-

tance to all living things.

tween the individual molecules in the frozen

state is on average greater than in the liquid

state, the density of ice is lower than that of

A. Water and methane

liquid water. This fact is of immense biological

The special properties of water (H₂O) become

importance—it means, for example, that in

apparent when it is compared with methane

winter, ice forms on the surface of open

(CH₄). The two molecules have a similar mass

stretches of water first, and the water rarely

and size. Nevertheless, the boiling point of

freezes to the bottom.

water is more than 250 °C above that of

methane. At temperatures on the earth’s sur-

C. Hydration

face, water is liquid, whereas methane is gas-

eous. The high boiling point of water results

In contrast to most other liquids, water is an

from its high vaporization enthalpy, which in

excellent solvent for ions. In the electrical

turn is due to the fact that the density of the

field of cations and anions, the dipolar water

electrons within the molecule is unevenly

molecules arrange themselves in a regular

distributed. Two corners of the tetrahedrally-

fashion corresponding to the charge of the

shaped water molecule are occupied by un-

ion. They form hydration shells and shield

shared electrons (green), and the other two

the central ion from oppositely charged ions.

by hydrogen atoms. As a result, the H-O-H

Metal ions are therefore often present as

bond has an angled shape. In addition, the

hexahydrates ([Me(H₂O)₆₂₊], on the right). In

O-H bonds are polarized due to the high elec-

the inner hydration sphere of this type of ion,

tronegativity of oxygen (see p. 6). One side of

the water molecules are practically immobi-

the molecule carries a partial charge (δ) of

lized and follow the central ion. Water has a

about -0.6 units, whereas the other is corre-

high dielectric constant of 78—i. e., the elec-

spondingly positively charged. The spatial

trostatic attraction force between ions is re-

separation of the positive and negative

duced to 1/78 by the solvent. Electrically

charges gives the molecule the properties of

charged groups in organic molecules (e. g.,

an electrical dipole. Water molecules are

carboxylate, phosphate, and ammonium

therefore attracted to one another like tiny

groups) are also well hydrated and contribute

magnets, and are also connected by hydrogen

to water solubility. Neutral molecules with

bonds (B) (see p. 6). When liquid water vapor-

several hydroxy groups, such as glycerol (on

izes, a large amount of energy has to be ex-

the left) or sugars, are also easily soluble,

pended to disrupt these interactions. By con-

because they can form H bonds with water

trast, methane molecules are not dipolar, and

molecules. The higher the proportion of polar

therefore interact with one another only

functional groups there is in a molecule, the

weakly. This is why liquid methane vaporizes

more water-soluble (hydrophilic) it is. By con-

at very low temperatures.

trast, molecules that consist exclusively or

mainly of hydrocarbons are poorly soluble or

insoluble in water. These compounds are

B. Structure of water and ice

called hydrophobic (see p. 28).

The dipolar nature of water molecules favors

the formation of hydrogen bonds (see p. 6).

Each molecule can act either as a donor or an

acceptor of H bonds, and many molecules in

liquid water are therefore connected by H

bonds (1). The bonds are in a state of constant

fluctuation. Tetrahedral networks of mole-

cules, known as water “clusters,” often arise.

As the temperature decreases, the proportion

Basics

is therefore positive (the disorder in the water

Hydrophobic interactions

increases), and the negative term

-T

∆S

Water is an excellent solvent for ions and for

makes the separation process exergonic

substances that contain polarized bonds (see

(∆G < 0), so that it proceeds spontaneously.

p. 20). Substances of this type are referred to

as polar or hydrophilic (“water-loving”). In

C. Arrangements of amphipathic substances

contrast, substances that consist mainly of

in water

hydrocarbon structures dissolve only poorly

in water. Such substances are said to be apolar

Molecules that contain both polar and apolar

or hydrophobic.

groups are called amphipathic or amphiphilic.

This group includes soaps (see p. 48), phos-

pholipids (see p. 50), and bile acids (see p. 56).

A. Solubility of methane

As a result of the “oil drop effect” amphi-

To understand the reasons for the poor water

pathic substances in water tend to arrange

solubility of hydrocarbons, it is useful first to

themselves in such a way as to minimize the

examine the energetics (see p. 16) of the pro-

area of surface contact between the apolar

cesses involved. In (1), the individual terms of

regions of the molecule and water. On water

the Gibbs-Helmholtz equation (see p. 20) for

surfaces, they usually form single-layer films

the simplest compound of this type, methane,

(top) in which the polar “head groups” face

are shown (see p. 4). As can be seen, the tran-

toward the water. Soap bubbles (right) consist

sition from gaseous methane to water is ac-

of double films, with a thin layer of water

tually exothermic (∆H⁰ < 0). Nevertheless, the

enclosed between them. In water, depending

change in the free enthalpy ∆G⁰ is positive

on their concentration, amphipathic com-

(the process is endergonic), because the en-

pounds form micelles—i. e., spherical aggre-

tropy term T

∆S⁰

has a strongly positive

gates with their head groups facing toward

value. The entropy change in the process

the outside, or extended bilayered double

(∆S⁰) is evidently negative—i. e., a solution of

membranes. Most biological membranes are

methane in water has a higher degree of order

assembled according to this principle (see

than either water or gaseous methane. One

p. 214). Closed hollow membrane sacs are

reason for this is that the methane molecules

known as vesicles. This type of structure

are less mobile when surrounded by water.

serves to transport substances within cells

More importantly, however, the water around

and in the blood (see p. 278).

the apolar molecules forms cage-like “clath-

The separation of oil and water (B) can be

rate” structures, which—as in ice—are stabi-

prevented by adding a strongly amphipathic

lized by H bonds. This strongly increases the

substance. During shaking, a more or less

degree of order in the water—and the more so

stable emulsion then forms, in which the sur-

the larger the area of surface contact between

face of the oil drops is occupied by amphi-

the water and the apolar phase.

pathic molecules that provide it with polar

properties externally. The emulsification of

fats in food by bile acids and phospholipids

B. The “oil drop effect”

is a vital precondition for the digestion of fats

The spontaneous separation of oil and water,

(see p. 314).

a familiar observation in everyday life, is due

to the energetically unfavorable formation of

clathrate structures. When a mixture of water

and oil is firmly shaken, lots of tiny oil drops

form to begin with, but these quickly coalesce

spontaneously to form larger drops—the two

phases separate. A larger drop has a smaller

surface area than several small drops with the

same volume. Separation therefore reduces

the area of surface contact between the water

and the oil, and consequently also the extent

of clathrate formation. The ∆S for this process

Basics

Acids and bases

B. pH values in the organism

pH values in the cell and in the extracellular

A. Acids and bases

fluid are kept constant within narrow limits.

In general, acids are defined as substances

In the blood, the pH value normally ranges

that can donate hydrogen ions

(protons),

only between 7.35 and 7.45 (see p. 288). This

while bases are compounds that accept pro-

corresponds to a maximum change in the H⁺

tons.

concentration of ca. 30%. The pH value of

Water enhances the acidic or basic proper-

cytoplasm is slightly lower than that of blood,

ties of dissolved substances, as water itself

7.0-7.3. In lysosomes

(see p. 234; pH

can act as either an acid or a base. For exam-

4.5-5.5), the H⁺ concentration is several hun-

ple, when hydrogen chloride (HCl) is in aque-

dred times higher than in the cytoplasm. In

ous solution, it donates protons to the solvent

the lumen of the gastrointestinal tract, which

(1). This results in the formation of chloride

forms part of the outside world relative to the

ions (Cl^-) and protonated water molecules

organism, and in the body’s excretion prod-

(hydronium ions, H₃O+, usually simply re-

ucts, the pH values are more variable. Ex-

ferred to as H⁺). The proton exchange be-

treme values are found in the stomach (ca.

tween HCl and water is virtually quantitative:

2) and in the small bowel (> 8). Since the

in water, HCl behaves as a very strong acid

kidney can excrete either acids or bases, de-

with a negative pK_a value (see p. 18).

pending on the state of the metabolism, the

Bases such as ammonia (NH₃) take over

pH of urine has a particularly wide range of

protons from water molecules. As a result of

variation (4.8-7.5).

this, hydroxyl ions

(OH^-) and positively

charged ammonium ions (NH₄₊, 3) form. Hy-

C. Buffers

dronium and hydroxyl ions, like other ions,

exist in water in hydrated rather than free

Short-term pH changes in the organism are

form (see p. 26).

cushioned by buffer systems. These are mix-

Acid-base reactions always involve pairs of

tures of a weak acid, HB, with its conjugate

acids and the associated conjugated bases

base, B^-, or of a weak base with its conjugate

(see p. 18). The stronger the acid or base, the

acid. This type of system can neutralize both

weaker the conjugate base or acid, respec-

hydronium ions and hydroxyl ions.

tively. For example, the very strongly acidic

In the first case (left), the base (B^-) binds a

hydrogen chloride belongs to the very weakly

large proportion of the added protons (H⁺)

basic chloride ion (1). The weakly acidic am-

and HB and water are formed. If hydroxyl

monium ion is conjugated with the moder-

ions (OH^-) are added, they react with HB to

ately strong base ammonia (3).

give B^- and water (right). In both cases, it is

The equilibrium constant K for the acid—

primarily the [HB]/[B^-] ratio that shifts, while

base reaction between H₂O molecules (2) is

the pH value only changes slightly. The titra-

very small. At 25 °C,

tion curve (top) shows that buffer systems are

most effective at the pH values that corre-

K = [H⁺]

[OH^-] / [H₂O] = 2

10^-16 mol L^-1

spond to the pK_a value of the acid. This is

where the curve is at its steepest, so that the

In pure water, the concentration

[H₂O] is

pH change, ∆pH, is at its smallest with a given

practically constant at 55 mol L^-1. Substitut-

increase ∆c in [H⁺] or [OH^-]. In other words,

ing this value into the equation, it gives:

the buffer capacity ∆c/ ∆pH is highest at the

pK_a value.

K_w = [H⁺]

[OH^-] = 1

10^-14 mol L^-1

The product [H⁺]

[OH^-]—the ion product of

water—is constant even when additional

acid-base pairs are dissolved in the water.

At 25 °C, pure water contains H⁺ and OH^- at

concentrations of 1

10^-7 mol L^-1 each; it is

neutral and has a pH value of exactly 7.

Physical Chemistry

A. Acids and bases

Proton

Hydrogen

Chloride ion

exchange

chloride

Very weak base

Very strong acid

pK_a= -7

Water

Hydronium ion

Very weak base

Very strong acid

Keq = 9 · 10⁶ mol · l^-1

Proton

Water

Hydroxyl ion

exchange

Very weak acid

Very strong base

pK_a= 15.7

Water

Hydronium ion

Very weak base

Very strong acid

Keq = 2 · 10^-16 mol · l^-1

Proton

exchange

Water

Hydroxyl ion

Very weak acid

Very strong base

pK_a= 9.2

Ammonia

Ammonium ion

Strong base

Weak acid

Keq = 6 · 10^-10 mol · l^-1

B. pH values in the body

C. Buffers

% B

∆ pH

pH 2

100

Base

pKa

Gastric juice

Acid

Lysosomes

∆ pH

Sweat

Acid

Base

Urine

Cytoplasm

Blood plasma

H₂O

Buffer solution:

Small intestine

mixture of a weak acid

with the conjugate base

Basics

other (see below). Only the combination 2 e^-/

Redox processes

1 H⁺, the hydride ion, is transferred as a unit.

A. Redox reactions

C. Biological redox systems

Redox reactions are chemical changes in

which electrons are transferred from one re-

In the cell, redox reactions are catalyzed by

action partner to another (1; see also p. 18).

enzymes, which work together with soluble

Like acid-base reactions (see p. 30), redox re-

or bound redox cofactors.

actions always involve pairs of compounds. A

Some of these factors contain metal ions as

pair of this type is referred to as a redox

redox-active components. In these cases, it is

system (2). The essential difference between

usually single electrons that are transferred,

the two components of a redox system is the

with the metal ion changing its valency. Un-

number of electrons they contain. The more

paired electrons often occur in this process,

electronrich component is called the reduced

but these are located in d orbitals (see p. 2)

form of the compound concerned, while the

and are therefore less dangerous than single

other one is referred to as the oxidized form.

electrons in non-metal atoms (“free radicals”;

The reduced form of one system (the reducing

see below).

agent) donates electrons to the oxidized form

We can only show here a few examples

of another one (the oxidizing agent). In the

from the many organic redox systems that

process, the reducing agent becomes oxidized

are found. In the complete reduction of the

and the oxidizing agent is reduced (3). Any

flavin coenzymes FMN and FAD (see p.104),

given reducing agent can reduce only certain

2 e^- and 2 H⁺ are transferred. This occurs in

other redox systems. On the basis of this type

two separate steps, with a semiquinone radi-

of observation, redox systems can be ar-

cal appearing as an intermediate. Since or-

ranged to form what are known as redox

ganic radicals of this type can cause damage

series (4).

to biomolecules, flavin coenzymes never oc-

The position of a system within one of

cur freely in solution, but remain firmly

these series is established by its redox

bound in the interior of proteins.

potential E (see p. 18). The redox potential

In the reduction or oxidation of quinone/

has a sign; it can be more negative or more

quinol systems, free radicals also appear as

positive than a reference potential arbitrarily

intermediate steps, but these are less reactive

set at zero (the normal potential of the system

than flavin radicals. Vitamin E, another qui-

[2 H⁺/H₂]). In addition, E depends on the con-

none-type redox system (see p. 104), even

centrations of the reactants and on the reac-

functions as a radical scavenger, by delocaliz-

tion conditions (see p. 18). In redox series (4),

ing unpaired electrons so effectively that they

the systems are arranged according to their

can no longer react with other molecules.

increasing redox potentials. Spontaneous

The pyridine nucleotides NAD⁺ and NADP⁺

electron transfers are only possible if the re-

always function in unbound form. The oxi-

dox potential of the donor is more negative

dized forms contain an aromatic nicotinamide

than that of the acceptor (see p. 18).

ring in which the positive charge is delocal-

ized. The right-hand example of the two res-

onance structures shown contains an elec-

B. Reduction equivalents

tron-poor, positively charged C atom at the

In redox reactions, protons (H⁺) are often

para position to nitrogen. If a hydride ion is

transferred along with electrons (e^-), or pro-

added at this point (see above), the reduced

tons may be released. The combinations of

forms NADH or NADPH arise. No radical inter-

electrons and protons that occur in redox

mediate steps occur. Because a proton is re-

processes are summed up in the term reduc-

leased at the same time, the reduced pyridine

tion equivalents. For example, the combina-

nucleotide coenzymes are correctly expressed

tion 1 e^-/1 H⁺ corresponds to a hydrogen

as NAD(P)H+H⁺.

atom, while 2 e^- and 2 H⁺ together produce

a hydrogen molecule. However, this does not

mean that atomic or molecular hydrogen is

actually transferred from one molecule to the

Physical Chemistry

A. Redox reactions

Possible

A _red

B _ox

Redox

Oxidizing

Not

system

agent

possible

Electron

Redox

exchange

system

Reducing

becomes

agent

reduced

Redox

A _ox

B _red

system

becomes

oxidized

1. Principle

2. Redox systems

3. Possible electron

4. Redox series

3. transfers

B. Reducing equivalents

Transferred

components

[H]

[H₂]

Equivalent

Electron

Hydrogen atom

Hydride ion

Hydrogen molecule

C. Biological redox systems

Metal

Me^m+

complexes

Oxidized

Reduced

H₃C

N N

H₃C

N N

H₃C

N N

Flavin

Oxidized flavin

Semiquinone radical

Reduced flavin

H₃CO C

H₃CO

C H

H₃CO

C H

H₃CO

Quinone/

hydro-

quinone

p-Benzoquinone

Semiquinone radical

Hydroquinone

Water H

H e

H O

O O

Reactive

O H

oxygen

Hydroperoxyl

Hydrogen

species

radical

peroxide

Oxygen

(ROS)

Hydroxyl radical

Water

Electron-poor

Hydride ion

CONH

C CONH

N H

NAD (P)

NAD(P)

(Resonance structures)

NAD(P)H + H

Biomolecules

The open-chained form of glucose shown

Overview

in (1) is found in neutral solution in less than

The carbohydrates are a group of naturally

0.1% of the molecules. The reason for this is an

occurring carbonyl compounds

(aldehydes

intramolecular reaction in which one of the

or ketones) that also contain several hydroxyl

OH groups of the sugar is added to the alde-

groups. The carbohydrates include single sug-

hyde group of the same molecule (2). This

ars

(monosaccharides) and their polymers,

gives rise to a cyclic hemiacetal (see p. 10). In

the oligosaccharides and polysaccharides.

aldohexoses, the hydroxy group at C-5 reacts

preferentially, and a six-membered pyran

ring is formed. Sugars that contain this ring

A. Carbohydrates: overview

are called pyranoses. By contrast, if the OH

Polymeric carbohydrates-above all starch, as

group at C-4 reacts, a five-part furan ring is

well as some disaccharides-are important

formed. In solution, pyranose forms and

(but not essential) components of food (see

furanose forms are present in equilibrium

p. 360). In the gut, they are broken down into

with each other and with the open-chained

monosaccharides and resorbed in this form

form, while in glucose polymers only the

(see p. 272). The form in which carbohydrates

pyranose form occurs.

are distributed by the blood of vertebrates is

The Haworth projection (2) is usually used

glucose (“blood sugar”). This is taken up by the

to depict sugars in the cyclic form, with the

cells and either broken down to obtain energy

ring being shown in perspective as viewed

(glycolysis) or converted into other metabo-

from above. Depending on the configuration,

lites (see pp. 150-159). Several organs (partic-

the substituents of the chiral C atoms are then

ularly the liver and muscles) store glycogen as

found above or below the ring. OH groups

a polymeric reserve carbohydrate (right; see

that lie on the right in the Fischer projection

p. 156). The glycogen molecules are covalently

(1) appear under the ring level in the Haworth

bound to a protein, glycogenin. Polysaccha-

projection, while those on the left appear

rides are used by many organisms as building

above it.

materials. For example, the cell walls of bac-

As a result of hemiacetal formation, an ad-

teria contain murein as a stabilizing compo-

ditional chiral center arises at C-1, which can

nent (see p. 40), while in plants cellulose and

be present in both possible configurations

other polysaccharides fulfill this role

(see

(anomers) (see p. 8). To emphasize this, the

p. 42). Oligomeric or polymeric carbohydrates

corresponding bonds are shown here using

are often covalently bound to lipids or pro-

wavy lines.

teins. The glycolipids and glycoproteins

The Haworth formula does not take ac-

formed in this way are found, for example,

count of the fact that the pyran ring is not

in cell membranes

(center). Glycoproteins

plain, but usually has a chair conformation. In

also occur in the blood in solute form (plasma

B3, two frequent conformations of D-glucopy-

proteins; see p. 276) and, as components of

ranose are shown as ball-and-stick models. In

proteoglycans, form important constituents of

the¹C₄ conformation (bottom), most of the

the intercellular substance (see p. 346).

OH groups appear vertical to the ring level, as

in the Haworth projection (axial or a posi-

tion). In the slightly more stable⁴C₁ confor-

B. Monosaccharides: structure

mation (top), the OH groups take the equato-

The most important natural monosaccharide,

rial or e position. At room temperature, each

D-glucose, is an aliphatic aldehyde with six C

form can change into the other, as well as into

atoms, five of which carry a hydroxyl group

other conformations.

(1). Since C atoms 2 to 5 represent chiral

centers

(see p. 8), there are

further

isomeric aldohexoses in addition to D-glucose,

although only a few of these are important in

nature (see p. 38). Most natural monosaccha-

rides have the same configuration at C-5 as

D-glyceraldehyde-they belong to the D series.

Carbohydrates

A. Carbohydrates: overview

Other monosaccharides

Transporter

Glycogenin

2OH

Glucose

OH H

Mono-

H OH

Gluconeo-

saccharide

Glycolysis

genesis

Pyruvate

Amino

acids

Glycoproteins

ATP

CO₂+H₂O

Glycogen

Glycolipids

Peptidoglycan

(Murein)

Proteoglycans

Periplasm

Bacterium

B. Monosaccharides: structure

HOCH2

Open-chained

form (< 0.1%)

HO₃

4C₁-conformation

Hemiacetal formation

2OH

HOCH2

CH₂OH

Open-chained

OH H

form of glucose

H OH

D-Gluco-

Chiral

1C₄-conformation

furanose (<1%)

pyranose (99%)

center

1. Fischer projection

2. Ring forms (Haworth projection)

3. Conformations

Biomolecules

5. Esterification. The hydroxyl groups of

Chemistry of sugars

monosaccharides can form esters with acids.

In metabolism, phosphoric acid esters such as

A. Reactions of the monosaccharides

glucose 6-phosphate and glucose 1-phosphate

The sugars (monosaccharides) occur in the

(6) are particularly important.

metabolism in many forms

(derivatives).

Only a few important conversion reactions

B. Polarimetry, mutarotation

are discussed here, using D-glucose as an ex-

ample.

Sugar solutions can be analyzed by polarim-

1. Mutarotation. In the cyclic form, as op-

etry, a method based on the interaction be-

posed to the open-chain form, aldoses have a

tween chiral centers and linearly polarized

chiral center at C-1 (see p. 34). The corre-

light—i. e., light that oscillates in only one

sponding isomeric forms are called anomers.

plane. It can be produced by passing normal

In the β-anomer (center left), the OH group at

light through a special filter (a polarizer). A

C-1 (the anomeric OH group) and the CH₂OH

second polarizing filter of the same type (the

group lie on the same side of the ring. In the α-

analyzer), placed behind the first, only lets the

anomer (right), they are on different sides.

polarized light pass through when the polar-

The reaction that interconverts anomers into

izer and the analyzer are in alignment. In this

each other is known as mutarotation (B).

case, the field of view appears bright when

2. Glycoside formation. When the anome-

one looks through the analyzer (1). Solutions

ric OH group of a sugar reacts with an alcohol,

of chiral substances rotate the plane of polar-

with elimination of water, it yields an

ized light by an angle α either to the left or to

O-glycoside (in the case shown, α -methylglu-

the right. When a solution of this type is

coside). The glycosidic bond is not a normal

placed between the polarizer and the ana-

ether bond, because the OH group at C-1 has a

lyzer, the field of view appears darker (2).

hemiacetal quality. Oligosaccharides and pol-

The angle of rotation, α, is determined by

ysaccharides also contain O-glycosidic bonds.

turning the analyzer until the field of view

Reaction of the anomeric OH group with an

becomes bright again (3). A solution’s optical

NH₂ or NH group yields an N-glycoside (not

rotation depends on the type of chiral com-

shown). N-glycosidic bonds occur in nucleo-

pound, its concentration, and the thickness of

tides

(see p. 80) and in glycoproteins (see

the layer of the solution. This method makes it

p. 44), for example.

possible to determine the sugar content of

3. Reduction and oxidation. Reduction of

wines, for example.

the anomeric center at C-1 of glucose (2) pro-

Certain procedures make it possible to ob-

duces the sugar alcohol sorbitol. Oxidation of

tain the α and β anomers of glucose in pure

the aldehyde group at C-1 gives the intramo-

form. A 1-molar solution of α-D-glucose has a

lecular ester (lactone) of gluconic acid (a gly-

rotation value [α]_D of +112°, while a corre-

conic acid). Phosphorylated gluconolactone is

sponding solution of β-D-glucose has a value

an intermediate of the pentose phosphate

of +19°. These values change spontaneously,

pathway (see p. 152). When glucose is oxi-

however, and after a certain time reach the

dized at C-6, glucuronic acid (a glycuronic

same end point of +52°. The reason for this is

acid) is formed. The strongly polar glucuronic

that, in solution, mutarotation leads to an

acid plays an important role in biotransforma-

equilibrium between the α and β forms in

tions in the liver (see pp. 194, 316).

which, independently of the starting condi-

4. Epimerization. In weakly alkaline solu-

tions, 62% of the molecules are present in the

tions, glucose is in equilibrium with the

β form and 38% in the α form.

ketohexose D-fructose and the aldohexose D-

mannose, via an enediol intermediate (not

shown). The only difference between glucose

and mannose is the configuration at C-2. Pairs

of sugars of this type are referred to as epi-

mers, and their interconversion is called epi-

merization.

Carbohydrates

A. Reactions of the monosaccharides

Glucuronate

Gluconolactone

Sorbitol

COO

HOCH₂

OOH

CH₂OH

Oxidation

Reduction

HOCH2

OOHβ

OH H

Mutarotation

β-D-Glucose

α-D-Glucose

Esterification

Epimerization

Glycoside formation

⁶CH₂

HOCH₂

OOH

CH₂OH

OH H

OHHO

O CH₃

Glucose 6-

-Fructose

α-D-Mannose

α-Methyl-

phosphate

glucoside

B. Polarimetry, mutarotation

Polarizer

Analyzer

α-D-Glucose: [ α ]

= +112°

)

α (˚

100

+ 52°

62% β

38% α

Time (min)

β-D-Glucose: [α]

= +19°

Biomolecules

Sugar alcohols

(6) such as sorbitol and

Monosaccharides and disaccharides

mannitol do not play an important role in

animal metabolism.

A. Important monosaccharides

Only the most important of the large number

B. Disaccharides

of naturally occurring monosaccharides are

mentioned here. They are classified according

When the anomeric hydroxyl group of one

to the number of C atoms (into pentoses,

monosaccharide is bound glycosidically with

hexoses, etc.) and according to the chemical

one of the OH groups of another, a disaccha-

nature of the carbonyl function into aldoses

ride is formed. As in all glycosides, the glyco-

and ketoses.

sidic bond does not allow mutarotation. Since

The best-known aldopentose (1), D-ribose,

this type of bond is formed stereospecifically

is a component of RNA and of nucleotide

by enzymes in natural disaccharides, they are

coenzymes and is widely distributed. In these

only found in one of the possible configura-

compounds, ribose always exists in the fura-

tions (α or β).

nose form (see p. 34). Like ribose, D-xylose and

Maltose (1) occurs as a breakdown product

L-arabinose are rarely found in free form.

of the starches contained in malt

(“malt

However, large amounts of both sugars are

sugar”; see p. 148) and as an intermediate in

found as constituents of polysaccharides in

intestinal digestion. In maltose, the anomeric

the walls of plant cells (see p. 42).

OH group of one glucose molecule has an α-

The most important of the aldohexoses (1)

glycosidic bond with C-4 in a second glucose

is D-glucose. A substantial proportion of the

residue.

biomass is accounted for by glucose polymers,

Lactose (“milk sugar,” 2) is the most impor-

above all cellulose and starch. Free D-glucose

tant carbohydrate in the milk of mammals.

is found in plant juices (“grape sugar”) and as

Cow’s milk contains 4.5% lactose, while hu-

“blood sugar” in the blood of higher animals.

man milk contains up to 7.5%. In lactose, the

As a constituent of lactose (milk sugar), D-

anomeric OH group of galactose forms a β-

galactose is part of the human diet. Together

glycosidic bond with C-4 of a glucose. The

with D-mannose, galactose is also found in

lactose molecule is consequently elongated,

glycolipids and glycoproteins (see p. 44).

and both of its pyran rings lie in the same

Phosphoric acid esters of the ketopentose

plane.

D-ribulose (2) are intermediates in the pen-

Sucrose (3) serves in plants as the form in

tose phosphate pathway (see p. 152) and in

which carbohydrates are transported, and as a

photosynthesis (see p. 128). The most widely

soluble carbohydrate reserve. Humans value

distributed of the ketohexoses is D-fructose. In

it because of its intensely sweet taste. Sources

free form, it is present in fruit juices and in

used for sucrose are plants that contain par-

honey. Bound fructose is found in sucrose (B)

ticularly high amounts of it, such as sugar

and plant polysaccharides (e. g., inulin).

cane and sugar beet (cane sugar, beet sugar).

In the deoxyaldoses (3), an OH group is

Enzymatic hydrolysis of sucrose-containing

replaced by a hydrogen atom. In addition to

flower nectar in the digestive tract of bees—

2-deoxy-D-ribose, a component of DNA (see

catalyzed by the enzyme invertase—produces

p. 84) that is reduced at C-2, L-fucose is shown

honey, a mixture of glucose and fructose. In

as another example of these. Fucose, a sugar

sucrose, the two anomeric OH groups of glu-

in the λ series (see p. 34) is reduced at C-6.

cose and fructose have a glycosidic bond; su-

The acetylated amino sugars N-acetyl-D-

crose is therefore one of the non-reducing

glucosamine and N-acetyl-D-Galactosamine

sugars.

(4) are often encountered as components of

glycoproteins.

N-acetylneuraminic acid (sialic acid, 5), is a

characteristic component of glycoproteins.

Other acidic monosaccharides such as D-glu-

curonic acid, D-galacturonic acid, and liduronic

acid, are typical constituents of the glycosa-

minoglycans found in connective tissue.

Carbohydrates

A. Important monosaccharides

Aldoses

Ketoses

D-Ribose (Rib)

D-Xylose (Xyl)

L-Arabinose (Ara)

D-Ribulose (Rub)

CH₂OH

HOCH2

C O

H H

OH H OH

H H

CH₂OH

HOH₂C

OH OH

H OH

OH OH

CH₂OH

Pentoses

-Glucose (Glc)

D-Mannose (Man)

D-Galactose (Gal)

D-Fructose (Fru)

CH₂OH

HOCH₂

C O

H OH

OHHO

OH H

HOCH₂

H HO

CH₂OH

Hexoses

CH₂OH

OH H

Deoxyaldoses

Acetylated amino sugars

2-Deoxy-

L-Fucose (Fuc)

N-Acetyl-D-glucos-

N -Acetyl-D-galac-

D-ribose (dRib)

amine (GlcNAc)

tosamine (GalNAc)

HOCH2

HOCH₂

H H OH

HO OH

OH H

C CH₃

Acidic monosaccharides

N-Acetylneuraminic acid

Sugar alcohols (alditoles)

(NeuAc)

D-Sorbitol

D-Mannitol

D-Glucuronic acid

L-Iduronic acid

CH₂OH

(GlcUA)

(IduUA)

CH₂OH

COO

C OH

C H

COO

C H

C CH₃

CH₂OH

B. Disaccharides

CH₂OH

H HO

CH₂OH

OH H

1. Maltose

2. Lactose

3. Sucrose

α-D-Glucopyranosyl-

β-D-Galactopyranosyl-

α-D-Glucopyranosyl-

4)-D-glucopyranose

2)-β-D-fructofuranoside

Biomolecules

Polysaccharides: overview

B. Important polysaccharides

Polysaccharides are ubiquitous in nature.

The table gives an overview of the composi-

They can be classified into three separate

tion and make-up both of the glycans men-

groups, based on their different functions.

tioned above and of several more.

Structural polysaccharides provide mechani-

In addition to murein, bacterial polysac-

cal stability to cells, organs, and organisms.

charides include dextrans—glucose polymers

Waterbinding polysaccharides are strongly

that are mostly α1

6-linked and α1

hydrated and prevent cells and tissues from

branched. In water, dextrans form viscous

drying out. Finally, reserve polysaccharides

slimes or gels that are used for chromato-

serve as carbohydrate stores that release

graphic separation of macromolecules after

monosaccharides as required. Due to their

chemical treatment (see p. 78). Dextrans are

polymeric nature, reserve carbohydrates are

also used as components of blood plasma

osmotically less active, and they can therefore

substitutes

(plasma expanders) and food-

be stored in large quantities within the cell.

stuffs.

Carbohydrates from algae (e. g., agarose

and carrageenan) can also be used to produce

A. Polysaccharides: structure

gels. Agarose has been used in microbiology

Polysaccharides that are formed from only

for more than 100 years to reinforce culture

one type of monosaccharide are called homo-

media (“agar-agar”). Algal polysaccharides are

glycans, while those formed from different

also added to cosmetics and ready-made

sugar constituents are called heteroglycans.

foods to modify the consistency of these prod-

Both forms can exist as either linear or

ucts.

branched chains.

The starches, the most important vegetable

A section of a glycogen molecule is shown

reserve carbohydrate and polysaccharides

here as an example of a branched homogly-

from plant cell walls, are discussed in greater

can. Amylopectin, the branched component of

detail on the following page. Inulin, a fructose

vegetable starch (see p. 42), has a very similar

polymer, is used as a starch substitute in dia-

structure. Both molecules mainly consist of

betics’ dietary products (see p. 160). In addi-

α1

4-linked glucose residues. In glycogen,

tion, it serves as a test substance for measur-

on average every 8th to 10th residue car-

ing renal clearance (see p. 322).

ries —via an α1

6 bond—another 1,4-linked

Chitin, a homopolymer from β1

4-linked

chain of glucose residues. This gives rise to

N-acetylglucosamine, is the most important

branched, tree-like structures, which in ani-

structural substance in insect and crustacean

mal glycogen are covalently bound to a

shells, and is thus the most common animal

protein, glycogenin (see p. 156).

polysaccharide. It also occurs in the cell wall

The linear heteroglycan murein, a struc-

of fungi.

tural polysaccharide that stabilizes the cell

Glycogen, the reserve carbohydrate of

walls of bacteria, has a more complex struc-

higher animals, is stored in the liver and mus-

ture. Only a short segment of this thread-like

culature in particular (A, see pp. 156, 336). The

molecule is shown here. In murein, two differ-

formation and breakdown of glycogen are

ent components, both β1

4-linked, alter-

subject to complex regulation by hormones

nate: N-acetylglucosamine

(GlcNAc) and

and other factors (see p. 120).

N-acetylmuraminic acid

(MurNAc), a lactic

acid ether of N-acetylglucosamine. Peptides

are bound to the carboxyl group of the lactyl

groups, and attach the individual strands of

murein to each other to form a three-dimen-

sional network (not shown). Synthesis of the

network-forming peptides in murein is inhib-

ited by penicillin (see p. 254).

Carbohydrates

A. Polysaccharides: structure

HOCH2

Glycogen -

branched

homopolymer

OH H

6CH2

HOCH2

Reducing end

OH H

HOCH2

NHCOCH₃

Murein - linear

H3C C

C O

H₃C

C O

heteropolymer

Peptide

B. Important polysaccharides

Poly-

Mono-

Linkage

Branch-

Occurrence

Function

saccharide

saccharide 1

saccharide 2

ing

Bacteria

Murein

D-GlcNAc

D-MurNAc¹⁾

Cell wall

Dextran

D-Glc

Slime

Plants

Agarose

D-Gal

L-aGal²⁾

Red algae (agar)

Carrageenan

D-Gal

Red algae

Cellulose

D-Glc

Cell wall

Xyloglucan

D-Glc

D-Xyl (D-Gal,

Cell wall

L-Fuc)

(

(Hemicellulose)

Arabinan

L-Ara

Cell wall (pectin)

Amylose

D-Glc

Amyloplasts

Amylopectin

D-Glc

Amyloplasts

Inulin

D-Fru

Storage cells

Animals

Chitin

D-GlcNAc

Insects, crabs

Glycogen

D-Glc

Liver, muscle

Hyaluronic

D-GlcUA

D-GlcNAc

Connective tissue

SK,WB

acid

SC= structural carbohydrate, RC= reserve carbohydrate,

WB = water-binding carbohydrate; ¹⁾N-acetylmuramic acid, ²⁾3,6-anhydrogalactose

Biomolecules

B. Starch

Plant polysaccharides

Starch, a reserve polysaccharide widely dis-

Two glucose polymers of plant origin are of

tributed in plants, is the most important car-

special importance among the polysac-

bohydrate in the human diet. In plants, starch

charides: β1

4-linked polymer cellulose

is present in the chloroplasts in leaves, as well

and starch, which is mostly α1

4-linked.

as in fruits, seeds, and tubers. The starch con-

tent is especially high in cereal grains (up to

A. Cellulose

75% of the dry weight), potato tubers (ap-

proximately 65%), and in other plant storage

Cellulose, a linear homoglycan of β1

organs.

linked glucose residues, is the most abundant

In these plant organs, starch is present in

organic substance in nature. Almost half of the

the form of microscopically small granules in

total biomass consists of cellulose. Some

special organelles known as amyloplasts.

40-50% of plant cell walls are formed by cel-

Starch granules are virtually insoluble in cold

lulose. The proportion of cellulose in cotton

water, but swell dramatically when the water

fibers, an important raw material, is 98%. Cel-

is heated. Some 15-25% of the starch goes

lulose molecules can contain more than 10⁴

into solution in colloidal form when the mix-

glucose residues (mass 1-2

10⁶ Da) and can

ture is subjected to prolonged boiling. This

reach lengths of 6-8 µm.

proportion is called amylose

(“soluble

Naturally occurring cellulose is extremely

starch”).

mechanically stable and is highly resistant to

Amylose consists of unbranched α1

chemical and enzymatic hydrolysis. These

linked chains of 200-300 glucose residues.

properties are due to the conformation of

Due the α configuration at C-1, these chains

the molecules and their supramolecular or-

form a helix with 6-8 residues per turn (1).

ganization. The unbranched β1

4 linkage re-

The blue coloring that soluble starch takes on

sults in linear chains that are stabilized by

when iodine is added (the “iodine-starch re-

hydrogen bonds within the chain and be-

action”) is caused by the presence of these

tween neighboring chains (1). Already during

helices—the iodine atoms form chains inside

biosynthesis, 50-100 cellulose molecules as-

the amylose helix, and in this largely non-

sociate to form an elementary fibril with a

aqueous environment take on a deep blue

diameter of 4 nm. About 20 such elementary

color. Highly branched polysaccharides turn

fibrils then form a microfibril (2), which is

brown or reddishbrown in the presence of

readily visible with the electron microscope.

iodine.

Cellulose microfibrils make up the basic

Unlike amylose, amylopectin, which is

framework of the primary wall of young plant

practically insoluble, is branched. On average,

cells (3), where they form a complex network

one in 20-25 glucose residues is linked to

with other polysaccharides. The linking poly-

another chain via an α1

6 bond. This leads

saccharides include hemicellulose, which is a

to an extended tree-like structure, which—

mixture of predominantly neutral heterogly-

like amylose—contains only one anomeric

cans (xylans, xyloglucans, arabinogalactans,

OH group (a “reducing end”). Amylopectin

etc.). Hemicellulose associates with the cellu-

molecules can contain hundreds of thousands

lose fibrils via noncovalent interactions. These

of glucose residues; their mass can be more

complexes are connected by neutral and

than 10⁸ Da.

acidic pectins, which typically contain galac-

turonic acid. Finally, a collagen-related

protein, extensin, is also involved in the for-

mation of primary walls.

In the higher animals, including humans,

cellulose is indigestible, but important as

roughage (see p. 273). Many herbivores (e. g.,

the ruminants) have symbiotic unicellular or-

ganisms in their digestive tracts that break

down cellulose and make it digestible by the

host.

Biomolecules

As an example of the carbohydrate compo-

Glycosaminoglycans and

nent of a glycoprotein, the structure of one of

glycoproteins

the oligosaccharide chains of immunoglobu-

lin G (IgG; see p. 300) is shown here. The

A. Hyaluronic acid

oligosaccharide has an N-glycosidic link to

the amide group of an asparagine residue in

As constituents of proteoglycans (see p. 346),

the F_c part of the protein. Its function is not

the glycosaminoglycans—a group of acidic

known.

heteropolysaccharides—are important struc-

Like all N-linked carbohydrates, the oligo-

tural elements of the extracellular matrix.

saccharide in IgG contains a T-shaped core

Glycosaminoglycans contain amino sugars

structure consisting of two N-acetylglucos-

as well as glucuronic acid and iduronic acid as

amines and three mannose residues (shown

characteristic components (see p. 38). In ad-

in violet). In addition, in this case the struc-

dition, most polysaccharides in this group are

ture contains two further N-acetylglucos-

esterified to varying extents by sulfuric acid,

amine residues, as well as a fucose residue

increasing their acidic quality. Glycosamino-

and a galactose residue. Glycoproteins show

glycans can be found in free form, or as com-

many different types of branching. In this

ponents of proteoglycans throughout the or-

case, we not only have β1

4 linkage, but

ganism.

also β1

2, α1

3, and α1

6 bonds.

Hyaluronic acid, an unesterified glycosami-

noglycan with a relatively simple structure,

consists of disaccharide units in which N-

C. Glycoproteins: forms

acetylglucosamine and glucuronic acid are

On the cell surface of certain glycoproteins,

alternately β1

4-linked and β1

3-linked.

O-glycosidic links are found between the car-

Due to the unusual β1

3 linkage, hyaluronic

bohydrate part and a serine or threonine res-

acid molecules-which may contain several

idue, instead of N-glycosidic links to aspara-

thousand monosaccharide residues—are

gine residues. This type of link is less common

coiled like a helix. Three disaccharide units

than the N-glycosidic one.

form each turn of the helix. The outwardfac-

There are two types of oligosaccharide

ing hydrophilic carboxylate groups of the glu-

structure with N-glycosidic links, which arise

curonic acid residues are able to bind Ca²⁺

through two different biosynthetic pathways.

ions. The strong hydration of these groups

During glycosylation in the ER, the protein is

enables hyaluronic acid and other glycosami-

initially linked to an oligosaccharide, which in

noglycans to bind water up to 10 000 times

addition to the core structure contains six

their own volume in gel form. This is the

further mannose residues and three terminal

function which hyaluronic acid has in the vit-

glucose residues

(see p. 230). The simpler

reous body of the eye, which contains approx-

from of oligosaccharide

(the mannose-rich

imately 1% hyaluronic acid and 98% water.

type) is produced when only the glucose res-

idues are cleaved from the primary product,

and no additional residues are added. In other

B. Oligosaccharide in immunoglobulin G

cases, the mannose residues that are located

(IgG)

outside the core structure are also removed

Many proteins on the surface of the plasma

and replaced by other sugars. This produces

membrane, and the majority of secreted pro-

oligosaccharides such as those shown on the

teins, contain oligosaccharide residues that

right (the complex type). At the external end

are post-translationally added to the endo-

of the structure, glycoproteins of the complex

plasmic reticulum and in the Golgi apparatus

type often contain N-acetylneuraminic acid

(see p. 230). By contrast, cytoplasmic proteins

residues, which give the oligosaccharide com-

are rarely glycosylated. Glycoproteins can

ponents negative charges.

contain more than 50 % carbohydrate; how-

ever, the proportion of protein is generally

much greater.

Carbohydrates

A. Hyaluronic acid

COO

HOCH

COO

HOCH₂

COO

HOCH₂

OH H

H HO

NHCOCH

NHCOCH₃

Disaccharide unit

III

[

3)-β-D-GlcNAc-(1

4)-β-D-GlcUA-(1

4]n

B. Oligosaccharide in immunoglobulin G (IgG)

D-Gal

D-GlcNAc

HOCH

HOCH2

Core structure

OH H

NHCOCH₃

HOH₂C

D-Man

CH₃

L-Fuc

N-glycosidic

HOCH₂

bond

HOCH₂

CH₂

D-GlcNAc

OH H

NHCOCH₃

HOH₂C

NHCOCH₃

CH₂

D-Man

D-GlcNAc

^H O

Asn-297

C. Glycoproteins: forms

NeuAc

O-linked

N-linked

NeuAc

Man

Gal

Man

GlcNAc GlcNAc

GlcNAc

Man

NeuAc

Man

Gal

GlcNAc

GalNAc

NeuAc

GlcNAc

Fuc

Ser

Protein

Asn

Mannose-rich type

Complex type

Biomolecules

are derivatives of the polyunsaturated fatty

Overview

acid arachidonic acid (see p. 390).

A. Classification

B. Biological roles

The lipids are a large and heterogeneous

group of substances of biological origin that

1. Fuel. Lipids are an important source of en-

are easily dissolved in organic solvents such

ergy in the diet. In quantitative terms, they

as methanol, acetone, chloroform, and ben-

represent the principal energy reserve in ani-

zene. By contrast, they are either insoluble or

mals. Neutral fats in particular are stored in

only poorly soluble in water. Their low water

specialized cells, known as adipocytes. Fatty

solubility is due to a lack of polarizing atoms

acids are released from these again as needed,

such as O, N, S, and P (see p. 6).

and these are then oxidized in the mitochon-

Lipids can be classified into substances that

dria to form water and carbon dioxide, with

are either hydrolyzable— i. e., able to undergo

oxygen being consumed. This process also

hydrolytic cleavage—or nonhydrolyzable. Only

gives rise to reduced coenzymes, which are

a few examples of the many lipids known can

used for ATP production in the respiratory

be mentioned here. The individual classes of

chain (see p. 140).

lipids are discussed in more detail in the fol-

2. Nutrients. Amphipathic lipids are used

lowing pages.

by cells to build membranes (see p. 214). Typ-

Hydrolyzable lipids (components shown in

ical membrane lipids include phospholipids,

brackets). The simple esters include the fats

glycolipids, and cholesterol. Fats are only

(triacylglycerol; one glycerol + three acyl res-

weakly amphiphilic and are therefore not

idues); the waxes (one fatty alcohol + one acyl

suitable as membrane components.

residue); and the sterol esters (one sterol + one

3. Insulation. Lipids are excellent insula-

acyl residue). The phospholipids are esters

tors. In the higher animals, neutral fats are

with more complex structures. Their charac-

found in the subcutaneous tissue and around

teristic component is a phosphate residue.

various organs, where they serve as mechan-

The phospholipids include the phosphatidic

ical and thermal insulators. As the principal

acids (one glycerol + two acyl residues + one

constituent of cell membranes, lipids also in-

phosphate) and the phosphatides (one glyc-

sulate cells from their environment mechan-

erol + two acyl residues + one phosphate +

ically and electrically. The impermeability of

one amino alcohol). In the sphingolipids, glyc-

lipid membranes to ions allows the formation

erol and one acyl residue are replaced by

of the membrane potential (see p. 126).

sphingosine. Particularly important in this

4. Special tasks. Some lipids have adopted

group are the sugar-containing glycolipids

special roles in the body. Steroids, eicosa-

(one sphingosine + one fatty acid + sugar).

noids, and some metabolites of phospholipids

The cerebrosides (one sphingosine + one fatty

have signaling functions. They serve as hor-

acid + one sugar) and gangliosides (one sphin-

mones, mediators, and second messengers

gosine + one fatty acid + several different

(see p. 370). Other lipids form anchors to at-

sugars, including neuraminic acid) are repre-

tach proteins to membranes (see p. 214). The

sentatives of this group.

lipids also produce cofactors for enzymatic re-

The components of the hydrolyzable lipids

actions—e. g., vitamin K (see p. 52) and ubiq-

are linked to one another by ester bonds. They

uinone (see p. 104). The carotenoid retinal, a

are easily broken down either enzymatically

light-sensitive lipid, is of central importance

or chemically.

in the process of vision (see p. 358).

Non-hydrolyzable lipids. The hydrocarbons

Several lipids are not formed indepen-

include the alkanes and carotenoids. The lipid

dently in the human body. These substances,

alcohols are also not hydrolyzable. They in-

as essential fatty acids and fat-soluble vita-

clude long-chained alkanols and cyclic sterols

mins, are indispensable components of nutri-

such as cholesterol, and steroids such as es-

tion (see pp. 364ff.)

tradiol and testosterone. The most important

acids among the lipids are fatty acids. The

eicosanoids also belong to this group; these

Lipids

A. Classification

Hydrolyzable lipids

C O CH₂

C O

CH₂

C O CH

C O CH₂

Esters

Fats

Non-hydrolyzable lipids

C O

Waxes

Sterol esters

Hydrocarbons

C O CH₂

Alkanes

C O CH

Carotenoids

H₂C O P

Phospholipids

Phosphatidates

Alcohols

Phosphatids

Sphingolipids

Long-chain alkanols

Sterols

Steroids

C O CH₂

COOH

C O CH

CH₂

H₂C O P

N CH₃

Acids

CH₃

Fatty acids

Eicosanoids

Glycolipids

CH₂

Cerebrosides

HO O

Gangliosides

B. Biological roles

Fat

Membrane

Cytoplasm

Glycerol

Fatty acid

ADP+P

ATP

Phospho-

lipid

Lipid

Mitochondrion

bilayer

CO2

H2O

1. Fuel

2. Building block

37 °C

Signaling

Anchor

0 °C

CoQ

Cell

Cofactor

Visual pigment

3. Thermal insulator

4. Special tasks

Biomolecules

(see p. 390). As the organism is capable of

Fatty acids and fats

elongating fatty acids by adding C₂ units, but

is not able to introduce double bonds into the

A. Carboxylic acids

end sections of fatty acids (after C-9), arachi-

The naturally occurring fatty acids are carbox-

donic acid has to be supplied with the diet.

ylic acids with unbranched hydrocarbon

Linoleic and linolenic acid can be converted

chains of

4-24

carbon atoms. They are

into arachidonic acid by elongation, and they

present in all organisms as components of

can therefore replace arachidonic acid in the

fats and membrane lipids. In these com-

diet.

pounds, they are esterified with alcohols

(glycerol, sphingosine, or cholesterol). How-

B. Structure of fats

ever, fatty acids are also found in small

amounts in unesterified form. In this case,

Fats are esters of the trivalent alcohol glycerol

they are known as free fatty acids (FFAs). As

with three fatty acids. When a single fatty acid

free fatty acids have strongly amphipathic

is esterified with glycerol, the product is re-

properties (see p. 28), they are usually present

ferred to as a monoacylglycerol (fatty acid res-

in protein-bound forms.

idue = acyl residue).

The table lists the full series of aliphatic

Formally, esterification with additional

carboxylic acids that are found in plants and

fatty acids leads to diacylglycerol and ulti-

animals. In higher plants and animals, un-

mately to triacylglycerol, the actual fat (for-

branched, longchain fatty acids with either

merly termed “triglyceride”). As triacylglycer-

16 or 18 carbon atoms are the most common—

ols are uncharged, they are also referred to as

e. g., palmitic and stearic acid. The number of

neutral fats. The carbon atoms of glycerol are

carbon atoms in the longer, natural fatty acids

not usually equivalent in fats. They are distin-

is always even. This is because they are bio-

guished by their

“sn” number, where sn

synthesized from C₂

building blocks

(see

stands for “stereospecific numbering.”

p. 168).

The three acyl residues of a fat molecule

Some fatty acids contain one or more

may differ in terms of their chain length and

isolated double bonds, and are therefore “un-

the number of double bonds they contain.

saturated.” Common unsaturated fatty acids

This results in a large number of possible

include oleic acid and linoleic acid. Of the two

combinations of individual fat molecules.

possible cis-trans isomers (see p. 8), usually

When extracted from biological materials,

only the cis forms are found in natural lipids.

fats always represent mixtures of very similar

Branched fatty acids only occur in bacteria. A

compounds, which differ in their fatty acid

shorthand notation with several numbers is

residues. A chiral center can arise at the mid-

used for precise characterization of the struc-

dle C atom (sn -C-2) of a triacylglycerol if the

ture of fatty acids—e g., 18:2;9,12 for linoleic

two external fatty acids are different. The

acid. The first figure stands for the number of

monoacylglycerols and diacylglycerols shown

C atoms, while the second gives the number

here are also chiral compounds. Nutritional

of double bonds. The positions of the double

fats contain palmitic, stearic, oleic acid, and

bonds follow after the semicolon. As usual,

linoleic acid particularly often. Unsaturated

numbering starts at the carbon with the high-

fatty acids are usually found at the central

est oxidation state (i. e., the carboxyl group

C atom of glycerol.

corresponds to C-1). Greek letters are also

The length of the fatty acid residues and

commonly used (α = C-2; β = C-3; ω = the

the number of their double bonds affect the

last carbon, ω-3 = the third last carbon).

melting point of the fats. The shorter the fatty

Essential fatty acids are fatty acids that

acid residues and the more double bonds they

have to be supplied in the diet. Without ex-

contain, the lower their melting points.

ception, these are all polyunsaturated fatty

acids: the C₂₀

fatty acid arachidonic acid

(20:4;5,8,11,14) and the two C₁₈ acids linoleic

acid

(18:2;9,12)

and linolenic acid

(18:3;9,12,15). The animal organism requires

arachidonic acid to synthesize eicosanoids

Lipids

A. Carboxylic acids

Name

Number of carbons

Number of double bonds

Position of double bonds

Formic acid

1 :

Not contained

Acetic acid

2 :0

in lipids

Propionic acid

3 :0

Butyric acid

4 :0

Valerianic acid

5 :0

HOOC

CH₂

CH₃

Caproic acid

6 :0

Caprylic acid

8 :0

Caproic acid

Capric acid

10 :0

Lauric acid

12 :0

Myristic acid

14 :0

Palmitic acid

16 :0

Stearic acid

18 :0

Oleic acid

18 :1;

Linoleic acid

18 :2;

9,12

Linolenic acid

18 :3;

9,12,15

Arachidic acid

20 :0

Arachidonic acid

20 :4;

5,8,11,14

Behenic acid

22 :0

Erucic acid

22 :1;

Lignoceric acid

24 :0

Nervonic acid

24 :1;

Essential in human nutrition

B. Structure of fats

Ester bonding

Chiral center

sn number

C-1

HO CH₂

CH₂

O CH₂

C-2

C H

R''

C H

CH₂

R'''

CH₂

C-3

Glycerol

Monoacylglycerol

Diacylglycerol

Triacylglycerol = Fat

Fatty acids

Glycerol

Acyl residue

Van der Waals

model

Acyl residue

of tristearylglycerol

Rotatable

around C-C bond

Biomolecules

Some phospholipids carry additional

Phospholipids and glycolipids

charges, in addition to the negative charge

at the phosphate residue. In phosphatidylcho-

A. Structure of phospholipids and

line and phosphatidylethanolamine, the

glycolipids

N-atom of the amino alcohol is positively

Fats (triacylglycerol, 1) are esters of glycerol

charged. As a whole, these two phosphatides

with three fatty acids (see p. 48). Within the

therefore appear to be neutral. In contrast,

cell, they mainly occur as fat droplets. In the

phosphatidylserine—with one additional pos-

blood, they are transported in the hydropho-

itive charge and one additional negative

bic interior of lipoproteins (see p. 278).

charge in the serine residue—and phosphati-

Phospholipids

(2) are the main consti-

dylinositol (with no additional charge) have a

tuents of biological membranes

(see

negative net charge, due to the phosphate

pp. 214-217). Their common feature is a phos-

residue.

phate residue that is esterified with the hy-

Sphingolipids (3), which are found in large

droxyl group at C-3 of glycerol. Due to this

quantities in the membranes of nerve cells in

residue, phospholipids have at least one neg-

the brain and in neural tissues, have a slightly

ative charge at a neutral pH.

different structure from the other membrane

Phosphatidates (anions of the phosphatidic

lipids discussed so far. In sphingolipids, sphin-

acids), the simplest phospholipids, are phos-

gosine, an amino alcohol with an unsaturated

phate esters of diacylglycerol. They are impor-

alkyl side chain, replaces glycerol and one of

tant intermediates in the biosynthesis of fats

the acyl residues. When sphingosine forms an

and phospholipids

(see p. 170). Phosphati-

amide bond to a fatty acid, the compound is

dates can also be released from phospholipids

called ceramide (3). This is the precursor of

by phospholipases.

the sphingolipids. Sphingomyelin

(2)—the

The other phospholipids can be derived

most important sphingolipid—has an addi-

from phosphatidates

(residue

= phospha-

tional phosphate residue with a choline group

tidyl). Their phosphate residues are esterified

attached to it on the sphingosine, in addition

with the hydroxyl group of an amino alcohol

to the fatty acid.

(choline, ethanolamine, or serine) or with the

Glycolipids (3) are present in all tissues on

cyclohexane derivative myo-inositol. Phos-

the outer surface of the plasma membrane.

phatidylcholine is shown here as an example

They consist of sphingosine, a fatty acid, and

of this type of compound. When two phos-

an oligosaccharide residue, which can some-

phatidyl residues are linked with one glyc-

times be quite large. The phosphate residue

erol, the result is cardiolipin (not shown), a

typical of phospholipids is absent. Galacto-

phospholipid that is characteristic of the inner

sylceramide and glucosylceramide (known as

mitochondrial membrane. Lysophospholipids

cerebroside) are simple representatives of

arise from phospholipids by enzymatic cleav-

this group. Cerebrosides in which the sugar

age of an acyl residue. The hemolytic effect of

is esterified with sulfuric acid are known as

bee and snake venoms is due in part to this

sulfatides. Gangliosides are the most complex

reaction.

glycolipids. They constitute a large family of

Phosphatidylcholine (lecithin) is the most

membrane lipids with receptor functions that

abundant phospholipid in membranes.

are as yet largely unknown. A characteristic

Phosphatidylethanolamine (cephalin) has an

component of many gangliosides is N-acetyl-

ethanolamine residue instead of choline, and

neuraminic acid (sialic acid; see p. 38).

phosphatidylserine has a serine residue. In

phosphatidylinositol, phosphatidate is esteri-

fied with the sugarlike cyclic polyalcohol

myo-inositol. A doubly phosphorylated deriv-

ative of this phospholipid, phosphatidylinosi-

tol 4,5-bisphosphate, is a special component

of membranes, which, by enzymatic cleavage,

can give rise to two second messengers, diacyl-

glycerol (DAG) and inositol 1,4,5trisphosphate

(InsP₃; see p. 386).

Lipids

A. Structure of fats, phospholipids, and glycolipids

Acyl residue 1

C O CH₂

C O C

CH₃

Acyl residue 2

H₂C O P O

(CH₂)₂

N CH₃

Acyl residue 3

CH₃

Fat

Phosphatide

1. Fats

(phosphatidylcholine,

lecithin)

Acyl residue 1

Acyl residue 2

CH₃

COO

CH₂

N CH₃

CH₂

CH NH₃

Phosphatidate

Choline

Serine

OH OH

Acyl residue 1

CH₂

NH₃

H H

Acyl residue 2

Amino alcohol

or sugar alcohol

Ethanolamine

myo-Inositol

Phosphatide

Acyl residue 1

Sphingosine

Amino alcohol

or sugar alcohol

Sphingophospholipid

Lysophospholipid

Acyl residue 1

CH₃

Sphingosine

CH₂

O P O

(CH₂)₂

N CH₃

CH₃

Choline

Sphingomyelin

2. Phospholipids

Acyl residue 1

Sphingosine

Sugar

Ceramide

Sphingosine

Sulfatide

Acyl residue 1

Sphingosine

Sugar

Glc

Gal

GalNAc

Gal

Cerebroside

Ganglioside G_M1

NeuAc

(galactosyl or glycosyl ceramide)

3. Sphingolipids

Biomolecules

tabolism, but cannot be produced by them

Isoprenoids

independently, are vitamins; this group

includes vitamins A, D, E, and K. Due to its

A. Activated acetic acid as a component of

structure and function, vitamin D is now usu-

lipids

ally classified as a steroid hormone

(see

Although the lipids found in plant and animal

pp. 56, 330).

organisms occur in many different forms,

Isoprene metabolism in plants is very com-

they are all closely related biogenetically;

plex. Plants can synthesize many types of ar-

they are all derived from acetyl-CoA, the “ac-

omatic substances and volatile oils from iso-

tivated acetic acid” (see pp. 12, 110).

prenoids. Examples include menthol (I= 2 ),

1. One major pathway leads from acetyl-

camphor (I = 2), and citronellal (I = 2). These

CoA to the activated fatty acids (acyl-CoA; for

C₁₀ compounds are also called monoterpenes.

details, see p. 168). Fats, phospholipids, and

Similarly, compounds consisting of three iso-

glycolipids are synthesized from these, and

prene units (I = 3) are termed sesquiterpenes,

fatty acid derivatives in particular are formed.

and the steroids (I = 6) are called triterpenes.

Quantitatively, this is the most important

Isoprenoids that have hormonal and sig-

pathway in animals and most plants.

naling functions form an important group.

2. The second pathway leads from acetyl-

These include steroid hormones (I = 6) and

CoA to isopentenyl diphosphate (“active iso-

retinoate (the anion of retinoic acid; I = 3) in

prene”), the basic component for the isopren-

vertebrates, and juvenile hormone (I = 3) in

oids. Its biosynthesis is discussed in connec-

arthropods. Some plant hormones also belong

tion with biosynthesis of the isoprenoid, cho-

to the isoprenoids—e. g., the cytokinins, absci-

lesterol (see p. 172).

sic acid, and brassinosteroids.

Isoprene chains are sometimes used as

lipid anchors to fix molecules to membranes

B. Isoprenoids

(see p. 214). Chlorophyll has a phytyl residue (I

Formally, isoprenoids are derived from a sin-

= 4) as a lipid anchor. Coenzymes with iso-

gle common building block, isoprene

(2-

prenoid anchors of various lengths include

methyl-1,3-butadiene), a methyl-branched

ubiquinone (coenzyme Q; I = 6-10), plastoqui-

compound with five C atoms. Activated

none (I = 9), and menaquinone (vitamin K; I =

isoprene, isopentenyl diphosphate, is used by

4-6). Proteins can also be anchored to mem-

plants and animals to biosynthesize linear

branes by isoprenylation.

and cyclic oligomers and polymers. For the

In some cases, an isoprene residue is used

isoprenoids listed here—which only represent

as an element to modify molecules chemi-

a small selection—the number of isoprene

cally. One example of this is N'-isopentenyl-

units (I) is shown.

AMP, which occurs as a modified component

From activated isoprene, the metabolic

in tRNA.

pathway leads via dimerization to activated

geraniol (I = 2) and then to activated farnesol (I

= 3). At this point, the pathway divides into

two. Further extension of farnesol leads to

chains with increasing numbers of isoprene

units—e. g., phytol (I = 4), dolichol (I = 14-24),

and rubber (I = 700-5000). The other pathway

involves a “head-to-head” linkage between

two farnesol residues, giving rise to squalene

(I = 6), which, in turn, is converted to choles-

terol (I = 6) and the other steroids.

The ability to synthesize particular iso-

prenoids is limited to a few species of plants

and animals. For example, rubber is only

formed by a few plant species, including the

rubber tree (Hevea brasiliensis). Several iso-

prenoids that are required by animals for me-

Lipids

A. Activated acetic acid as a component of lipids

Activated acetic acid

Isoprene

H₃C

Acetyl-CoA

Activated fatty acid

Active isoprene

O P P

Acyl-CoA

Isopentenyl diphosphate

Fats

Phospholipids Glycolipids

Isoprenoids

B. Isoprenoids

Biosynthesis only in plants

Metabolite

Building block of

and micro-organisms

modified

all isoprenoids

with isoprene

Camphor

Isopentenyl-AMP

Active isoprene

I = 2

I =1

CH₃

H₃C

Chain-like

Citronellol

Geraniol

isoprenoids

I = 2

Menthol

I = 2

Juvenile hormone

Farnesol

Squalene

Cholesterol

I = 3

I = 6

CH₂OH

Retinoic

Phytol

I = 4

Carotenoids

CH₂OH

(Vitamin A)

Steroid hormones

CH₂OH

Bile acids

Menaquinone

I = 4 - 6

Steroid glycosides

I = 6

Dolichol

Plastoquinone

I = 14 - 24

I = 9

Tocopherol

CH₃

(Vitamin E)

Cyclic

isoprenoids

I = 4

Rubber

I = 700 - 5 000

H₃C

CH₃

Ubiquinone

H₃C

CH₃

I = 6 - 10

Phylloquinone

H₃C

CH₃

(Vitamin K)

n = 6-10

I = 4

Biomolecules

onto which the much more mobile side chain

Steroid structure

is attached.

Steroids are relatively apolar (hydropho-

A. Steroid building blocks

bic). Some polar groups—e. g., hydroxyl and

Common to all of the steroids is a molecular

oxo groups—give them amphipathic proper-

core structure consisting of four saturated

ties. This characteristic is especially pro-

rings, known as gonane. At the end of the

nounced with the bile acids (see p. 314).

steroid core, many steroids also carry a side

chain, as seen in cholestane, the basic compo-

C. Thin-layer chromatography

nent of the sterols (steroid alcohols).

Thin-layer chromatography (TLC) is a power-

ful, mainly analytic, technique for rapidly sep-

B. Spatial structure

arating lipids and other small molecules such

The four rings of the steroids are distin-

as amino acids, nucleotides, vitamins, and

guished using the letters A, B, C, and D. Due

drugs. The sample being analyzed is applied

to the tetrahedral arrangement of the single

to a plate made of glass, aluminum, or plastic,

carbon bonds, the rings are not flat, but puck-

which is covered with a thin layer of silica gel

ered. Various ring conformations are known

or other material (1). The plate is then placed

by the terms “chair,” “boat,” and “twisted”

in a chromatography chamber that contains

(not shown). The chair and boat conforma-

some solvent. Drawn by capillary forces, the

tions are common. Fivemembered rings fre-

solvent moves up the plate (2). The substan-

quently adopt a conformation referred to as

ces in the sample move with the solvent. The

an “envelope”. Some rings can be converted

speed at which they move is determined by

from one conformation to another at room

their distribution between the stationary

temperature, but with steroids this is dif cult.

phase (the hydrophilic silica), and the mobile

Substituents of the steroid core lie either

phase (the hydrophobic solvent). When the

approximately in the same plane as the ring

solvent reaches the top edge of the plate,

(e = equatorial) or nearly perpendicular to it

the chromatography is stopped. After evapo-

(a = axial). In threedimensional representa-

ration of the solvent, the separated substan-

tions, substituents pointing toward the ob-

ces can be made visible using appropriate

server are indicated by an unbroken line (β

staining methods or with physical processes

position), while bonds pointing into the plane

(e. g., ultraviolet light) (3). The movement of a

of the page are indicated by a dashed line (α

substance in a given TLC system is expressed

position). The so-called angular methyl

as its R_f value. In this way, compounds that are

groups at C-10 and C-13 of the steroids always

not known can be identified by comparison

adopt the β position.

with reference substances.

Neighboring rings can lie in the same plane

A process in which the polarity of the sta-

(trans; 2) or at an angle to one another (cis; 1).

tionary and mobile phases is reversed—i. e.,

This depends on the positions of the substitu-

the stationary phase is apolar and the solvent

ents of the shared ring carbons, which can be

is polar—is known as “reversed-phase thin-

arranged either cis or trans to the angular

layer chromatography” (RP-TLC).

methyl group at C-10. The substituents of ste-

roid that lie at the points of intersection of the

individual rings are usually in trans position.

As a whole, the core of most steroids is more

or less planar, and looks like a flat disk. The

only exceptions to this are the ecdysteroids,

bile acids (in which A:B is cis), cardiac glyco-

sides, and toad toxins.

A more realistic impression of the three-

dimensional structure of steroids is provided

by the space-filling model of cholesterol (3).

The four rings form a fairly rigid scaffolding,

Lipids

A. Steroid building blocks

B. 3D structure

Angular

methyl groups

Gonane

111213

Methyl-branched side

chain with 8 carbons

Cholesterol

Double bond

Cholestane

Hydroxyl group

in ring B: ∆⁵

at C-3 adopts

β conformation

β con-

CH3

H and CH

3 in cis position

formation,

β con-

axial

formation,

CH3

equatorial

CH3

Cholestanol

H and CH₃ in

α con-

transposition

formation,

axial

Chair

Boat

Envelope

Ring conformations

Cholesterol (Van der Waals model)

C. Thin-layer chromatography

Thin-

Chromato-

Front

Cholesterol

layer

graphy tank

esters

plate with

Triacyl-

silica gel

glycerols

surface

R_f =b

Free fatty acids

Cholesterol

Running

1,3-

Diacyl-

solvent:

1,2-

glycerols

Hexane/

Diethylether/

Monoacyl-

Sample:

Formic acid

glycerols

lipid

80 : 80 : 2

mixture

(v/v/v)

Start

Phospholipids

1. Load

2. Develop

3. Make visible

Biomolecules

A and B are in cis position relative to each

Steroids: overview

other

(see p. 54). One to three hydroxyl

The three most important groups of steroids

groups (in α position) are found in the steroid

are the sterols, bile acids, and steroid hor-

core at positions 3, 7, and 12. Bile acids keep

mones. Particularly in plants, compounds

bile cholesterol in a soluble state as micelles

with steroid structures are also found that

and promote the digestion of lipids in the

are notable for their pharmacological ef-

intestine (see p. 270). Cholic acid and cheno-

fects—steroid alkaloids, digitalis glycosides,

deoxycholic acid are primary bile acids that

and saponins.

are formed by the liver. Their dehydroxylation

at C-7 by microorganisms from the intestinal

flora gives rise to the secondary bile acids

A. Sterols

lithocholic acid and deoxycholic acid.

Sterols are steroid alcohols. They have a

β-positioned hydroxyl group at C-3 and one

C. Steroid hormones

or more double bonds in ring B and in the side

chain. There are no further oxygen functions,

The conversion of cholesterol to steroid

as in the carbonyl and carboxyl groups.

hormones (see p. 376) is of minor importance

The most important sterol in animals is

quantitatively, but of major importance in

cholesterol. Plants and microorganisms have

terms of physiology. The steroid hormones

a wide variety of closely related sterols in-

are a group of lipophilic signal substances

stead of cholesterol—e. g., ergosterol, β-sitos-

that regulate metabolism, growth, and repro-

terol, and stigmasterol.

duction (see p. 374).

Cholesterol is present in all animal tissues,

Humans have six steroid hormones:

and particularly in neural tissue. It is a major

progesterone, cortisol, aldosterone, testos-

constituent of cellular membranes, in which it

terone, estradiol, and calcitriol. With the ex-

regulates fluidity (see p. 216). The storage and

ception of calcitriol, these steroids have either

transport forms of cholesterol are its esters

no side chain or only a short side one consist-

with fatty acids. In lipoproteins, cholesterol

ing of two carbons. Characteristic for most of

and its fatty acid esters are associated with

them is an oxo group at C-3, conjugated with

other lipids (see p. 278). Cholesterol is a con-

a double bond between C-4 and C-5 of ring A.

stituent of the bile and is therefore found in

Differences occur in rings C and D. Estradiol is

many gallstones. Its biosynthesis, metabo-

aromatic in ring A, and its hydroxyl group at

lism, and transport are discussed elsewhere

C-3 is therefore phenolic. Calcitriol differs

(see pp. 172, 312).

from other vertebrate steroid hormones; it

Cholesterol-rich lipoproteins of the LDL

still contains the complete carbon framework

type are particularly important in the devel-

of cholesterol, but lightdependent opening of

opment of arteriosclerosis, in which the arte-

ring B turns it into what is termed a “secoste-

rial walls are altered in connection with an

roid” (a steroid with an open ring).

excess plasma cholesterol level. In terms of

Ecdysone is the steroid hormone of the

dietary physiology, it is important that plant

arthropods. It can be regarded as an early

foodstuffs are low in cholesterol. By contrast,

form of the steroid hormones. Steroid hor-

animal foods can contain large amounts of

mones with signaling functions also occur in

cholesterol—particularly butter, egg yolk,

plants.

meat, liver, and brain.

B. Bile acids

Bile acids are synthesized from cholesterol in

the liver

(see p. 314). Their structures can

therefore be derived from that of cholesterol.

Characteristic for the bile acids is a side chain

shortened by three C atoms in which the last

carbon atom is oxidized to a carboxyl group.

The double bond in ring B is reduced and rings

Biomolecules

mensional structure as follows: firstly, the

Amino acids: chemistry and

tetrahedron is rotated in such a way that the

properties

most oxidized group (the carboxylate group)

is at the top. Rotation is then continued until

the line connecting line COO^- and R (red) is

A. Amino acids: functions

level with the page. In L-amino acids, the

The amino acids (2-aminocarboxylic acids)

NH₃₊ group is then on the left, while in D-

fulfill various functions in the organism.

amino acids it is on the right.

Above all, they serve as the components of

peptides and proteins. Only the 20 proteino-

C. Dissociation curve of histidine

genic amino acids (see p. 60) are included in

the genetic code and therefore regularly

All amino acids have at least two ionizable

found in proteins. Some of these amino acids

groups, and their net charge therefore de-

undergo further (post-translational) change

pends on the pH value. The COOH groups at

following their incorporation into proteins

the α-C atom have pK_a values of between 1.8

(see p. 62). Amino acids or their derivatives

and 2.8 and are therefore more acidic than

are also form components of lipids—e. g., ser-

simple monocarboxylic acids. The basicity of

ine in phospholipids and glycine in bile salts.

the α-amino function also varies, with pK_a

Several

amino acids function

values of between 8.8 and 10.6, depending

neurotransmitters themselves

(see p. 352),

on the amino acid. Acidic and basic amino

while others are precursors of neurotransmit-

acids have additional ionizable groups in their

ters, mediators, or hormones

(see p. 380).

side chain. The pK_a values of these side chains

Amino acids are important (and sometimes

are listed on p. 60. The electrical charges of

essential) components of food (see p. 360).

peptides and proteins are mainly determined

Specific amino acids form precursors for other

by groups in the side chains, as most α-car-

metabolites—e. g., for glucose in gluconeogen-

boxyl and α-amino functions are linked to

esis, for purine and pyrimidine bases, for

peptide bonds (see p. 66).

heme, and for other molecules. Several non-

Histidine can be used here as an example of

proteinogenic amino acids function as inter-

the pH-dependence of the net charge of an

mediates in the synthesis and breakdown of

amino acid. In addition to the carboxyl group

proteinogenic amino acids (see p. 412) and in

and the amino group at the α-C atom with pK_a

the urea cycle (see p. 182).

values of 1.8 and 9.2, respectively, histidine

also has an imidazole residue in its side chain

with a pK_a value of 6.0. As the pH increases,

B. Optical activity

the net charge (the sum of the positive and

The natural amino acids are mainly α-amino

negative charges) therefore changes from +2

acids, in contrast to β-amino acids such as β-

to -1. At pH 7.6, the net charge is zero, even

alanine and taurine. Most α-amino acids have

though the molecule contains two almost

four different substituents at C-2 (Cα). The α

completely ionized groups in these condi-

atom therefore represents a chiral center—i. e.,

tions. This pH value is called the isoelectric

there are two different enantiomers (L- and

point.

D-amino acids; see p. 8). Among the proteino-

At its isoelectric point, histidine is said to

genic amino acids, only glycine is not chiral (R

be zwitterionic, as it has both anionic and

= H). In nature, it is almost exclusively

cationic properties. Most other amino acids

L-amino acids that are found. D-Amino acids

are also zwitterionic at neutral pH. Peptides

occur in bacteria—e. g., in murein

(see

and proteins also have isoelectric points,

p. 40)—and in peptide antibiotics. In animal

which can vary widely depending on the

metabolism, D-Amino acids would disturb

composition of the amino acids.

the enzymatic reactions of L-amino acids

and they are therefore broken down in the

liver by the enzyme D-amino acid oxidase.

The Fischer projection (center) is used to

present the formulas for chiral centers in bio-

molecules. It is derived from their three-di-

Biomolecules

The aromatic amino acids (class III) contain

Proteinogenic amino acids

resonancestabilized rings. In this group, only

phenylalanine has strongly apolar properties.

A. The proteinogenic amino acids

Tyrosine and tryptophan are moderately polar,

The amino acids that are included in the ge-

and histidine is even strongly polar. The imi-

netic code (see p. 248) are described as “pro-

dazole ring of histidine is already protonated

teinogenic.” With a few exceptions (see p. 58),

at weakly acidic pH values. Histidine, which is

only these amino acids can be incorporated

only aromatic in protonated form (see p. 58),

into proteins through translation. Only the

can therefore also be classified as a basic

side chains of the 20 proteinogenic amino

amino acid. Tyrosine and tryptophan show

acids are shown here. Their classification is

strong light absorption at wavelengths of

based on the chemical structure of the side

250-300 nm.

chains, on the one hand, and on their polarity

The neutral amino acids (class IV) have

on the other (see p. 6). The literature includes

hydroxyl groups (serine, threonine) or amide

several slightly different systems for classify-

groups (asparagine, glutamine). Despite their

ing amino acids, and details may differ from

nonionic nature, the amide groups of aspara-

those in the system used here.

gine and glutamine are markedly polar.

The carboxyl groups in the side chains of

For each amino acid, the illustration names:

the acidic amino acids aspartic acid and glu-

• Membership of structural classes I-VII (see

tamic acid (class V) are almost completely

below; e. g., III and VI for histidine)

ionized at physiological pH values. The side

• Name and abbreviation, formed from the

chains of the basic amino acids lysine and

first three letters of the name (e. g., histi-

arginine are also fully ionized—i. e., positively

dine, His)

charged—at neutral pH. Arginine, with its

• The one-letter symbol introduced to save

positively charge guanidinium group, is par-

space in the electronic processing of se-

ticularly strongly basic, and therefore ex-

quence data (H for histidine)

tremely polar.

• A quantitative value for the polarity of the

Proline (VII) is a special case. Together with

side chain (bottom left; 10.3 for histidine).

the α-C atom and the α-NH₂ group, its side

The more positive this value is, the more

chain forms a fivemembered ring. Its nitrogen

polar the amino acid is.

atom is only weakly basic and is not proto-

In addition, the polarity of the side chains is

nated at physiological pH. Due to its ring

indicated by color. It increases from yellow,

structure, proline causes bending of the pep-

through light and dark green, to bluish green.

tide chain in proteins (this is important in

For ionizing side chains, the corresponding

collagen, for example; see p. 70).

pK_a values are also given (red numbers).

Several proteinogenic amino acids cannot

The aliphatic amino acids (class I) include

be synthesized by the human organism, and

glycine, alanine, valine, leucine, and isoleucine.

therefore have to be supplied from the diet.

These amino acids do not contain heteroa-

These essential amino acids (see p. 360) are

toms (N, O, or S) in their side chains and do

marked with a star in the illustration. Histi-

not contain a ring system. Their side chains

dine and possibly also arginine are essential

are markedly apolar. Together with threonine

for infants and small children.

(see below), valine, leucine, and isoleucine

form the group of branched-chain amino

acids. The sulfurcontaining amino acids cys-

teine and methionine (class II), are also apolar.

However, in the case of cysteine, this only

applies to the undissociated state. Due to its

ability to form disulfide bonds, cysteine plays

an important role in the stabilization of pro-

teins (see p. 72). Two cysteine residues linked

by a disulfide bridge are referred to as cystine

(not shown).

Amino Acids

A. The proteinogenic amino acids

Aliphatic

Sulfur-containing

Glycine

Alanine

Valine

Leucine

Isoleucine

Cysteine

Methionine

(Gly, G)

(Ala, A)

(Val, V)

(Leu, L)

(Ile, I)

(Cys, C)

(Met, M)

CH₃

H₃C

CH₂

CH₃

H₃C

CH₂

8.3

CH₃

pKa value

Polarity

-2.4

-1.9

-2.0

-2.3

-2.2

-1.2

-1.5

Aromatic

Cyclic

Neutral

Phenylalanine

Tyrosine

Tryptophan

Proline

Serine

Threonine

(Phe, F)

(Tyr, Y)

(Trp, W)

(Pro, P)

(Ser, S)

(Thr, T)

CH₂

COO

H₃C

CH₂

H₂C CH₂

Indole ring

Pyrrolidine ring

10.1

+0.8

+6.1

+5.9

+6.0

+5.1

+4.9

Essential amino acids

Chiral center

Neutral

Acidic

Basic

Asparagine

Glutamine

Aspartic acid

Glutamic acid

Histidine

Lysine

Arginine

(Asn,N)

(Gln, Q)

(Asp, D)

(Glu, E)

(His, H)

(Lys,K)

(Arg, R)

CH₂

CONH₂

CH₂

COO

CH₂

4.0

HN CH

CONH₂

COO

CH₂

HC N

4.3

6.0

CH₂

Imidazole ring

NH₃

10.8

H₂N

NH₂

12.5

+9.7

+9.4

+11.0

+10.2

+10.3

+15.0

+20.0

Biomolecules

The ε-amino group of lysine residues is sub-

Non-proteinogenic amino acids

ject to a particularly large number of modifi-

In addition to the 20 proteinogenic amino

cations. Its acetylation (or deacetylation) is an

acids (see p. 60), there are also many more

important mechanism for controlling genetic

compounds of the same type in nature. These

activity

(see p. 244). Many coenzymes and

arise during metabolic reactions (A) or as a

cofactors are covalently linked to lysine resi-

result of enzymatic modifications of amino

dues. These include biotin (see p. 108), lipoic

acid residues in peptides or proteins (B). The

acid

(see p. 106), and pyridoxal phosphate

“biogenic amines” (C) are synthesized from α-

(see p. 108), as well as retinal (see p. 358).

amino acids by decarboxylation.

Covalent modification with ubiquitin marks

proteins for breakdown (see p. 176). In colla-

gen, lysine and proline residues are modified

A. Rare amino acids

by hydroxylation to prepare for the formation

Only a few important representatives of the

of stable fibrils (see p. 70). Cysteine residues

non-proteinogenic amino acids are men-

form disulfide bonds with one another (see

tioned here. The basic amino acid ornithine

p. 72). Cysteine prenylation serves to anchor

is an analogue of lysine with a shortened side

proteins in membranes (see p. 214). Covalent

chain. Transfer of a carbamoyl residue to or-

bonding of a cysteine residue with heme oc-

nithine yields citrulline. Both of these amino

curs in cytochrome c. Flavins are sometimes

acids are intermediates in the urea cycle (see

covalently bound to cysteine or histidine res-

p. 182). Dopa (an acronym of 3,4-dihydroxy-

idues of enzymes. Among the modifications of

phenylalanine) is synthesized by hydroxyla-

tyrosine residues, conversion into iodinated

tion of tyrosine. It is an intermediate in the

thyroxine (see p. 374) is particularly interest-

biosynthesis of catecholamines (see p. 352)

ing.

and of melanin. It is in clinical use in the

treatment of Parkinson’s disease. Selenocys-

C. Biogenic amines

teine, a cysteine analogue, occurs as a compo-

nent of a few proteins—e. g., in the enzyme

Several amino acids are broken down by de-

glutathione peroxidase (see p. 284).

carboxylation. This reaction gives rise to what

are known as biogenic amines, which have

various functions. Some of them are compo-

B. Post-translational protein modification

nents of biomolecules, such as ethanolamine

Subsequent alteration of amino acid residues

in phospholipids (see p. 50). Cysteamine and

in finished peptides and proteins is referred

b-alanine are components of coenzyme A (see

to as post-translational modification. These re-

p. 12) and of pantetheine (see pp. 108, 168).

actions usually only involve polar amino acid

Other amines function as signaling substan-

residues, and they serve various purposes.

ces. An important neurotransmitter derived

The free α-amino group at the N-terminus

from glutamate is γ-aminobutyrate (GABA,

is blocked in many proteins by an acetyl res-

see p. 356). The transmitter dopamine is also

idue or a longer acyl residue (acylation). N-

a precursor for the catecholamines epineph-

terminal glutamate can cyclize into a pyroglu-

rine and norepinephrine (see p. 352). The bio-

tamate residue, while the C-terminal carbox-

genic amine serotonin, a substance that has

ylate group can be present in an amidated

many effects, is synthesized from tryptophan

form (see TSH, p. 380). The side chains of ser-

via the intermediate 5-hydroxytryptophan.

ine and asparagine residues are often linked

Monamines are inactivated into aldehydes

to oligosaccharides (glycosylation, see p. 230).

by amine oxidase

(monoamine oxidase,

Phosphorylation of proteins mainly affects

“MAO”) with deamination and simultaneous

serine and tyrosine residues. These reactions

oxidation. MAO inhibitors therefore play an

have mainly regulatory functions (see p. 114).

important role in pharmacological interven-

Aspartate and histidine residues of enzymes

tions in neurotransmitter metabolism.

are sometimes phosphorylated, too. A special

modification of glutamate residues, J-carbox-

ylation, is found in coagulation factors. It is

essential for blood coagulation (see p. 290).

Amino Acids

A. Rare amino acids

COO

H₃N

CH₂

Se H

CH₂

NH₃

HN C NH2

Seleno-

Ornithine

Citrulline

L-Dopa

cysteine

B. Post-translational protein modification

D: Pyroglutamyl-

B: Oligo-

D: Phospho-

D: Acetyl-

B: Pyridoxal-

Acetyl-

saccharide

Methyl-

Liponat

(O-glyco-

(N-glyco-

Formyl-

γ-Carboxy-

γ-Hydroxy-

Biotin

sylation)

Myristoyl-

(Glu)

Retinal

Ubiquitin

CONH

COO

NH₃

H₃N

Ser, Thr

Asn, Gln

Asp, Glu

Lys

D: derivative B: bonds with

Pro

Tyr

Phe

His

Cys

OOC

D: 3-Hydroxy-

HN N

4-Hydroxy-

D: Amido-

D: Phospho-

D: 4-Hydroxy-

D: Phospho-

D: Disulfide

(CONH2)

Iodo-

(Tyrosine)

Methyl-

Prenyl-

Sulfato-

B: Flavin

B: Heme

Adenyl-

Flavin

C. Biogenic amines

Amino acid

Amine

Function

Amino acid

Amine

Function

Serine

Ethanol-

Glutamate

γ-Amino-

Neurotrans-

amine

butyrate

mitter (GABA)

Cysteine

Cysteamine

Component of

Histidine

Histamine

Mediator, neuro-

coenzyme A

transmitter

Threonine

Amino-

Component of

Dopa

Dopamine

Neurotransmitter

propanol

vitamin B12

Aspartate

β-Alanine

Component of

5-Hydroxy-

Serotonin

Mediator, neuro-

coenzyme A

tryptophan

transmitter

Biomolecules

hormone somatotropin and its receptor is

Peptides and proteins: overview

shown here as an example (middle). Here,

the extracellular domains of two receptor

A. Proteins

molecules here bind one molecule of the hor-

When amino acids are linked together by

mone. This binding activates the cytoplasmic

acid-amide bonds, linear macromolecules

domains of the complex, leading to further

(peptides) are produced. Those containing

conduction of the signal to the interior of

more than ca. 100 amino acid residues are

the cell

(see p. 384). The small peptide

described as proteins (polypeptides). Every

hormone insulin is discussed in detail else-

organism contains thousands of different pro-

where (see pp. 76, 160). DNA-binding proteins

teins, which have a variety of functions. At a

(transcription factors; see p. 118) are decisively

magnification of ca. 1.5 million, the semi-

involved in regulating the metabolism and in

schematic illustration shows the structures

differentiation processes. The structure and

of a few intra and extracellular proteins, giv-

function of the catabolite activator protein

ing an impression of their variety. The func-

(top left) and similar bacterial transcription

tions of proteins can be classified as follows.

factors have been particularly well investi-

Establishment and maintenance of struc-

gated.

ture. Structural proteins are responsible for

Catalysis. Enzymes, with more than 2000

the shape and stability of cells and tissues. A

known representatives, are the largest group

small part of a collagen molecule is shown as

of proteins in terms of numbers (see p. 88).

an example (right; see p. 70). The complete

The smallest enzymes have molecular masses

molecule is 1.5

300 nm in size, and at the

10-15 kDa. Intermediatesized enzymes,

magnification used here it would be as long as

such as alcohol dehydrogenase (top left) are

three pages of the book. Histones are also

around

100-200 kDa, and the largest—

structural proteins. They organize the ar-

including glutamine synthetase with its 12

rangement of DNA in chromatin. The basic

monomers (top right)—can reach more than

components of chromatin, the nucleosomes

500 kDa.

(top right; see p. 218) consist of an octameric

Movement. The interaction between actin

complex of histones, around which the DNA is

and myosin is responsible for muscle contrac-

coiled.

tion and cell movement (see p. 332). Myosin

Transport. A wellknown transport protein

(right), with a length of over

150 nm, is

is hemoglobin in the erythrocytes (bottom

among the largest proteins there are. Actin

left). It is responsible for the transport of oxy-

filaments (F-actin) arise due to the polymer-

gen and carbon dioxide between the lungs

ization of relatively small protein subunits (G-

and tissues (see p. 282). The blood plasma

actin). Along with other proteins, tropomyo-

also contains many other proteins with trans-

sin, which is associated with F-actin, controls

port functions. Prealbumin

(transthyretin;

contraction.

middle), for example, transports the thyroid

Storage. Plants contain special storage pro-

hormones thyroxin and triiodothyronine. Ion

teins, which are also important for human

channels and other integral membrane pro-

nutrition

(not shown). In animals, muscle

teins (see p. 220) facilitate the transport of

proteins constitute a nutrient reserve that

ions and metabolites across biological mem-

can be mobilized in emergencies.

branes.

Protection and defense. The immune sys-

tem protects the body from pathogens and

foreign substances. An important component

of this system is immunoglobulin G (bottom

left; see p. 300). The molecule shown here is

bound to an erythrocyte by complex forma-

tion with surface glycolipids (see p. 292).

Control and regulation. In biochemical sig-

nal chains, proteins function as signaling sub-

stances (hormones) and as hormone recep-

tors. The complex between the growth

Biomolecules

example, the peptide hormone angiotensin II

Peptide bonds

(see p. 330) has the sequence Asp-Arg-Val-

Tyr-Ile-His-Pro-Phe, or DRVYIHPF.

A. Peptide bond

The amino acid components of peptides and

D. Conformational space of the peptide

proteins are linked together by amide bonds

chain

(see p. 60) between α-carboxyl and α-amino

groups. This type of bonding is therefore also

With the exception of the terminal residues,

known as peptide bonding. In the dipeptide

every amino acid in a peptide is involved in

shown here, the serine residue has a free

two peptide bonds (one with the preceding

ammonium group, while the carboxylate

residue and one with the following one). Due

group in alanine is free. Since the amino acid

to the restricted rotation around the C-N

with the free NH₃₊ group is named first, the

bond, rotations are only possible around the

peptide is known as seryl alanine, or in abbre-

N-C_α and C_α-C bonds (2). As mentioned

viated form Ser-Ala or SA.

above, these rotations are described by the

dihedral angles φ (phi) and ψ (psi). The angle

describes rotation around the N-C_α bond; ψ

B. Resonance

describes rotation around C_α-C—i. e., the po-

Like all acid-amide bonds, the peptide bond is

sition of the subsequent bond.

stabilized by resonance (see p. 4). In the con-

For steric reasons, only specific combina-

ventional notation (top right) it is represented

tions of the dihedral angles are possible.

as a combination of a C=O double bond with a

These relationships can be illustrated clearly

C-N single bond. However, a C=N double bond

by a so-called φ/ ψ diagram (1). Most combi-

with charges at O and N could also be written

nations of φ and ψ are sterically “forbidden”

(middle). Both of these are only extreme cases

(red areas). For example, the combination φ =

of electron distribution, known as resonance

0° and ψ = 180° (4) would place the two

structures. In reality, the π electrons are

carbonyl oxygen atoms less than

115 pm

delocalized throughout all the atoms (bot-

apart—i. e., at a distance much smaller than

tom). As a mesomeric system, the peptide

the sum of their van der Waals radii (see p. 6).

bond is planar. Rotation around the C-N

Similarly, in the case of φ = 180° and ψ = 0° (5),

bond would only be possible at the expense

the two NH hydrogen atoms would collide.

of large amounts of energy, and the bond is

The combinations located within the green

therefore not freely rotatable. Rotations are

areas are the only ones that are sterically

only possible around the single bonds marked

feasible (e. g., 2 and 3). The important secon-

with arrows. The state of these is expressed

dary structures that are discussed in the fol-

using the angles φ and ψ (see D). The plane in

lowing pages are also located in these areas.

which the atoms of the peptide bond lie is

The conformations located in the yellow areas

highlighted in light blue here and on the fol-

are energetically less favorable, but still pos-

lowing pages.

sible.

The φ/ ψ diagram (also known as a Rama-

chandran plot) was developed from modeling

C. Peptide nomenclature

studies of small peptides. However, the con-

Peptide chains have a direction and therefore

formations of most of the amino acids in pro-

two different ends. The amino terminus (N

teins are also located in the permitted areas.

terminus) of a peptide has a free ammonium

The corresponding data for the small protein,

group, while the carboxy terminus (C termi-

insulin (see p. 76), are represented by black

nus) is formed by the carboxylate group of the

dots in 1.

last amino acid. In peptides and proteins, the

amino acid components are usually linked in

linear fashion. To express the sequence of a

peptide, it is therefore suf cient to combine

the three-letter or single-letter abbreviations

for the amino acid residues (see p. 60). This

sequence always starts at the N terminus. For

Peptides and Proteins

A. Peptide bonds

B. Resonance

C N

Resonance

structures

C N

ϕ ψ

C N

Seryl alanine

(Ser-Ala, H₃N-Ser-Ala-COO

, SA)

Mesomeric

structure

C. Peptide nomenclature

Residue 1

Residue 2

Residue 3

Residue 4

Residue

R₁

O R₃

H O

Amino

Carboxy-

terminus

(N terminus)

H₃N

COO

(C terminus)

O R₂

H O R₄

D. Conformation space of the peptide chain

ϕ =

0°

ϕ (Phi): Rotation about

ψ = 180°

(Phi): N - C_α

ψ (Psi): Rotation about

y (Psi): C_α - C

ϕ = -139°

180

ψ = -135°

B-23

β_a

120

d = 115 pm

αl

Allowed

Forbidden

ψ 0

αr

ϕ = 180°

-60

ψ=

0°

ϕ = -57°

ψ= -47°

d =

-120

A-9

B-20

155 pm

B-8

-180

-120

-60

120

180

Pleated sheet (antiparallel)

β_a

α Helix (right-handed)

αr

Pleated sheet (parallel)

β_p

α Helix (left-handed)

Collagen helix

αl

Biomolecules

B. Collagen helix

Secondary structures

Another type of helix occurs in the collagens,

In proteins, specific combinations of the dihe-

which are important constituents of the con-

dral angles φ and ψ (see p. 66) are much more

nectivetissue matrix (see pp. 70, 344). The

common than others. When several succes-

collagen helix is left-handed, and with a pitch

sive residues adopt one of these conforma-

of 0.96 nm and 3.3 residues per turn, it is

tions, defined secondary structures arise,

steeper than the α-helix. In contrast to the

which are stabilized by hydrogen bonds ei-

α-helix, H bonds are not possible within the

ther within the peptide chain or between

collagen helix. However, the conformation is

neighboring chains. When a large part of a

stabilized by the association of three helices

protein takes on a defined secondary struc-

to form a righthanded collagen triple helix

ture, the protein often forms mechanically

(see p. 70).

stable filaments or fibers. Structural proteins

of this type (see p. 70) usually have character-

istic amino acid compositions.

C. Pleated-sheet structures

The most important secondary structural

Two additional, almost stretched, conforma-

elements of proteins are discussed here first.

tions of the peptide chain are known as E

The illustrations only show the course of the

pleated sheets, as the peptide planes are ar-

peptide chain; the side chains are omitted. To

ranged like a regularly folded sheet of paper.

make the course of the chains clearer, the

Again, H bonds can only form between neigh-

levels of the peptide bonds are shown as

boring chains (“strands”) in pleated sheets.

blue planes. The dihedral angles of the struc-

When the two strands run in opposite direc-

tures shown here are also marked in diagram

tions (1), the structure is referred to as an

D1 on p. 67.

antiparallel pleated sheet (β_a). When they

run in the same direction (2), it is a parallel

A. D-Helix

pleated sheet (β_p). In both cases, the α-C

atoms occupy the highest and lowest points

The right-handed α-helix (α_R) is one of the

in the structure, and the side chains point

most common secondary structures. In this

alternately straight up or straight down (see

conformation, the peptide chain is wound

p. 71 C). The β_a structure, with its almost lin-

like a screw. Each turn of the screw (the screw

ear H bonds, is energetically more favorable.

axis in shown in orange) covers approxi-

In extended pleated sheets, the individual

mately 3.6 amino acid residues. The pitch of

strands of the sheet are usually not parallel,

the screw (i. e., the smallest distance between

but twisted relative to one another (see p. 74).

two equivalent points) is 0.54 nm. α-Helices

are stabilized by almost linear hydrogen bonds

between the NH and CO groups of residues,

D. E Turns

which are four positions apart from each an-

E Turns are often found at sites where the

other in the sequence (indicated by red dots;

peptide chain changes direction. These are

see p. 6). In longer helices, most amino acid

sections in which four amino acid residues

residues thus enter into two H bonds. Apolar

are arranged in such a way that the course

or amphipathic α-helices with five to seven

of the chain reverses by about 180° into the

turns often serve to anchor proteins in bio-

opposite direction. The two turns shown

logical membranes (transmembrane helices;

(types I and II) are particularly frequent.

see p. 214).

Both are stabilized by hydrogen bonds be-

The mirror image of the α_R helix, the left-

tween residues 1 and 4. β Turns are often

handed D-helix (α_L), is rarely found in nature,

located between the individual strands of

although it would be energetically “permissi-

antiparallel pleated sheets, or between

ble.”

strands of pleated sheets and α helices.

Biomolecules

two latter amino acids are only formed during

Structural proteins

collagen biosynthesis as a result of posttrans-

The structural proteins give extracellular

lational modification (see p. 344).

structures mechanical stability, and are in-

The triplet Gly-X-Y (2) is constantly re-

volved in the structure of the cytoskeleton

peated in the sequence of collagen, with the

(see p. 204). Most of these proteins contain a

X position often being occupied by Pro and

high percentage of specific secondary struc-

the Y position by Hyp. The reason for this is

tures (see p. 68). For this reason, the amino

that collagen is largely present as a triple helix

acid composition of many structural proteins

made up of three individual collagen helices

is also characteristic (see below).

(1). In triple helices, every third residue lies

on the inside of the molecule, where for steric

reasons there is only room for glycine resi-

A. D Keratin

dues (3; the glycine residues are shown in

D-Keratin is a structural protein that predom-

yellow). Only a small section of a triple helix

inantly consists of α helices. Hair

(wool),

is illustrated here. The complete collagen

feathers, nails, claws and the hooves of ani-

molecule is approximately 300 nm long.

mals consist largely of keratin. It is also an

important component of the cytoskeleton

C. Silk fibroin

(cytokeratin), where it appears in intermedi-

ate filaments (see p. 204).

Silk is produced from the spun threads from

In the keratins, large parts of the peptide

silkworms (the larvae of the moth Bombyx

chain show right-handed α-helical coiling.

mori and related species). The main protein

Two chains each form a left-handed super-

in silk, fibroin, consists of antiparallel pleated

helix, as is also seen in myosin (see p. 65).

sheet structures arranged one on top of the

The superhelical keratin dimers join to form

other in numerous layers (1). Since the amino

tetramers, and these aggregate further to

acid side chains in pleated sheets point either

form protofilaments, with a diameter of

straight up or straight down (see p. 68), only

3 nm. Finally, eight protofilaments then

compact side chains fit between the layers. In

form an intermediate filament, with a diam-

fact, more than 80% of fibroin consists of gly-

eter of 10 nm (see p. 204).

cine, alanine, and serine, the three amino

Similar keratin filaments are found in hair.

acids with the shortest side chains. A typical

In a single wool fiber with a diameter of about

repetitive amino acid sequence is (Gly-Ala-

20 µm, millions of filaments are bundled to-

Gly-Ala-Gly-Ser). The individual pleated sheet

gether within dead cells. The individual kera-

layers in fibroin are found to lie alternately

tin helices are cross-linked and stabilized by

0.35 nm and 0.57 nm apart. In the first case,

numerous disulfide bonds (see p. 72). This fact

only glycine residues (R = H) are opposed to

is exploited in the perming of hair. Initially,

one another. The slightly greater distance of

the disulfide bonds of hair keratin are dis-

0.57 nm results from repulsion forces be-

rupted by reduction with thiol compounds

tween the side chains of alanine and serine

(see p. 8). The hair is then styled in the desired

residues (2).

shape and heat-dried. In the process, new

disulfide bonds are formed by oxidation,

which maintain the hairstyle for some time.

B. Collagen

Collagen is the quantitatively most important

protein in mammals, making up about 25% of

the total protein. There are many different

types of collagen, particularly in connective

tissue. Collagen has an unusual amino acid

composition. Approximately one-third of the

amino acids are glycine (Gly), about 10 % pro-

line (Pro), and 10% hydroxyproline (Hyp). The

Biomolecules

tively cleaved again. The small plant protein

Globular proteins

crambin (46 amino acids) contains three di-

Soluble proteins have a more complex struc-

sulfide bonds and is therefore very stable. The

ture than the fibrous, completely insoluble

high degree of stability of insulin (see p. 76)

structural proteins. The shape of soluble pro-

has a similar reason.

teins is more or less spherical (globular). In

their biologically active form, globular

C. Protein dynamics

proteins have a defined spatial structure

(the native conformation). If this structure is

The conformations of globular proteins are

destroyed (denaturation; see p. 74), not only

not rigid, but can change dramatically on

does the biological effect disappear, but the

binding of ligands or in contact with other

protein also usually precipitates in insoluble

proteins. For example, the enzyme adenylate

form. This happens, for example, when eggs

kinase (see p. 336) has a mobile domain (do-

are boiled; the proteins dissolved in the egg

main = independently folded partial struc-

white are denatured by the heat and produce

ture), which folds shut after binding of the

the solid egg white.

substrate (yellow). The larger domain (bot-

To illustrate protein conformations in a

tom) also markedly alters its conformation.

clear (but extremely simplified) way, Richard-

There are large numbers of allosteric

son diagrams are often used. In these

proteins of this type. This group includes, for

diagrams, α-helices are symbolized by red

example, hemoglobin (see p. 280), calmodulin

cylinders or spirals and strands of pleated

(see p. 386), and many allosteric enzymes

sheets by green arrows. Less structured areas

such as aspartate carbamoyltransferase (see

of the chain, including the β-turns, are shown

p. 116).

as sections of gray tubing.

D. Folding patterns

A. Conformation-stabilizing interactions

The globular proteins show a high degree of

The native conformation of proteins is stabi-

variability in folding of their peptide chains.

lized by a number of different interactions.

Only a few examples are shown here. Purely

Among these, only the disulfide bonds (B)

helically folded proteins such as myoglobin (1;

represent covalent bonds. Hydrogen bonds,

see p. 74, heme yellow) are rare. In general,

which can form inside secondary structures,

pleated sheet and helical elements exist

as well as between more distant residues, are

alongside each other. In the hormone-binding

involved in all proteins (see p. 6). Many pro-

domain of the estrogen receptor (2; see p. 378),

teins are also stabilized by complex formation

a small, two-stranded pleated sheet functions

with metal ions (see pp. 76, 342, and 378, for

as a “cover” for the hormone binding site

example). The hydrophobic effect is particu-

(estradiol yellow). In flavodoxin, a small flavo-

larly important for protein stability. In glob-

protein with a redox function (3; FMN yel-

ular proteins, most hydrophobic amino acid

low), a fan-shaped, pleated sheet made up of

residues are arranged in the interior of the

five parallel strands forms the core of the

structure in the native conformation, while

molecule. The conformation of the β subunit

the polar amino acids are mainly found on

of the G-protein transducin (4; see pp. 224,

the surface (see pp. 28, 76).

358) is very unusual. Seven pleated sheets

form a large, symmetrical “β propeller.” The

N-terminal section of the protein contains one

B. Disulfide bonds

long and one short helix.

Disulfide bonds arise when the SH groups of

two cysteine residues are covalently linked as

a dithiol by oxidation. Bonds of this type are

only found (with a few exceptions) in extra-

cellular proteins, because in the interior of the

cell glutathione (see p. 284) and other reduc-

ing compounds are present in such high con-

centrations that disulfides would be reduc-

Biomolecules

When the urea and thiol are removed by

Protein folding

dialysis

(see p. 78), secondary and tertiary

Information about the biologically active (na-

structures develop again spontaneously. The

tive) conformation of proteins is already en-

cysteine residues thus return to a suf ciently

coded in their amino acid sequences. The na-

close spatial vicinity that disulfide bonds can

tive forms of many proteins arise spontane-

once again form under the oxidative effect of

ously in the test tube and within a few mi-

atmospheric oxygen. The active center also

nutes. Nevertheless, there are special

reestablishes itself. In comparison with the

auxiliary proteins (chaperonines) that sup-

denatured protein, the native form is aston-

port the folding of other proteins in the con-

ishingly compact, at 4.5

2.5 nm. In this state,

ditions present within the cell (see p. 232). An

the apolar side chains (yellow) predominate

important goal of biochemistry is to under-

in the interior of the protein, while the polar

stand the laws governing protein folding. This

residues are mainly found on the surface. This

would make it possible to predict the confor-

distribution is due to the “hydrophobic effect”

mation of a protein from the easily accessible

(see p. 28), and it makes a vital contribution to

DNA sequence (see p. 260).

the stability of the native conformation (B).

A. Folding and denaturation of

B. Energetics of protein folding

ribonuclease A

The energetics of protein folding are not at

The folding of proteins to the native form is

present satisfactorily understood. Only a sim-

favored under physiological conditions. The

plified model is discussed here. The confor-

native conformation is lost, as the result of

mation of a molecule is stable in any given

denaturation, at extreme pH values, at high

conditions if the change in its free enthalpy

temperatures, and in the presence of organic

during folding (∆G_fold) is negative (see p. 16).

solvents, detergents, and other denaturing

The magnitude of the folding enthalpy is af-

substances, such as urea.

fected by several factors. The main factor

The fact that a denatured protein can spon-

working against folding is the strong increase

taneously return to its native conformation

in the ordering of the molecule involved. As

was demonstrated for the first time with ri-

discussed on p. 20, this leads to a negative

bonuclease, a digestive enzyme (see p. 266)

change in entropy of ∆S_conf and therefore to

consisting of 124 amino acids. In the native

a strongly positive entropy term -T

∆S (violet

form (top right), there are extensive pleated

arrow). By contrast, the covalent and nonco-

sheet structures and three α helices. The eight

valent bonds in the interior of the protein

cysteine residues of the protein are forming

have a stabilizing influence. For this reason,

four disulfide bonds. Residues His-12, Lys-41

the change in folding enthalpy ∆H_fold is neg-

and His-119 (pink) are particularly important

ative (red arrow). A third factor is the change

for catalysis. Together with additional amino

in the system’s entropy due to the hydropho-

acids, they form the enzyme’s active center.

bic effect. During folding, the degree of order

The disulfide bonds can be reductively

in the surrounding water decreases—i. e.,

cleaved by thiols

(e. g., mercaptoethanol,

∆S_water is positive and therefore

-T

∆S is

HO-CH₂-CH₂-SH). If urea at a high concentra-

negative (blue arrow). When the sum of these

tion is also added, the protein unfolds com-

effects is negative (green arrow), the protein

pletely. In this form (left), it is up to 35 nm

folds spontaneously into its native conforma-

long. Polar (green) and apolar (yellow) side

tion.

chains are distributed randomly. The dena-

tured enzyme is completely inactive, because

the catalytically important amino acids (pink)

are too far away from each other to be able to

interact with each other and with the sub-

strate.

Biomolecules

as the tertiary structure. In insulin, it is com-

Molecular models: insulin

pact and wedge-shaped (B). The tip of the

The opposite page presents models of insulin,

wedge is formed by the B chain, which

a small protein. The biosynthesis and function

changes its direction at this point.

of this important hormone are discussed else-

Quaternary structure. Due to non-covalent

where in this book (pp. 160, 388). Monomeric

interactions, many proteins assemble to form

insulin consists of 51 amino acids, and with a

symmetrical complexes (oligomers). The indi-

molecular mass of 5.5 kDa it is only half the

vidual components of oligomeric proteins

size of the smallest enzymes. Nevertheless, it

(usually 2-12) are termed subunits or mono-

has the typical properties of a globular pro-

mers. Insulin also forms quaternary struc-

tein.

tures. In the blood, it is partly present as a

Large quantities of pure insulin are re-

dimer. In addition, there are also hexamers

quired for the treatment of diabetes mellitus

stabilized by Zn²⁺ ions (light blue) (3), which

(see p. 160). The annual requirement for insu-

represent the form in which insulin is stored

lin is over 500 kg in a country the size of

in the pancreas (see p. 160).

Germany. Formerly, the hormone had to be

obtained from the pancreas of slaughtered

B. Insulin (monomer)

animals in a complicated and expensive

procedure. Human insulin, which is produced

The van der Waals model of monomeric in-

by overexpression in genetically engineered

sulin (1) once again shows the wedge-shaped

bacteria, is now mainly used (see p. 262).

tertiary structure formed by the two chains

together. In the second model (3, bottom), the

side chains of polar amino acids are shown in

A. Structure of insulin

blue, while apolar residues are yellow or pink.

There are various different structural levels in

This model emphasizes the importance of the

proteins, and these can be briefly discussed

“hydrophobic effect” for protein folding (see

again here using the example of insulin.

p. 74). In insulin as well, most hydrophobic

The primary structure of a protein is its

side chains are located on the inside of the

amino acid sequence. During the biosynthesis

molecule, while the hydrophilic residues are

of insulin in the pancreas, a continuous pep-

located on the surface. Apparently in contra-

tide chain with 84 residues is first synthesi-

diction to this rule, several apolar side chains

zed—proinsulin (see p. 160). After folding of

(pink) are found on the surface. However, all

the molecule, the three disulfide bonds are

of these residues are involved in hydrophobic

first formed, and residues 31 to 63 are then

interactions that stabilize the dimeric and

proteolytically cleaved releasing the so-called

hexameric forms of insulin.

C peptide. The molecule that is left over (1)

In the third model (2, right), the colored

now consists of two peptide chains, the A

residues are those that are located on the

chain (21 residues, shown in yellow) and the

surface and occur invariably (red) or almost

B chain (30 residues, orange). One of the di-

invariably (orange) in all known insulins. It is

sulfide bonds is located inside the A chain,

assumed that amino acid residues that are not

and the two others link the two chains to-

replaced by other residues during the course

gether.

of evolution are essential for the protein’s

Secondary structures are regions of the

function. In the case of insulin, almost all of

peptide chain with a defined conformation

these residues are located on one side of the

(see p. 68) that are stabilized by H-bonds. In

molecule. They are probably involved in the

insulin (2), the α-helical areas are predomi-

binding of the hormone to its receptor (see

nant, making up 57% of the molecule; 6%

p. 224).

consists of β-pleated-sheet structures, and

10% of β-turns, while the remainder (27%)

cannot be assigned to any of the secondary

structures.

The three-dimensional conformation of a

protein, made up of secondary structural ele-

ments and unordered sections, is referred to

Biomolecules

spherical gel particles (diameter 10-500 µm)

Isolation and analysis of proteins

of polymeric material (shown schematically

Purified proteins are nowadays required for a

in 1a). The insides of the particles are tra-

wide variety of applications in research, med-

versed by channels that have defined diame-

icine, and biotechnology. Since the globular

ters. A protein mixture is then introduced at

proteins in particular are very unstable (see

the upper end of the column (1b) and elution

p. 72), purification is carried out at low tem-

is carried out by passing a buffer solution

peratures

(0-5 °C) and particularly gentle

through the column. Large protein molecules

separation processes are used. A few of the

(red) are unable to penetrate the particles,

methods of purifying and characterizing pro-

and therefore pass through the column

teins are discussed on this page.

quickly. Medium-sized (green) and small par-

ticles (blue) are delayed for longer or shorter

periods (1c). The proteins can be collected

A. Salt precipitation

separately from the ef uent (eluate) (2). Their

The solubility of proteins is strongly depen-

elution volume V_e depends mainly on their

dent on the salt concentration (ionic strength)

molecular mass (3).

of the medium. Proteins are usually poorly

soluble in pure water. Their solubility in-

D. SDS gel electrophoresis

creases as the ionic strength increases, be-

cause more and more of the well-hydrated

The most commonly used procedure for

anorganic ions (blue circles) are bound to

checking the purity of proteins is sodium do-

the protein’s surface, preventing aggregation

decyl sulfate polyacrylamide gel electropho-

of the molecules (salting in). At very high

resis

(SDS-PAGE). In electrophoresis, mole-

ionic strengths, the salt withdraws the hy-

cules move in an electrical field (see p. 276).

drate water from the proteins and thus leads

Normally, the speed of their movement de-

to aggregation and precipitation of the mole-

pends on three factors—their size, their shape,

cules (salting out). For this reason, adding

and their electrical charge.

salts such as ammonium sulfate (NH₄)₂SO₄

In SDS-PAGE, the protein mixture is treated

makes it possible to separate proteins from a

in such a way that only the molecules’ mass

mixture according to their degree of solubility

affects their movement. This is achieved by

(fractionation).

adding sodium dodecyl sulfate

(C₁₂H₂₅-

OSO₃Na), the sulfuric acid ester of lauryl alco-

hol (dodecyl alcohol). SDS is a detergent with

B. Dialysis

strongly amphipathic properties (see p. 28). It

Dialysis is used to remove lower-molecular

separates oligomeric proteins into their sub-

components from protein solutions, or to ex-

units and denatures them. SDS molecules

change the medium. Dialysis is based on the

bind to the unfolded peptide chains

(ca.

fact that due to their size, protein molecules

0.4 g SDS / g protein) and give them a strongly

are unable to pass through the pores of a

negative charge. To achieve complete denatu-

semipermeable membrane, while lower-mo-

ration, thiols are also added in order to cleave

lecular substances distribute themselves

the disulfide bonds (1).

evenly between the inner and outer spaces

Following electrophoresis, which is carried

over time. After repeated exchanging of the

out in a vertically arranged gel of polymeric

external solution, the conditions inside the

acrylamide (2), the separated proteins are

dialysis tube

(salt concentration, pH, etc.)

made visible by staining. In example (3), the

will be the same as in the surrounding solu-

following were separated: a) a cell extract

tion.

with hundreds of different proteins, b) a pro-

tein purified from this, and c) a mixture of

proteins with known masses.

C. Gel filtration

Gel permeation chromatography (“gel filtra-

tion”) separates proteins according to their

size and shape. This is done using a chroma-

tography column, which is filled with

Biomolecules

residues, it yields nucleoside diphosphates

Bases and nucleotides

and triphosphates—e. g., ADP and ATP, which

The nucleic acids play a central role in the

are important coenzymes in energy metabo-

storage and expression of genetic information

lism (see p. 106). All of these nucleoside phos-

(see p. 236). They are divided into two major

phates are classified as nucleotides.

classes: deoxyribonucleic acid

(DNA) func-

In nucleosides and nucleotides, the pentose

tions solely in information storage, while ri-

residues are present in the furanose form (see

bonucleic acids (RNAs) are involved in most

p. 34). The sugars and bases are linked by an

steps of gene expression and protein biosyn-

N-glycosidic bond between the C-1 of the

thesis. All nucleic acids are made up from

sugar and either the N-9 of the purine ring

nucleotide components, which in turn consist

or N-1 of the pyrimidine ring. This bond al-

of a base, a sugar, and a phosphate residue.

ways adopts the β-configuration.

DNA and RNA differ from one another in the

type of the sugar and in one of the bases that

C. Oligonucleotides, polynucleotides

they contain.

Phosphoric acid molecules can form acid-an-

hydride bonds with each other. It is therefore

A. Nucleic acid bases

possible for two nucleotides to be linked via

The bases that occur in nucleic acids are

the phosphate residues. This gives rise to di-

aromatic heterocyclic compounds derived

nucleotides with a phosphoric acid-anhydride

from either pyrimidine or purine. Five of these

structure. This group includes the coenzymes

bases are the main components of nucleic

NAD(P)⁺ and CoA, as well as the flavin

acids in all living creatures. The purine bases

derivative FAD (1; see p. 104).

adenine (abbreviation Ade, not “A”!) and gua-

If the phosphate residue of a nucleotide

nine (Gua) and the pyrimidine base cytosine

reacts with the 3 -OH group of a second nu-

(Cyt) are present in both RNA and DNA. In

cleotide, the result is a dinucleotide with a

contrast, uracil (Ura) is only found in RNA. In

phosphoric acid diester structure. Dinucleo-

DNA, uracil is replaced by thymine (Thy), the

tides of this type have a free phosphate resi-

5-methyl derivative of uracil. 5-methylcyto-

due at the 5 end and a free OH group at the 3

sine also occurs in small amounts in the DNA

end. They can therefore be extended with

of the higher animals. A large number of other

additional mononucleotides by adding fur-

modified bases occur in tRNA (see p. 82) and

ther phosphoric acid diester bonds. This is

in other types of RNA.

the way in which oligonucleotides, and ulti-

mately polynucleotides, are synthesized.

Polynucleotides consisting of ribonucleo-

B. Nucleosides, nucleotides

tide components are called ribonucleic acid

When a nucleic acid base is N-glycosidically

(RNA), while those consisting of deoxyribonu-

linked to ribose or 2-deoxyribose (see p. 38), it

cleotide monomers are called deoxyribonu-

yields a nucleoside. The nucleoside adenosine

cleic acid (DNA; see p. 84). To describe the

(abbreviation: A) is formed in this way from

structure of polynucleotides, the abbrevia-

adenine and ribose, for example. The corre-

tions for the nucleoside components are writ-

sponding derivatives of the other bases are

ten from left to right in the 5

direction.

called guanosine (G), uridine (U), thymidine

The position of the phosphate residue is also

(T) and cytidine (C). When the sugar compo-

sometimes indicated by a “p”. In this way, the

nent is

2-deoxyribose, the product is a

structure of the RNA segment shown Fig. 2

deoxyribonucleoside—e. g.,

2 -deoxyadeno-

can be abbreviated as ..pUpG.. or simply as

sine (dA, not shown). In the cell, the 5 OH

..^UG .. .

group of the sugar component of the nucleo-

side is usually esterified with phosphoric acid.

2 -Deoxythymidine (dT) therefore gives rise

2 -deoxythymidine-5 -monophosphate

(dTMP), one of the components of DNA (2).

If the 5 phosphate residue is linked via an

acid-anhydride bond to additional phosphate

Nucleotides and Nucleic Acids

A. Nucleic acid bases

Pyrimidine bases

CH₃

Pyrimidine

Uracil (Ura)

Thymine (Thy)

Cytosine (Cyt)

Purine bases

H₂N

Purine

Adenine (Ade)

Guanine (Gua)

B. Nucleosides, nucleotides

NH₂

CH₃

CH₂

H H

OH OH

OH H

1. Adenosine (Ado)

2. 2'-Deoxythymidine 5'-monophosphate (dtMP)

C. Oligonucleotides, polynucleotides

Flavin

To the 5' end

H₃C

Phosphoric acid-

CH₂

anhydride bond

H₃C

CH₂

NH₂

Ribitol

H H

H₂C

CH₂

Phosphoric acid

O OH

H H

Ribose

diester bond

To the 3' end

1. Flavin adenine dinucleotide

OH OH

(FAD)

2. RNA (section)

Biomolecules

Messenger RNAs (mRNAs) transfer genetic

RNA

information from the cell nucleus to the cyto-

Ribonucleic acids (RNAs) are polymers con-

plasm. The primary transcripts are substan-

sisting of nucleoside phosphate components

tially modified while still in the nucleus

that are linked by phosphoric acid diester

(mRNA maturation; see p. 246). Since mRNAs

bonds (see p. 80). The bases the contain are

have to be read codon by codon in the ribo-

mainly uracil, cytosine, adenine, and guanine,

some, they must not form a stable tertiary

but many unusual and modified bases are also

structure. This is ensured in part by the at-

found in RNAs (B).

tachment of RNA-binding proteins, which pre-

vent base pairing. Due to the varying amounts

of information that they carry, the lengths of

A. Ribonucleic acids (RNAs)

mRNAs also vary widely. Their lifespan is usu-

RNAs are involved in all the individual steps of

ally short, as they are quickly broken down

gene expression and protein biosynthesis (see

after translation.

pp. 242-253). The properties of the most im-

Small nuclear RNAs (snRNAs) are involved

portant forms of RNA are summarized in the

in the splicing of mRNA precursors

(see

table. The schematic diagram also gives an

p. 246). They associate with numerous pro-

idea of the secondary structure of these mol-

teins to form “spliceosomes.”

ecules.

In contrast to DNA, RNAs do not form ex-

B. Transfer RNA (tRNA^Phe)

tended double helices. In RNAs, the base pairs

(see p. 84) usually only extend over a few

The transfer RNAs (tRNAs) function during

residues. For this reason, substructures often

translation (see p. 250) as links between the

arise that have a finger shape or clover-leaf

nucleic acids and proteins. They are small

shape in two-dimensional representations. In

RNA molecules consisting of 70-90 nucleoti-

these, the paired stem regions are linked by

des, which “recognize” specific mRNA codons

loops. Large RNAs such as ribosomal 16S-

with their anticodons through base pairing. At

rRNA (center) contain numerous “stem and

the same time, at their 3

end (sequence

loop” regions of this type. These sections are

.. CCA-3 ) they carry the amino acid that is

again folded three-dimensionally—i. e., like

assigned to the relevant mRNA codon accord-

proteins, RNAs have a tertiary structure (see

ing to the genetic code (see p. 248).

p. 86). However, tertiary structures are only

The base sequence and the tertiary struc-

known of small RNAs, mainly tRNAs. The dia-

ture of the yeast tRNA specific for phenylala-

grams in Fig. B and on p. 86 show that the

nine (tRNA^Phe) is typical of all tRNAs. The

“clover-leaf” structure is not recognizable in

molecule (see also p. 86) contains a high pro-

a three-dimensional representation.

portion of unusual and modified components

Cellular RNAs vary widely in their size,

(shaded in dark green in Fig. 1). These include

structure, and lifespan. The great majority of

pseudouridine (Ψ), dihydrouridine (D), thymi-

them are ribosomal RNA (rRNA), which in

dine (T), which otherwise only occurs in DNA,

several forms is a structural and functional

and many methylated nucleotides such as 7-

component of ribosomes (see p. 250). Riboso-

methylguanidine

(m⁷G) and—in the anti-

mal RNA is produced from DNA by transcrip-

codon—2 -O-methylguanidine (m²G). Numer-

tion in the nucleolus, and it is processed there

ous base pairs, sometimes deviating from the

and assembled with proteins to form ribo-

usual pattern, stabilize the molecule’s confor-

some subunits (see pp. 208, 242). The bacte-

mation (2).

rial 16S-rRNA shown in Fig. A, with 1542 nu-

cleotides (nt), is a component of the small

ribosomae subunit, while the much smaller

5S-rRNA (118 nt) is located in the large sub-

unit.

Nucleic Acids

A. Ribonucleic acids (RNAs)

tRNA

mRNA U1-snRNA

16S-RNA

5S-rRNA

tRNA

rRNA

Type

mRNA

snRNA

>50

Species per cell

> 1000

~ 10

74 - 95

120 - 5000

Length (b)

400 - 6000

100 - 300

10-20%

80%

Proportion

< 1%

Long

Lifespan

Short

Long

Translation

Function

Translation

Splicing

B. Transfer RNA (tRNA^Phe)

Phe

TΨ loop

H₂C

D loop

CH₂

H H

Variable

loop

O OH

Phe

mRNA

Dihydrouridine (D)

Pseudouridine (Ψ)

Anticodon

Codon

TΨ loop

Normal base

pairing

C U

2. Conformation

Unusual base

G A C AC

pairing

C U G U

CUCG

G AG C

D loop

2'-O-methylguanidine (m

²G)

7-methylguanidine (m⁷G)

Variable

CH₃

loop

A A

Anticodon

CH₂

NH₂

CH₂

H H

* Methylated base

O OCH₃

O OH

1. Structure

Biomolecules

sugar and phosphate residues in the back-

DNA

bone. Along the whole length of the DNA

molecule, there are two depressions—re-

A. DNA: structure

ferred to as the “minor groove” and the “ma-

Like RNAs (see p. 82), deoxyribonucleic acids

jor groove”—that lie between the strands.

(DNAs) are polymeric molecules consisting of

nucleotide building blocks. Instead of ribose,

B. Coding of genetic information

however, DNA contains 2 -deoxyribose, and

the uracil base in RNA is replaced by thymine.

In all living cells, DNA serves to store genetic

The spatial structure of the two molecules

information. Specific segments of DNA

also differs (see p. 86).

(“genes”) are transcribed as needed into

The first evidence of the special structure

RNAs, which either carry out structural or

of DNA was the observation that the amounts

catalytic tasks themselves or provide the basis

of adenine and thymine are almost equal in

for synthesizing proteins (see p. 82). In the

every type of DNA. The same applies to gua-

latter case, the DNA codes for the primary

nine and cytosine. The model of DNA struc-

structure of proteins. The “language” used in

ture formulated in 1953 explains these con-

this process has four letters (A, G, C, and T). All

stant base ratios: intact DNA consists of two

of the words (“codons”) contain three letters

polydeoxynucleotide molecules

(“strands”).

(“triplets”), and each triplet stands for one of

Each base in one strand is linked to a comple-

the 20 proteinogenic amino acids.

mentary base in the other strand by H-bonds.

The two strands of DNA are not function-

Adenine is complementary to thymine, and

ally equivalent. The template strand (the (-)

guanine is complementary to cytosine. One

strand or “codogenic strand,” shown in light

purine base and one pyrimidine base are

gray in Fig. 1) is the one that is read during the

thus involved in each base pair.

synthesis of RNA (transcription; see p. 242).

The complementarity of A with T and of G

Its sequence is complementary to the RNA

with C can be understood by considering the

formed. The sense strand (the (+) strand or

H bonds that are possible between the differ-

“coding strand,” shown in color in Figs. 1 and

ent bases. Potential donors

(see p. 6) are

2) has the same sequence as the RNA, except

amino groups (Ade, Cyt, Gua) and ring NH

that T is exchanged for U. By convention, it is

groups. Possible acceptors are carbonyl oxy-

agreed that gene sequences are expressed by

gen atoms (Thy, Cyt, Gua) and ring nitrogen

reading the sequence of the sense strand in

atoms. Two linear and therefore highly stable

the 5

direction. Using the genetic code

bonds can thus be formed in A-T pairs, and

(see p. 248), in this case the protein sequence

three in G-C pairs.

(3) is obtained directly in the reading direc-

Base pairings of this type are only possible,

tion usual for proteins—i. e., from the N termi-

however, when the polarity of the two strands

nus to the C terminus.

differs—i. e., when they run in opposite direc-

tions (see p. 80). In addition, the two strands

have to be intertwined to form a double helix.

Due to steric hindrance by the 2 -OH groups

of the ribose residues, RNA is unable to form a

double helix. The structure of RNA is therefore

less regular than that of DNA (see p. 82).

The conformation of DNA that predomi-

nates within the cell (known as B-DNA) is

shown schematically in Fig. A2 and as a van

der Waals model in Fig. B1. In the schematic

diagram

(A2), the deoxyribose-phosphate

“backbone” is shown as a ribbon. The bases

(indicated by lines) are located on the inside

of the double helix. This area of DNA is there-

fore apolar. By contrast, the molecule’s surface

is polar and negatively charged, due to the

Biomolecules

A-DNA arises when B-DNA is dehydrated. It

Molecular models: DNA and RNA

probably does not occur in the cell.

The illustration opposite shows selected nuc-

In the Z-conformation (3), which can occur

leic acid molecules. Fig. A shows various con-

within GC-rich regions of B-DNA, the organ-

formations of DNA, and Fig. B shows the spa-

ization of the nucleotides is completely differ-

tial structures of two small RNA molecules. In

ent. In this case, the helix is left-handed, and

both, the van der Waals models (see p. 6) are

the backbone adopts a characteristic zig-zag

accompanied by ribbon diagrams that make

conformation (hence “Z-DNA”). The Z double

the course of the chains clear. In all of the

helix has a smaller pitch than B-DNA. DNA

models, the polynucleotide

“backbone” of

segments in the Z conformation probably

the molecule is shown in a darker color, while

have physiological significance, but details

the bases are lighter.

are not yet known.

A. DNA: conformation

B. RNA

Investigations of synthetic DNA molecules

RNA molecules are unable to form extended

have shown that DNA can adopt several dif-

double helices, and are therefore less highly

ferent conformations. All of the DNA seg-

ordered than DNA molecules. Nevertheless,

ments shown consist of 21 base pairs (bp)

they have defined secondary and tertiary

and have the same sequence.

structures, and a large proportion of the nu-

By far the most common form is B-DNA (2).

cleotide components enter into base pairings

As discussed on p. 84, this consists of two

with other nucleotides. The examples shown

antiparallel polydeoxynucleotide strands in-

here are 5S-rRNA (see p. 242), which occurs as

tertwined with one another to form a right-

a structural component in ribosomes, and a

handed double helix. The “backbone” of these

tRNA molecule from yeast (see p. 82) that is

strands is formed by deoxyribose and phos-

specific for phenylalanine.

phate residues linked by phosphoric acid di-

Both molecules are folded in such a way

ester bonds.

that the 3

end and the 5

end are close to-

In the B conformation, the aromatic rings of

gether. As in DNA, most of the bases are lo-

the nucleobases are stacked at a distance of

cated in the inside of the structures, while the

0.34 nm almost at right angles to the axis of

much more polar “backbone” is turned out-

the helix. Each base is rotated relative to the

wards. An exception to this is seen in the

preceding one by an angle of 35°. A complete

three bases of the anticodon of the tRNA

turn of the double helix (360°) therefore con-

(pink), which have to interact with mRNA

tains around 10 base pairs (abbreviation: bp),

and therefore lie on the surface of the mole-

i. e., the pitch of the helix is 3.4 nm. Between

cule. The bases of the conserved CCA triplet at

the backbones of the two individual strands

the 3

end (red) also jut outward. During

there are two grooves with different widths.

amino acid activation (see p. 248), they are

The major groove is visible at the top and

recognized and bound by the ligases.

bottom, while the narrower minor groove is

seen in the middle. DNA-binding proteins and

transcription factors (see pp. 118, 244) usually

enter into interactions in the area of the major

groove, with its more easily accessible bases.

In certain conditions, DNA can adopt the A

conformation (1). In this arrangement, the

double helix is still right-handed, but the

bases are no longer arranged at right angles

to the axis of the helix, as in the B form. As can

be seen, the A conformation is more compact

than the other two conformations. The minor

groove almost completely disappears, and the

major groove is narrower than in the B form.

Metabolism

Enzymes: basics

C. Enzyme classes

Enzymes are biological catalysts—i. e., sub-

More than 2000 different enzymes are cur-

stances of biological origin that accelerate

rently known. A system of classification has

chemical reactions (see p. 24). The orderly

been developed that takes into account both

course of metabolic processes is only possible

their reaction specificity and their substrate

because each cell is equipped with its own

specificity. Each enzyme is entered in the En-

genetically determined set of enzymes. It is

zyme Catalogue with a four-digit Enzyme

only this that allows coordinated sequences

Commission number (EC number). The first

of reactions (metabolic pathways; see p. 112).

digit indicates membership of one of the six

Enzymes are also involved in many regulatory

major classes. The next two indicate sub-

mechanisms that allow the metabolism to

classes and subsubclasses. The last digit indi-

adapt to changing conditions (see p. 114). Al-

cates where the enzyme belongs in the sub-

most all enzymes are proteins. However,

subclass. For example, lactate dehydrogenase

there are also catalytically active ribonucleic

(see pp. 98-101) has the EC number 1.1.1.27

acids, the “ribozymes” (see pp. 246, 252).

(class 1, oxidoreductases; subclass 1.1, CH-OH

group as electron donor; sub-subclass 1.1.1,

NAD(P)⁺ as electron acceptor).

A. Enzymatic activity

Enzymes with similar reaction specificities

The catalytic action of an enzyme, its activity,

are grouped into each of the six major classes:

is measured by determining the increase in

The oxidoreductases (class 1) catalyze the

the reaction rate under precisely defined con-

transfer of reducing equivalents from one re-

ditions—i. e., the difference between the turn-

dox system to another.

over (violet) of the catalyzed reaction (or-

The transferases

(class

2) catalyze the

ange) and uncatalyzed reaction (yellow) in a

transfer of other groups from one molecule

specific time interval. Normally, reaction rates

to another. Oxidoreductases and transferases

are expressed as the change in concentration

generally require coenzymes (see pp. 104ff.).

per unit of time (mol

1-1 s^-1; see p. 22).

The hydrolases (class 3) are also involved in

Since the catalytic activity of an enzyme is

group transfer, but the acceptor is always a

independent of the volume, the unit used

water molecule.

for enzymes is usually turnover per unit time,

Lyases (class 4, often also referred to as

expressed in katal (kat, mol s^-1). However,

“synthases”) catalyze reactions involving ei-

the international unit U is still more com-

ther the cleavage or formation of chemical

monly used (µmol turnover min^-1; 1 U =

bonds, with double bonds either arising or

16.7 nkat).

disappearing.

The isomerases

(class

5) move groups

within a molecule, without changing the

B. Reaction and substrate specificity

gross composition of the substrate.

The action of enzymes is usually very specific.

The ligation reactions catalyzed by ligases

This applies not only to the type of reaction

(“synthetases,” class 6) are energy-dependent

being catalyzed (reaction specificity), but also

and are therefore always coupled to the hy-

to the nature of the reactants (“substrates”)

drolysis of nucleoside triphosphates.

that are involved (substrate specificity; see

p. 94). In Fig. B, this is illustrated schemati-

In addition to the enzyme name, we also

cally using a bond-breaking enzyme as an

usually give its EC number. The annotated

example. Highly specific enzymes (type A,

enzyme list (pp. 420ff.) includes all of the en-

top) catalyze the cleavage of only one type

zymes mentioned in this book, classified ac-

of bond, and only when the structure of the

cording to the Enzyme Catalog system.

substrate is the correct one. Other enzymes

(type B, middle) have narrow reaction specif-

icity, but broad substrate specificity. Type C

enzymes (with low reaction specificity and

low substrate specificity, bottom) are very

rare.

Enzymes

A. Enzymatic activity

B. Reaction and substrate specificity

Group

Bond

Turnover (mol product. s^-1)

without enzyme

Group

Turnover (mol product. s^-1) with enzyme

Enzyme activity (mol. s^-1= kat)

Reaction specificity

Substrate specificity

1 Katal (kat): Amount of enzyme

High

which increases

-1

High

Low

turnover by 1 mol . s

Low

C. The enzyme classes

Class

Reaction type

Important subclasses

= Reduction equivalent

Dehydrogenases

Oxidases, peroxidases

1 Oxidoreductases

Reductases

Monooxygenases

Dioxygenases

Ared

Box

Aox

Bred

C₁-Transferases

Glycosyltransferases

2 Transferases

Aminotransferases

Phosphotransferases

A-B

B-C

Esterases

Glycosidases

3 Hydrolases

Peptidases

Amidases

A-B

H₂O

A-H

B-OH

C-C-Lyases

C-O-Lyases

4 Lyases

C-N-Lyases

(“synthases”)

C-S-Lyases

A-B

Epimerases

cis trans Isomerases

5 Isomerases

Intramolecular

transferases

Iso-A

X=A,G,U,C

XDP

C-C-Ligases

C-O-Ligases

6 Ligases

P P P

P P

C-N-Ligases

(“synthetases”)

C-S-Ligases

XTP

A-B

Metabolism

that productive A-B complexes will arise. In

Enzyme catalysis

addition, binding of the substrates results in

Enzymes are extremely effective catalysts.

removal of their hydration shells. As a result

They can increase the rate of a catalyzed re-

of the exclusion of water, very different con-

action by a factor of 10¹² or more. To grasp the

ditions apply in the active center of the en-

mechanisms involved in enzyme catalysis, we

zyme during catalysis than in solution (3-5).

can start by looking at the course of an un-

A third important factor is the stabilization of

catalyzed reaction more closely.

the transition state as a result of interactions

between the amino acid residues of the pro-

tein and the substrate (4). This further re-

A. Uncatalyzed reaction

duces the activation energy needed to create

The reaction A + B

C + D is used as an

the transition state. Many enzymes also take

example. In solution, reactants A and B are

up groups from the substrates or transfer

surrounded by a shell of water molecules

them to the substrates during catalysis.

(the hydration shell), and they move in ran-

Proton transfers are particularly common.

dom directions due to thermal agitation. They

This acid-base catalysis by enzymes is much

can only react with each other if they collide

more effective than the exchange of protons

in a favorable orientation. This is not very

between acids and bases in solution. In many

probable, and therefore only occurs rarely.

cases, chemical groups are temporarily bound

Before conversion into the products C + D,

covalently to the amino acid residues of the

the collision complex A-B has to pass through

enzyme or to coenzymes during the catalytic

a transition state, the formation of which usu-

cycle. This effect is referred to as covalent

ally requires a large amount of activation

catalysis (see the transaminases, for example;

energy, E_a (see p. 22). Since only a few A-B

p. 178). The principles of enzyme catalysis

complexes can produce this amount of en-

sketched out here are discussed in greater

ergy, a productive transition state arises

detail on p. 100 using the example of lactate

even less often than a collision complex. In

dehydrogenase.

solution, a large proportion of the activation

energy is required for the removal of the hy-

C. Principles of enzyme catalysis

dration shells between A and B. However,

charge displacements and other chemical

Although it is dif cult to provide quantitative

processes within the reactants also play a

estimates of the contributions made by indi-

role. As a result of these limitations, conver-

vidual catalytic effects, it is now thought that

sion only happens occasionally in the absence

the enzyme’s stabilization of the transition

of a catalyst, and the reaction rate v is low,

state is the most important factor. It is not

even when the reaction is thermodynamically

tight binding of the substrate that is impor-

possible—i. e., when ∆G < 0 (see p. 18).

tant, therefore—this would increase the acti-

vation energy required by the reaction, rather

than reducing it—but rather the binding of the

B. Enzyme-catalyzed reaction

transition state. This conclusion is supported

Shown here is a sequential mechanism in

by the very high af nity of many enzymes for

which substrates A and B are bound and prod-

analogues of the transition state (see p. 96). A

ucts C and D are released, in that order. An-

simple mechanical analogy may help clarify

other possible reaction sequence, known as

this (right). To transfer the metal balls (the

the “ping-pong mechanism,” is discussed on

reactants) from location EA (the substrate

p. 94.

state) via the higher-energy transition state

Enzymes are able to bind the reactants

to EP (the product state), the magnet (the

(their substrates) specifically at the active cen-

catalyst) has to be orientated in such a way

ter. In the process, the substrates are oriented

that its attractive force acts on the transition

in relation to each other in such a way that

state (bottom) rather than on EA (top).

they take on the optimal orientation for the

formation of the transition state (1-3). The

proximity and orientation of the substrates

therefore strongly increase the likelihood

Metabolism

enzymes whose substrate saturation curves

Enzyme kinetics I

are shown in diagram 1, enzyme 2 has the

The kinetics of enzyme-catalyzed reactions

higher af nity for A

[K_m = 1 mmol l^-1);

(i. e., the dependence of the reaction rate on

Vmax, by contrast, is much lower than with

the reaction conditions) is mainly determined

enzyme 1.

by the properties of the catalyst. It is therefore

Since v approaches V asymptotically with

more complex than the kinetics of an uncata-

increasing values of [A], it is dif cult to obtain

lyzed reaction (see p. 22). Here we discuss

reliable values for V_max—and thus for K_m as

these issues using the example of a simple

well—from diagrams plotting v against [A]. To

first-order reaction (see p. 22)

get around this, the Michaelis-Menten equa-

tion can be arranged in such a way that the

measured points lie on a straight line. In the

A. Michaelis-Menten kinetics

Lineweaver-Burk plot

(2),

1/v is plotted

In the absence of an enzyme, the reaction rate v

against 1/[A]. The intersections of the line of

is proportional to the concentration of sub-

best fit with the axes then produce 1/V_max

stance A (top). The constant k is the rate con-

and—1/K_m. This type of diagram is very clear,

stant of the uncatalyzed reaction. Like all cat-

but for practical purposes it is less suitable for

alysts, the enzyme E (total concentration [E]_t)

determining V_max and K_m. Calculation meth-

creates a new reaction pathway. Initially, A is

ods using personal computers are faster and

bound to E (partial reaction 1, left). If this

more objective.

reaction is in chemical equilibrium, then

with the help of the law of mass action—and

B. Isosteric and allosteric enzymes

taking into account the fact that [E]_t = [E] +

[EA]—one can express the concentration [EA]

Many enzymes can occur in various conforma-

of the enzyme-substrate complex as a func-

tions (see p. 72), which have different catalytic

tion of [A] (left). The Michaelis constant K_m

properties and whose proportion of the total

thus describes the state of equilibrium of the

number of enzyme molecules is influenced by

reaction. In addition, we know that k_cat > k—in

substrates and other ligands (see pp. 116 and

other words, enzyme-bound substrate reacts

280, for example). Allosteric enzymes of this

to B much faster than A alone (partial reaction

type, which are usually present in oligomeric

2, right). k_cat, the enzyme’s turnover number,

form, can be recognized by their S-shaped

corresponds to the number of substrate mol-

(sigmoidal) saturation curves, which cannot

ecules converted by one enzyme molecule per

be described using the Michaelis model. In

second. Like the conversion A B, the forma-

the case of isosteric enzymes (with only one

tion of B from EA is a first-order reaction—i. e.,

enzyme conformation, 1), the ef ciency of

v = k

[EA] applies. When this equation is

substrate binding

(dashed curve) declines

combined with the expression already de-

constantly with increasing [A], because the

rived for EA, the result is the Michaelis-

number of free binding sites is constantly

Menten equation.

decreasing. In most allosteric enzymes (2),

In addition to the variables v and [A], the

the binding ef ciency initially rises with in-

equation also contains two parameters that do

creasing

[A], because the free enzyme is

not depend on the substrate concentration

present

in a low-af nity conformation

[A], but describe properties of the enzyme

(square symbols), which is gradually con-

itself: the product k_cat

[E]_g is the limiting

verted into a higher-af nity form (round sym-

value for the reaction rate at a very high [A],

bols) as a result of binding with A. It is only at

the maximum velocity V_max of the reaction

high [A] values that a lack of free binding sites

(recommended abbreviation: V). The Michae-

becomes noticeable and the binding strength

lis constant K_m characterizes the af nity of the

decreases again. In other words, the af nity of

enzyme for a substrate. It corresponds to the

allosteric enzymes is not constant, but de-

substrate concentration at which v reaches

pends on the type and concentration of the

half of V_max (if v = V_max/2, then [A]/(K_m +

ligand.

[A]) = 1/2, i. e. [A] is then = K_m). A high af nity

of the enzyme for a substrate therefore leads

to a low K_m value, and vice versa. Of the two

Enzymes

A. Michaelis Menten kinetics

Uncatalyzed reaction

Enzyme-catalyzed reaction

v = k · [A ]

Partial reaction 1:

Partial reaction 2:

formation and decay

formation of the

of enzyme-substrate

product of EA

complex EA

kcat

E + A

[EA]

E + B

[A]

[EA] = [E]

v = k

cat · [EA]

m + [A]

Michaelis constant

Maximum velocity

Km (mol · l-1)

[A]

Vmax = kcat · [E]g (mol · l-1· s-1)

kcat [E]g

v =

[A]

1.0

Enzyme 1

0.8

0.6

-1/K

0.4

-1/K

Enzyme 2

0.2

1/V

max

1/V

Vmax

max

0.0

100

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

Concentration [A] (mM)

Reciprocal concentration 1/[A] (mM^-1)

1. Hyperbolic plot

2. Lineweaver-Burk plot

B. Isosteric and allosteric enzymes

Isosteric

Allosteric

(n=1)

(n=3)

Vmax

Bonding

strenght

Bonding

strenght

[A]

O.5

[A] (mmol · l^-1)

Metabolism

B. Substrate specificity

Enzyme kinetics II

Enzymes “recognize” their substrates in a

The catalytic properties of enzymes, and con-

highly specific way (see p. 88). It is only the

sequently their activity (see p. 90), are influ-

marked substrate specificity of the enzymes

enced by numerous factors, which all have to

that makes a regulated metabolism possible.

be optimized and controlled if activity meas-

This principle can be illustrated using the ex-

urements are to be carried out in a useful and

ample of the two closely related proteinases

reproducible fashion. These factors include

trypsin and chymotrypsin. Both belong to the

physical quantities (temperature, pressure),

group of serine proteinases and contain the

the chemical properties of the solution (pH

same “triad” of catalytically active residues

value, ionic strength), and the concentrations

(Asp-His-Ser, shown here in green; see

of the relevant substrates, cofactors, and in-

p. 176). Trypsin selectively cleaves peptide

hibitors.

bonds on the C-terminal side of basic amino

acids (lysine and arginine), while chymotryp-

A. pH and temperature dependency of

sin is specific for hydrophobic residues. The

enzyme activity

substrate binding “pockets” of both enzymes

have a similar structure, but their amino acid

The effect of enzymes is strongly dependent

sequences differ slightly. In trypsin, a nega-

on the pH value (see p. 30). When the activity

tively charged aspartate residue

(Asp-189,

is plotted against pH, a bell-shaped curve is

red) is arranged in such a way that it can

usually obtained (1). With animal enzymes,

bind and fix the basic group in the side chain

the pH optimum—i. e., the pH value at which

of the substrate. In chymotrypsin, the “bind-

enzyme activity is at its maximum—is often

ing pocket” is slightly narrower, and it is lined

close to the pH value of the cells (i. e., pH 7).

with neutral and hydrophobic residues that

However, there are also exceptions to this. For

stabilize the side chains of apolar substrate

example, the proteinase pepsin (see p. 270),

amino acids through hydrophobic interac-

which is active in the acidic gastric lumen,

tions (see p. 28).

has a pH optimum of 2, while other enzymes

(at least in the test tube) are at their most

active at pH values higher than 9. The bell

C. Bisubstrate kinetics

shape of the activity-pH profile results from

Almost all enzymes—in contrast to the sim-

the fact that amino acid residues with ioniz-

plified description given on p. 92—have more

able groups in the side chain are essential for

than one substrate or product. On the other

catalysis. In example (1), these are a basic

hand, it is rare for more than two substrates to

group B (pK_a = 8), which has to be protonated

be bound simultaneously. In bisubstrate reac-

in order to become active, and a second acidic

tions of the type A + B C + D, a number of

amino acid AH (pK_a = 6), which is only active

reaction sequences are possible. In addition to

in a dissociated state. At the optimum pH of 7,

the sequential mechanisms

(see p. 90), in

around 90% of both groups are present in the

which all substrates are bound in a specific

active form; at higher and lower values, one

sequence before the product is released, there

or the other of the groups increasingly passes

are also mechanisms in which the first sub-

into the inactive state.

strate A is bound and immediately cleaved. A

The temperature dependency of enzymatic

part of this substrate remains bound to the

activity is usually asymmetric. With increas-

enzyme, and is then transferred to the second

ing temperature, the increased thermal

substrate B after the first product C has been

movement of the molecules initially leads to

released. This is known as the ping-pong

a rate acceleration (see p.22). At a certain

mechanism, and it is used by transaminases,

temperature, the enzyme then becomes un-

for example (see p. 178). In the Lineweaver—

stable, and its activity is lost within a narrow

Burk plot (right; see p. 92), it can be recog-

temperature difference as a result of denatu-

nized in the parallel shifting of the lines when

ration (see p. 74). The optimal temperatures of

[B] is varied.

the enzymes in higher organisms rarely ex-

ceed 50 °C, while enzymes from thermophilic

bacteria found in hot springs, for instance,

may still be active at 100 °C.

Enzymes

A. pH and temperature dependency of enzyme activity

Proportion BH

Proportion A

1.0

BH⁺

A-

Denaturation

Enzyme

0.8

active

Increased

0.6

activity due

BH⁺

A-

to temperature

increase

0.4

BH⁺

0.2

A-

Enzyme

0.0

denatured

Temperature (°C)

B. Substrate specificity

Asp-189

Substrate (-X-Arg-Y-)

Ser-189

Substrate (-X-Phe-Y-)

Ser-195

His-57

Asp-102

Trypsin (3.4.21.4)

Chymotrypsin (3.4.21.1)

-X-Y-Arg (Lys)-Z-

-X-Y-Tyr (Trp, Phe, Leu)-Z-

C. Bisubstrate kinetics

3. Covalent

intermediate

2. EA complex

product E'

{B}

Active center

1. Free enzyme E

5. EP2 complex

4. E'B complex

1/{A}(mM-1)

Metabolism

“Suicide substrates” (5) are substrate ana-

Inhibitors

logs that also contain a reactive group. Ini-

Many substances can affect metabolic pro-

tially, they bind reversibly, and then they

cesses by influencing the activity of

form a covalent bond with the active center

enzymes. Enzyme inhibitors are particularly

of the enzyme. Their effect is therefore also

important here. A large proportion of

non-competitive. A well-known example of

medicines act as enzyme inhibitors. Enzyme-

this is the antibiotic penicillin (see p. 254).

kinetic experiments are therefore an impor-

Allosteric inhibitors bind to a separate

tant aspect of drug development and testing

binding site outside the active center

(6).

procedures. Natural metabolites are also in-

This results in a conformational change in

volved in regulatory processes as inhibitors

the enzyme protein that indirectly reduces

(see p. 114).

its activity (see p. 116). Allosteric effects prac-

tically only occur in oligomeric enzymes. The

kinetics of this type of system can no longer

A. Types of inhibitor

be described using the simple Micha-

Most enzyme inhibitors act reversibly—i. e.,

elis-Menten model.

they do not cause any permanent changes in

the enzyme. However, there are also irrever-

B. Inhibition kinetics

sible inhibitors that permanently modify the

target enzyme. The mechanism of action of an

In addition to the Lineweaver-Burk plot (see

inhibitor—its inhibition type—can be deter-

p. 92), the Eadie-Hofstee plot is also com-

mined by comparing the kinetics (see p. 92)

monly used. In this case, the velocity v is

of the inhibited and uninhibited reactions (B).

plotted against v /[A]. In this type of plot,

This makes it possible to distinguish compet-

Vmax corresponds to the intersection of the

itive inhibitors

(left) from noncompetitive

approximation lines with the v axis, while

inhibitors

(right), for example. Allosteric

Km is derived from the gradient of the lines.

inhibition is particularly important for meta-

Competitive and non-competitive inhibitors

bolic regulation (see below).

are also easily distinguishable in the Eadie—

Substrate analogs (2) have properties sim-

Hofstee plot. As mentioned earlier, competi-

ilar to those of one of the substrates of the

tive inhibitors only influence K_m, and not

target enzyme. They are bound by the en-

Vmax. The lines obtained in the absence and

zyme, but cannot be converted further and

presence of an inhibitor therefore intersect on

therefore reversibly block some of the enzyme

the ordinate. Non-competitive inhibitors pro-

molecules present. A higher substrate concen-

duce lines that have the same slope (K_m un-

tration is therefore needed to achieve a half-

changed) but intersect with the ordinate at a

maximum rate; the Michaelis constant K_m

lower level. Another type of inhibitor, not

increases (B). High concentrations of the sub-

shown here, in which V_max and K_m are re-

strate displace the inhibitor again. The max-

duced by the same factor, is referred to as

imum rate V_max is therefore not influenced by

uncompetitive. Inhibitors with purely uncom-

this type of inhibition. Because the substrate

petitive effects are rare. A possible explana-

and the inhibitor compete with one another

tion for this type of inhibition is selective

for the same binding site on the enzyme, this

binding of the inhibitor to the EA complex.

type of inhibition is referred to as compe-

Allosteric enzymes shift the target en-

titive. Analogs of the transition state (3) usu-

zyme’s saturation curve to the left

(see

ally also act competitively.

p. 92). In Eadie-Hofstee and Lineweaver-Burk

When an inhibitor interacts with a group

plots (see p. 92), allosteric enzymes are recog-

that is important for enzyme activity, but does

nizable because they produce curved lines

not affect binding of the substrate, the inhi-

(not shown).

bition is non-competitive (right). In this case,

Km remains unchanged, but the concentration

of functional enzyme [E]_t, and thus V_max, de-

crease. Non-competitive inhibitors generally

act irreversibly, by modifying functional

groups of the target enzyme (4).

Metabolism

The differences in sequence between the M

Lactate dehydrogenase: structure

and H subunits are mainly conservative—i. e.,

Lactate dehydrogenase (LDH, EC 1.1.1.27) is

both residues are of the same type, e. g. gly-

discussed in some detail here and on the

cine (G) and alanine (A), or arginine (R) and

next page as an example of the structure

lysine (K). Non-conservative exchanges are

and function of an enzyme.

less frequent—e. g., lysine (K) for glutamine

(Q), or threonine (T) for glutamic acid (E).

Overall, the H subunit contains more acidic

A. Lactate dehydrogenase: structure

and fewer basic residues than the M form, and

The active form of lactate dehydrogenase

it therefore has a more strongly negative

(mass 144 kDa) is a tetramer consisting of

charge. This fact is exploited to separate the

four subunits (1). Each monomer is formed

isoenzymes using electrophoresis

(2; see

by a peptide chain of

334

amino acids

pp. 78, 276). The isoenzyme LDH-1, consisting

(36 kDa). In the tetramer, the subunits

of four H subunits, migrates fastest, and the

occupy equivalent positions (1); each mono-

M₄ isoenzyme is slowest.

mer has an active center. Depending on met-

abolic conditions, LDH catalyzes NADH-de-

The separation and analysis of isoenzymes

pendent reduction of pyruvate to lactate, or

in blood samples is important in the diagnosis

NAD⁺-dependent oxidation of lactate to pyru-

of certain diseases. Normally, only small

vate (see p. 18).

amounts of enzyme activity are found in se-

The active center of an LDH subunit is

rum. When an organ is damaged, intracellular

shown schematically in Fig. 2. The peptide

enzymes enter the blood and can be demon-

backbone is shown as a light blue tube. Also

strated in it (serum enzyme diagnosis). The

shown are the substrate lactate (red), the

total activity of an enzyme reflects the se-

coenzyme NAD⁺ (yellow), and three amino

verity of the damage, while the type of iso-

acid side chains (Arg-109, Arg-171, and His-

enzyme found in the blood provides evidence

195; green), which are directly involved in the

of the site of cellular injury, since each of the

catalysis. A peptide loop

(pink) formed by

genes is expressed in the various organs at

amino acid residues 98-111 is also shown. In

different levels. For example, the liver and

the absence of substrate and coenzyme, this

skeletal muscles mainly produce M subunits

partial structure is open and allows access to

of lactate dehydrogenase

(M for muscle),

the substrate binding site (not shown). In the

while the brain and cardiac muscle mainly

enzyme lactate NAD⁺ complex shown, the

express H subunits (H for heart). In conse-

peptide loop closes the active center. The cat-

quence, each organ has a characteristic isoen-

alytic cycle of lactate dehydrogenase is dis-

zyme pattern (3). Following cardiac infarction,

cussed on the next page.

for example, there is a strong increase in the

amount of LDH-1 in the blood, while the con-

centration of LDH-5 hardly changes. The iso-

B. Isoenzymes

enzymes of creatine kinase (see p. 336) are

There are two different LDH subunits in the

also of diagnostic importance.

organism—M and H—which have a slightly

different amino acid sequence and conse-

quently different catalytic properties. As these

two subunits can associate to form tetramers

randomly, a total of five different isoenzymes

of LDH are found in the body.

Fig. 1 shows sections from the amino acid

sequences of the two subunits, using the sin-

gle-letter notation (see p. 60). A common pre-

cursor gene was probably duplicated at some

point in evolution. The two genes then con-

tinued to develop further independently of

each other through mutation and selection.

100

Metabolism

and coenzyme, so that water molecules are

Lactate dehydrogenase:

largely excluded during the electron transfer.

mechanism

We can now look at the partial reactions

involved in LDH-catalyzed pyruvate reduc-

The principles of enzyme catalysis discussed

tion.

on p. 90 can be illustrated using the reaction

mechanism of lactate dehydrogenase (LDH)

In the free enzyme, His195 is protonated

as an example.

(1). This form of the enzyme is therefore de-

scribed as E H⁺. The coenzyme NADH is

A. Lactate dehydrogenase: catalytic cycle

bound first (2), followed by pyruvate (3). It

is important that the carbonyl group of the

LDH catalyzes the transfer of hydride ions (see

pyruvate in the enzyme and the active site in

p. 32) from lactate to NAD⁺ or from NADH to

the nicotinamide ring of the coenzyme should

pyruvate.

have a fairly optimal position in relation to

each other, and that this orientation should

L-lactate + NAD⁺ ↔pyruvate + NADH + H⁺

become fixed (proximity and orientation of the

substrates). The 98-111 loop now closes over

The equilibrium of the reaction strongly fa-

the active center. This produces a marked

vors lactate formation. At high concentrations

decrease in polarity, which makes it easier

of lactate and NAD⁺, however, oxidation of

to achieve the transition state (4; water ex-

lactate to pyruvate is also possible

(see

clusion). In the transition state, a hydride ion,

p. 18). LDH catalyzes the reaction in both di-

H- (see p. 32), is transferred from the coen-

rections, but—like all enzymes—it has no ef-

zyme to the carbonyl carbon (group transfer).

fect on chemical equilibrium.

The transient—and energetically unfavora-

As the reaction is reversible, the catalytic

ble—negative charge on the oxygen that oc-

process can be represented as a closed loop.

curs here is stabilized by electrostatic inter-

The catalytic cycle of LDH is reduced to six

action with Arg-109 (stabilization of the tran-

“snapshots” here. Intermediate steps in catal-

sition state). At the same time, a proton from

ysis such as those shown here are extremely

His-195 is transferred to this oxygen atom

short-lived and therefore dif cult to detect.

(group transfer), giving rise to the enzyme-

Their existence was deduced indirectly from a

bound products lactate and NAD⁺ (5). After

large number of experimental findings—e. g.,

the loop opens, lactate dissociates from the

kinetic and binding measurements.

enzyme, and the temporarily uncharged imi-

Many amino acid residues play a role in the

dazole group in His-195 again binds a proton

active center of LDH. They can mediate the

from the surrounding water (6). Finally, the

binding of the substrate and coenzyme, or

oxidized coenzyme NAD⁺ is released, and the

take part in one of the steps in the catalytic

initial state (1) is restored. As the diagram

cycle directly. Only the side chains of three

shows, the proton that appears in the reaction

particularly important residues are shown

equation (NADH + H⁺) is not bound together

here. The positively charged guanidinium

with NADH, but after release of the lacta-

group of arginine-171 binds the carboxylate

te—i. e., between steps

(5) and

(6) of the

group of the substrate by electrostatic inter-

previous cycle.

action. The imidazole group of histidine-195 is

Exactly the same steps occur during the

involved in acid-base catalysis, and the side

oxidation of lactate to pyruvate, but in the

chain of arginine-109 is important for the sta-

opposite direction. As mentioned earlier, the

bilization of the transition state. In contrast to

direction which the reaction takes depends

His-195, which changes its charge during cat-

not on the enzyme, but on the equilibrium

alysis, the two essential arginine residues are

state—i. e., on the concentrations of all the

constantly protonated. In addition to these

reactants and the pH value (see p. 18).

three residues, the peptide loop 98-111 men-

tioned on p. 98 is also shown here schemati-

cally (red). Its function consists of closing the

active center after binding of the substrate

Enzymes

101

A. Lactate dehydrogenase: catalytic cycle

E. H

E . H . NADH

Arg-109

HN NH₂

NH₂

H₂N

Loop

98-111

NADH

His-195

H₂N

NH₂

H₂N

NH₂

Arg-171

1. Free enzyme

2. NADH bound

NH₂

HN NH₂

NH₂

HN NH

H₂N

H₃C

NAD

Pyruvat

H₂N

NH₂

H₂N

NH₂

6. NAD bound

3. Pyruvate bound

NH₂

HN NH₂

H₂N

H₃C

N H

O O

Lactate

H₂N

NH₂

O O

Proton

Hydride

transfer

H₂N

NH₂

5. Lactate bound

4. Redox reaction

E . NAD . Lactate

Transition state

102

Metabolism

absorption is recorded at a constant

Enzymatic analysis

wavelength of 340 nm. The uncatalyzed LDH

Enzymes play an important role in biochem-

reaction is very slow. It is only after addition

ical analysis. In biological material—e. g., in

of the enzyme that measurable quantities of

body fluids—even tiny quantities of an en-

NADH are formed and absorption increases.

zyme can be detected by measuring its cata-

Since according to the Beer-Lambert law the

lytic activity. However, enzymes are also used

rate of the increase in absorption ∆A/∆t is

as reagents to determine the concentrations

proportional to the reaction rate ∆c/∆t. The

of metabolites—e. g., the blood glucose level

absorption coef cient ε at 340 nm or compar-

(C). Most enzymatic analysis procedures use

ison with a standard solution can be used to

the method of spectrophotometry (A).

calculate LDH activity.

A. Principle of spectrophotometry

C. Enzymatic determination of glucose

Many substances absorb light in the visible or

Most biomolecules do not show any absorp-

ultraviolet region of the spectrum. This prop-

tion in the visible or ultraviolet spectrum. In

erty can be used to determine the concentra-

addition, they are usually present in the form

tion of such a substance. The extent of light

of mixtures with other—similar—compounds

absorption depends on the type and concen-

that would also react to a chemical test pro-

tration of the substance and on the wave-

cedure. These two problems can be avoided

length of the light used. Monochromatic

by using an appropriate enzyme to produce a

light—i. e., light with a defined wavelength

colored dye selectively from the metabolite

isolated from white light using a monochrom-

that is being analyzed. The absorption of the

ator—is therefore used. Monochromatic light

dye can then be measured.

with an intensity of I₀ is passed through a

A procedure (1) that is often used to mea-

rectangular vessel made of glass or quartz (a

sure glucose when monitoring blood glucose

cuvet), which contains a solution of the ab-

levels (see p. 160) involves two successive re-

sorbing substance. The absorption A of the

actions. The glucose-specific enzyme glucose

solution (often also referred to as its extinc-

oxidase (obtained from fungi) first produces

tion) is defined as the negative decadic loga-

hydrogen peroxide, H₂O₂, which in the second

rithm of the quotient I/I₀. The Beer-Lambert

step—catalyzed by a peroxidase—oxidizes a

law states that A is proportional to the con-

colorless precursor into a green dye

(2).

centration c of the absorbing substance and

When all of the glucose in the sample has

the thickness d of the solution it passes

been used up, the amount of dye formed—

through. As mentioned earlier, the absorption

which can be measured on the basis of its

coef•cient ε depends on the type of substance

light absorption—is equivalent to the quantity

and the wavelength.

of glucose originally present.

B. Measurement of lactate dehydrogenase

activity

Measurement of lactate dehydrogenase (LDH)

activity takes advantage of the fact that while

the reduced coenzyme NADH + H⁺ absorbs

light at 340 nm, oxidized NAD⁺ does not. Ab-

sorption spectra (i. e., plots of A against the

wavelength) for the substrates and the coen-

zymes of the LDH reaction are shown in Fig. 1.

Differences in absorption behavior between

NAD⁺ and NADH between 300 and 400 nm

result from changes in the nicotinamide ring

during oxidation or reduction (see p. 32). To

measure the activity, a solution containing

lactate and NAD⁺ is placed in a cuvet, and

Enzymes

103

A. Principle of spectrophotometry

Monochroma-

White light

tic light,

intensity

Absorption

Light source

Monochromator

Detector

Instrument

Light

Sample solution,

absorption

concentration c

Beer Lambert

Absorption

A = -log I

= ε . c. d

law

B. Assay of lactate dehydrogenase activity

∆A

∆c

2.0

∆A =

v ≈ Activity

;

∆t · ε

∆t

;

Lactate

Pyruvate

0.1 mM

NAD

each

1.5

NADH

Addition

3 nkat

1.0

of LDH

2 nkat

NADH

1 nkat

Lactate; NAD

0.5

Lactate

∆A

NAD

Pyruvate

240

280

320

360

400

∆t

Time

Wavelength (nm)

C. Enzymatic determination of glucose

O₂

Glucose-containing

sample solution

Glucose

Glucono-

Glucose

oxidase

lactone

1.1.3.4 [FAD]

Enzymes

2 H₂O

Colorless

H2O2

precursor

∆A

—

[Green dye]

∞ =

Peroxidase

Green

Colorless

[Green dye]

∞ = [Glucose]₀

1.11.1.7

dye

precursor

[Heme]

Time (min)

1. Reaction

2. Procedure

104

Metabolism

metabolism. In contrast, reduced NADP⁺ is the

Coenzymes 1

most important reductant involved in biosyn-

thesis (see p. 112).

A. Coenzymes: definitions

The flavin coenzymes FMN and FAD (2, 3)

In many enzyme-catalyzed reactions, elec-

contain flavin (isoalloxazine) as a redox-active

trons or groups of atoms are transferred

group. This is a three-membered, N-contain-

from one substrate to another. This type of

ing ring system that can accept a maximum of

reaction always also involves additional mol-

two electrons and two protons during reduc-

ecules, which temporarily accept the group

tion. FMN carries the phosphorylated sugar

being transferred. Helper molecules of this

alcohol ribitol at the flavin ring. FAD arises

type are called coenzymes. As they are not

from FMN through bonding with AMP. The

catalytically active themselves, the less fre-

two coenzymes are functionally similar.

quently used term “cosubstrate” would be

They are found in dehydrogenases, oxidases,

more appropriate. In contrast to substrates

and monooxygenases. In contrast to the pyri-

for which a given enzyme is usually specific

dine nucleotides, flavin reactions give rise to

(see p. 88), coenzymes cooperate with many

radical intermediates (see p. 32). To prevent

enzymes of varying substrate specificity. We

damage to cell components, the flavins al-

have rather arbitrarily divided the coenzymes

ways remain bound as prosthetic groups in

here into group-transferring and redox coen-

the enzyme protein.

zymes. Strictly speaking, redox coenzymes

The role of ubiquinone (coenzyme Q, 4) in

also transfer groups—namely, reducing equiv-

transferring reducing equivalents in the res-

alents (see p. 32).

piratory chain is discussed on p. 140. During

Depending on the type of interaction with

reduction, the quinone is converted into the

the enzyme, a distinction is made between

hydroquinone (ubiquinol). The isoprenoid side

soluble coenzymes and prosthetic groups.

chain of ubiquinone can have various lengths.

Soluble coenzymes

(1) are bound like

It holds the molecule in the membrane, where

substrates during a reaction, undergo a chem-

it is freely mobile. Similar coenzymes are also

ical change, and are then released again. The

found in photosynthesis (plastoquinone; see

original form of the coenzyme is regenerated

p. 132). Vitamins E and K (see p. 52) also be-

by a second, independent reaction. Prosthetic

long to the quinone/hydroquinone systems.

groups (2), on the other hand, are coenzymes

L-Ascorbic acid (vitamin C, 5) is a powerful

that are tightly bound to the enzyme and re-

reducing agent. As an antioxidant, it provides

main associated with it during the reaction.

nonspecific protection against oxidative dam-

The part of the substrate bound by the coen-

age (see p. 284), but it is also an essential

zyme is later transferred to another substrate

cofactor for various monooxygenases and di-

or coenzyme of the same enzyme (not shown

oxygenases. Ascorbic acid is involved in the

in Fig. 2).

hydroxylation of proline and lysine residues

during the biosynthesis of collagen

(see

p. 344), in the synthesis of catecholamines

B. Redox coenzymes 1

(see p. 352) and bile acids (see p. 314), as

All oxidoreductases (see p. 88) require coen-

well as in the breakdown of tyrosine (see

zymes. The most important of these redox

p. 415). The reduced form of the coenzyme

coenzymes are shown here. They can act in

is a relatively strong acid and forms salts,

soluble form (S) or prosthetically (P). Their

the ascorbates. The oxidized form is known

normal potentials E⁰

are shown in addition

as dehydroascorbic acid. The stimulation of

to the type of reducing equivalent that they

the immune system caused by ascorbic acid

transfer (see p. 18).

has not yet been fully explained.

The pyridine nucleotides NAD⁺ and NADP⁺

(1) are widely distributed as coenzymes of

dehydrogenases. They transport hydride ions

(2e^- and 1 H⁺; see p. 32) and always act in

soluble form. NAD⁺ transfers reducing equiv-

alents from catabolic pathways to the respi-

ratory chain and thus contributes to energy

Enzymes

105

A. Coenzymes: definitions

Substrate 1

Coenzyme

Substrate 2

Coenzyme

Group

(form 1)

transfer

(form 2)

Prosthetic

group (form1)

Substrate 1

Substrate 2

group (form 2)

B. Redox coenzymes

Trans-

Eol

Coenzyme

Oxidized form

Reduced form

Type

ferred

(V)

1. NAD(P)

-0.32

NH₂

O H

CH₂O P O

P O CH₂

NH₂

H H

ox.

red.

OH OH

2. Flavin

2[H]

-0.3

mononucleotide

H₃C

(FMN)

+0.2

H₃C

CH₂

Ribitol (Rit)

ox.

red.

H₂C O P

3. Flavin

2[H]

-0.3

adenine

H₃C

dinucleotide

+0.2

(FAD)

H₃C

N N

O P O P O CH₂

H₃C

Ribitol

ox.

red.

H H

OH OH

4. Ubiquinone

2[H]

-0

(coenzym Q)

H₃CO

CH₃

H₃CO

CH₃

+0.2

H₃CO

CH₃

6 -10

5. Ascorbic

2[H]

+0.1

acid

C H

CH₂OH

106

Metabolism

of energetic coupling (see p. 124) also allow

Coenzymes 2

endergonic processes to proceed. Metabolites

are often made more reactive (“activated”) as

A. Redox coenzymes 2

a result of the transfer of phosphate residues

In lipoic acid (6), an intramolecular disulfide

(phosphorylation). Bonding with nucleoside

bond functions as a redox-active structure. As

diphosphate residues (mainly UDP and CDP)

a result of reduction, it is converted into the

provides activated precursors for polysac-

corresponding dithiol. As a prosthetic group,

charides and lipids (see p. 110). Endergonic

lipoic acid is usually covalently bound to a

formation of bonds by ligases (enzyme class

lysine residue (R) of the enzyme, and it is

6) also depends on nucleoside triphosphates.

then referred to as lipoamide. Lipoamide is

Acyl residues are usually activated by

mainly involved in oxidative decarboxylation

transfer to coenzyme A (2). In coenzyme A

2-oxo acids

(see p. 134). The peptide

(see p. 12), pantetheine is linked to 3 -phos-

coenzyme glutathione is a similar disulfide/

pho-ADP by a phosphoric acid anhydride

dithiol system (not shown; see p. 284).

bond. Pantetheine consists of three compo-

Iron-sulfur clusters (7) occur as prosthetic

nents connected by amide bonds—pantoic

groups in oxidoreductases, but they are also

acid, E-alanine, and cysteamine. The latter

found in lyases—e. g., aconitase (see p. 136)

two components are biogenic amines formed

and other enzymes. Iron-sulfur clusters con-

by the decarboxylation of aspartate and

sist of 2-4 iron ions that are coordinated with

cysteine, respectively. The compound formed

cysteine residues of the protein (-SR) and

from pantoic acid and β−alanine (pantothenic

with anorganic sulfide ions (S). Structures of

acid) has vitamin-like characteristics for hu-

this type are only stable in the interior of

mans (see p. 368). Reactions between the

proteins. Depending on the number of iron

thiol group of the cysteamine residue and

and sulfide ions, distinctions are made be-

carboxylic acids give rise to thioesters, such

tween [Fe₂S₂], [Fe₃S₄], and [Fe₄S₄] clusters.

as acetyl CoA. This reaction is strongly ender-

These structures are particularly numerous

gonic, and it is therefore coupled to exergonic

in the respiratory chain

(see p. 140), and

processes. Thioesters represent the activated

they are found in all complexes except com-

form of carboxylic acids, because acyl residues

plex IV.

of this type have a high chemical potential

Heme coenzymes (8) with redox functions

and are easily transferred to other molecules.

exist in the respiratory chain (see p. 140), in

This property is often exploited in metabo-

photosynthesis (see p. 128), and in monooxy-

lism.

genases and peroxidases (see p. 24). Heme-

Thiamine diphosphate (TPP, 3), in coopera-

containing proteins with redox functions are

tion with enzymes, is able to activate alde-

also referred to as cytochromes. In cyto-

hydes or ketones as hydroxyalkyl groups and

chromes, in contrast to hemoglobin and myo-

then to pass them on to other molecules. This

globin, the iron changes its valence (usually

type of transfer is important in the transketo-

between +2 and +3). There are several classes

lase reaction, for example (see p. 152). Hy-

of heme (a, b, and c), which have different

droxyalkyl residues also arise in the decar-

types of substituent - R₁ to - R₃. Hemoglobin,

boxylation of oxo acids. In this case, they are

myoglobin, and the heme enzymes contain

released as aldehydes or transferred to lipo-

heme b. Two types of heme a are found in

amide residues of 2-oxoacid dehydrogenases

cytochrome c oxidase

(see p. 132), while

(see p. 134). The functional component of TPP

heme c mainly occurs in cytochrome c, where

is the sulfur- and nitrogen-containing thiazole

it is covalently bound with cysteine residues

ring.

of the protein part via thioester bonds.

B. Group-transferring coenzymes 1

The nucleoside phosphates (1) are not only

precursors for nucleic acid biosynthesis; many

of them also have coenzyme functions. They

serve for energy conservation, and as a result

Enzymes

107

A. Redox coenzymes 2

Coenzyme

Oxidized form

Reduced form

Type

Trans-

Eol

ferred

6. Lipoamide

2[H]

–0.29

S S

HS SH

H₂

ox.

red.

-0.6

7. Iron-

[Fe₂ S₂]

[Fe₄ S₄]

sulfur

S Fe

Fe S

+0.5

cluster

S Fe

8. Heme

R₂

CH₃

R₂

CH₃

H₃C

R₃

H₃C

R₃

+0.5

Fe³⁺

Fe²⁺

R₁

CH₃

R₁

CH₃

ox.

red.

COO

B. Group-transferring coenzymes 1

Coenzyme

Free form

Charged form

Group(s)

Important

(symbol)

trans-

enzymes

ferred

1. Nucleoside

Phospho-

1. phosphates

transferases

Base

Nucleotidyl-

B-Rib

transferases

CH₂

B-Rib-

(2.7.n.n)

Ligases

P P P

(6.n.n.n)

B-Rib- P

OH OH

H CH₃

2. Coenzyme A

Acyl

Acyltrans-

CH₂

N C C C CH₂

O P O

residues

ferases

CH₂

O OH CH₃

NH₂

(2.3.n.n)

C O

P O

CoA trans-

CH₂

ferases

CH₂

(2.8.3.n)

H H

CH₂

C O

O OH

CH₃

P O

3. Thiamine

Hydroxy-

Decarboxy-

3. diphosphate

alkyl

lases (4.1.1.n)

H₃C

NH₂

residues

Oxoacid de-

N S

hydrogenases

CH2 N S

(1.2.4. n)

TPP

Transketolase

H₃C

CH₂

(2.2.1.1)

H₃C

CH₂

CH₂O

P P

108

Metabolism

THF derivatives in the biosynthesis of DNA

Coenzymes 3

precursors, the enzymes involved in THF me-

tabolism are primary targets for cytostatic

A. Group-transferring coenzymes 2

drugs (see p. 402).

Pyridoxal phosphate (4) is the most important

coenzyme in amino acid metabolism. Its role

The cobalamins (7) are the chemically most

in transamination reactions is discussed in

complex form of coenzyme. They also repre-

detail on p. 178. Pyridoxal phosphate is also

sent the only natural substances that contain

involved in other reactions involving amino

the transition metal cobalt (Co) as an essential

acids, such as decarboxylations and dehydra-

component. Higher organisms are unable to

tions. The aldehyde form of pyridoxal phos-

synthesize cobalamins themselves, and are

phate shown here (left) is not generally found

therefore dependent on a supply of vitamin

in free form. In the absence of substrates, the

B₁₂ synthesized by bacteria (see p. 368).

aldehyde group is covalently bound to the ε-

The central component of the cobalamins

amino group of a lysine residue as aldimine

is the corrin ring, a member of the tetrapyr-

(“Schiff’s base”). Pyridoxamine phosphate

roles, at the center of which the cobalt ion is

(right) is an intermediate of transamination

located. The end of one of the side chains of

reactions. It reverts to the aldehyde form by

the ring carries a nucleotide with the unusual

reacting with 2-oxoacids (see p. 178).

base dimethylbenzimidazole. The ligands for

the metal ion are the four N atoms of the

Biotin (5) is the coenzyme of the carboxy-

pyrrole ring, a nitrogen from dimethylbenzi-

lases. Like pyridoxal phosphate, it has an

midazole, and a group X, which is organo-

amide-type bond via the carboxyl group

metallically bound—i. e., mainly covalently.

with a lysine residue of the carboxylase. This

bond is catalyzed by a specific enzyme. Using

In methylcobalamin, X is a methyl group.

ATP, biotin reacts with hydrogen carbonate

This compound functions as a coenzyme for

(HCO_3-) to form N-carboxybiotin . From this

several methyltransferases, and among other

activated form, carbon dioxide (CO₂) is then

things is involved in the synthesis of methio-

transferred to other molecules, into which a

nine from homocysteine (see p. 418). How-

carboxyl group is introduced in this way. Ex-

ever, in human metabolism, in which methio-

amples of biotindependent reactions of this

nine is an essential amino acid, this reaction

type include the formation of oxaloacetic acid

does not occur.

from pyruvate (see p. 154) and the synthesis

of malonyl-CoA from acetyl-CoA (see p. 162).

Adenosylcobalamin (coenzyme B₁₂) carries

a covalently bound adenosyl residue at the

Tetrahydrofolate (THF, 6) is a coenzyme

metal atom. This is a coenzyme of various

that can transfer C₁ residues in different oxi-

isomerases, which catalyze rearrangements

dation states. THF arises from the vitamin folic

following a radical mechanism. The radical

acid (see p. 366) by double hydrogenation of

arises here through homolytic cleavage of the

the heterocyclic pterin ring. The C₁

units

bond between the metal and the adenosyl

being transferred are bound to N-5, N-10, or

group. The most important reaction of this

both nitrogen atoms. The most important de-

type in animal metabolism is the rearrange-

rivatives are:

ment of methylmalonyl-CoA to form succinyl-

a) N⁵-formyl-THF and N¹⁰-formyl-THF, in

CoA, which completes the breakdown of odd-

which the formyl residue has the oxidation

numbered fatty acids and of the branched

state of a carboxylic acid;

amino acids valine and isoleucine

(see

b) N⁵-methylene-THF, with a C₁ residue in

pp. 166 and 414).

the oxidation state of an aldehyde; and

c) N⁵-methyl-THF, in which the methyl

group has the oxidation state of an alcohol.

C₁ units transferred by THF play a role in

the synthesis of methionine (see p. 412), pu-

rine nucleotides (see p. 188), and dTMP (see

p. 190), for example. Due to the central role of

110

Metabolism

3. Phosphoadenosine phosphosulfate (PAPS)

Activated metabolites

Sulfate residues occur as strongly polar

Many coenzymes (see pp. 104ff.) serve to ac-

groups in various biomolecules—e. g., in gly-

tivate molecules or groups that are poorly

cosaminoglycans (see p. 346) and conjugates

reactive. Activation consists of the formation

of steroid hormones and xenobiotics

(see

of reactive intermediate compounds in which

p. 316). In the synthesis of the “activated sul-

the group concerned is located at a higher

fate” PAPS, ATP first reacts with anorganic

chemical potential and can therefore be

sulfate to form adenosine phosphosulfate

transferred to other molecules in an exer-

(APS, a). This intermediate already contains

gonic reaction (see p. 124). Acetyl-CoA is an

the “energy-rich” mixed anhydride bond be-

example of this type of compound (see p. 12).

tween phosphoric acid and sulfuric acid. In

ATP and the other nucleoside triphosphate

the second step, the 3 -OH group of APS is

coenzymes not only transfer phosphate resi-

phosphorylated, with ATP being used again.

dues, but also provide the nucleotide compo-

After transfer of the sulfate residue to OH

nents for this type of activation reaction. On

groups (c), adenosine-3 ,5 -bisphosphate re-

this page, we discuss metabolites or groups

mains.

that are activated in the metabolism by bond-

ing with nucleosides or nucleotides. Inter-

mediates of this type are mainly found in

4. S-adenosyl methionine (SAM)

the metabolism of complex carbohydrates

The coenzyme tetrahydrofolate (THF) is the

and lipids.

main agent by which C₁ fragments are trans-

ferred in the metabolism. THF can bind this

A. Activated metabolites

type of group in various oxidation states and

pass it on (see p. 108). In addition, there is

1. Uridine diphosphate glucose (UDPglucose)

“activated methyl,” in the form of S-adenosyl

The inclusion of glucose residues into poly-

methionine (SAM). SAM is involved in many

mers such as glycogen or starches is an ender-

methylation reactions—e. g., in creatine syn-

gonic process. The activation of the glucose

thesis (see p. 336), the conversion of norepi-

building blocks that is required for this takes

nephrine into epinephrine (see p. 352), the

places in several steps, in which two ATPs are

inactivation of norepinephrine by methyla-

used per glucose. After the phosphorylation of

tion of a phenolic OH group (see p. 316), and

free glucose, glucose 6-phosphate is isomer-

in the formation of the active form of the

ized to glucose 1-phosphate (a), reaction with

cytostatic drug

6-mercaptopurine

(see

UTP (b) then gives rise to UDPglucose, in

p. 402).

which the anomeric OH group at C-1 of the

SAM is derived from degradation of the

sugar is bound with phosphate. This “energy-

proteinogenic amino acid methionine, to

rich” compound (an acetal phosphate) allows

which the adenosyl residue of an ATP mole-

exergonic transfer of glucose residues to gly-

cule is transferred. After release of the acti-

cogen (c; see pp. 156, 408) or other acceptors.

vated methyl group, S-adenosyl homocys-

teine (SAH) is left over. This can be converted

back into methionine in two further steps.

2. Cytidine diphosphate choline (CDPcholine)

Firstly, cleavage of the adenosine residue

The amino alcohol choline is activated for in-

gives rise to the non-proteinogenic amino

clusion in phospholipids following a similar

acid homocysteine, to which a methyl group

principle (see p. 170). Choline is first phos-

is transferred once again with the help of N⁵-

phorylated by ATP to form choline phosphate

methyl-THF (see p. 418). Alternatively, homo-

(a), which by reaction with CTP and cleavage

cysteine can also be broken down into pro-

of diphosphate, then becomes CDPcholine. In

pionyl-CoA.

contrast to (1), it is not choline that is trans-

ferred from CDPcholine, but rather choline

phosphate, which with diacylglycerol yields

phosphatidylcholine (lecithin).

Enzymes

111

A. Activated metabolites

ADP

Glc

HOCH2

Glucose

Glc

1-phosphate

^H H

Glycogen

Extended glycogen

O P O

CH₂

Glc

H H

OH OH

Glc

UDP-glucose

1. Uridine diphosphate glucose (UDP-glucose)

ADP

NH₂

Choline P

Choline

CH₃

Diacylglycerol

Phosphatidylcholine

H₃C

(CH₂)₂

O P O

P O

CH₂

H H

Choline

OH OH

CDP-choline

Choline

2. Cytidine diphosphate choline (CDPcholine)

P P

O₃S

SO₄₂

CH₂

SO₃

H H

Sulfated

substrate

O OH

O₃S

P O

PAPS

3. Phosphoadenosine phosphosulfate (PAPS)

Methionine

Homocysteine

CH₃

N5-Methyl-

THF

Adenosine

THF

COO

H₃N

CH₂

CH₃

Methylated

H₃C

CH₂

substrate

H₃C

H H

4. S-adenosyl methionine (SAM)

S-adenosyl-

OH OH

homocysteine

SAM

112

Metabolism

arrows). Of the numerous metabolites in the

Intermediary metabolism

pool, only three particularly important repre-

Hundreds of chemical reactions are con-

sentatives—pyruvate, acetyl-CoA, and gly-

stantly taking place in every cell, and taken

cerol—are shown here. These molecules

together these are referred to as the metabo-

represent connecting links between the

lism. The chemical compounds involved in

metabolism of proteins, carbohydrates, and

this are known as metabolites. Outside of

lipids. The metabolite pool also includes the

the cell, almost all of the chemical changes

intermediates of the tricarboxylic acid cycle

in metabolites would only take place very

(6). This cyclic pathway has both catabolic and

slowly and without any specific direction. By

anabolic functions—i. e., it is amphibolic (vio-

contrast, organized sequences of chemical re-

let; see p. 138).

actions with a high rate of throughput, known

Waste products from the degradation of

as metabolic pathways, become possible

organic substances in animal metabolism

through the existence of specific enzymes

include carbon dioxide (CO₂), water (H₂O),

(see p. 88).

and ammonia (NH₃). In mammals, the toxic

substance ammonia is incorporated into urea

and excreted in this form (see p. 182).

A. Intermediary metabolism: overview

The most important form of storage for

A number of central metabolic pathways are

chemical energy in all cells is adenosine

common to most cells and organisms. These

triphosphate (ATP, see p. 122). ATP synthesis

pathways, which serve for synthesis, degra-

requires energy—i. e., the reaction is ender-

dation, and interconversion of important me-

gonic. Conversely, cleavage of ATP into ADP

tabolites, and also for energy conservation,

and phosphate releases energy. Exergonic hy-

are referred to as the intermediary metabo-

drolysis of ATP, as a result of energetic

lism.

coupling (see p. 16), makes energy-depend-

In order to survive, all cells constantly re-

ent (endergonic) processes possible. For ex-

quire organic and inorganic nutrients, as well

ample, most anabolic pathways, as well as

as chemical energy, which is mainly derived

movement and transport processes, are en-

from ATP (see below). Depending on the way

ergy-dependent.

in which these needs are satisfied, organisms

The most important pathway for the syn-

can be classified into autotrophic and hetero-

thesis of ATP is oxidative phosphorylation

trophic groups. The autotrophs, which in-

(see p. 122). In this process, catabolic path-

clude plants and many microorganisms, can

ways first form reduced cofactors (NADH+H⁺,

synthesize organic molecules from inorganic

QH₂, ETFH₂). Electrons are then transferred

precursors (CO₂). An autotrophic lifestyle is

from these compounds to oxygen. This

possible through photosynthesis, for exam-

strongly exergonic process is catalyzed by

ple (see p. 128). The heterotrophs—e. g., ani-

the respiratory chain and used indirectly for

mals and fungi—depend on organic substan-

the ATP synthesis (see p. 140). In anaerobic

ces supplied in their diet. The schema shown

conditions—i. e., in the absence of oxygen—

on this page provides an overview of animal

most organisms can fall back on ATP that

metabolism.

arises in glycolysis

(3). This less ef cient

The polymeric substances contained in the

type of ATP synthesis is referred to as fermen-

diet

(proteins, carbohydrates, and nucleic

tation (see p. 146).

acids—top) cannot be used by the organism

While NADH exclusively supplies oxidative

directly. Digestive processes first have to de-

phosphorylation, NADPH+H⁺—a very similar

grade them to monomers (amino acids, sug-

coenzyme—is the reducing agent for anabolic

ars, nucleotides). These are then mostly bro-

pathways. NADPH + H⁺ is mainly formed in

ken down by catabolic pathways (pink ar-

the pentose phosphate pathway (PPP, 1; see

rows) into smaller fragments. The metabolites

p. 152).

produced in this way (generally referred to as

the “metabolite pool”) are then either used to

obtain energy through further catabolic con-

version, or are built up again into more com-

plex molecules by anabolic pathways (blue

114

Metabolism

Interconversion processes in most cases

Regulatory mechanisms

involve ATP-dependent phosphorylation of

the enzyme protein by a protein kinase or

A. Fundamental mechanisms of metabolic

dephosphorylation of it by a protein phospha-

regulation

tase (see p. 120). The phosphorylated form of

The activities of all metabolic pathways are

the key enzyme is usually the more active

subject to precise regulation in order to adjust

one, but the reverse may also occur.

the synthesis and degradation of metabolites

Modulation by ligands. An important vari-

to physiological requirements. An overview of

able that regulates flow through a metabolic

the regulatory mechanisms is presented here.

pathway is precursor availability (metabolite

Further details are shown on pp. 116ff.

A in the case shown here). The availability of

Metabolite flow along a metabolic pathway

precursor A increases along with the activity

is mainly determined by the activities of the

of the metabolic pathways that form A (3) and

enzymes involved (see p. 88). To regulate the

it decreases with increasing activity of other

pathway, it is suf cient to change the activity

pathways that also consume A (4). Transport

of the enzyme that catalyzes the slowest step

from one cell compartment to another can

in the reaction chain. Most metabolic path-

also restrict the availability of A.

ways have key enzymes of this type on which

Coenzyme availability can also often have a

the regulatory mechanisms operate. The ac-

limiting effect (5). If the coenzyme is regen-

tivity of key enzymes is regulated at three

erated by a second, independent metabolic

independent levels:

pathway, the speed of the second pathway

Transcriptional control. Here, Biosynthesis

can limit that of the first one. For example,

of the enzyme protein is influenced at the

glycolysis and the tricarboxylic acid cycle are

genetic level

(1). Interventions in enzyme

mainly regulated by the availability of NAD⁺

synthesis mainly affect synthesis of the cor-

(see p. 146). Since NAD⁺ is regenerated by the

responding mRNA—i. e., transcription of the

respiratory chain, the latter indirectly con-

gene coding for the enzyme. The term “tran-

trols the breakdown of glucose and fatty acids

scriptional control” is therefore used

(see

(respiratory control, see p. 144).

pp. 118, 244). This mechanism is mediated by

Finally, the activity of key enzymes can be

regulatory proteins (transcription factors) that

regulated by ligands

(substrates, products,

act directly on DNA. The genes have a special

coenzymes, or other effectors), which as allo-

regulatory segment for this purpose, known

steric effectors do not bind at the active center

as the promoter region, which contains bind-

itself, but at another site in the enzyme,

ing sites

(control elements) for regulatory

thereby modulating enzyme activity (6; see

proteins. The activity of these proteins is, in

p. 116). Key enzymes are often inhibited by

turn, affected by metabolites or hormones.

immediate reaction products, by end prod-

When synthesis of a protein is increased by

ucts of the reaction chain concerned (“feed-

transcriptional control, the process is referred

back” inhibition), or by metabolites from com-

to as induction; when it is reduced or sup-

pletely different metabolic pathways. The

pressed, it is referred to as repression. Induc-

precursors for a reaction chain can stimulate

tion and repression processes take some time

their own utilization through enzyme activa-

and are therefore not immediately effective.

tion.

Interconversion of key enzymes (2) takes

effect considerably faster than transcriptional

control. In this case, the enzyme is already

present at its site of effect, but it is initially

still inactive. It is only when needed that it is

converted into the catalytically active form,

after signaling and mediation from second

messengers (see p. 120) through an activating

enzyme (E₁). If the metabolic pathway is no

longer required, an inactivating enzyme (E₂)

returns the key enzyme to its inactive resting

state.

116

Metabolism

causes a left shift; it reduces both [A]_0.5 and

Allosteric regulation

h (curve III). This type of allosteric effect was

The regulation of aspartate carbamoyltrans-

first observed in hemoglobin

(see p. 280),

ferase (ACTase), a key enzyme of pyrimidine

which can be regarded as an “honorary” en-

biosynthesis (see p. 188) is discussed here as

zyme.

an example of allosteric regulation of enzyme

activity. Allosteric effects are mediated by the

C. R and T states

substrate itself or by inhibitors and activators

(allosteric effectors, see p. 114). The latter bind

Allosteric enzymes are almost always oligo-

at special sites outside the active center, pro-

mers with 2-12 subunits. ACTase consists of

ducing a conformational change in the en-

six catalytic subunits (blue) and six regulatory

zyme protein and thus indirectly lead to an

subunits (yellow). The latter bind the allo-

alteration in its activity.

steric effectors CTP and ATP. Like hemoglobin,

ACTase can also be present in two conforma-

tions—the less active T state (for “tense”) and

A. Aspartate carbamoyltransferase:

the more active R state (for “relaxed”). Sub-

reaction

strates and effectors influence the equili-

ACTase catalyzes the transfer of a carbamoyl

brium between the two states, and thereby

residue from carbamoyl phosphate to the

give rise to sigmoidal saturation behavior.

amino group of L-aspartate. The N-carbamoyl

With increasing aspartate concentration, the

L-aspartate formed in this way already con-

equilibrium is shifted more and more toward

tains all of the atoms of the later pyrimidine

the R form. ATP also stabilizes the R confor-

ring (see p. 188). The ACTase of the bacterium

mation by binding to the regulatory subunits.

Escherichia coli is inhibited by cytidine tri-

By contrast, binding of CTP to the same sites

phosphate (CTP), an end product of the ana-

promotes a transition to the T state. In the

bolic metabolism of pyrimidines, and is ac-

case of ACTase, the structural differences be-

tivated by the precursor ATP.

tween the R and T conformations are partic-

ularly dramatic. In T R conversion, the cat-

alytic subunits separate from one another by

B. Kinetics

1.2 nm, and the subunits also rotate around

In contrast to the kinetics of isosteric (normal)

the axis of symmetry. The conformations of

enzymes, allosteric enzymes such as ACTase

the subunits themselves change only slightly,

have sigmoidal (S-shaped) substrate satura-

however.

tion curves (see p. 92). In allosteric systems,

the enzyme’s af nity to the substrate is not

D. Structure of a dimer

constant, but depends on the substrate con-

centration [A]. Instead of the Michaelis con-

The subunits of ACTase each consist of two

stant K_m (see p. 92), the substrate concentra-

domains—i. e., independently folded partial

tion at half-maximal rate ([A]_0.5) is given. The

structures. The N-terminal domain of the reg-

sigmoidal character of the curve is described

ulatory subunit (right) mediates interaction

by the Hill coef•cient h. In isosteric systems,

with CTP or ATP (green). A second, Zn²⁺-con-

h = 1, and h increases with increasing sig-

taining domain (Zn²⁺ shown in light blue)

moidicity.

establishes contact with the neighboring cat-

Depending on the enzyme, allosteric effec-

alytic subunit. Between the two domains of

tors can influence the maximum rate V_max,

the catalytic subunit lies the active center,

the semi-saturation concentration [A]_0.5, and

which is occupied here by two substrate ana-

the Hill coef cient h. If it is mainly V_max that is

logs (red).

changed, the term “V system” is used. Much

more common are “K systems”, in which al-

losteric effects only influence [A]_0.5 and h.

The K type also includes ACTase. The inhib-

itor CTP in this case leads to right-shifting of

the curve, with an increase in [A]_0.5 and h

(curve II). By contrast, the activator ATP

Metabolic Regulation

117

A. Aspartate carbamoyltransferase: reaction

COO

P P P

L-Aspartate

CH₂

CTP

H₃N H COO

COO

Aspartate

H₂N

CH₂

carbamoyl-

UMP

CO₂

NH₂

transferase

R-NH₂

COO

2.1.3.2 [ Zn²

]

ATP

N-Carbamoyl

N-Carbamoyl-

L-aspartate

ATP

B. Kinetics

C. R and T conformation

Active

C₁

C₃

center

2 mM ATP

h = 1.4

III

R₁

R₂

Effector-

C₄

C₆

binding

C₅

Without

site

[A]_0.5

effector

h = 2.0

T conformation

(less active)

0.5 mM CTP

h = 2.3

C₂

C₁

C₃

0.0

5.0

10.0

15.0

R₃

[Aspartate] (mM)

R₁

R₂

C₄

C₆

D. Structure of a dimer

C₅

R conformation

(more active)

Regulatory

Substrate

subunit

ATP (CTP)

Catalytic

subunit

Zn² domain

ATP/CTP-binding domain

118

Metabolism

B. Lactose operon

Transcription control

The well-investigated lactose operon of the

A. Functioning of regulatory proteins

bacterium Escherichial coli can be used here

as an example of transcriptional control. The

Regulatory proteins (transcription factors) are

lac operon is a DNA sequence that is simul-

involved in controlling gene expression in all

taneously subject to negative and positive

cells. These regulatory proteins bind to spe-

control. The operon contains the structural

cific DNA sequences and thereby activate or

genes for three proteins that are required for

inhibit the transcription of genes

(Tran-

the utilization of lactose (one transporter and

scription control). The effects of transcription

two enzymes), as well as control elements that

factors are usually reversible and are often

serve to regulate the operon.

controlled by ligands or by interconversion.

Since lactose is converted to glucose in the

The nomenclature for transcription factors

cell, there is no point in expressing the genes

is confusing. Depending on their mode of ac-

if glucose is already available. And indeed, the

tion, various terms are in use both for the

genes are in fact only transcribed when glu-

proteins themselves and for the DNA sequen-

cose is absent and lactose is present (3). This is

ces to which they bind. If a factor blocks tran-

achieved by interaction between two regula-

scription, it is referred to as a repressor; oth-

tory proteins. In the absence of lactose, the lac

erwise, it is called an inducer. DNA sequences

repressor blocks the promoter region

(2).

to which regulatory proteins bind are referred

When lactose is available, it is converted

to as control elements. In prokaryotes, control

into allolactose, which binds to the repressor

elements that serve as binding sites for RNA

and thereby detaches it from the operator (3).

polymerases are called promoters, whereas

However, this is still not suf cient for the

repressor-binding sequences are usually

transcription of the structural genes. For bind-

called operators. Control elements that bind

ing of the RNA polymerase to take place, an

activating factors are termed enhancers,

inducer—the catabolite activator protein

while elements that bind inhibiting factors

(CAP)—is required, which only binds to the

are known as silencers.

DNA when it is present as a complex with

The numerous regulatory proteins that are

3,5 -cyclo-AMP (cAMP; see p. 386). cAMP, a

known can be classified into four different

signal for nutrient deficiency, is only formed

groups (1-4), based on their mechanisms of

by E. coli in the absence of glucose.

action. Negative gene regulation—i. e.,

The interaction between the CAP-cAMP

switching off of the gene concerned—is car-

complex and DNA is shown in Fig. 4. Each

ried out by repressors. Some repressors only

subunit of the dimeric inducer (yellow or or-

bind to DNA (1a) in the absence of specific

ange) binds one molecule of cAMP (red). Con-

ligands (L). In this case, the complex between

tact with the DNA (blue) is mediated by two

the repressor and the ligand loses its ability to

“recognition helices” that interact with the

bind to the DNA, and the promoter region

major groove of the DNA. The bending of the

becomes accesible for binding of RNA poly-

DNA strand caused by CAP has functional sig-

merase (1b). It is often the free repressor that

nificance.

does not bind to the DNA, so that transcrip-

Transcription control is much more com-

tion is only blocked in the presence of the

plex in eukaryotes (see p. 244). The number

ligand (2a, 2b). A distinction between two

of transcription factors involved is larger, and

different types of positive gene regulation

in addition the gene activity is influenced by

can be made in the same way. If it is only

the state of the chromatin (see p. 238).

the free inducer that binds, then transcription

is inhibited by the appropriate ligand

(3).

Conversely, many inducers only become ac-

tive when they have bound a ligand (4). This

group includes the receptors for steroid hor-

mones, for example (see p. 378).

120

Metabolism

glycogen breakdown, releasing glucose, and

Hormonal control

at the same time inhibits glycogen synthesis.

In higher organisms, metabolic and other

Glucagon binds to receptors in the plasma

processes (growth, differentiation, control of

membrane (bottom left) and, with mediation

the internal environment) are controlled by

by a G-protein (see p. 386), activates the

hormones (see pp. 370 ff.)

enzyme adenylate cyclase, which forms the

second messenger

3,5 -cyclo-AMP

(cAMP)

from ATP. cAMP binds to another enzyme,

A. Principles of hormone action

protein kinase A

(PK-A), and activates it.

Depending on the type of hormone, hormone

PK-A has several points of attack. Through

signals are transmitted to the target cells in

phosphorylation, it converts the active form

different ways. Apolar (lipophilic) hormones

of glycogen synthase into the inactive form,

penetrate the cell and act in the cell nucleus,

thereby terminating the synthesis of glyco-

while polar (hydrophilic) hormones act on the

gen. Secondly, it activates another protein

external cell membrane.

kinase (not shown), which ultimately con-

Lipophilic hormones, which include the

verts the inactive form of glycogen phosphor-

steroid hormones, thyroxine, and retinoic

ylase into the active form through phosphor-

acid, bind to a specific receptor protein inside

ylation. The active phosphorylase releases glu-

their target cells. The complex formed by the

cose 1-phosphate from glycogen, which after

hormone and the receptor then influences

conversion into glucose 6-phosphate supplies

transcription of specific genes in the cell nu-

free glucose. In addition, via an inhibitor (I) of

cleus (see pp. 118, 244). The group of hydro-

protein phosphatase (PP), active PK-A inhibits

philic hormones (see p. 380) consists of hor-

inactivation of glycogen phosphorylase. When

mones derived from amino acids, as well as

the cAMP level falls again, phosphoprotein

peptide hormones and proteohormones.

phosphatases become active, which dephos-

Their receptors are located in the plasma

phorylate the various phosphoproteins in the

membrane. Binding of the hormone to this

cascade described, and thereby arrest glyco-

type of receptor triggers a signal that is trans-

gen breakdown and re-start glycogen synthe-

mitted to the interior of the cell, where it

sis. Activation and inactivation of proteins

controls the processes that allow the hor-

through phosphorylation or dephosphoryla-

mone signal to take effect (signal transduc-

tion is referred to as interconversion.

tion; see pp. 384ff.)

In contrast to glucagon, the peptide

hormone insulin (see p. 76) increases glyco-

gen synthesis and inhibits glycogen break-

B. Hormonal regulation of glucose

down. Via several intermediates, it inhibits

metabolism in the liver

protein kinase GSK-3 (bottom right; for de-

The liver plays a major role in glucose homeo-

tails, see p. 388) and thereby prevents inacti-

stasis in the organism (see p. 310). If glucose

vation of glycogen synthase. In addition, in-

deficiency arises, the liver releases glucose

sulin reduces the cAMP level by activating

into the blood, and when blood sugar levels

cAMP phosphodiesterase (PDE).

are high, it takes glucose up from the blood

Regulation by transcriptional control (top).

and converts it into different metabolites.

If the liver’s glycogen reserves have been ex-

Several hormones from both groups are in-

hausted, the steroid hormone cortisol main-

volved in controlling these processes. A very

tains glucose release by initiating the conver-

simplified version of the way in which they

sion of amino acids into glucose (gluconeo-

work is presented here. Glycogen is the form

genesis; see p. 154). In the cell nucleus, the

in which glucose is stored in the liver and

complex of cortisol and its receptor

(see

muscles. The rate of glycogen synthesis is

p. 378) binds to the promoter regions of var-

determined by glycogen synthase

(bottom

ious key enzymes of gluconeogenesis and

right), while its breakdown is catalyzed by

leads to their transcription. The active en-

glycogen phosphorylase (bottom left).

zymes are produced through translation of

Regulation by interconversion (bottom). If

the mRNA formed. Control of the transcrip-

the blood glucose level falls, the peptide

tion of the gluconeogenesis enzyme PEP car-

hormone glucagon is released. This activates

boxykinase is discussed on p. 244.

122

Metabolism

In standard conditions, the change in free

ATP

enthalpy ∆G⁰

(see p. 18) that occurs in the

The nucleotide coenzyme adenosine

hydrolysis of phosphoric acid anhydride

triphosphate

(ATP) is the most important

bonds amounts to -30 to -35 kJ mol^-1 at

form of chemical energy in all cells. Cleavage

pH 7. The particular anhydride bond of ATP

of ATP is strongly exergonic. The energy this

that is cleaved only has a minor influence on

provides (∆G; see p. 16) is used to drive ender-

∆G⁰

(1-2). Even the hydrolysis of diphos-

gonic processes (such as biosynthesis and

phate (also known as pyrophosphate; 4) still

movement and transport processes) through

yields more than -30 kJ mol^-1. By contrast,

energetic coupling (see p. 124). The other nu-

cleavage of the ester bond between ribose and

cleoside triphosphate coenzymes (GTP, CTP, and

phosphate only provides -9 kJ mol^-1 (3).

UTP) have similar chemical properties to ATP,

In the cell, the ∆G of ATP hydrolysis is sub-

but they are used for different tasks in metab-

stantially larger, because the concentrations

olism (see p. 110).

of ATP, ADP and P_i are much lower than in

standard conditions and there is an excess of

ATP over ADP (see p. 18). The pH value and

A. ATP: structure

Mg²⁺ concentration also affect the value of ∆G.

In ATP, a chain of three phosphate residues is

The physiological energy yield of ATP hydrol-

linked to the 5 -OH group of the nucleoside

ysis to ADP and anorganic phosphate (P_i) is

adenosine (see p. 80). These phosphate resi-

probably around -50 kJ mol^-1.

dues are termed α, β, and γ. The α phosphate

is bound to ribose by a phosphoric acid ester

C. Types of ATP formation

bond. The linkages between the three phos-

phate residues, on the other hand, involve

Only a few compounds contain phosphate

much more unstable phosphoric acid anhy-

residues with a group transfer potential (see

dride bonds. The active coenzyme is in fact

p. 18) that is high enough to transfer them to

generally a complex of ATP with an Mg²⁺

ADP and thus allow ATP synthesis. Processes

ion, which is coordinatively bound to the α

that raise anorganic phosphate to this type of

and β phosphates (Mg²⁺ ATP^4-). However,

high potential are called substrate level phos-

the term “ATP” is usually used for the sake

phorylations (see p. 124). Reactions of this

of simplicity.

type take place in glycolysis (see p. 150) and

in the tricarboxylic acid cycle (see p. 136).

Another “energy-rich” phosphate compound

B. Hydrolysis energies

is creatine phosphate, which is formed from

The formula for phosphate residues shown in

ATP in muscle and can regenerate ATP as

Fig. A, with single and double bonds, is not an

needed (see p. 336).

accurate representation of the actual charge

Most cellular ATP does not arise in the way

distribution. In ATP, the oxygen atoms of all

described above (i. e., by transfer of phosphate

three phosphate residues have similarly

residues from organic molecules to ADP), but

strong negative charges (orange), while the

rather by oxidative phosphorylation. This

phosphorus atoms represent centers of posi-

process takes place in mitochondria (or as

tive charge. One of the reasons for the insta-

light-driven phosphorylation in chloroplasts)

bility of phosphoric anhydride bonds is the

and is energetically coupled to a proton gra-

repulsion between these negatively charged

dient over a membrane. These H⁺ gradients

oxygen atoms, which is partly relieved by

are established by electron transport chains

cleavage of a phosphate residue. In addition,

and are used by the enzyme ATP synthase as a

the free phosphate anion formed by hydroly-

source of energy for direct linking of anor-

sis of ATP is better hydrated and more strongly

ganic phosphate to ADP. In contrast to sub-

resonance-stabilized than the corresponding

strate level phosphorylation, oxidative phos-

residue in ATP. This also contributes to the

phorylation requires the presence of oxygen

strongly exergonic character of ATP hydroly-

(i. e., aerobic conditions).

sis.

Energy Metabolism

123

A. ATP: structure

Phosphoric acid

N-glycosidic

anhydride bonds

ester bond

bond

CH₂

H H

1. Formula

OH OH

CH₂

Ribose

Phosphate residue

Adenosine

2. Mg² -Complex

B. Hydrolysis energies

∆G^OI

kJ · mol^-1

-10

Positive

-20

Neutral

-30

Negative

1. Hydrolysis energies

2. ATP: charge density

C. Types of ATP formation

Electrons

Phosphorylated

substrate

Protons

ATP

synthase

ATP

A_red

ATP

Enzyme

Substrate

chain phos-

phorylation

P P

Substrate

ADP

1. Phosphate transfer

2. Oxidative phosphorylation

124

Metabolism

phorylations,” as they represent individual

Energetic coupling

steps within metabolic pathways.

The cell stores chemical energy in the form of

In the glyceraldehyde 3-phosphate dehy-

“energy-rich” metabolites. The most impor-

drogenation reaction, a step involved in gly-

tant metabolite of this type is adenosine tri-

colysis (1; see also C), the aldehyde group in

phosphate (ATP), which drives a large number

glyceraldehyde 3-phosphate is oxidized into a

of energy-dependent reactions via energetic

carboxyl group. During the reaction, an anor-

coupling (see p. 16).

ganic phosphate is also introduced into the

product, producing a mixed acid anhy-

dride—1,3-bisphosphoglycerate. Phosphopyr-

A. Energetic coupling

uvate hydratase (“enolase”, 2) catalyzes the

The change in free enthalpy ∆G⁰ during hy-

elimination of water from 2-phosphoglycer-

drolysis (see p. 18) has been arbitrarily se-

ate. In the enol phosphate formed (phosphoe-

lected as a measure of the group transfer

nol pyruvate), the phosphate residue—in con-

potential of “energy-rich” compounds. How-

trast to

2-phosphoglycerate—is at an ex-

ever, this does not mean that ATP is in fact

tremely high potential (∆G⁰

of hydrolysis:

hydrolyzed in energetically coupled reactions.

-62 kJ mol^-1). A third reaction of this type

If ATP hydrolysis and an endergonic process

is the formation of succinyl phosphate, which

were simply allowed to run alongside each

occurs in the tricarboxylic acid cycle as an

other, the hydrolysis would only produce

individual step in the succinyl CoA ligase re-

heat, without influencing the endergonic

action. Here again, anorganic phosphate is

process. For coupling, the two reactions have

introduced into a mixed acid anhydride

to be linked in such a way that a common

bond to be transferred from there to GDP.

intermediate arises. This connection is illus-

Succinyl phosphate is only an intermediate

trated here using the example of the gluta-

here, and is not released by the enzyme.

mine synthetase reaction.

In the literature, the term “substrate level

Direct transfer of NH₃ to glutamate is en-

phosphorylation” is used inconsistently.

dergonic

(∆G⁰ = +14 kJ mol^-1; see p. 18),

Some authors use it to refer to reactions in

and can therefore not take place. In the cell,

which anorganic phosphate is raised to a high

the reaction is divided into two exergonic

potential, while others use it for the subse-

steps. First, the γ-phophate residue is trans-

quent reactions, in which ATP or GTP is

ferred from ATP to glutamate. This gives rise

formed from the energy-rich intermediates.

to an “energy-rich” mixed acid anhydride. In

the second step, the phosphate residue from

C. Glyceraldehyde-3-phosphate

the intermediate is substituted by NH₃, and

dehydrogenase

glutamine and free phosphate are produced.

The energy balance of the reaction as a whole

The reaction catalyzed during glycolysis by

(∆G⁰ = -17 kJ mol^-1) is the sum of the

glyceraldehyde-3-phosphate dehydrogenase

changes in free enthalpy of direct glutamine

(GADPH) is shown here in detail. Initially,

synthesis (∆G⁰ = 14 kJ mol^-1) plus ATP hy-

the SH group of a cysteine residue of the

drolysis (∆G⁰

= -31 kJ mol^-1), although ATP

enzyme is added to the carbonyl group of

has not been hydrolyzed at all.

glyceraldehyde 3-phosphate (a). This inter-

mediate is oxidized by NAD⁺ into an “en-

ergy-rich” thioester (b). In the third step (c),

B. Substrate-level phosphorylation

anorganic phosphate displaces the thiol, and

As mentioned earlier (see p. 122), there are a

the mixed anhydride 1,3-bisphosphoglycerate

few metabolites that transfer phosphate to

arises. In this bond, the phosphate residue is

ADP in an exergonic reaction and can there-

at a high enough potential for it to be trans-

fore form ATP. In ATP synthesis, anorganic

ferred to ADP in the next step (not shown; see

phosphate or phosphate bound in an ester-

p. 150).

like fashion is transferred to bonds with a

high phosphate transfer potential. Reactions

of this type are termed “substrate-level phos-

Energy Metabolism

125

A. Energetic coupling

COO

Glu-γ-

Gln

phosphate

COO

C H

NH₃

H₃N

C H

(CH

)

2 2

H₂O

(CH )

2 2

NH₂

∆G^OI=

∆G^OI= -17 kJ . mol^-1

+14 kJ .

COO

mol^-1

NH₄

C H

(CH )

2 2

P P

ATP

P P

ADP

–

Glu

1. Glutamine synthetase reaction

Reaction 1: Glutamate + NH₃

+14 kJ . mol^-1

Glutamine

+ H₂O

Reaction 2: ATP

+ H₂O

- 31 kJ . mol-1

ADP

Total:

Glutamate + NH₃+ ATP

- 17 kJ . mol-1

Glutamine +

ADP

2. Energy balance

B. Substrate level phosphorylation

C. Glyceraldehyde 3-phosphate

dehydrogenase

Chemical

Phospho-

potential

enolpyruvate

Glyceraldehyde

3-phosphate

Glycer-

1,3-bisphospho-

aldehyde-

glycerate

3-phosphate

Succinyl-

dehydro-

phosphate

genase

Inter-

mediate 1

P P P

ATP (GTP)

Inter-

mediate 2

CoA

Inorganic

Thioester

Succinyl-

phosphate

CoA

Glycer-

2-Phospho-

aldehyde

glycerate

3-phos-

1,3-Bisphos-

O P

phate

phoglycerate

Inorganic

phosphate

Mixed anhydride

126

Metabolism

constantly maintained by the enzyme Na⁺/

Energy conservation at membranes

K+-ATPase, which consumes ATP.

Metabolic energy can be stored not only in the

form of “energy-rich” bonds (see p. 122), but

B. Proton motive force

also by separating electric charges from each

other using an insulating layer to prevent

Hydronium ions (“H⁺ ions”) can also develop

them from redistributing. In the field of tech-

electrochemical gradients. Such a proton gra-

nology, this type of system would be called a

dient plays a decisive part in cellular ATP syn-

condenser. Using the same principle, energy is

thesis (see p. 142). As usual, the energy con-

also stored (“conserved”) at cell membranes.

tent of the gradient depends on the concen-

The membrane functions as an insulator;

tration gradients—i. e., on the pH difference

electrically charged atoms and molecules

∋pH between the two sides of the membrane.

(ions) function as charges.

In addition, the membrane potential ∆ψ also

makes a contribution. Together, these two

values give the proton motive force ∆p, a

A. Electrochemical gradient

measure for the work that the H⁺ gradient

Although artificial lipid membranes are al-

can do. The proton gradient across the inner

most impermeable to ions, biological mem-

mitochondrial membrane thus delivers ap-

branes contain ion channels that selectively

proximately 24 kJ per mol H⁺.

allow individual ion types to pass through

(see p. 222). Whether an ion can cross this

C. Energy conservation in proton gradients

type of membrane, and if so in which direc-

tion, depends on the electrochemical gra-

Proton gradients can be built up in various

dient—i. e., on the concentrations of the ion

ways. A very unusual type is represented by

on each side of the membrane (the concen-

bacteriorhodopsin (1), a light-driven proton

tration gradient) and on the difference in the

pump that various bacteria use to produce

electrical potential between the interior and

energy. As with rhodopsin in the eye, the

exterior, the membrane potential.

light-sensitive component used here is cova-

The membrane potential of resting cells

lently bound retinal (see p. 358). In photosyn-

(resting potential; see p. 350) is

-0.05 to

thesis

(see p. 130), reduced plastoquinone

-0.09 V—i. e., there is an excess negative

(QH₂) transports protons, as well as electrons,

charge on the inner side of the plasma mem-

through the membrane (Q cycle, 2). The for-

brane. The main contributors to the resting

mation of the proton gradient by the respira-

potential are the two cations Na⁺ and K⁺, as

tory chain is also coupled to redox processes

well as Cl^- and organic anions (1). Data on the

(see p. 140). In complex III, a Q cycle is respon-

concentrations of these ions outside and in-

sible for proton translocation (not shown). In

side animal cells, and permeability coef -

cytochrome c oxidase (complex IV, 3), H⁺ trans-

cients, are shown in the table (2).

port is coupled to electron flow from

The behavior of an ion type is described

cytochrome c to O₂.

quantitatively by the Nernst equation

(3).

In each of these cases, the H⁺ gradient is

∆ψ_G is the membrane potential (in volts, V)

utilized by an ATP synthase (4) to form ATP.

at which there is no net transport of the ion

ATP synthases consist of two components—a

concerned across the membrane (equilibrium

proton channel (F₀) and an inwardly directed

potential). The factor R T/F n has a value of

protein complex (F₁), which conserves the

0.026 V for monovalent ions at 25 °C. Thus,

energy of back-flowing protons through ATP

for K⁺, the table (2) gives an equilibrium po-

synthesis (see p. 142).

tential of ca. -0.09 V—i. e., a value more or less

the same as that of the resting potential. By

contrast, for Na⁺ ions, ∆ψ_G is much higher than

the resting potential, at

+0.07 V. Na⁺ ions

therefore immediately flow into the cell

when Na⁺ channels open (see p. 350). The

disequilibrium between Na⁺ and K⁺ ions is

Energy Metabolism

127

C. Energy conservation

A. Electrochemical gradient

in proton gradients

Inside

Outside

1. Light-driven

proton pump

Retinal

Organic anions

(bacterio-

1. Cause

rhodopsin)

Ion

Concentrations

Permeability

coefficient

PS II

Cyto-

Extracelluar

plasm space

(mM)

(cm · s-1 · 10⁹)

100

500

2. Q cycle

QH2

150

(plasto-

quinone

Ca²

0.0002

cycle

in plants)

150

Organic

138

anions

QH2

2. Concentrations

b/f-

complex

Cyto-

outside

R · T

chrome C

∆Ψ_G =

F · n

inside

O₂

Cu_A

R = gas constant

n = Ion charge

T = temperature (K)

F = Faraday constant

2 H₂O

3. Nernst equation

Cu_B

3. Electron-

Heme/a₃

B. Proton motive force

driven

proton

pump

(cyto-

chrome C

oxidase)

Membrane

pH gradient

potential

∆pH = pHa - pH

∆ψ = ψa - ψ

(in pH units)

Protein

P P

Proton motive force

≈ 0.06 V

P P P

ATP

2.3 · R · T

∆p = ∆ψ -

∆pH

4. Proton-

∆G

= -F · ∆p

driven ATP

Proton flow

Ha H i

synthesis

Electron flow

128

Metabolism

koids or flattened membrane sacs are stacked

Photosynthesis: light reactions

on top of each other to form grana. The inside

Sunlight is the most important source of en-

of the thylakoid is referred to as the lumen.

ergy for nearly all living organisms. With the

The light reactions are catalyzed by enzymes

help of photosynthesis, light energy is used to

located in the thylakoid membrane, whereas

produce organic substances from CO₂ and

the dark reactions take place in the stroma.

water. This property of phototrophic organ-

As in the respiratory chain (see p. 140), the

isms (plants, algae, and some bacteria) is ex-

light reactions cause electrons to pass from

ploited by heterotrophic organisms (e. g., ani-

one redox system to the next in an electron

mals), which are dependent on a supply of

transport chain. However, the direction of

organic substances in their diet (see p. 112).

transport is opposite to that found in the res-

The atmospheric oxygen that is vital to higher

piratory chain. In the respiratory chain, elec-

organisms is also derived from photosynthe-

trons flow from NADH+H⁺ to O₂, with the

sis.

production of water and energy.

In photosynthesis, electrons are taken up

from water and transferred to NADP⁺, with an

A. Photosynthesis: overview

expenditure of energy. Photosynthetic electron

The chemical balance of photosynthesis is

transport is therefore energetically

“uphill

simple. Six molecules of CO₂

are used to

work.” To make this possible, the transport

form one hexose molecule (right). The hydro-

is stimulated at two points by the absorption

gen required for this reduction process is

of light energy. This occurs through two pho-

taken from water, and molecular oxygen is

tosystems—protein complexes that contain

formed as a by-product (left). Light energy is

large numbers of chlorophyll molecules and

required, since water is a very poor reducing

other pigments (see p. 132). Another compo-

agent and is therefore not capable of reducing

nent of the transport chain is the cytochrome

CO₂.

b/f complex, an aggregate of integral mem-

In the light-dependent part of photosyn-

brane proteins that includes two cytochromes

thesis—the “light reactions ”—H₂O molecules

(b₅₆₃

and f). Plastoquinone, which is com-

are split into protons, electrons, and oxygen

parable to ubiquinone, and two soluble pro-

atoms. The electrons undergo excitation by

teins, the coppercontaining plastocyanin and

light energy and are raised to an energy level

ferredoxin, function as mobile electron car-

that is high enough to reduce NADP⁺. The

riers. At the end of the chain, there is an

NADPH+H⁺ formed in this way, in contrast to

enzyme that transfers the electrons to NADP⁺.

H₂O, is capable of “fixing” CO₂

reductive-

Because photosystem II and the cyto-

ly—i. e., of incorporating it into organic bonds.

chrome b/f complex release protons from re-

Another product of the light reactions is ATP,

duced plastoquinone into the lumen (via a Q

which is also required for CO₂ fixation. If

cycle), photosynthetic electron transport es-

NADPH+H⁺, ATP, and the appropriate en-

tablishes an electrochemical gradient across

zymes are available, CO₂ fixation can also

the thylakoid membrane (see p. 126), which is

take place in darkness. This process is there-

used for ATP synthesis by an ATP synthase.

fore known as the “dark reaction.”

ATP and NADPH+H⁺, which are both needed

The excitation of electrons to form NADPH

for the dark reactions, are formed in the

is a complex photochemical process that

stroma.

involves chlorophyll, a tetrapyrrole dye con-

taining Mg²⁺ that bears an extra phytol resi-

due (see p. 132).

B. Light reactions

In green algae and higher plants, photosyn-

thesis occurs in chloroplasts. These are organ-

elles, which—like mitochondria—are sur-

rounded by two membranes and contain their

own DNA. In their interior, the stroma, thyla-

Energy Metabolism

129

A. Photosynthesis: overview

Phytol residue

Hexose

12 NADPH + H

H₃C

CH₃

H₃C

P P P

“Dark

CH₃

18 ATP

reactions”

(Calvin

CH₃

cycle)

H₃C

P P

Chlorophyll a

3 O₂

12 H

18 ADP + P_i

Electron flow

6 H₂O

Proton flow

12 NADP

6 CO₂

Cytoplasm

Nucleus

Outer

Thylakoid

Lumen

membrane

Inner

membrane

Plasma

membrane

Stroma

Granum

Chloroplast

Vacuole

B. Light reactions

P P

P P P

ATP

Stroma

NADPH + H

Thylakoid membrane

Lumen

NADP

Ferredoxin (Fd)

2 H

H2O

[O]

Mg²⁺

Light

Photosystem I

Plasto-

quinone

Ferredoxin-

Plasto-

NADP

cyanin

reductase

1.18.1.2

QH2

(PC)

ATP synthase

3.6.1.34

Photosystem II

2 H

Cytochrome b/f complex

130

Metabolism

quinone pool takes place as described on the

Photosynthesis: dark reactions

preceding page and shown in B.

The “light reactions” in photosynthesis bring

about two strongly endergonic reactions—the

B. Redox series

reduction of NADP⁺ to NADPH+H⁺ and ATP

synthesis (see p. 122). The chemical energy

It can be seen from the normal potentials E⁰

needed for this is produced from radiant en-

(see p. 18) of the most important redox sys-

ergy by two photosystems.

tems involved in the light reactions why two

excitation processes are needed in order to

transfer electrons from H₂O to NADP⁺. After

A. Photosystem II

excitation in PS II, E⁰ rises from around -1 V

The photosynthetic electron transport chain

back to positive values in plastocyanin

in plants starts in photosystem II (PS II; see

(PC)—i. e., the energy of the electrons has to

p. 128). PS II consists of numerous protein

be increased again in PS I. If there is no NADP⁺

subunits

(brown) that contain bound pig-

available, photosynthetic electron transport

ments—i. e., dye molecules that are involved

can still be used for ATP synthesis. During

in the absorption and transfer of light energy.

cyclic photophosphorylation, electrons return

The schematic overview of PS II presented

from ferredoxin (Fd) via the plastoquinone

here (1) only shows the important pigments.

pool to the b/f complex. This type of electron

These include a special chlorophyll molecule,

transport does not produce any NADPH, but

the reaction center P₆₈₀; a neighboring Mg²⁺

does lead to the formation of an H⁺ gradient

free chlorophyll (pheophytin); and two bound

and thus to ATP synthesis.

plastoquinones (Q_A and Q_B). A third quinone

(Q_P) is not linked to PS II, but belongs to the

C. Calvin cycle

plastoquinone pool. The white arrows indi-

cate the direction of electron flow from water

The synthesis of hexoses from CO₂ is only

to Q_P. Only about 1 % of the chlorophyll mol-

shown in a very simplified form here; a com-

ecules in PS II are directly involved in photo-

plete reaction scheme is given on p. 407. The

chemical excitation (see p. 128). Most of them

actual CO₂ fixation—i. e., the incorporation of

are found, along with other pigments, in what

CO₂ into an organic compound—is catalyzed

are known as light-harvesting or antenna

by ribulose bisphosphate carboxylase/oxygen-

complexes (green). The energy of light quanta

ase (“rubisco”). Rubisco, the most abundant

striking these can be passed on to the reaction

enzyme on Earth, converts ribulose 1,5-bis-

center, where it can be utilized.

phosphate, CO₂ and water into two mole-

In Fig. 2, photosynthetic electron transport

cules of 3-phosphoglycerate. These are then

in PS II is separated into the individual steps

converted, via 1,3-bisphosphoglycerate and

involved. Light energy from the light-harvest-

3-phosphoglycerate, into glyceraldehyde

ing complexes (a) raises an electron of the

3-phosphate (glyceral 3-phosphate). In this

chlorophyll in the reaction center to an

way, 12 glyceraldehyde 3-phosphates are syn-

excited “singlet state.” The excited electron is

thesized from six CO₂. Two molecules of this

immediately passed on to the neighboring

intermediate are used by gluconeogenesis re-

pheophytin. This leaves behind an “electron

actions to synthesize glucose

6-phosphate

gap” in the reaction center—i. e., a positively

(bottom right). From the remaining 10 mole-

charged P₆₈₀ radical (b). This gap is now filled

cules, six molecules of ribulose 1,5-bisphos-

by an electron removed from an H₂O mole-

phate are regenerated, and the cycle then

cule by the water-splitting enzyme (b). The

starts over again. In the Calvin cycle, ATP is

excited electron passes on from the pheophy-

required for phosphorylation of 3-phospho-

tin via Q_A to Q_B, converting the latter into a

glycerate

and ribulose

5-phosphate.

semiquinone radical (c). Q_B is then reduced to

NADPH+H⁺, the second product of the light

hydroquinone by a second excited electron,

reaction, is consumed in the reduction of 1,3-

and is then exchanged for an oxidized qui-

bisphosphoglycerate to glyceraldehyde

none (Q_P) from the plastoquinone pool. Fur-

phosphate.

ther transport of electrons from the plasto-

Energy Metabolism

131

A. Photosystem II

B. Redox series

EOl (V)

Photo-

Bound

Exchangeable Plasto-

chemical

-1.2

quinone

excitation

-1.0

-0.8

Fe/S

Mg²⁺

Q_A

-0.6

Mg²⁺

-0.4

-0.2

b/f

Light-

Reaction

NADP

harvesting

Mg²⁺

center

complex

(P₆₈₀)

+0.2

PS I

Pheophytin

+0.4

PS II

700)

680)

+0.6

Cyclic

Water-

+0.8

photophos-

splitting

4 Mn²⁺

H2O

phorylation

enzyme

H₂O

4 ions

2 H

1/2 O₂

Plasto-

quinone

(ox.)

Mg²⁺

Exchange

Q_P(ox)

B (red)

H2O

C. Calvin cycle

6 ADP

6 ATP

H O O

H₂C C

C C CH₂

O OH OH

6 CO₂

H2O

O C O

CO₂, Mg²

CO₂

Light

6 H₂O

4 P

Light

H₂C C

CH₂

Light

P O OHO

Ribulose-bisphosphate

carboxylase 4.1.1.39

Phosphoglycerate kinase

Glucose

6-phosphate

2.7.2.3

12 ATP

P P

Glyceraldehyde 3-phosphate

dehydrogenase (NADP

) 1.2.1.13

12 ADP

Gluco-

neogenesis

Phosphoribulokinase 2.7.1.19

12 NADPH

12 NADP

Glyceraldehyde

3-phosphate

132

Metabolism

are taken up by two channels (D and K, not

Molecular models:

shown). The mechanism that links proton

membrane proteins

transport to electron transfer is still being

investigated.

The plates show, in simplified form, the struc-

tures of cytochrome c oxidase (A; complex IV

of the respiratory chain) and of photosystem I

B. Reaction center of Synechococcus

of a cyanobacterium (B). These two molecules

elongatus

are among the few integral membrane pro-

Photosystem I (PS I) in the cyanobacterium

teins for which the structure is known in de-

Synechococcus elongatus is the first system of

tail. Both structures were determined by X-

this type for which the structure has been

ray crystallography.

solved in atomic detail. Although the bacterial

photosystem differs slightly from the systems

in higher plants, the structure provides val-

A. Cytochrome c oxidase

uable hints about the course of the light re-

The enzyme cytochrome c oxidase (“COX,” EC

actions in photosynthesis (see p. 128). The

1.9.3.1) catalyzes the final step of the respira-

functioning of the photosystem is discussed

tory chain. It receives electrons from the small

in greater detail on p. 130.

heme protein cytochrome c and transfers

The functional form of PS I in S. elongatus

them to molecular oxygen, which is thereby

consists of a trimer with a mass of more than

reduced to water (see p. 140). At the same

10⁶ Da that is integrated into the membrane.

time, 2-4 protons per water molecule formed

Only one of the three subunits is shown here.

are pumped from the matrix into the inter-

This consists of

12 different polypeptides

membrane space.

(gray-blue), 96 chlorophyll molecules (green),

Mammalian COX (the illustration shows

22 carotenoids (orange), several phylloqui-

the enzyme from bovine heart) is a dimer

nones (yellow), and other components. Most

that has two identical subunits with masses

of the chlorophyll molecules are so-called an-

of 204 kDa each. Only one subunit is shown in

tenna pigments. These collect light energy

detail here; the other is indicated by gray

and conduct it to the reaction center, which

lines. Each subunit consists of 13 different

is located in the center of the structure and

polypeptides, which all span the inner mito-

therefore not visible. In the reaction center, an

chondrial membrane. Only polypeptides I

electron is excited and transferred via various

(light blue) and II (dark blue) and the linked

intermediate steps to a ferredoxin molecule

cofactors are involved in electron transport.

(see p. 128). The chlorophylls (see formula)

The other chains, which are differently ex-

are heme-like pigments with a highly modi-

pressed in the different organs, probably

fied tetrapyrrole ring, a central Mg²⁺ ion, and

have regulatory functions. The two heme

an apolar phytol side chain. Shown here is

groups, heme a (orange) and heme a₁ (red)

chlorophyll a, which is also found in the re-

are bound in polypeptide 1. The copper center

action center of the S. elongatus photosystem.

Cu_A consists of two copper ions

(green),

The yellow and orange-colored carot-

which are coordinated by amino acid residues

enoids—e. g., E-carotene

(see formula)—are

in polypeptide II. The second copper (Cu_B) is

auxiliary pigments that serve to protect the

located in polypeptide I near heme a₃.

chloroplasts from oxidative damage. Danger-

To reduce an O₂ molecule to two molecules

ous radicals can be produced during the light

of H₂O, a total of four electrons are needed,

reaction—particularly singlet oxygen. Caroten-

which are supplied by cytochrome c (pink, top

oids prevent compounds of this type from

left) and initially given off to Cu_A. From there,

arising, or render them inactive. Carotenoids

they are passed on via heme a and heme a₃ to

are also responsible for the coloring of leaves

the enzyme’s reaction center, which is located

seen during fall. They are left behind when

between heme a₃ and Cu_B. The reduction of

plants break down chlorophyll in order to

the oxygen takes place in several steps, with-

recover the nitrogen it contains.

out any intermediate being released. The four

protons needed to produce water and the H⁺

ions pumped into the intermembrane space

134

Metabolism

An important aspect of PDH catalysis is the

Oxoacid dehydrogenases

spatial relationship between the components

The intermediary metabolism has multien-

of the complex. The covalently bound lipo-

zyme complexes which, in a complex reaction,

amide coenzyme is part of a mobile domain

catalyze the oxidative decarboxylation of 2-

of E2, and is therefore highly mobile. This

oxoacids and the transfer to coenzyme A of

structure is known as the lipoamide arm, and

the acyl residue produced. NAD⁺ acts as the

swings back and forth between E1 and E3

electron acceptor. In addition, thiamine di-

during catalysis. In this way, lipoamide can

phosphate, lipoamide, and FAD are also in-

interact with the TPP bound at E1, with solute

volved in the reaction. The oxoacid

coenzyme A, and also with the FAD that

dehydrogenases include a) the pyruvate dehy-

serves as the electron acceptor in E3.

drogenase complex (PDH, pyruvate

acetyl

CoA), b) the

2-oxoglutarate dehydrogenase

B. PDH complex of Escherichia coli

complex of the tricarboxylic acid cycle (ODH,

2-oxoglutarate

succinyl CoA), and c) the

The PDH complex of the bacterium Escheri-

branched chain dehydrogenase complex, which

chia coli has been particularly well studied. It

is involved in the catabolism of valine, leu-

has a molecular mass of 5.3

10⁶, and with a

cine, and isoleucine (see p. 414).

diameter of more than 30 nm it is larger than

a ribosome. The complex consists of a total of

60 polypeptides (1, 2): 24 molecules of E2

A. Pyruvate dehydrogenase: reactions

(eight trimers) form the almost cube-shaped

The pyruvate dehydrogenase reaction takes

core of the complex. Each of the six surfaces of

place in the mitochondrial matrix

(see

the cube is occupied by a dimer of E3 compo-

p. 210). Three different enzymes

[E1-E3]

nents, while each of the twelve edges of the

form the PDH multienzyme complex (see B).

cube is occupied by dimers of E1 molecules.

[1] Initially, pyruvate dehydrogenase [E1]

Animal oxoacid dehydrogenases have similar

catalyzes the decarboxylation of pyruvate

structures, but differ in the numbers of sub-

and the transfer of the resulting hydroxyethyl

units and their molecular masses.

residue to thiamine diphosphate (TPP, 1a). The

same enzyme then catalyzes oxidation of the

Further information

TPP-bound hydroxyethyl group to yield an

acetyl residue. This residue and the reducing

The PDH reaction, which is practically irrever-

equivalents obtained are then transferred to

sible, occupies a strategic position at the inter-

lipoamide (1b).

face between carbohydrate and fatty acid me-

[2] The second enzyme, dihydrolipoamide

tabolism, and also supplies acetyl residues to

acetyltransferase [E2], shifts the acetyl residue

the tricarboxylic acid cycle. PDH activity is

from lipoamide to coenzyme A (2), with dihy-

therefore strictly regulated (see p. 144). Inter-

drolipoamide being left over.

conversion is particularly important in animal

[3] The third enzyme, dihydrolipoamide de-

cells (see p. 120). Several PDH-specific protein

hydrogenase

[E3], reoxidizes dihydrolipo-

kinases inactivate the E1 components through

amide, with NADH+H⁺ being formed. The

phosphorylation, while equally specific pro-

electrons are first taken over by enzyme-

tein phosphatases reactivate it again. The

bound FAD (3a) and then transferred via a

binding of the kinases and phosphatases to

catalytically active disulfide bond in the E3

the complex is in turn regulated by metabo-

subunit (not shown) to soluble NAD⁺ (3b).

lites. For example, high concentrations of ace-

The five different coenzymes involved are

tyl CoA promote binding of kinases and

associated with the enzyme components in

thereby inhibit the reaction, while Ca²⁺ in-

different ways. Thiamine diphosphate is

creases the activity of the phosphatase. Insu-

non-covalently bound to E1, whereas lipo-

lin activates PDH via inhibition of phosphor-

amide is covalently bound to a lysine residue

ylation.

of E2 and FAD is bound as a prosthetic group to

E3. NAD⁺ and coenzyme A, being soluble

coenzymes, are only temporarily associated

with the complex.

136

Metabolism

p. 134). NADH+H⁺ is once again formed in

Tricarboxylic acid cycle: reactions

this reaction.

The tricarboxylic acid cycle (TCA cycle, also

[5] The subsequent cleavage of the thio-

known as the citric acid cycle or Krebs cycle)

ester succinylCoA into succinate and coen-

is a cyclic metabolic pathway in the mitochon-

zyme A by succinic acid-CoA ligase (succinyl

drial matrix (see p. 210). In eight steps, it oxi-

CoA synthetase, succinic thiokinase) is

dizes acetyl residues (CH₃-CO-) to carbon di-

strongly exergonic and is used to synthesize

oxide (CO₂). The reducing equivalents ob-

a phosphoric acid anhydride bond (“substrate

tained in this process are transferred to

level phosphorylation ”, see p. 124). However, it

NAD⁺ or ubiquinone, and from there to the

is not ATP that is produced here as is other-

respiratory chain (see p. 140). Additional met-

wise usually the case, but instead guanosine

abolic functions of the cycle are discussed on

triphosphate (GTP). However, GTP can be con-

p. 138.

verted into ATP by a nucleoside diphosphate

kinase (not shown).

[6] Via the reactions described so far, the

A. Tricarboxylic acid cycle

acetyl residue has been completely oxidized

The acetyl-CoA that supplies the cycle with

to CO₂. At the same time, however, the carrier

acetyl residues is mainly derived from E-

molecule oxaloacetate has been reduced to

oxidation of fatty acids (see p. 164) and from

succinate. Three further reactions in the cycle

the pyruvate dehydrogenase reaction. Both of

now regenerate oxaloacetate from succinate.

these processes take place in the mitochon-

Initially, succinate dehydrogenase oxidizes

drial matrix.

succinate to fumarate. In contrast to the other

[1] In the first step of the cycle, citrate

enzymes in the cycle, succinate dehydrogenase

synthase catalyzes the transfer of an acetyl

is an integral protein of the inner mitochondrial

residue from acetyl CoA to a carrier molecule,

membrane. It is therefore also assigned to the

oxaloacetic acid. The product of this reaction,

respiratory chain as complex II. Although suc-

tricarboxylic acid, gives the cycle its name.

cinate dehydrogenase contains FAD as a pros-

[2] In the next step, tricarboxylic acid

thetic group, ubiquinone is the real electron

undergoes isomerization to yield isocitrate.

acceptor of the reaction.

In the process, only the hydroxyl group is

[7] Water is now added to the double bond

shifted within the molecule. The correspond-

of fumarate by fumarate hydratase (“fuma-

ing enzyme is called aconitate hydratase

rase”), and chiral (2S)-malate is produced.

(“aconitase”), because unsaturated aconitate

[8] In the last step of the cycle, malate is

arises as an enzyme-bound intermediate dur-

again oxidized by malate dehydrogenase into

ing the reaction (not shown; see p. 8). Due to

oxaloacetate, with NADH+H⁺ again being pro-

the properties of aconitase, the isomerization

duced. With this reaction, the cycle is com-

is absolutely stereospecific. Although citrate is

plete and can start again from the beginning.

not chiral, isocitrate has two chiral centers, so

As the equilibrium of the reaction lies well on

that it could potentially appear in four iso-

the side of malate, the formation of oxaloace-

meric forms. However, in the tricarboxylic

tic acid by reaction

[8] depends on the

acid cycle, only one of these stereoisomers,

strongly exergonic reaction [1], which imme-

(2R,3S)-isocitrate, is produced.

diately removes it from the equilibrium.

[3] The first oxidative step now follows.

The net outcome is that each rotation of

Isocitrate dehydrogenase oxidizes the hy-

the tricarboxylic acid cycle converts one ace-

droxyl group of isocitrate into an oxo group.

tyl residue and two molecules of H₂O into two

At the same time, a carboxyl group is released

molecules of CO₂. At the same time, one GTP,

as CO₂, and 2-oxoglutarate (also known as α-

three NADH+H⁺ and one reduced ubiquinone

ketoglutarate) and NADH+H⁺ are formed.

(QH₂) are produced. By oxidative phosphory-

[4] The next step, the formation of succinyl

lation (see p. 122), the cell obtains around

CoA, also involves one oxidation and one de-

nine molecules of ATP from these reduced

carboxylation. It is catalyzed by 2-oxogluta-

coenzymes (see p. 146). Together with the

rate dehydrogenase, a multienzyme complex

directly formed GTP, this yields a total of 10

closely resembling the PDH complex

(see

ATP per acetyl group.

Energy Metabolism

137

A. Tricarboxylic acid cycle

Center of chirality

COO

Acetyl CoA

C H

+28.1

C CH₃

H₂O

-3.8

COO

∆G0I

(2S) - Malate

COO

kJ · mol-1

COO

C H

CH₂

COO

Fumarate

Oxaloacetate

Ubiquinol

QH₂

H₂O

±0

-38.2

Respiratory

OOC

COO

chain

H₂C

CH₂

COO

Citrate

Succinate

P P

GTP

-8.8

+6.7

P P

OOC

COO

H₂C

CH₂

H₂C

C O

COO

Succinyl CoA

(2R,3S)-Isocitrate

OOC

-37.0

-7.1

H₂C

CH₂

O C O

CO₂

O C O

CO₂

COO

2-Oxoglutarate

Citrate synthase

2-Oxoglutarate DH complex

Succinate DH 1.3.5.1

4.1.3.7

1.2.4.2, 1.8.1.4, 2.3.1.61

[FAD, Fe₂S₂, Fe₄S₄]

Aconitase

Succinate-CoA ligase

Fumarate hydratase

4.2.1.3 [Fe₄S₄]

6.2.1.4

4.2.1.2

Isocitrate DH 1.1.1.41

DH = dehydrogenase

Malate DH 1.1.1.37

138

Metabolism

carboxylase [1]. It allows pyruvate yielding

Tricarboxylic acid cycle: functions

amino acids and lactate to be used for gluco-

neogenesis.

A. Tricarboxylic acid cycle: functions

By contrast, acetyl CoA does not have ana-

The tricarboxylic acid cycle (see p. 136) is

plerotic effects in animal metabolism. Its car-

often described as the “hub of intermediary

bon skeleton is completely oxidized to CO₂

metabolism.” It has both catabolic and ana-

and is therefore no longer available for bio-

bolic functions—it is amphibolic.

synthesis. Since fatty acid degradation only

As a catabolic pathway, it initiates the “ter-

supplies acetyl CoA, animals are unable to

minal oxidation” of energy substrates. Many

convert fatty acids into glucose. During peri-

catabolic pathways lead to intermediates of

ods of hunger, it is therefore not the fat re-

the tricarboxylic acid cycle, or supply metab-

serves that are initially drawn on, but pro-

olites such as pyruvate and acetyl-CoA that

teins. In contrast to fatty acids, the amino

can enter the cycle, where their C atoms are

acids released are able to maintain the blood

oxidized to CO₂. The reducing equivalents

glucose level (see p. 308).

(see p. 14) obtained in this way are then

used for oxidative phosphorylation—i. e., to

The tricarboxylic acid cycle not only takes

aerobically synthesize ATP (see p. 122).

up acetyl CoA from fatty acid degradation, but

also supplies the material for the biosynthesis

The tricarboxylic acid cycle also supplies

of fatty acids and isoprenoids. Acetyl CoA,

important precursors for anabolic pathways.

which is formed in the matrix space of mito-

Intermediates in the cycle are converted into:

chondria by pyruvate dehydrogenase

(see

p. 134), is not capable of passing through the

• Glucose (gluconeogenesis; precursors: oxa-

inner mitochondrial membrane. The acetyl

loacetate and malate—see p. 154)

residue is therefore condensed with oxalo-

• Porphyrins

(precursor: succinyl-CoA—see

acetate by mitochondrial citrate synthase to

p. 192)

form citrate. This then leaves the mitochon-

• Amino acids (precursors: 2-oxoglutarate,

dria by antiport with malate

(right; see

oxaloacetate—see p. 184)

p. 212). In the cytoplasm, it is cleaved again

• Fatty acids and isoprenoids (precursor: cit-

by ATP-dependent citrate lyase [4] into acetyl-

rate—see below)

CoA and oxaloacetate. The oxaloacetate

The intermediates of the tricarboxylic acid

formed is reduced by a cytoplasmic malate

cycle are present in the mitochondria only in

dehydrogenase to malate [2], which then re-

very small quantities. After the oxidation of

turns to the mitochondrion via the antiport

acetyl-CoA to CO₂, they are constantly regen-

already mentioned. Alternatively, the malate

erated, and their concentrations therefore re-

can be oxidized by “malic enzyme” [5], with

main constant, averaged over time. Anabolic

decarboxylation, to pyruvate. The NADPH+H⁺

pathways, which remove intermediates of the

formed in this process is also used for fatty

cycle (e. g., gluconeogenesis) would quickly

acid biosynthesis.

use up the small quantities present in the

mitochondria if metabolites did not reenter

Additional information

the cycle at other sites to replace the com-

pounds consumed. Processes that replenish

Using the so-called glyoxylic acid cycle, plants

the cycle in this way are called anaplerotic

and bacteria are able to convert acetyl-CoA

reactions.

into succinate, which then enters the tricar-

The degradation of most amino acids is

boxylic acid cycle. For these organisms, fat

anaplerotic, because it produces either inter-

degradation therefore functions as an ana-

mediates of the cycle or pyruvate (glucogenic

plerotic process. In plants, this pathway is

amino acids; see p. 180). Gluconeogenesis is in

located in special organelles, the glyoxysomes.

fact largely sustained by the degradation of

amino acids. A particularly important ana-

plerotic step in animal metabolism leads

from pyruvate to oxaloacetic acid. This ATP-

dependent reaction is catalyzed by pyruvate

Energy Metabolism

139

A. Tricarboxylic acid cycle: functions

* Essential

Asp, Asn,

Glucose

* amino acid

Arg, Met*,

GTP

Thr*, Ile*

Fat

Oxaloacetate

PEP

Phe*, Tyr, Trp*

Irreversible

Ala, Ser, Thr*,

Cys, Gly

Acyl-

Ala, Leu*,

Carbo-

Malate

Pyruvate

CoA

Val*

hydrates

CO₂

Cytoplasm

Carnitine

shuttle

CO₂

Pyruvate

Irreversible

ATP

Oxalo-

Malate

acetate

Acyl

Acetyl

CoA

β-Oxidation

Mitochondrial

Malate

ATP

ADP+P

matrix

Oxalo-

acetate

Citrate

Fumarate

Asp

Phe*

Asn

Citrate

Tyr

His

CoA

Acetyl

Ile*

Pro

CoA

Val*

Arg

Succinate

Met*

Gln

Trp*

Glu

Isocitrate

Fatty

GTP

acids

Succinyl

2-Oxo-

CoA

CO₂

glutarate

Fat

CO₂

Glu, Gln,

Porphyrins

Pro, Arg

Pyruvate carboxylase

6.4.1.1

Malate dehydrogenase

1.1.1.37

NADH+H

2[H]

O₂

2[H]

Ubiquinol

PEP carboxykinase

(QH₂)

4.1.1.32

Citrate lyase 4.1.3.8

Oxidative

P P

phosphorylation

P P P

Malic enzyme 1.1.1.40

ADP

ATP

Catabolic pathway

H₂O

Anabolic pathway

Anaplerotic reaction

140

Metabolism

zyme-bound FADH₂ and the electron-trans-

Respiratory chain

porting flavoprotein (ETF; see p. 164). Ubiq-

The respiratory chain is one of the pathways

uinol passes electrons on to complex III, which

involved in oxidative phosphorylation

(see

transfers them via two b-type heme groups,

p. 122). It catalyzes the steps by which elec-

one Fe/S cluster, and heme c₁ to the small

trons are transported from NADH+H⁺ or re-

heme protein cytochrome c. Cytochrome c

duced ubiquinone (QH₂) to molecular oxygen.

then transports the electrons to complex

Due to the wide difference between the redox

IV—cytochrome c oxidase. Cytochrome c oxi-

potentials of the donor (NADH+H⁺ or QH₂)

dase contains redox-active components in the

and the acceptor (O₂), this reaction is strongly

form of two copper centers (Cu_A and Cu_B) and

exergonic (see p. 18). Most of the energy re-

hemes a and a₃, through which the electrons

leased is used to establish a proton gradient

finally reach oxygen (see p. 132). As the result

across the inner mitochondrial membrane

of the two-electron reduction of O₂, the

(see p. 126), which is then ultimately used to

strongly basic O^2- anion is produced (at least

synthesize ATP with the help of ATP synthase.

formally), and this is converted into water by

binding of two protons. The electron transfer

is coupled to the formation of a proton gradi-

A. Components of the respiratory chain

ent by complexes I, III, and IV (see p. 126).

The electron transport chain consists of three

protein complexes (complexes I, III, and IV),

B. Organization

which are integrated into the inner mitochon-

drial membrane, and two mobile carrier mol-

Proton transport via complexes I, III, and IV

ecules—ubiquinone (coenzyme Q) and cyto-

takes place vectorially from the matrix into

chrome c. Succinate dehydrogenase, which ac-

the intermembrane space. When electrons

tually belongs to the tricarboxylic acid cycle,

are being transported through the respiratory

is also assigned to the respiratory chain as

chain, the H⁺ concentration in this space in-

complex II. ATP synthase (see p. 142) is some-

creases—i. e., the pH value there is reduced by

times referred to as complex V, although it is

about one pH unit. For each H₂O molecule

not involved in electron transport. With the

formed, around 10 H⁺ ions are pumped into

exception of complex I, detailed structural in-

the intermembrane space. If the inner mem-

formation is now available for every complex

brane is intact, then generally only ATP syn-

of the respiratory chain.

thase (see p. 142) can allow protons to flow

All of the complexes in the respiratory

back into the matrix. This is the basis for the

chain are made up of numerous polypeptides

coupling of electron transport to ATP synthe-

and contain a series of different protein

sis, which is important for regulation pur-

bound redox coenzymes (see pp. 104, 106).

poses (see p. 144).

These include flavins (FMN or FAD in com-

As mentioned, although complexes I

plexes I and II), iron-sulfur clusters (in I, II,

through V are all integrated into the inner

and III), and heme groups (in II, III, and IV).

membrane of the mitochondrion, they are not

Of the more than 80 polypeptides in the res-

usually in contact with one another, since the

piratory chain, only 13 are coded by the mi-

electrons are transferred by ubiquinone and

tochondrial genome (see p. 210). The remain-

cytochrome c. With its long apolar side chain,

der are encoded by nuclear genes, and have to

ubiquinone is freely mobile within the mem-

be imported into the mitochondria after

brane. Cytochrome c is water-soluble and is

being synthesized in the cytoplasm

(see

located on the outside of the inner membrane.

p. 228).

NADH oxidation via complex I takes place

Electrons enter the respiratory chain in var-

on the inside of the membrane—i. e., in the

ious different ways. In the oxidation of

matrix space, where the tricarboxylic acid

NADH+H⁺ by complex I, electrons pass via

cycle and β-oxidation (the most important

FMN and Fe/S clusters to ubiquinone (Q). Elec-

sources of NADH) are also located. O₂ reduc-

trons arising during the oxidation of succinate,

tion and ATP formation also take place in the

acyl CoA, and other substrates are passed to

matrix.

ubiquinone by succinate dehydrogenase or

other mitochondrial dehydrogenases via en-

Energy Metabolism

141

A. Components of the respiratory chain

Liponamide-H

Pyruvate

Complex I

EOI

2-Oxoglutarate

HS SH

NADH dehydrogenase (ubiquinone)

1.6.5.3

M_r 700 - 800 kDa, 25 - 30 subunits

-0.3

1 FMN, 2 Fe₂S₂, 4 - 5 Fe₄S

Succinate

Complex II

3-Hydroxybutyrate

3-Hydroxyacyl CoA

Succinate dehydrogenase 1.3.5.1

Malate

Isocitrate

M_r 125 kDa, 4 - 6 subunits

NADH

+0.1

1 FAD, 1 Fe₂S₂, 1 Fe₄S₄, 1Fe₃S

2 ubiquinone, 1 heme b

Complex III

Fumarate

Ubiquinol-cytochrome C

Acyl CoA

reductase 1.10.2.2

III

α-Glycerophosphate

ETF

M_r ≈ 400 kDa, 11 subunits

Dihydroorotat

2 Fe₂S₂, 2 heme b, 1 heme c

Cholin

Complex IV

Cytochrome C

Mr 12 kDa

Cytochrome Coxidase 1.9.3.1

1 heme

+0.3

M_r ≈ 200 kDa, 8 - 13 subunits

2 Cu, 1 Zn, 1 heme a, 1 heme a₃

Complex V

H -transporting ATP synthase

3.6.1.34

P P

P P P

M_r >400 kDa, >20 subunits

2 H

1/2 O

Electron flow

+0.8

Proton flow

H₂O

B. Organization

Outer

mitochon-

drial

membrane

Inter-

membrane

space

4 H

2 H

4 H

Inner

Cyto-

mitochon-

∆p

chrome C

drial

III

membrane

4 H

2-4 H

1/2 O

Matrix

4 H

O²

3 P

space

2 H

P P

P P P

ATP

Tricarboxylic

10 H

NAD

H₂O

acid cycle

NADH+H

β-Oxidation

142

Metabolism

form complexes with inorganic sulfide and

ATP synthesis

the SH groups of cysteine residues

(see

In the respiratory chain (see p. 140), electrons

p. 286). Ubiquinone

(coenzyme Q; see

are transferred from NADH or ubiquinol (QH₂)

p. 104) is a mobile carrier that takes up elec-

to O₂. The energy obtained in this process is

trons from complexes I and II and from re-

used to establish a proton gradient across the

duced ETF and passes them on to complex III.

inner mitochondrial membrane. ATP synthe-

Heme groups are also involved in electron

sis is ultimately coupled to the return of pro-

transport in a variety of ways. Type b hemes

tons from the intermembrane space into the

correspond to that found in hemoglobin (see

matrix.

p. 280). Heme c in cytochrome c is covalently

bound to the protein, while the tetrapyrrole

ring of heme a is isoprenylated and carries a

A. Redox systems of the respiratory chain

formyl group. In complex IV, a copper ion (Cu_B)

The electrons provided by NADH do not reach

and heme a₃ react directly with oxygen.

oxygen directly, but instead are transferred to

it in various steps. They pass through at least

B. ATP synthase

10 intermediate redox systems, most of which

are bound as prosthetic groups in complexes

The ATP synthase (EC 3.6.1.34, complex V) that

I, III, and IV. The large number of coenzymes

transports H⁺ is a complex molecular ma-

involved in electron transport may initially

chine. The enzyme consists of two parts—a

appear surprising. However, as discussed on

proton channel (F_o, for “oligomycin-sensitive”)

p. 18, in redox reactions, the change in free

that is integrated into the membrane; and a

enthalpy ∆G—i. e., the chemical work that is

catalytic unit (F₁) that protrudes into the ma-

done—depends only on the difference in re-

trix. The F_o part consists of 12 membrane-

dox potentials ∆E between the donor and the

spanning c-peptides and one a-subunit. The

acceptor. Introducing additional redox sys-

“head” of the F₁ part is composed of three α

tems does not alter the reaction’s overall en-

and three β subunits, between which there

ergy yield. In the case of the respiratory chain,

are three active centers. The “stem” between

the difference between the normal potential

Fo and F1 consists of one γ and one ε subunit.

of the donor (NAD⁺/NADH+H⁺, E⁰ = -0.32 V)

Two more polypeptides, b and δ, form a kind

and that of the acceptor

(O₂/H₂O, E⁰ =

of “stator,” fixing the α and β subunits relative

+0.82 V) corresponds to an energy difference

to the F_o part.

∆G⁰

of more than 200 kJ mol^-1. This large

The catalytic cycle can be divided into

amount is divided into smaller, more

three phases, through each of which the three

manageable “packages,” the size of which is

active sites pass in sequence. First, ADP and P_i

determined by the difference in redox poten-

are bound (1), then the anhydride bond forms

tials between the respective intermediates. It

(2), and finally the product is released (3).

is assumed that this division is responsible for

Each time protons pass through the F_o chan-

the astonishingly high energy yield (about

nel protein into the matrix, all three active

60%) achieved by the respiratory chain.

sites change from their current state to the

The illustration shows the important redox

next. It has been shown that the energy for

systems involved in mitochondrial electron

proton transport is initially converted into a

transport and their approximate redox poten-

rotation of the γ subunit, which in turn cycli-

tials. These potentials determine the path fol-

cally alters the conformation of the α and β

lowed by the electrons, as the members of a

subunits, which are stationary relative to the

redox series have to be arranged in order of

Fo part, and thereby drives ATP synthesis.

increasing redox potential if transport is to

occur spontaneously (see p. 32).

In complex 1, the electrons are passed from

NADH+H⁺ first to FMN (see p. 104) and then

on to several iron-sulfur (Fe/S) clusters. These

redox systems are only stable in the interior

of proteins. Depending on the type, Fe/S clus-

ters may contain two to six iron ions, which

Energy Metabolism

143

A. Redox systems of the respiratory chain

∆G'

FMN/FMNH₂

(kJ · mol-1)

(V)

NAD

-0.4

CoQ

Hemes b

(ubi-

quinone)

–0.2

NADH

III

Cyto-

chrome C

Heme a

Cu2

+0.2

Fe/S centers

+0.4

Fe/S center

Cu2

+0.6

Heme c₁

∆G = -n · F · ∆E

-220

+0.8

Heme a

B. ATP synthase

Inside:

P P

matrix

Formation of ATP

H₂O

P P P

Outside:

P P P

Inter-

membrane

space

outside

α β

F₁

P P

inside

P P

P P P

F₀

H₂O

P P

H₂O

P P

P P P

H₂O

Binding of ADP and Pi

Release of ATP

outside

1. Structure and location

2. Catalytic cycle

144

Metabolism

to the inner membrane (1) or by lipid-soluble

Regulation

substances that can transport protons

The amount of nutrient degradation and ATP

through the membrane, such as

2,4-

synthesis have to be continually adjusted to

dinitrophenol (DNP, 2). Thermogenin (uncou-

the body’s changing energy requirements.

pling protein-1, UCP-1,

3)—an ion channel

The need to coordinate the production and

(see p. 222) in mitochondria of brown fat tis-

consumption of ATP is already evident from

sue—is a naturally occurring uncoupler.

the fact that the total amounts of coenzymes

Brown fat is found, for example, in newborns

in the organism are low. The human body

and in hibernating animals, and serves exclu-

forms about 65 kg ATP per day, but only con-

sively to generate heat. In cold periods, nor-

tains 3-4 g of adenine nucleotides (AMP, ADP,

epinephrine activates the hormone-sensitive

and ATP). Each ADP molecule therefore has to

lipase (see p. 162). Increased lipolysis leads

be phosphorylated to ATP and dephosphory-

to the production of large quantities of free

lated again many thousand times a day.

fatty acids. Like DNP, these bind H⁺ ions in the

intermembrane space, pass the UCP in this

form, and then release the protons in the

A. Respiratory control

matrix again. This makes fatty acid degrada-

The simple regulatory mechanism which en-

tion independent of ADP availability—i. e., it

sures that ATP synthesis is “automatically”

takes place at maximum velocity and only

coordinated with ATP consumption is known

produces heat (A). It is becoming increasingly

as respiratory control. It is based on the fact

clear that there are also UCPs in other cells,

that the different parts of the oxidative phos-

which are controlled by hormones such as

phorylation process are coupled via shared

thyroxine

(see p. 374). This regulates the

coenzymes and other factors (left).

ATP yield and what is known as the basal

If a cell is not using any ATP, hardly any ADP

metabolic rate.

will be available in the mitochondria. Without

ADP, ATP synthase (3) is unable to break down

C. Regulation of the tricarboxylic acid cycle

the proton gradient across the inner mito-

chondrial membrane. This in turn inhibits

The most important factor in the regulation of

electron transport in the respiratory chain

the cycle is the NADH/NAD⁺ ratio. In addition

(2), which means that NADH+H⁺ can no lon-

to pyruvate dehydrogenase (PDH) and oxoglu-

ger be reoxidized to NAD⁺. Finally, the result-

tarate dehydrogenase (ODH; see p. 134), cit-

ing high NADH/NAD⁺ ratio inhibits the tricar-

rate synthase and isocitrate dehydrogenase are

boxylic acid cycle (C), and thus slows down

also inhibited by NAD⁺ deficiency or an excess

the degradation of the substrate SH₂ (1). Con-

of NADH+H⁺. With the exception of isocitrate

versely, high rates of ATP utilization stimulate

dehydrogenase, these enzymes are also sub-

nutrient degradation and the respiratory

ject to product inhibition by acetyl-CoA, suc-

chain via the same mechanism.

cinyl-CoA, or citrate.

If the formation of a proton gradient is

Interconversion processes (see p. 120) also

prevented

(right), substrate oxidation

(1)

play an important role. They are shown here

and electron transport

(2) proceed much

in detail using the example of the PDH com-

more rapidly. However, instead of ATP, only

plex

(see p. 134). The inactivating protein

heat is produced.

kinase [1a] is inhibited by the substrate pyru-

vate and is activated by the products acetyl-

CoA and NADH+H⁺. The protein phosphatase

B. Uncouplers

[1b]—like isocitrate dehydrogenase [3] and the

Substances that functionally separate oxida-

ODH complex [4]—is activated by Ca²⁺. This is

tion and phosphorylation from one another

particularly important during muscle con-

are referred to as uncouplers. They break

traction, when large amounts of ATP are

down the proton gradient by allowing H⁺

needed. Insulin also activates the PDH com-

ions to pass from the intermembrane space

plex (through inhibition of phosphorylation)

back into the mitochondrial matrix without

and thereby promotes the breakdown of glu-

the involvement of ATP synthase. Uncoupling

cose and its conversion into fatty acids.

effects are produced by mechanical damage

Energy Metabolism

145

A. Respiratory control

AH₂

Coupling

points

Dehydro-

genases

Respira-

outside

tory chain

inside

ATP syn-

outside

inside

thesis

uncoupled

Heat

from proton

transport

ATP

P P

synthase

P P

Endergonic

processes

Endergonic

processes

1. Coupled

2. Uncoupled

B. Uncouplers

C. Regulation of the

tricarboxylic acid cycle

1. Membrane

Insulin

Pyruvate

1. damage

Ca²

NO₂

NADH

NO₂

2. Mobile

Acetyl CoA

2. carriers

O₂N

NO₂

Oxalo-

2,4-Dinitrophenol

Citrate

acetate

Inner

mitochochondrial

Most important

Isocitrate

factor: con-

membrane

centration ratio

NADH

[NADH] / [NAD

]

Norepinephrine

2-Oxo-

Succinyl

glutarate

Fatty

CoA

Fat

acids

Ca²

PDH kinase

Isocitrate dehydro-

2.7.1.99

genase 1.1.1.42

Thermo-

genin

PDH phosphatase

2-Oxoglutarate

3. Gated proton

(UCP1)

3.1.3.43

dehydrogenase 1.2.4.2,

3. channels

1.8.1.4, 2.3.1.61

Citrate synthase

4.1.3.7

146

Metabolism

ylic acid cycle and the pyruvate dehydro-

Respiration and fermentation

genase reaction

(see p. 144). β-Oxidation

and the malate shuttle, which are dependent

A. Aerobic and anaerobic oxidation of

on free NAD⁺, also come to a standstill. Since

glucose

amino acid degradation is also no longer able

In the presence of oxygen (i. e., in aerobic

to contribute to energy production, the cell

conditions), most animal cells are capable of

becomes totally dependent on ATP synthe-

“respiring” various types of nutrient (lipids,

sized via the degradation of glucose by

amino acids, and carbohydrates)—i. e., using

glycolysis. For this process to proceed contin-

oxidative processes to break them down com-

uously, the NADH+H⁺ formed in the cyto-

pletely. If oxygen is lacking (i. e., in anaerobic

plasm has to be constantly reoxidized. Since

conditions), only glucose can be used for ATP

this can no longer occur in the mitochondria,

synthesis. Although in these conditions glu-

in anaerobic conditions animal cells reduce

cose breakdown in animals already ends in

pyruvate to lactate and pass it into the blood.

lactate and only produces small quantities of

This type of process is called fermentation

ATP, it is decisively important for the survival

(see p. 148). The ATP yield is low, with only

of cells at times of oxygen deficiency.

two ATPs per glucose arising during lactate

synthesis.

In aerobic conditions (left), ATP is derived

almost exclusively from oxidative phosphor-

To estimate the number of ATP molecules

ylation (see p. 140). Fatty acids enter the mi-

formed in an aerobic state, it is necessary to

tochondria with the help of carnitine (see

know the P/O quotient—i. e., the molar ratio

p. 164), and are broken down there into CoA-

between synthesized ATP (“P”) and the water

bound acetyl residues. Glucose is converted

formed (“O”). During transport of two elec-

into pyruvate by glycolysis (see p. 150) in the

trons from NADH+H⁺ to oxygen, about 10 pro-

cytoplasm. Pyruvate is then also transported

tons are transported into the intermembrane

into the mitochondrial matrix, where it is

space, while from ubiquinol (QH₂), the num-

oxidatively decarboxylated by the pyruvate

ber is only six. ATP synthase (see p. 142) prob-

dehydrogenase complex (see p. 134) to yield

ably requires three H⁺ to synthesize one ATP,

acetyl-CoA. The reducing equivalents

so that maximum P/O quotients of around 3

NADH+H⁺ per glucose) that arise in glycolysis

or 2 are possible. This implies a yield of up to

enter the mitochondrial matrix via the malate

38 ATP per mol of glucose. However, the ac-

shuttle (see p. 212). The acetyl residues that

tual value is much lower. It needs to be taken

are formed are oxidized to CO₂ in the tricar-

into account that the transport of specific me-

boxylic acid cycle (see p. 136). Breakdown of

tabolites into the mitochondrial matrix and

amino acids also produces acetyl residues or

the exchange of ATP^4- for ADP^3- are also

products that can directly enter the tricarbox-

driven by the proton gradient (see p. 212).

ylic acid cycle

(see p. 180). The reducing

The P/O quotients for the oxidation of

equivalents that are obtained are transferred

NADH+H⁺ and QH₂ are therefore more in the

to oxygen via the respiratory chain as re-

range of 2.5 and 1.5. If the energy balance of

quired. In the process, chemical energy is re-

aerobic glycolysis is calculated on this basis,

leased, which is used (via a proton gradient)

the result is a yield of around 32 ATP per

to synthesize ATP (see p. 140).

glucose. However, this value is also not con-

stant, and can be adjusted as required by the

In the absence of oxygen—i. e., in anaerobic

cell’s own uncouplers (UCPs; see p. 144) and

conditions—the picture changes completely.

other mechanisms.

Since O₂ is missing as the electron acceptor

for the respiratory chain, NADH+H⁺ and QH₂

can no longer be reoxidized. Consequently,

not only is mitochondrial ATP synthesis

halted, but also almost the whole metabolism

in the mitochondrial matrix. The main reason

for this is the high NADH+H⁺ concentration

and lack of NAD⁺, which inhibit the tricarbox-

Energy Metabolism

147

A. Aerobic and anaerobic oxidation of glucose

Glucose

P P P

P P

Glyco-

lysis

PEP

P P

P P P

Pyruvate

Lactate

Malate shuttle

Pyruvate

Acetyl

CoA

Tricarboxylic

acid cycle

inhibited due

to high ratio of

NADH/NAD

O₂

2 GTP

H₂O

P P

1. Aerobic

2. Anaerobic

ATP

Coenzymes

Enzymes

Coenzymes

ATP

-1

–1 ATP

Hexokinase

–1 ATP

-1

-2

–1 ATP

6-Phosphofructokinase

–1 ATP

-2

+5 ATP

+2 NADH

Glyceraldehyde-3 P DH

+2 NADH

-2

+2 ATP

Phosphoglycerate kinase

+2 ATP

NAD

+2 ATP

Pyruvate kinase

+2 ATP

recycled

Lactate dehydrogenase

-2 NADH

+12

+5 ATP

+2 NADH

Pyruvate dehydrogenase

+17

+5 ATP

+2 NADH

Isocitrate dehydrogenase

+22

+5 ATP

+2 NADH

Oxoglutarate dehydrogenase

+27

+5 ATP

+2 NADH

Malate dehydrogenase

+30

+3 ATP

+2 QH₂

Succinate dehydrogenase

+32

+2 ATP

+2 GTP

Succinate-CoA ligase

DH = dehydrogenase

Sum: 32 ATP/glucose

Sum: 2 ATP/glucose

148

Metabolism

lated by pyruvate decarboxylase [2], which

Fermentations

does not occur in animal metabolism, to pro-

As discussed on p. 146, degradation of glucose

duce acetaldehyde (ethanal). When this is re-

to pyruvate is the only way for most organ-

duced by alcohol dehydrogenase [3], with

isms to synthesize ATP in the absence of oxy-

NADH being consumed, ethanol [3] is formed.

gen. The NADH+H⁺ that is also formed in this

Yeasts, unicellular fungi that belong to the

process has to be constantly reoxidized to

eukaryotes (3), rather than bacteria, are re-

NAD⁺ in order to maintain glycolysis and

sponsible for this type of fermentation. Yeasts

thus ATP synthesis. In the animal organism,

are also often used in baking. They produce

this is achieved by the reduction of pyruvate

CO₂ and ethanol, which raise the dough.

to lactate. In microorganisms, there are many

Brewers’ and bakers’ yeasts (Saccharomyces

other forms of NAD⁺ regeneration. Processes

cerevisiae) are usually haploid and reproduce

of this type are referred to as fermentations.

asexually by budding (3). They can live both

Microbial fermentation processes are often

aerobically and anaerobically. Wine is pro-

used to produce foodstuffs and alcoholic bev-

duced by other types of yeast, some of which

erages, or to preserve food. Features common

already live on the grapes. To promote the

to all fermentation processes are that they

formation of ethanol, efforts are made to gen-

start with pyruvate and only occur under

erally exclude oxygen during alcoholic fer-

anaerobic conditions.

mentation—for example, by covering dough

with a cloth when it is rising and by ferment-

ing liquids in barrels that exclude air.

A. Lactic acid and propionic acid

fermentation

C. Beer brewing

Many milk products, such as sour milk, yo-

gurt, and cheese are made by bacterial lactic

Barley is the traditional starting material for

acid fermentation (1). The reaction is the same

the brewing of beer. Although cereal grains

as in animals. Pyruvate, which is mainly de-

contain starch, they hardly have any free sug-

rived from degradation of the disaccharide

ars. The barley grains are therefore first al-

lactose (see p. 38), is reduced to lactate by

lowed to germinate so that starch-cleaving

lactate dehydrogenase [1]. Lactic acid fermen-

amylases are formed. Careful warming of the

tation also plays an important role in the

sprouting grain produces malt. This is then

production of sauerkraut and silage. These

ground, soaked in water, and kept warm for

products usually keep for a long time, because

a certain time. In the process, a substantial

the pH reduction that occurs during fermen-

proportion of the starch is broken down into

tation inhibits the growth of putrefying bac-

the disaccharide maltose

(see p. 38). The

teria.

product (the wort) is then boiled, yeast and

Bacteria from the genera Lactobacillus and

hops are added, and the mixture is allowed to

Streptococcus are involved in the first steps of

ferment for several days. The addition of hops

dairy production (3). The raw materials pro-

makes the beer less perishable and gives it its

duced by their effects usually only acquire

slightly bitter taste. Other substances con-

their final properties after additional fermen-

tained in hops act as sedatives and diuretics.

tation processes. For example, the character-

istic taste of Swiss cheese develops during a

subsequent propionic acid fermentation. In

this process, bacteria from the genus

Propionibacterium convert pyruvate to propi-

onate in a complex series of reactions (2).

B. Alcoholic fermentation

Alcoholic beverages are produced by the fer-

mentation of plant products that have a high

carbohydrate content. Pyruvate, which is

formed from glucose, is initially decarboxy-

Energy Metabolism

149

A. Lactic acid and propionic acid fermentation

Propionate

Lactobacillus

C C

H H

Propioni-

bacterium

Lactate

C C

Streptococcus

H O

10 µm

2[H]

DNA Cell wall

C C

B. Alcoholic fermentation

Lactate dehydrogenase

10 µm

1.1.1.27

Pyruvate

Pyruvate decarboxylase

[TPP] 4.1.1.1

Alcohol dehydrogenase

Yeast

[Zn2 ] 1.1.1.1

CO₂

(Saccharomyces

cerevisiae)

Vacuole

Septum Daughter cell

C C

Ethanal

(Acet-

H H

aldehyde)

Nucleus

Cell wall

C C

Tonoplast

Mitochondrium

H H

Ethanol

C. Beer brewing

Germinate,

Malt

Grind,

Wort

Hops

dry

incubate

O₂

in water

Barley

Fermentation

Starch

Maltose

Amylases

Yeast

Glucose

formed in

Maltose

Ethanol

+ CO₂

seedling

150

Metabolism

phorylation; see p. 124), and

1,3-bisphos-

Glycolysis

phoglycerate is produced. This intermediate

contains a mixed acid-anhydride bond, the

A. Balance

phosphate part of which is at a high chemical

Glycolysis is a catabolic pathway in the cyto-

potential.

plasm that is found in almost all organisms—

[7] Catalyzed by phosphoglycerate kinase,

irrespective of whether they live aerobically

this phosphate residue is transferred to ADP,

or anaerobically. The balance of glycolysis is

producing 3-phosphoglycerate and ATP. The

simple: glucose is broken down into two mol-

ATP balance is thus once again in equilibrium.

ecules of pyruvate, and in addition two mol-

[8] As a result of shifting of the remaining

ecules of ATP and two of NADH+H⁺ are

phosphate residue within the molecule, the

formed.

isomer 2-phosphoglycerate is formed.

In the presence of oxygen, pyruvate and

[9] Elimination of water from 2-phospho-

NADH+H⁺ reach the mitochondria, where

glycerate produces the phosphate ester of the

they undergo further transformation (aerobic

enol form of pyruvate—phosphoenolpyruvate

glycolysis; see p. 146). In anaerobic condi-

(PEP). This reaction also raises the second

tions, fermentation products such as lactate

phosphate residue to a high potential.

or ethanol have to be formed in the cytoplasm

[10] In the last step, pyruvate kinase trans-

from pyruvate and NADH+H⁺, in order to re-

fers this residue to ADP. The remaining enol

generate NAD⁺ so that glycolysis can continue

pyruvate is immediately rearranged into

(anaerobic glycolysis; see p. 146). In the anae-

pyruvate, which is much more stable. Along

robic state, glycolysis is the only means of

with step [7] and the thiokinase reaction in

obtaining ATP that animal cells have.

the tricarboxylic acid cycle (see p. 136), the

pyruvate kinase reaction is one of the three

reactions in animal metabolism that are able

B. Reactions

to produce ATP independently of the respira-

Glycolysis involves ten individual steps, in-

tory chain.

cluding three isomerizations and four phos-

In glycolysis, two molecules of ATP are ini-

phate transfers. The only redox reaction takes

tially used for activation ([1], [3]). Later, two

place in step [6].

ATPs are formed per C₃ fragment. Overall,

[1] Glucose, which is taken up by animal

therefore, there is a small net gain of 2 mol

cells from the blood and other sources, is first

ATP per mol of glucose.

phosphorylated to glucose 6-phosphate, with

ATP being consumed. The glucose 6-phos-

C. Energy profile

phate is not capable of leaving the cell.

[2] In the next step, glucose 6-phosphate is

The energy balance of metabolic pathways de-

isomerized into fructose 6-phosphate.

pends not only on the standard changes in

[3] Using ATP again, another phosphoryla-

enthalpy ∆G⁰, but also on the concentrations

tion takes place, giving rise to fructose 1,6-

of the metabolites (see p. 18). Fig. C shows the

bisphosphate. Phosphofructokinase is the

actual enthalpy changes ∆G for the individual

most important key enzyme in glycolysis

steps of glycolysis in erythrocytes.

(see p. 144).

As can be seen, only three reactions ([1],

[4] Fructose

1,6-bisphosphate is broken

[3], and

[10]), are associated with large

down by aldolase into the C₃ compounds glyc-

changes in free enthalpy. In these cases, the

eraldehyde 3-phosphate (also known as glyc-

equilibrium lies well on the side of the prod-

eral 3-phosphate) and glycerone 3-phosphate

ucts (see p. 18). All of the other steps are

(dihydroxyacetone 3-phosphate).

freely reversible. The same steps are also fol-

[5] The latter two products are placed in

lowed—in the reverse direction—in gluconeo-

fast equilibrium by triosephosphate isomerase.

genesis (see p. 154), with the same enzymes

[6] Glyceraldehyde

3-phosphate is now

being activated as in glucose degradation. The

oxidized by glyceraldehyde-3-phosphate de-

non-reversible steps [1], [3], and [10] are by-

hydrogenase, with NADH+H⁺ being formed.

passed in glucose biosynthesis (see p. 154).

In this reaction, inorganic phosphate is taken

up into the molecule (substrate-level phos-

Carbohydrate Metabolism

151

A. Glycolysis: balance

COO

Glycolysis

C O

OH H

∆G^OI = -35 kJ · mol^-1

CH₃

P P

P P P

Glucose

Pyruvate

B. Reactions

Glucose

Fructose

Glucose

6-phosphate

1,6-bisphosphate

CH₂

O OH

H HO

^H H

CH₂OH

CH₂

OH H

P P

O P

H₂C OH

HC O

HC OH

C O

H₂C OH

H₂C O

CH₂

2 P

2-Phospho-

3-Phospho-

1,3-Bisphospho-

Glyceraldehyde

Glycerone

glycerate

3-phosphate

2 H₂O

C. Energy profile

O O

Steps 1, 3 and 10

P P P

are bypassed in

gluconeogenesis

C O P

C O

CH₂

CH₃

-20

P P

Phospho-

2 Pyruvate

enolpyruvate

P P

P P P

P P

P P P

-40

P P P

Glyceraldehyde-

Hexokinase 2.7.1.1

dehydro-

genase 1.2.1.12

Glucose 6-phosphate

Isomerase 5.3.1.9

Phosphoglycerate

P P

kinase 2.7.2.3

6-Phosphofructo-

-60

kinase 2.7.1.11

Phosphoglycerate

P P

Fructose bisphosphate

mutase 5.4.2.1

aldolase 4.1.2.13

Phosphopyruvate

P P P

hydratase 4.2.1.11

Triose-phosphate

isomerase 5.3.1.1

-80

Pyruvate kinase

Pyruvate

2.7.1.40

∆G^' (kJ · mol^-1)

152

Metabolism

of the regenerative branch is to adjust the net

Pentose phosphate pathway

production of NADPH+H⁺ and pentose phos-

The pentose phosphate pathway (PPP, also

phates to the cell’s current requirements. Nor-

known as the hexose monophosphate

mally, the demand for NADPH+H⁺ is much

pathway) is an oxidative metabolic pathway

higher than that for pentose phosphates. In

located in the cytoplasm, which, like glycoly-

these conditions, the reaction steps shown

sis, starts from glucose 6-phosphate. It sup-

first convert six ribulose

5-phosphates to

plies two important precursors for anabolic

five molecules of fructose 6-phosphate and

pathways: NADPH+H+, which is required for

then, by isomerization, regenerate five glu-

the biosynthesis of fatty acids and isopren-

cose 6-phosphates. These can once again sup-

oids, for example (see p. 168), and ribose 5-

ply NADPH+H⁺ to the oxidative part of the

phosphate, a precursor in nucleotide biosyn-

PPP. Repeating these reactions finally results

thesis (see p. 188).

in the oxidation of one glucose 6-phosphate

into six CO₂. Twelve NADPH+H⁺ arise in the

same process. In sum, no pentose phosphates

A. Pentose phosphate pathway:

are produced via this pathway.

oxidative part

In the recombination of sugar phosphates

The oxidative segment of the PPP converts

in the regenerative part of the PPP, there are

glucose 6-phosphate to ribulose 5-phosphate.

two enzymes that are particularly important:

One CO₂ and two NADPH+H⁺ are formed in

[5] Transaldolase transfers C₃ units from

the process. Depending on the metabolic

sedoheptulose 7-phosphate, a ketose with

state, the much more complex regenerative

seven C atoms, to the aldehyde group of glyc-

part of the pathway (see B) can convert some

eraldehyde 3-phosphate.

of the pentose phosphates back to hexose

[4] Transketolase, which contains thiamine

phosphates, or it can pass them on to glycol-

diphosphate, transfers C₂ fragments from one

ysis for breakdown. In most cells, less than

sugar phosphate to another.

10% of glucose 6-phosphate is degraded via

The reactions in the regenerative segment

the pentose phosphate pathway.

of the PPP are freely reversible. It is therefore

easily possible to use the regenerative part of

the pathway to convert hexose phosphates

B. Reactions

into pentose phosphates. This can occur

[1] The oxidative part starts with the oxida-

when there is a high demand for pentose

tion of glucose

6-phosphate by glucose-6-

phosphates—e. g., during DNA replication in

phosphate dehydrogenase. This forms

the S phase of the cell cycle (see p. 394).

NADPH+H⁺ for the first time. The second

product, 6-phosphogluconolactone, is an in-

Additional information

tramolecular ester

(lactone) of

6-phospho-

gluconate.

When energy in the form of ATP is required in

[2] A specific hydrolase then cleaves the

addition to NADPH+H⁺, the cell is able to

lactone, exposing the carboxyl group of

channel the products of the regenerative

6-phosphogluconate.

part of the PPP (fructose 6-phosphate and

[3] The last enzyme in the oxidative part is

glyceraldehyde 3-phosphate) into glycolysis.

phosphogluconate dehydrogenase [3], which

Further degradation is carried out via the tri-

releases the carboxylate group of 6-phospho-

carboxylic acid cycle and the respiratory chain

gluconate as CO₂ and at the same time oxi-

to CO₂ and water. Overall, the cell in this way

dizes the hydroxyl group at C₃ to an oxo

obtains

12 mol NADPH+H⁺ and around

group. In addition to a second NADPH+H⁺,

150 mol ATP from 6 mol glucose 6-phos-

this also produces the ketopentose ribulose

phate. PPP activity is stimulated by insulin

5-phosphate. This is converted by an isomer-

(see p. 388). This not only increases the rate

ase to ribose 5-phosphate, the initial com-

of glucose degradation, but also produces ad-

pound for nucleotide synthesis (top).

ditional NADPH+H⁺ for fatty acid synthesis

The regenerative part of the PPP is only

(see p. 168).

shown here schematically. A complete reac-

tion scheme is given on p. 408. The function

Carbohydrate Metabolism

153

A. Pentose phosphate pathway: oxidative part

CH₂

H H O H

PPP -

oxidative

C C

C C C H

^H H

part

H OH OH OH

Glucose 6-phosphate

NADP

NADPH + H

Ribulose 5-phosphate

B. Reactions

O H H O H

P P

Ribulose

C C

C C C H

5-phosphate

H OH OH OH

6 CO

P P

Ribose

Xylulose

O H H OH H

6-Phospho-

C C

C C C

gluconate

H OH OH H OH

Sedo-

Anabolic

heptulose

P P

pathways

H₂O

Glyceral

6-Phospho-

glucono-

lactone

OH H

Fructose

P P

Erythrose

CH₂

Fructose

Glucose

O OH

6-phosphate

P P

Glycer-

^H H

aldehyde

Glucose 6-phosphate dehydrogenase 1.1.1.49

Transketolase 2.2.1.1

Gluconolactonase 3.1.1.17

Transaldolase 2.2.1.2

Phosphogluconate dehydrogenase (decarboxylating) 1.1.1.44

154

Metabolism

from lactate or amino acids is therefore ini-

Gluconeogenesis

tially transported into the mitochondrial ma-

Some tissues, such as brain and erythrocytes,

trix, and—in a biotin-dependent reaction cat-

depend on a constant supply of glucose. If the

alyzed by pyruvate carboxylase—is carboxy-

amount of carbohydrate taken up in food is

lated there to oxaloacetate. Oxaloacetate is

not suf cient, the blood sugar level can be

also an intermediate in the tricarboxylic acid

maintained for a limited time by degradation

cycle. Amino acids with breakdown products

of hepatic glycogen (see p. 156). If these re-

that enter the cycle or supply pyruvate can

serves are also exhausted, de-novo synthesis

therefore be converted into glucose

(see

of glucose (gluconeogenesis) begins. The liver

p. 180).

is also mainly responsible for this (see p. 310),

[3] The oxaloacetate formed in the mito-

but the tubular cells of the kidney also show a

chondrial matrix is initially reduced to ma-

high level of gluconeogenetic activity (see

late, which can leave the mitochondria via

p. 328). The main precursors for gluconeo-

inner membrane transport systems

(see

genesis are amino acids derived from muscle

p. 212).

proteins. Another important precursor is

[4] In the cytoplasm, oxaloacetate is re-

lactate, which is formed in erythrocytes and

formed and then converted into phospho-

muscle proteins when there is oxygen de-

enol pyruvate by a GTP-dependent PEP car-

ficiency. Glycerol produced from the degrada-

boxykinase. The subsequent steps up to fruc-

tion of fats can also be used for gluconeogen-

tose 1,6-bisphosphate represent the reverse

esis. However, the conversion of fatty acids

of the corresponding reactions involved in

into glucose is not possible in animal metab-

glycolysis. One additional ATP per C₃ frag-

olism (see p. 138). The human organism can

ment is used for the synthesis of 1,3-bisphos-

synthesize several hundred grams of glucose

phoglycerate.

per day by gluconeogenesis.

Two gluconeogenesis-specific phosphat-

ases then successively cleave off the phos-

phate residues from fructose

1,6-bisphos-

A. Gluconeogenesis

phate. In between these reactions lies the

Many of the reaction steps involved in gluco-

isomerization of fructose 6-phosphate to glu-

neogenesis are catalyzed by the same en-

cose

6-phosphate—another glycolytic reac-

zymes that are used in glycolysis

(see

tion.

p. 150). Other enzymes are specific to gluco-

[5] The reaction catalyzed by fructose

neogenesis and are only synthesized, under

1,6-bisphosphatase is an important regulation

the influence of cortisol and glucagon when

point in gluconeogenesis (see p. 158).

needed (see p. 158). Glycolysis takes place

[6] The last enzyme in the pathway, glucose

exclusively when needed in the cytoplasm,

6-phosphatase, occurs in the liver, but not in

but gluconeogenesis also involves the mito-

muscle. It is located in the interior of the

chondria and the endoplasmic reticulum (ER).

smooth endoplasmic reticulum. Specific

Gluconeogenesis consumes 4 ATP (3 ATP + 1

transporters allow glucose

6-phosphate to

GTP) per glucose—i. e., twice as many as gly-

enter the ER and allow the glucose formed

colysis produces.

there to return to the cytoplasm. From there,

it is ultimately released into the blood.

[1] Lactate as a precursor for gluconeogen-

esis is mainly derived from muscle (see Cori

Glycerol initially undergoes phosphoryla-

cycle, p. 338) and erythrocytes. LDH

(see

tion at C-3

[7]. The glycerol

3-phosphate

p. 98) oxidizes lactate to pyruvate, with

formed is then oxidized by an NAD⁺-depen-

NADH+H⁺ formation.

dent dehydrogenase to form glycerone 3-

[2] The first steps of actual gluconeogenesis

phosphate [8] and thereby channeled into

take place in the mitochondria. The reason for

gluconeogenesis. An FAD-dependent mito-

this “detour” is the equilibrium state of the

chondrial enzyme is also able to catalyze

pyruvate kinase reaction (see p. 150). Even

this reaction

(known as the “glycerophos-

coupling to ATP hydrolysis would not be suf-

phate shuttle”; see p. 212).

ficient to convert pyruvate directly into phos-

phoenol pyruvate

(PEP). Pyruvate derived

Carbohydrate Metabolism

155

A. Gluconeogenesis

Lactate

Glucose

dehydrogenase

1.1.1.27

Glucose 6-phosphate

Glucose

Pyruvate

CH₂

H₂O

CH₂

carboxylase

(biotin)6.4.1.1

OOH

^H H

Malate

dehydrogenase

1.1.1.37

gER

PEP

carboxykinase

4.1.1.32

Glucose 6-phosphate

Fructose 1,6-

bisphosphate

CH₂

3.1.3.11

O OH

H HO

Glucose 6-

phosphatase

CH₂OH

CH₂

3.1.3.9

H₂O

OH H

Fructose 6-phosphate

Fructose 1,6-bisphosphate

Glycerol kinase

2.7.1.30

ATP ADP

Glycerol 3-

3-Phospho-

1,3-Bisphospho- Glyceraldehyde

Glycerone

phosphate

glycerate

3-phosphate

dehydrogenase

1.1.1.8

NADH

NAD NADH

NAD

2-Phospho-

NADH+H NAD

Glycerol

glycerate

3-phosphate

ADP

GTP GDP

ATP

COO

H₂C OH

C O

HC OH

Malate

CH₂

CO₂

CH₂

CH₃

H₂C OH

COO

Pyruvate

Lactate

Glycerol

Phospho-

Oxaloacetate

enolpyruvate

COO

CO₂

COO

C O

CH₂

NAD

NADH

ADP ATP

CH₃

COO

Pyruvate

Malate

Oxaloacetate

Mitochrondrion

Amino acids

Glycerol

Cytoplasm

Lactate

Amino acids

156

Metabolism

important degradative enzyme, glycogen

Glycogen metabolism

phosphorylase, cleaves residues from a non-

Glycogen (see p. 40) is used in animals as a

reducing end one after another as glucose

carbohydrate reserve, from which glucose

1-phosphate. The larger the number of these

phosphates and glucose can be released

ends, the more phosphorylase molecules can

when needed. Glucose storage itself would

attack simultaneously. The formation of glu-

not be useful, as high concentrations within

cose 1-phosphate instead of glucose has the

cells would make them strongly hypertonic

advantage that no ATP is needed to channel

and would therefore cause an influx of water.

the released residues into glycolysis or the

By contrast, insoluble glycogen has only low

PPP.

osmotic activity.

[5] [6] Due to the structure of glycogen

phosphorylase, degradation comes to a halt

four residues away from each branching

A. Glycogen balance

point. Two more enzymes overcome this

Animal glycogen, like amylopectin in plants, is

blockage. First, a glucanotransferase moves a

a branched homopolymer of glucose. The glu-

trisaccharide from the side chain to the end of

cose residues are linked by an α1

4-glyco-

the main chain [5]. A 1,6-glucosidase [6] then

sidic bond. Every tenth or so glucose residue

cleaves the single remaining residue as a free

has an additional α1

6 bond to another

glucose and leaves behind an unbranched

glucose. These branches are extended by

chain that is once again accessible to phos-

additional α1

4-linked glucose residues.

phorylase.

This structure produces tree-shaped mole-

The regulation of glycogen metabolism by

cules consisting of up to

50000 residues

interconversion, and the role of hormones in

(M > 1

10⁷ Da).

these processes, are discussed on p. 120.

Hepatic glycogen is never completely de-

graded. In general, only the nonreducing ends

B. Glycogen balance

of the “tree” are shortened, or—when glucose

is abundant—elongated. The reducing end of

The human organism can store up to 450 g of

the tree is linked to a special protein, glyco-

glycogen—one-third in the liver and almost all

genin. Glycogenin carries out autocatalytic

of the remainder in muscle. The glycogen

covalent bonding of the first glucose at one

content of the other organs is low.

of its tyrosine residues and elongation of this

Hepatic glycogen is mainly used to main-

by up to seven additional glucose residues. It

tain the blood glucose level in the postresorp-

is only at this point that glycogen synthase

tive phase (see p. 308). The glycogen content

becomes active to supply further elongation.

of the liver therefore varies widely, and can

[1] The formation of glycosidic bonds be-

decline to almost zero in periods of extended

tween sugars is endergonic. Initially, there-

hunger. After this, gluconeogenesis

(see

fore, the activated form—UDP-glucose—is

p. 154) takes over the glucose supply for the

synthesized by reaction of glucose 1-phos-

organism. Muscle glycogen serves as an energy

phate with UTP (see p. 110).

reserve and is not involved in blood glucose

[2] Glycogen synthase now transfers glu-

regulation. Muscle does not contain any glu-

cose residues one by one from UDP-glucose

cose 6-phosphatase and is therefore unable to

to the non-reducing ends of the available

release glucose into the blood. The glycogen

“branches.”

content of muscle therefore does not fluctuate

[3] Once the growing chain has reached a

as widely as that of the liver.

specific length (> 11 residues), the branching

enzyme cleaves an oligosaccharide consisting

of 6-7 residues from the end of it, and adds

this into the interior of the same chain or a

neighboring one with α1

6 linkage. These

branches are then further extended by glyco-

gen synthase.

[4] The branched structure of glycogen al-

lows rapid release of sugar residues. The most

Carbohydrate Metabolism

157

A. Glycogen metabolism

α-1,4-Glucan chain

(unbranched)

(α-1,6-branched)

Reducing

end

P P

UDP-

Degra-

dation

glucose

P P

Glucose 1-

phosphate

P P

UTP

Further

degradation

Glucose

1-phosphate

Building block

synthesis

Glucose

UTP-glucose 1-phosphate

Phosphorylase 2.4.1.1

uridyltransferase 2.7.7.9

Glycogen synthase 2.4.1.11

4-α-Glucanotransferase 2.4.1.25

Glucan branching enzyme

Amylo-1,6-glucosidase

2.4.1.18

3.2.1.33

B. Glycogen balance

Liver

Blood

Muscle

Liver

Muscle

glycogen

4 - 6 g · l^-1

300 g

Blood

Glucose

glucose

1-phosphate

200 g

150 g

De-

Glucose

Degra-

grad-

6-phosphate

dation

ation

Glucose

Liver

Muscle

glycogen

158

Metabolism

Glucocorticoids—mainly cortisol

(see

Regulation

p. 374)—induce all of the key enzymes in-

volved in gluconeogenesis [4, 6, 8, 9]. At the

A. Regulation of carbohydrate metabolism

same time, they also induce enzymes in-

In all organisms, carbohydrate metabolism is

volved in amino acid degradation and thereby

subject to complex regulatory mechanisms

provide precursors for gluconeogenesis. Reg-

involving hormones, metabolites, and

ulation of the expression of PEP carboxy-

coenzymes. The scheme shown here (still a

kinase, a key enzyme in gluconeogenesis, is

simplified one) applies to the liver, which

discussed in detail on p. 244.

has central functions in carbohydrate metab-

Metabolites. High concentrations of ATP

olism (see p. 306). Some of the control mech-

and citrate inhibit glycolysis by allosteric reg-

anisms shown here are not effective in other

ulation of phosphofructokinase. ATP also

tissues.

inhibits pyruvate kinase. Acetyl-CoA, an inhib-

One of the liver’s most important tasks is to

itor of pyruvate kinase, has a similar effect. All

store excess glucose in the form of glycogen

of these metabolites arise from glucose

and to release glucose from glycogen when

degradation (feedback inhibition). AMP and

required (buffer function). When the glycogen

ADP, signals for ATP deficiency, activate gly-

reserves are exhausted, the liver can provide

cogen degradation and inhibit gluconeogene-

glucose by de novo synthesis (gluconeogene-

sis.

sis; see p. 154). In addition, like all tissues, the

liver breaks glucose down via glycolysis.

B. Fructose 2,6-bisphosphate

These functions have to be coordinated with

each other. For example, there is no point in

Fructose 2,6-bisphosphate (Fru-2,6-bP) plays

glycolysis and gluconeogenesis taking place

an important part in carbohydrate metabo-

simultaneously, and glycogen synthesis and

lism. This metabolite is formed in small quan-

glycogen degradation should not occur simul-

tities from fructose

6-phosphate and has

taneously either. This is ensured by the fact

purely regulatory functions. It stimulates gly-

that two different enzymes exist for important

colysis by allosteric activation of phospho-

steps in both pathways, each of which cata-

fructokinase and inhibits gluconeogenesis by

lyzes only the anabolic or the catabolic reac-

inhibition of fructose 1,6-bisphosphatase.

tion. The enzymes are also regulated differ-

The synthesis and degradation of Fru-2,6-

ently. Only these key enzymes are shown

bP are catalyzed by one and the same protein

here.

[10a, 10b]. If the enzyme is present in an un-

Hormones. The hormones that influence

phosphorylated form [10a], it acts as a kinase

carbohydrate metabolism include the pepti-

and leads to the formation of Fru-2,6-bP. After

des insulin and glucagon; a glucocorticoid,

phosphorylation by cAMP-dependent protein

cortisol; and a catecholamine, epinephrine

kinase A (PK-A), it acts as a phosphatase [10b]

(see p. 380). Insulin activates glycogen

and now catalyzes the degradation of Fru-2,6-

synthase ([1]; see p. 388), and induces several

bP to fructose 6-phosphate. The equilibrium

enzymes involved in glycolysis [3, 5, 7]. At the

between [10a] and [10b] is regulated by hor-

same time, insulin inhibits the synthesis of

mones. Epinephrine and glucagon increase

enzymes involved in gluconeogenesis

the cAMP level (see p. 120). As a result of

(repression; [4, 6, 8, 9]). Glucagon, the antag-

increased PK-A activity, this reduces the Fru-

onist of insulin, has the opposite effect. It

2,6-bP concentration and inhibits glycolysis,

induces gluconeogenesis enzymes [4, 6, 8, 9]

while at the same time activating gluconeo-

and represses pyruvate kinase [7], a key en-

genesis. Conversely, via [10a], insulin acti-

zyme of glycolysis. Additional effects of glu-

vates the synthesis of Fru-2,6-bP and thus

cagon are based on the interconversion of en-

glycolysis. In addition, insulin also inhibits

zymes and are mediated by the second mes-

the action of glucagon by reducing the cAMP

senger cAMP. This inhibits glycogen synthesis

level (see p. 120).

[1] and activates glycogenolysis

[2].

Epinephrine acts in a similar fashion. The in-

hibition of pyruvate kinase [7] by glucagon is

also due to interconversion.

Carbohydrate Metabolism

159

A. Regulation of carbohydrate metabolism

Epinephrine

Glycogen

Epinephrine

Glucagon

Insulin

AMP

Fru-2,6-bis P

ATP

Insulin

AMP

Citrate

Glucose

1-phosphate

Glucose

Fructose

Fructose 1,6-

Glucose

6-phosphate

bisphosphate

Insulin

Cortisol

Fru 2,6-bis P

Insulin

Glucagon

AMP

Glucagon

ATP

Acetyl CoA

Glycogen synthase 2.4.1.11

Insulin

Glycogen phosphorylase 2.4.1.1

Hexokinase 2.7.1.1

Hexokinase (liver) 2.7.1.1

PEP

Pyruvate

Glucose 6-phosphatase 3.1.3.9

Acetyl

Insulin

CoA

6-Phosphofructokinase 2.7.1.11

Fructose 1,6-bisphosphatase 3.1.3.11

Cortisol

Pyruvate kinase 2.7.1.40

Glucagon

Pyruvate carboxylase 6.4.1.1

Oxalo-

PEP carboxykinase (GTP) 4.1.1.32

acetate

B. Fructose 2,6-bisphosphate

Insulin

Citrate, PEP

10a

ATP

Fructose 6-

Fructose 2,6-

Fructose 1,6-

phosphate

bisphosphate

ADP

10b

Insulin

cAMP

Glucagon

10a

6-Phosphofructo-2-kinase 2.7.1.105

10b

Fructose 2,6-bisphosphatase 3.1.3.46

160

Metabolism

sensitive lipases (see p. 162) and prevents the

Diabetes mellitus

breakdown of muscle protein.

Diabetes mellitus is a very common metabolic

The effects of insulin deficiency on metab-

disease that is caused by absolute or relative

olism are shown by arrows in the illustration.

insulin deficiency. The lack of this peptide

Particularly noticeable is the increase in the

hormone (see p. 76) mainly affects carbohy-

glucose concentration in the blood, from

drate and lipid metabolism. Diabetes mellitus

5 mM to 9 mM (90 mg dL^-1) or more

occurs in two forms. In type 1 diabetes (in-

(hyperglycemia, elevated blood glucose

sulin-dependent diabetes mellitus, IDDM),

level). In muscle and adipose tissue - the two

the insulin-forming cells are destroyed in

most important glucose consumers—glucose

young individuals by an autoimmune reac-

uptake and glucose utilization are impaired

tion. The less severe type 2 diabetes (non-

by insulin deficiency. Glucose utilization in

insulin-dependent diabetes mellitus, NIDDM)

the liver is also reduced. At the same time,

usually has its first onset in elderly individu-

gluconeogenesis is stimulated, partly due to

als. The causes have not yet been explained in

increased proteolysis in the muscles. This in-

detail in this type.

creases the blood sugar level still further.

When the capacity of the kidneys to resorb

glucose is exceeded (at plasma concentrations

A. Insulin biosynthesis

of 9 mM or more), glucose is excreted in the

Insulin is produced by the B cells of the islets

urine (glucosuria).

of Langerhans in the pancreas. As is usual with

The increased degradation of fat that oc-

secretory proteins, the hormone’s precursor

curs in insulin deficiency also has serious ef-

(preproinsulin) carries a signal peptide that

fects. Some of the fatty acids that accumulate

directs the peptide chain to the interior of

in large quantities are taken up by the liver

the endoplasmic reticulum (see p. 210). Proin-

and used for lipoprotein synthesis (hyperlipi-

sulin is produced in the ER by cleavage of the

demia), and the rest are broken down into

signal peptide and formation of disulfide

acetyl CoA. As the tricarboxylic acid cycle is

bonds. Proinsulin passes to the Golgi appara-

not capable of taking up such large quantities

tus, where it is packed into vesicles—the β-

of acetyl CoA, the excess is used to form ke-

granules. After cleavage of the C peptide, ma-

tone bodies

(acetoacetate and E-hydroxy-

ture insulin is formed in the β-granules and is

butyrate see p. 312). As H⁺ ions are released

stored in the form of zinc-containing hexam-

in this process, diabetics not receiving ad-

ers until secretion.

equate treatment can suffer severe metabolic

acidosis (diabetic coma). The acetone that is

also formed gives these patients’ breath a

B. Effects of insulin deficiency

characteristic odor. In addition, large amounts

The effects of insulin on carbohydrate

of ketone body anions appear in the urine

metabolism are discussed on p. 158. In sim-

(ketonuria).

plified terms, they can be described as stim-

Diabetes mellitus can have serious secon-

ulation of glucose utilization and inhibition of

dary effects. A constantly raised blood sugar

gluconeogenesis. In addition, the transport of

level can lead in the long term to changes in

glucose from the blood into most tissues is

the blood vessels (diabetic angiopathy), kid-

also insulin-dependent (exceptions to this in-

ney damage (nephropathy) and damage to

clude the liver, CNS, and erythrocytes).

the nervous system (neuropathy), as well as

The lipid metabolism of adipose tissue is

to cataracts in the eyes.

also influenced by the hormone. In these cells,

insulin stimulates the reorganization of glu-

cose into fatty acids. This is mainly based on

activation of acetyl CoA carboxylase

(see

p. 162) and increased availability of

NADPH+H⁺ due to increased PPP activity

(see p. 152). On the other hand, insulin also

inhibits the degradation of fat by hormone-

Carbohydrate Metabolism

161

A. Insulin biosynthesis

B cells

Preproinsulin

Proinsulin

Insulin

104 AS

84 AS

51 AS

Nucleus

H3N

Zn²

Exo-

cytosis

β-Granules

Rough

Signal

Golgi apparatus

peptide

C peptide

Insulin

hexamer

OOC

B. Effects of insulin deficiency

Muscle and

Blood

Adipose

other insulin-

tissue

Fat

dependent tissues

Glucose

uptake

impaired

Glucose

Lipolysis

Amino

Protein

Fatty acids

acids

Proteo-

Maximal

lysis

resorption

capacity

Hyper-

exceeded

glycemia

Glucose

Amino

acids

Fatty acids

Hyper-

lipid-

Glyco-

Glucose

emia

gen

Lipo-

Kidney

proteins

Fatty

acids

Anions

of ketone

bodies

Urine

Acetyl

Ketone

Pyruvate

Liver

CoA

bodies

Glucose

Anions

of ketone

Metabolic

bodies

Insulin deficiency

acidosis

Water

Electrolytes

162

Metabolism

coenzyme and ATP derived from it by oxida-

Overview

tive phosphorylation. If acetyl CoA production

exceeds the energy requirements of the hepa-

A. Fat metabolism

tocytes—as is the case when there is a high

Fat metabolism in adipose tissue (top). Fats

level of fatty acids in the blood plasma (typical

(triacylglycerols) are the most important en-

in hunger and diabetes mellitus)—then the

ergy reserve in the animal organism. They are

excess is converted into ketone bodies (see

mostly stored in insoluble form in the cells of

p. 312). These serve exclusively to supply

adipose tissue—the adipocytes—where they

other tissues with energy.

are constantly being synthesized and broken

down again.

Fat synthesis in the liver (right). Fatty acids

and fats are mainly synthesized in the liver

As precursors for the biosynthesis of fats

and in adipose tissue, as well as in the kid-

(lipogenesis), the adipocytes use triacylgly-

neys, lungs, and mammary glands. Fatty acid

cerols from lipoproteins (VLDLs and chylomi-

biosynthesis occurs in the cytoplasm—in con-

crons; see p. 278), which are formed in the

trast to fatty acid degradation. The most im-

liver and intestines and delivered by the

portant precursor is glucose, but certain

blood. Lipoprotein lipase [1], which is located

amino acids can also be used.

on the inner surface of the blood capillaries,

The first step is carboxylation of acetyl CoA

cleaves these triacylglycerols into glycerol

to malonyl CoA. This reaction is catalyzed by

and fatty acids, which are taken up by the

acetyl-CoA carboxylase [5], which is the key

adipocytes and converted back into fats.

enzyme in fatty acid biosynthesis. Synthesis

The degradation of fats (lipolysis) is cata-

into fatty acids is carried out by fatty acid

lyzed in adipocytes by hormone-sensitive

synthase

[6]. This multifunctional enzyme

lipase

[2]—an enzyme that is regulated by

(see p. 168) starts with one molecule of ace-

various hormones by cAMP-dependent inter-

tyl-CoA and elongates it by adding malonyl

conversion (see p. 120). The amount of fatty

groups in seven reaction cycles until palmi-

acids released depends on the activity of this

tate is reached. One CO₂ molecule is released

lipase; in this way, the enzyme regulates the

in each reaction cycle. The fatty acid therefore

plasma levels of fatty acids.

grows by two carbon units each time.

In the blood plasma, fatty acids are trans-

NADPH+H⁺ is used as the reducing agent

ported in free form—i. e., non-esterified. Only

and is derived either from the pentose phos-

short-chain fatty acids are soluble in the

phate pathway (see p. 152) or from isocitrate

blood; longer, less water-soluble fatty acids

dehydrogenase and malic enzyme reactions.

are transported bound to albumin.

The elongation of the fatty acid by fatty acid

synthase concludes at C₁₆, and the product,

Degradation of fatty acids in the liver (left).

palmitate

(16:0), is released. Unsaturated

Many tissues take up fatty acids from the

fatty acids and long-chain fatty acids can arise

blood plasma in order to synthesize fats or

from palmitate in subsequent reactions. Fats

to obtain energy by oxidizing them. The me-

are finally synthesized from activated fatty

tabolism of fatty acids is particularly intensive

acids

(acyl CoA) and glycerol 3-phosphate

in the hepatocytes in the liver.

(see p. 170). To supply peripheral tissues,

The most important process in the degra-

fats are packed by the hepatocytes into lipo-

dation of fatty acids is E-oxidation—a meta-

protein complexes of the VLDL type and re-

bolic pathway in the mitochondrial matrix

leased into the blood in this form (see p. 278).

(see p. 164). Initially, the fatty acids in the

cytoplasm are activated by binding to coen-

zyme A into acyl CoA [3]. Then, with the help

of a transport system (the carnitine shuttle

[4]; see p. 164), the activated fatty acids enter

the mitochondrial matrix, where they are

broken down into acetyl CoA. The resulting

acetyl residues can be oxidized to CO₂ in the

tricarboxylic acid cycle, producing reduced

Lipid Metabolism

163

A. Fat metabolism

Lipoprotein

Acetyl-CoA

lipase 3.1.1.34

carboxylase

Epinephrine

Largest

6.4.1.2 [Biotin]

Hormone-sensitive

Norepinephrine

Adipocyte

energy

lipase 3.1.1.3

Fatty acid

Glucagon etc.

store

synthase

Fatty acid-CoA

2.3.1.85

Triacylglycerols

ligase 6.2.1.3

Carnitine O-

Insulin

palmitoyltrans-

COO

ferase 2.3.1.21

Free fatty acids

From the

intestine

Insulin

COO

Chylo-

microns

Fatty acid-albumin complex

Blood

VLDL

Hepatocyte

Free fatty acids

CoA

ATP

Triacylglycerols

AMP+

Acyl CoA

Fat biosynthesis

Mitochondrion

Acyl CoA

Unsaturated

Elongated

fatty acids

NADH

Palmitate

β-Oxidation

NADP

CO₂

Acetyl CoA

NADPH

or acyl CoA

Malonyl CoA

ADP+

Ketone bodies

Citrate

Insulin

Glucagon

ATP

HCO₃

Citric acid

cycle

Acetyl CoA

Respiratory

chain

Amino acid

Glycolysis

degradation

Supply

of energy

to other

tissues

CO₂+ATP

Amino acids

Glucose

Most important

Fatty acid

precursor

degradation

biosynthesis

164

Metabolism

[4] β-Ketoacyl-CoA is now broken down by

Fatty acid degradation

an acyl transferase into acetyl CoA and an acyl

CoA shortened by 2 C atoms (“thioclastic

A. Fatty acid degradation: E-oxidation

cleavage”).

After uptake by the cell, fatty acids are

Several cycles are required for complete

activated by conversion into their CoA deriva-

degradation of long-chain fatty acids—eight

tives—acyl CoA is formed. This uses up two

cycles in the case of stearyl-CoA (C18:0), for

energy-rich anhydride bonds of ATP per fatty

example. The acetyl CoA formed can then

acid (see p. 162). For channeling into the mi-

undergo further metabolism in the tricarbox-

tochondria, the acyl residues are first trans-

ylic acid cycle (see p. 136), or can be used for

ferred to carnitine and then transported

biosynthesis. When there is an excess of ace-

across the inner membrane as acyl carnitine

tyl CoA, the liver can also form ketone bodies

(see B).

(see p. 312).

The degradation of the fatty acids occurs in

When oxidative degradation is complete,

the mitochondrial matrix through an oxida-

one molecule of palmitic acid supplies around

tive cycle in which C₂ units are successively

106 molecules of ATP, corresponding to an

cleaved off as acetyl CoA (activated acetic

energy of 3300 kJ mol^-1. This high energy

acid). Before the release of the acetyl groups,

yield makes fats an ideal form of storage for

each CH₂ group at C-3 of the acyl residue (the

metabolic energy. Hibernating animals such

β-C atom) is oxidized to the keto group—

as polar bears can meet their own energy

hence the term

-oxidation for this metabolic

requirements for up to 6 months solely by

pathway. Both spatially and functionally, it is

fat degradation, while at the same time pro-

closely linked to the tricarboxylic acid cycle

ducing the vital water they need via the res-

(see p. 136) and to the respiratory chain (see

piratory chain (“respiratory water”).

p. 140).

B. Fatty acid transport

[1] The first step is dehydrogenation of acyl

CoA at C-2 and C-3. This yields an unsaturated

The inner mitochondrial membrane has a

∆²-enoyl-CoA derivative with a trans-config-

group-specific transport system for fatty

ured double bond. The two hydrogen atoms

acids. In the cytoplasm, the acyl groups of

are initially transferred from FAD-containing

activated fatty acids are transferred to carni-

acyl CoA dehydrogenase to the electron-trans-

tine by carnitine acyltransferase [1]. They are

ferring flavoprotein (ETF). ETF dehydrogenase

then channeled into the matrix by an acylcar-

[5] passes them on from ETF to ubiquinone

nitine/carnitine antiport as acyl carnitine, in

(coenzyme Q), a component of the respiratory

exchange for free carnitine. In the matrix, the

chain (see p. 140). Other FAD-containing mi-

mitochondrial enzyme carnitine acyltransfer-

tochondrial dehydrogenases are also able to

ase catalyzes the return transfer of the acyl

supply the respiratory chain with electrons in

residue to CoA.

this fashion.

The carnitine shuttle is the rate-determin-

There are three isoenzymes (see p. 98) of

ing step in mitochondrial fatty acid degrada-

acyl CoA dehydrogenase that are specialized

tion. Malonyl CoA, a precursor of fatty acid

for long-chain fatty acids (12-18 C atoms),

biosynthesis, inhibits carnitine acyltransferase

medium-chain fatty acids (4-14), and short-

(see p. 162), and therefore also inhibits uptake

chain fatty acids (4-8).

of fatty acids into the mitochondrial matrix.

[2] The next step in fatty acid degradation

The most important regulator of β-oxida-

is the addition of a water molecule to the

tion is the NAD⁺/NADH+H⁺ ratio. If the respi-

double bond of the enoyl CoA (hydration),

ratory chain is not using any NADH+H⁺, then

with formation of

-hydroxyacyl CoA.

not only the tricarboxylic acid cycle

(see

[3] In the next reaction, the OH group at C-

p. 136) but also β-oxidation come to a stand-

3 is oxidized to a carbonyl group (dehydro-

still due to the lack of NAD⁺.

genation). This gives rise to

-ketoacyl CoA,

and the reduction equivalents are transferred

to NAD⁺, which also passes them on to the

respiratory chain.

Lipid Metabolism

165

A. Fatty acid degradation: β-oxidation

Electron-

transferring

QH₂

flavoprotein (ETF)

Respiratory

chain

β-Carbon

C C C

C C

Acyl CoA

(n - 2 carbons)

C C

H O

C C

C C C

Acetyl CoA

H₂O

Tricarboxylic acid cycle

Acyl-CoA dehydrogenase 1.3.99.3

H O

Enoyl-CoA hydratase 4.2.1.17

Respiratory

C C C

chain

3-Hydroxyacyl-CoA dehydrogenase

1.1.1.35

Acetyl-CoA acyltransferase 2.3.1.16

ETF dehydrogenase [FAD, Fe₄S₄] 1.5.5.1

B. Fatty acid transport

Carnitine

Acyl

O-palmitoyltransferase

carnitine

2.3.1.21

CH₃

Fat degradation

β-Oxidation

OOC

CH₂

N CH₃

CH₃

Acyl

Carnitine

Acyl

carnitine

166

Metabolism

boxylic acid cycle and is available for gluco-

Minor pathways of fatty acid

neogenesis through conversion into oxaloace-

degradation

tate. Odd-numbered fatty acids from pro-

pionyl-CoA can therefore be used to synthe-

Most fatty acids are saturated and even-num-

size glucose.

bered. They are broken down via E-oxidation

This pathway is also important for rumi-

(see p.164). In addition, there are special path-

nant animals, which are dependent on sym-

ways involving degradation of unsaturated

biotic microorganisms to break down their

fatty acids

(A), degradation of fatty acids

food. The microorganisms produce large

with an odd number of C atoms (B), α and ω

amounts of propionic acid as a degradation

oxidation of fatty acids, and degradation in

product, which the host can channel into the

peroxisomes.

metabolism in the way described.

A. Degradation of unsaturated fatty acids

Further information

Unsaturated fatty acids usually contain a cis

In addition to the degradation pathways de-

double bond at position 9 or 12—e. g., linoleic

scribed above, there are also additional spe-

acid (18:2; 9,12). As with saturated fatty acids,

cial pathways for particular fatty acids found

degradation in this case occurs via β-oxida-

in food.

tion until the C-9-cis double bond is reached.

a Oxidation is used to break down methyl-

Since enoyl-CoA hydratase only accepts sub-

branched fatty acids. It takes place through

strates with trans double bonds, the corre-

step-by-step removal of C₁ residues, begins

sponding enoyl-CoA is converted by an iso-

with a hydroxylation, does not require coen-

merase from the cis-∆³, cis- ∆⁶ isomer into the

zyme A, and does not produce any ATP.

trans-∆³,cis-∆⁶ isomer [1]. Degradation by β-

w Oxidation—i. e., oxidation starting at the

oxidation can now continue until a shortened

end of the fatty acid—also starts with a hy-

trans-∆², cis-∆⁴ derivative occurs in the next

droxylation catalyzed by a monooxygenase

cycle. This cannot be isomerized in the same

(see p. 316), and leads via subsequent oxida-

way as before, and instead is reduced in an

tion to fatty acids with two carboxyl groups,

NADPH-dependent way to the trans-∆³ com-

which can undergo β-oxidation from both

pound [2]. After rearrangement by enoyl-CoA

ends until C₈ or C₆ dicarboxylic acids are

isomerase [1], degradation can finally be com-

reached, which can be excreted in the urine

pleted via normal β-oxidation.

in this form.

Degradation of unusually long fatty acids.

B. Degradation of oddnumbered fatty acids

An alternative form of β-oxidation takes place

in hepatic peroxisomes, which are specialized

Fatty acids with an odd number of C atoms are

for the degradation of particularly long fatty

treated in the same way as “normal” fatty

acids (n > 20). The degradation products are

acids—i. e., they are taken up by the cell with

acetyl-CoA and hydrogen peroxide (H₂O₂),

ATP-dependent activation to acyl CoA and are

which is detoxified by the catalase

(see

transported into the mitochondria with the

p. 32) common in peroxisomes.

help of the carnitine shuttle and broken

down there by β−oxidation (see p. 164). In

Enzyme defects are also known to exist in

the last step, propionyl CoA arises instead of

the minor pathways of fatty acid degradation.

acetyl CoA. This is first carboxylated by pro-

In Refsum disease, the methyl-branched phy-

pionyl CoA carboxylase into (S)-methylmalonyl

tanic acid (obtained from vegetable foods)

CoA [3], which—after isomerization into the

cannot be degraded by α-oxidation. In Zell-

(R) enantiomer (not shown; see p. 411)—is

weger syndrome, a peroxisomal defect means

isomerized into succinyl CoA [4].

that long-chain fatty acids cannot be de-

Various coenzymes are involved in these

graded.

reactions. The carboxylase [3] requires biotin,

and the mutase [4] is dependent on coenzyme

B₁₂ (5 -deoxyadenosyl cobalamin; see p. 108).

Succinyl-CoA is an intermediate in the tricar-

Lipid Metabolism

167

A. Degradation of unsaturated fatty acids

Linoleoyl CoA (18 : 2; 9,12)

Shift and

Reduction and

izomerization

shift of the

cis

3 CoA

of the

marked

double bonds

double bond

β-Oxidation

3 Acetyl CoA

trans

cis

β-Oxidation

cis

CoA

Acetyl CoA

NADPH

4 CoA

trans

NADP

β-Oxidation

Enoyl-CoA isomerase

5.3.3.8

5 Acetyl CoA

2,4-Dienoyl-CoA reductase

1.3.1.34

B. Degradation of odd-numbered fatty acids

Propionyl-CoA carboxylase

Odd-numbered

6.4.1.3 [biotin]

fatty acids

Methylmalonyl-CoA mutase

5.4.99.2 [cobamide]

β-Oxidation

H C C

P P

Tricarboxylic acid cycle

P P

n Acetyl CoA

C C C

C C

C H

COO

H COO

Propionyl CoA

CO₂

Methylmalonyl CoA

Succinyl CoA

168

Metabolism

ductase [6]. Finally, domain 3 serves to release

Fatty acid synthesis

the finished product by acyl-[ACP]-hydrolase

In the vertebrates, biosynthesis of fatty acids

[7] after seven steps of chain elongation.

is catalyzed by fatty acid synthase, a multi-

functional enzyme. Located in the cytoplasm,

B. Reactions of fatty acid synthase

the enzyme requires acetyl CoA as a starter

molecule. In a cyclic reaction, the acetyl resi-

The key enzyme in fatty acid synthesis is ace-

due is elongated by one C₂ unit at a time for

tyl CoA carboxylase (see p. 162), which pre-

seven cycles. NADPH+H⁺ is used as a reducing

cedes the synthase and supplies the malonyl-

agent in the process. The end product of the

CoA required for elongation. Like all carbox-

reaction is the saturated C₁₆ acid, palmitic

ylases, the enzyme contains covalently bound

acid.

biotin as a prosthetic group and is hormone-

dependently inactivated by phosphorylation

or activated by dephosphorylation

(see

A. Fatty acid synthase

p. 120). The precursor citrate (see p. 138) is

Fatty acid synthase in vertebrates consists of

an allosteric activator, while palmitoyl-CoA

two identical peptide chains—i. e., it is a ho-

inhibits the end product of the synthesis

modimer. Each of the two peptide chains,

pathway.

which are shown here as hemispheres, cata-

[1] The first cycle (n = 1) starts with the

lyzes all seven of the partial reactions re-

transfer of an acetyl residue from acetyl CoA

quired to synthesize palmitate. The spatial

to the peripheral cysteine residue (Cys-SH). At

compression of several successive reactions

the same time,

into a single multifunctional enzyme has ad-

[2] a malonyl residue is transferred from

vantages in comparison with separate en-

malonyl CoA to 4-phosphopantetheine (Pan-

zymes. Competing reactions are prevented,

SH).

the individual reactions proceed in a coordi-

[3] By condensation of the acetyl resi-

nated way as if on a production line, and due

due—or (in later cycles) the acyl residue—with

to low diffusion losses they are particularly

the malonyl group, with simultaneous decar-

ef cient.

boxylation, the chain is elongated.

Each subunit of the enzyme binds acetyl

[4]-[6] The following three reactions (re-

residues as thioesters at two different SH

duction of the 3-oxo group, dehydrogenation

groups: at one peripheral cysteine residue

of the 3-hydroxyl derivative, and renewed

(CysSH) and one central

4 -phosphopante-

reduction of it) correspond in principle to a

theine group (Pan-SH). Pan-SH, which is very

reversal of β-oxidation, but they are catalyzed

similar to coenzyme A (see p. 12), is cova-

by other enzymes and use NADPH+H⁺ instead

lently bound to a protein segment of the syn-

of NADH+H⁺ for reduction. They lead to an

thase known as the acyl-carrier protein (ACP).

acyl residue bound at Pan-SH with 2n + 2 C

This part functions like a long arm that passes

atoms (n = the number of the cycle). Finally,

the substrate from one reaction center to the

depending on the length of the product,

next. The two subunits of fatty acid synthase

[1 ] The acyl residue is transferred back to

cooperate in this process; the enzyme is

the peripheral cysteine, so that the next cycle

therefore only capable of functioning as a

can begin again with renewed loading of the

dimer.

ACP with a malonyl residue, or:

Spatially, the enzyme activities are ar-

[7] After seven cycles, the completed pal-

ranged into three different domains.

mitic acid is hydrolytically released.

Domain 1 catalyzes the entry of the substrates

acetyl CoA and malonyl CoA by

[ACP]-S-

In all, one acetyl-CoA and seven malonyl-

acetyltransferase

[1] and

[ACP]-Smalonyl

CoA are converted with the help of

transferase [2] and subsequent condensation

NADPH+H⁺ into one palmitic acid, 7 CO₂,

of the two partners by

3-oxoacyl-[ACP]-

6 H₂O, 8 CoA and 14 NADP⁺. Acetyl CoA car-

synthase [3]. Domain 2 catalyzes the conver-

boxylase also uses up seven ATP.

sion of the 3-oxo group to a CH₂ group by 3-

oxoacyl-[ACP]-reductase

[4],

3-hydroxyacyl-

[ACP]-dehydratase

[5], and enoyl-[ACP]-re-

Lipid Metabolism

169

A. Fatty acid synthase

B. Reactions of fatty acid synthesis

Substrate entry

Water cleavage

Palmitate

Chain elongation

Reduction

H₂O

Product

release

Reduction

Product release

Pan-S

C H

Acyl-

Palmitate

Cys-SH

H H H

NADP

ACP

NADP+H

-Pantethein

Cys

trans-Enoyl-

Pan-S

C C H

ACP

Cys-SH

H H

H₂O

Pan-S

3-Hydroxy-

C C H

Acetyl

acyl-

Cys-SH

H H

Malonyl

NADP

NADP+H

[ACP]-S-Acetyl-

transferase 2.3.1.38

[ACP]-S-Malonyl-

3-Oxoacyl-

Pan-S

C C H

transferase 2.3.1.39

Cys-SH

3-Oxoacyl-[ACP]

synthase 2.3.1.41

CO2

3-Oxoacyl-[ACP]

reductase 1.1.1.100

3-Hydroxypalmitoyl-[ACP]

Pan-S

COO

dehydratase 4.2.1.61

Enoyl-[ACP]

reductase (NADPH) 1.3.1.10

Acyl-[ACP]

Cys-S

hydrolase 3.1.2.14

Acetyl or

Malonyl

Starting reaction

Acetyl

acyl residue

170

Metabolism

The biosynthesis of most phospholipids

Biosynthesis of complex lipids

also starts from DAG.

[7] Transfer of a phosphocholine residue to

A. Biosynthesis of fats and phospholipids

the free OH group gives rise to phosphatidyl-

Complex lipids, such as neutral fats (triacyl-

choline

(lecithin; enzyme:

1-alkyl-2-acetyl-

glycerols), phospholipids, and glycolipids, are

glycerolcholine phosphotransferase

2.7.8.16).

synthesized via common reaction pathways.

The phosphocholine residue is derived from

Most of the enzymes involved are associated

the precursor CDP-choline (see p. 110). Phos-

with the membranes of the smooth endoplas-

phatidylethanolamine is similarly formed

mic reticulum.

from CDP-ethanolamine and DAG. By

contrast, phosphatidylserine is derived from

The synthesis of fats and phospholipids

phosphatidylethanolamine by an exchange of

starts with glycerol 3-phosphate. This com-

the amino alcohol. Further reactions serve to

pound can arise via two pathways:

interconvert the phospholipids—e. g., phos-

[1] By reduction from the glycolytic

phatidylserine can be converted into phos-

intermediate glycerone 3-phosphate (dihy-

phatidylethanolamine by decarboxylation,

droxyacetone

3-phosphate; enzyme: glyc-

and the latter can then be converted into

erol-3-phosphate dehydrogenase

(NAD+)

phosphatidylcholine by methylation with S-

1.1.1.8), or:

adenosyl methionine (not shown; see also

[2] By phosphorylation of glycerol deriving

p. 409). The biosynthesis of phosphatidylino-

from fat degradation (enzyme: glycerol kinase

sitol starts from phosphatidate rather than

2.7.1.30).

DAG.

[3] Esterification of glycerol 3-phosphate

[8] In the lumen of the intestine, fats from

with a long-chain fatty acid produces a

food are mainly broken down into monoacyl-

strongly amphipathic lysophosphatidate (en-

glycerols (see p. 270). The cells of the intesti-

zyme: glycerol-3-phosphate acyltransferase

nal mucosa re-synthesize these into neutral

2.3.1.15). In this reaction, an acyl residue is

fats. This pathway also passes via DAG

transferred from the activated precursor

(enzyme: acylglycerolpalmitoyl transferase

acyl-CoA to the hydroxy group at C-1.

2.3.1.22).

[4] A second esterification of this type leads

[9] Transfer of a CMP residue gives rise first

to a phosphatidate (enzyme: 1-acylglycerol-3-

to CDP-diacylglycerol (enzyme: phosphatida-

phosphate acyltransferase

2.3.1.51). Unsatu-

tecytidyl transferase 2.3.1.22).

rated acyl residues, particularly oleic acid,

[10] Substitution of the CMP residue by

are usually incorporated at C-2 of the glycerol.

inositol then provides phosphatidylinositol

Phosphatidates (anions of phosphatidic acids)

(PtdIns; enzyme: CDPdiacylglycerolinositol-3-

are the key molecules in the biosynthesis of

phosphatidyl transferase 2.7.8.11).

fats, phospholipids, and glycolipids.

[12] An additional phosphorylation (en-

[5] To biosynthesize fats (triacylglycerols),

zyme: phosphatidylinositol-4-phosphate kin-

the phosphate residue is again removed by

ase 2.7.1.68) finally provides phosphaditylino-

hydrolysis (enzyme: phosphatidate phospha-

sitol-4,5-bisphosphate

(PIP₂, PtdIns(4,5)P₂).

tase

3.1.3.4). This produces diacylglycerols

PIP₂ is the precursor for the second messen-

(DAG).

gers

2,3-diacylglycerol

(DAG) and inositol-

[6] Transfer of an additional acyl residue to

1,4,5-trisphosphate (InsP₃, IP₃; see p. 367).

DAG forms triacylglycerols (enzyme: diacyl-

The biosynthesis of the sphingolipids is

glycerol acyltransferase

2.3.1.20). This com-

shown in schematic form on p. 409.

pletes the biosynthesis of neutral fats. They

are packaged into VLDLs by the liver and re-

leased into the blood. Finally, they are stored

by adipocytes in the form of insoluble fat

droplets.

172

Metabolism

(effectors: hormones). Insulin and thyroxine

Biosynthesis of cholesterol

stimulate the enzyme and glucagon inhibits it

Cholesterol is a major constituent of the cell

by cAMP-dependent phosphorylation. A large

membranes of animal cells (see p. 216). It

supply of cholesterol from food also inhibits

would be possible for the body to provide its

3-HMG-CoA reductase.

full daily cholesterol requirement (ca. 1 g) by

(2) Formation of isopentenyl diphosphate.

synthesizing it itself. However, with a mixed

After phosphorylation, mevalonate is decar-

diet, only about half of the cholesterol is de-

boxylated to isopentenyl diphosphate, with

rived from endogenous biosynthesis, which

consumption of ATP. This is the component

takes place in the intestine and skin, and

from which all of the isoprenoids are built

mainly in the liver (about 50%). The rest is

(see p. 53).

taken up from food. Most of the cholesterol

(3) Formation of squalene. Isopentenyl

is incorporated into the lipid layer of plasma

diphosphate undergoes isomerization to

membranes, or converted into bile acids (see

form dimethylallyl diphosphate. The two C₅

p. 314). A very small amount of cholesterol is

molecules condense to yield geranyl diphos-

used for biosynthesis of the steroid hormones

phate, and the addition of another isopen-

(see p. 376). In addition, up to 1 g cholesterol

tenyl diphosphate produces farnesyl diphos-

per day is released into the bile and thus

phate. This can then undergo dimerization, in

excreted.

a head-to-head reaction, to yield squalene.

Farnesyl diphosphate is also the starting-

point for other polyisoprenoids, such as doli-

A. Cholesterol biosynthesis

chol (see p. 230) and ubiquinone (see p. 52).

Cholesterol is one of the isoprenoids, synthe-

(4) Formation of cholesterol. Squalene, a

sis of which starts from acetyl CoA (see p. 52).

linear isoprenoid, is cyclized, with O₂ being

In a long and complex reaction chain, the C₂₇

consumed, to form lanosterol, a C₃₀ sterol.

sterol is built up from C₂ components. The

Three methyl groups are cleaved from this

biosynthesis of cholesterol can be divided

in the subsequent reaction steps, to yield the

into four sections. In the first

(1),

end product cholesterol. Some of these reac-

mevalonate, a C₆

compound, arises from

tions are catalyzed by cytochrome P450 sys-

three molecules of acetyl CoA. In the second

tems (see p. 318).

part (2), mevalonate is converted into isopen-

The endergonic biosynthetic pathway de-

tenyl diphosphate, the “active isoprene.” In

scribed above is located entirely in the smooth

the third part (3), six of these C₅ molecules

endoplasmic reticulum. The energy needed

are linked to produce squalene, a C₃₀ com-

comes from the CoA derivatives used and

pound. Finally, squalene undergoes cycliza-

from ATP. The reducing agent in the formation

tion, with three C atoms being removed, to

of mevalonate and squalene, as well as in the

yield cholesterol

(4). The illustration only

final steps of cholesterol biosynthesis, is

shows the most important intermediates in

NADPH+H⁺.

biosynthesis.

The division of the intermediates of the

(1) Formation of mevalonate. The conver-

reaction pathway into three groups is charac-

sion of acetyl CoA to acetoacetyl CoA and then

teristic: CoA compounds, diphosphates, and

3-hydroxy-3-methylglutaryl CoA

(3-HMG

highly lipophilic, poorly soluble compounds

CoA) corresponds to the biosynthetic path-

(squalene to cholesterol), which are bound to

way for ketone bodies (details on p. 312). In

sterol carriers in the cell.

this case, however, the synthesis occurs not in

the mitochondria as in ketone body synthesis,

but in the smooth endoplasmic reticulum. In

the next step, the 3-HMG group is cleaved

from the CoA and at the same time reduced

to mevalonate with the help of NADPH+H⁺. 3-

HMG CoA reductase is the key enzyme in cho-

lesterol biosynthesis. It is regulated by repres-

sion of transcription

(effectors: oxysterols

such as cholesterol) and by interconversion

Lipid Metabolism

173

A. Cholesterol biosynthesis

Acetyl CoA

Mevalonate

Isopentenyl diphosphate

Squalene

Cholesterol

C₂

C₆

C₃₀

C₂₇

CH₃

3x H₃C C

Acetyl CoA

OOC

CH₂

C CH

CH₂OH

Mevalonate

3-Hydroxy-

3-methyl-

P P P

glutaryl CoA

CH₃

P P

OOC CH₂

C CH₂

OOC

CH₂

C CH₂

CH₂

O P P

Insulin

HMG-CoA

Mevalonyl

Thyroxin

Cholesterol

reductase

diphosphate

1.1.1.34

Glucagon

Key enzyme

CO₂

P P

CH₃

OOC

CH₂

C CH₂

CH₂OH

H₂C

P P

Mevalonate

Isopentenyl diphosphate

Dimethylallyl

Isopentenyl diphosphate

diphosphate

Squalene

P P

O2 +

Two steps

H₂O +

Geranyl

P P

diphosphate

P P

Lanosterol

Farnesyl

diphosphate

P P

x O₂ + x

O P P

2 CO₂

x H₂O + x

1 HCOOH

Multiple steps

NADPH+H

P P

NADP

Squalene

Cholesterol

174

Metabolism

is reincorporated into proteins (protein bio-

Protein metabolism: overview

synthesis). The body’s high level of protein

Quantitatively, proteins are the most impor-

turnover is due to the fact that many proteins

tant group of endogenous macromolecules. A

are relatively short-lived. On average, their

person weighing 70 kg contains about 10 kg

half-lives amount to 2-8 days. The key en-

protein, with most of it located in muscle. By

zymes of the intermediary metabolism have

comparison, the proportion made up by other

even shorter half-lives. They are sometimes

nitrogencontaining compounds is minor. The

broken down only a few hours after being

organism’s nitrogen balance is therefore pri-

synthesized, and are replaced by new mole-

marily determined by protein metabolism.

cules. This constant process of synthesis and

Several hormones—mainly testosterone and

degradation makes it possible for the cells to

cortisol—regulate the nitrogen balance (see

quickly adjust the quantities, and therefore

p. 374).

the activity, of important enzymes in order

to meet current requirements. By contrast,

structural proteins such as the histones, he-

A. Protein metabolism: overview

moglobin, and the components of the cyto-

In adults, the nitrogen balance is generally in

skeleton are particularly long-lived.

equilibrium—i. e., the quantities of protein ni-

Almost all cells are capable of carrying out

trogen taken in and excreted per day are ap-

biosynthesis of proteins (top left). The forma-

proximately equal. If only some of the nitro-

tion of peptide chains by translation at the

gen taken in is excreted again, then the bal-

ribosome is described in greater detail on

ance is positive. This is the case during growth,

pp. 250-253. However, the functional forms

for example. Negative balances are rare and

of most proteins arise only after a series of

usually occur due to disease.

additional steps. To begin with, supported by

Proteins taken up in food are initially bro-

auxiliary proteins, the biologically active con-

ken down in the gastrointestinal tract into

formation of the peptide chain has to be

amino acids, which are resorbed and distrib-

formed (folding; see pp. 74,

232). During

uted in the organism via the blood

(see

subsequent “post-translational” maturation,

p. 266). The human body is not capable of

many proteins remove part of the peptide

synthesizing 8-10 of the 20 proteinogenic

chain again and attach additional groups—

amino acids it requires (see p. 60). These

e. g., oligosaccharides or lipids. These pro-

amino acids are essential, and have to be sup-

cesses take place in the endoplasmic reticu-

plied from food (see p. 184).

lum and in the Golgi apparatus (see p. 232).

Proteins are constantly being lost via the

Finally, the proteins have to be transported to

intestine and, to a lesser extent, via the kid-

their site of action (sorting; see p. 228).

neys. To balance these inevitable losses, at

Some intracellular protein degradation

least 30 g of protein have to be taken up

(proteolysis) takes place in the lysosomes

with food every day. Although this minimum

(see p. 234). In addition, there are protein

value is barely reached in some countries, in

complexes in the cytoplasm, known as pro-

the industrial nations the protein content of

teasomes, in which incorrectly folded or old

food is usually much higher than necessary.

proteins are degraded. These molecules are

As it is not possible to store amino acids, up to

recognized by a special marking (see p. 176).

100 g of excess amino acids per day are used

The proteasome also plays an important part

for biosynthesis or degraded in the liver in

in the presentation of antigens by immune

this situation. The nitrogen from this excess

cells (see p. 296).

is converted into urea (see p. 182) and ex-

creted in the urine in this form. The carbon

skeletons are used to synthesize carbohy-

drates or lipids (see p. 180), or are used to

form ATP.

It is thought that adults break down

300-400 g of protein per day into amino

acids (proteolysis). On the other hand, ap-

proximately the same amount of amino acids

176

Metabolism

molecules) are marked by covalent linkage

Proteolysis

with chains of the small protein ubiquitin.

The ubiquitin is previously activated by the

A. Proteolytic enzymes

introduction of reactive thioester groups.

Combinations of several enzymes with differ-

Molecules marked with ubiquitin (“ubiquiti-

ent specificities are required for complete

nated”) are recognized by the 19S particle,

degradation of proteins into free amino

unfolded using ATP, and then shifted into

acids. Proteinases and peptidases are found

the interior of the nucleus, where degradation

not only in the gastrointestinal tract

(see

takes place. Ubiquitin is not degraded, but is

p. 268), but also inside the cell (see below).

reused after renewed activation.

The proteolytic enzymes are classified into

endopeptidases and exopeptidases, according

C. Serine proteases

to their site of attack in the substrate mole-

cule. The endopeptidases or proteinases cleave

A large group of proteinases contain serine in

peptide bonds inside peptide chains. They

their active center. The serine proteases in-

“recognize” and bind to short sections of the

clude, for example, the digestive enzymes

substrate’s sequence, and then hydrolyze

trypsin, chymotrypsin, and elastase

(see

bonds between particular amino acid residues

pp. 94 and 268), many coagulation factors

in a relatively specific way (see p. 94). The

(see p. 290), and the fibrinolytic enzyme plas-

proteinases are classified according to their

min and its activators (see p. 292).

reaction mechanism. In serine proteinases,

As described on p. 270, pancreatic protein-

for example (see C), a serine residue in the

ases are secreted as proenzymes (zymogens).

enzyme is important for catalysis, while in

Activation of these is also based on proteolytic

cysteine proteinases, it is a cysteine residue,

cleavages. This is illustrated here in detail us-

and so on.

ing the example of trypsinogen, the precursor

The exopeptidases attack peptides from

of trypsin (1). Activation of trypsinogen starts

their termini. Peptidases that act at the N

with cleavage of an N-terminal hexapeptide

terminus are known as aminopeptidases,

by enteropeptidase (enterokinase), a specific

while those that recognize the C terminus

serine proteinase that is located in the mem-

are called carboxypeptidases. The dipepti-

brane of the intestinal epithelium. The cleav-

dases only hydrolyze dipeptides.

age product (β-trypsin) is already catalytically

active, and it cleaves additional trypsinogen

molecules at the sites marked in red in the

B. Proteasome

illustration (autocatalytic cleavage). The pre-

The functional proteins in the cell have to be

cursors of chymotrypsin, elastase, and car-

protected in order to prevent premature deg-

boxypeptidase A, among others, are also acti-

radation. Some of the intracellularly active

vated by trypsin.

proteolytic enzymes are therefore enclosed

The active center of trypsin is shown in

in lysosomes (see p. 234). The proteinases

Fig. 2. A serine residue in the enzyme (Ser-

that act there are also known as cathepsins.

195), supported by a histidine residue and

Another carefully regulated system for pro-

an aspartate residue (His-57, Asp-102), nucle-

tein degradation is located in the cytoplasm.

ophilically attacks the bond that is to be

This consists of large protein complexes (mass

cleaved (red arrow). The cleavage site in the

10⁶ Da), the proteasomes. Proteasomes

substrate peptide is located on the C-terminal

contain a barrel-shaped core consisting of 28

side of a lysine residue, the side chain of

subunits that has a sedimentation coef cient

which is fixed in a special “binding pocket”

(see p. 200) of

20 S.Proteolytic activity

of the enzyme (left) during catalysis

(see

(shown here by the scissors) is localized in

p. 94).

the interior of the 20-S core and is therefore

protected. The openings in the barrel are

sealed by 19-S particles with a complex struc-

ture that control access to the core.

Proteins destined for degradation in the

proteasome (e. g., incorrectly folded or old

Protein Metabolism

177

A. Proteolytic enzymes

C-Terminus

COO

Serine proteinase

H₃N

N-Terminus

3.4.21.n

Aminopeptidase

H₃N

COO

Cysteine proteinase

Exopeptidase

[Zn2

] 3.4.11.n

3.4.22.n

Endopeptidase

Aspartate proteinase

3.4.23.n

Metalloproteinase

Dipeptidase

H₃N

3.4.24.n

[Zn2

] 3.4.13.n

Carboxy-

peptidase

3.4.17.n

Amino acid residue

COO

B. Proteasome

C. Serine proteases

Folded

Activated

Disulfide Autocatalytic

protein

ubiquitin

bond

cleavage

Auto-

cata-

lytic

cleavage

Marking

Activation

with

ubiquitin

Ubiquitinated

protein

Cleavage

by entero-

peptidase

Active

19 S

and trypsin

center

particle

Enteropeptidase

Trypsin

Binding

3.4.21.9

3.4.21.4

20 S

1. Trypsinogen activation

nucleus

19 S

particle

Asp-102

Ser-195

Lysine residue

His-57

Unfolding

Degradation

Substrate

2. Trypsin: active center

178

Metabolism

The ketimine (3) is hydrolyzed to yield the 2-

Transamination and deamination

oxoacid and pyridoxamine phosphate (4).

Amino nitrogen accumulates during protein

In the second part of the reaction (see A,

degradation. In contrast to carbon, amino ni-

1b), these steps take place in the opposite

trogen is not suitable for oxidative energy

direction: pyridoxamine phosphate and the

production. If they are not being reused for

second 2-oxoacid form a ketimine, which is

biosynthesis, the amino groups of amino acids

isomerized into aldimine. Finally, the second

are therefore incorporated into urea

(see

amino acid is cleaved and the coenzyme is

p. 182) and excreted in this form.

regenerated.

A. Transamination and deamination

C. NH₃ metabolism in the liver

Among the NH₂ transfer reactions, trans-

In addition to urea synthesis itself

(see

aminations

(1) are particularly important.

p. 182), the precursors NH₃ and aspartate are

They are catalyzed by transaminases, and oc-

also mainly formed in the liver. Amino nitro-

cur in both catabolic and anabolic amino acid

gen arising in tissue is transported to the liver

metabolism. During transamination, the

by the blood, mainly in the form of glutamine

amino group of an amino acid (amino acid

(Gln) and alanine (Ala; see p. 338). In the liver,

1) is transferred to a 2-oxoacid (oxoacid 2).

Gln is hydrolytically deaminated by glutami-

From the amino acid, this produces a 2-oxo-

nase [3] into glutamate (Glu) and NH₃. The

acid (a), while from the original oxoacid, an

amino group of the alanine is transferred by

amino acid is formed (b). The NH₂ group is

alanine transaminase [1] to 2-oxoglutarate (2-

temporarily taken over by enzyme-bound

OG; formerly known as α-ketoglutarate). This

pyridoxal phosphate (PLP; see p. 106), which

transamination (A) produces another gluta-

thus becomes pyridoxamine phosphate.

mate. NH₃ is finally released from glutamate

If the NH₂ is released as ammonia, the

by oxidative deamination (A). This reaction is

process is referred to as deamination. There

catalyzed by glutamate dehydrogenase [4], a

are different mechanisms for this (see p. 180).

typical liver enzyme. Aspartate (Asp), the sec-

A particularly important one is oxidative

ond amino group donor in the urea cycle, also

deamination (2). In this reaction, the α-amino

arises from glutamate. The aspartate

group is initially oxidized into an imino group

transaminase [2] responsible for this reaction

(2a), and the reducing equivalents are trans-

is found with a high level of activity in the

ferred to NAD⁺ or NADP⁺. In the second step,

liver, as is alanine transaminase [1].

the imino group is then cleaved by hydrolysis.

Transaminases are also found in other tis-

As in transamination, this produces a 2-oxo-

sues, from which they leak from the cells into

acid (C). Oxidative deamination mainly takes

the blood when injury occurs. Measurement

place in the liver, where glutamate is broken

of serum enzyme activity (serum enzyme di-

down in this way into 2-oxoglutarate and

agnosis; see also p. 98) is an important

ammonia, catalyzed by glutamate dehydro-

method of recognizing and monitoring the

genase. The reverse reaction initiates biosyn-

course of such injuries. Transaminase activity

thesis of the amino acids in the glutamate

in the blood is for instance important for di-

family (see p. 184).

agnosing liver disease (e. g., hepatitis) and

myocardial disease (cardiac infarction).

B. Mechanism of transamination

In the absence of substrates, the aldehyde

group of pyridoxal phosphate is covalently

bound to a lysine residue of the transaminase

(1). This type of compound is known as an

aldimine or “Schiff’s base.” During the reac-

tion, amino acid 1 (A, 1a) displaces the lysine

residue, and a new aldimine is formed (2). The

double bond is then shifted by isomerization.

Protein Metabolism

179

A. Transamination and deamination

B. Mechanism of transamination

Amino

Lysine residue

acid

OOC C R

H₃N

C H

H C

R₁

Aldimine 2

Amino acid 1

Oxoacid 1

OOC C R

Pyridoxamine

PLP

H₃N

phosphate

H₃C

H C

PLP (Aldimine 1)

H₃C

O C

H₃N

C H

Aldimine 2

R₂

Oxoacid 2

Amino acid 2

Rearrangement

1. Transamination

OOC

Imino acid

Ketimine

H CH₂

H₃N

C H

H₂N

R₂

Amino acid

H₂O

H₃C

NH₂

CH₂

H₂O

NH₄

Oxoacid

H₃C

OOC

R₂

2. Oxidative deamination

Oxoacid

Pyridoxamine-P

C. NH₃ metabolism in the liver

Alanine trans-

aminase [PLP]

2.6.1.2

Aspartate trans-

aminase [PLP]

2.6.1.1

Glutaminase

3.5.1.2

Glutamate

dehydrogenase

1.4.1.2

Transamination

Oxidative

deamination

Hydrolytic

deamination

180

Metabolism

and ketogenic. This group includes phenylala-

Amino acid degradation

nine, tyrosine, tryptophan, and isoleucine.

A large number of metabolic pathways are

Degradation of acetoacetate to acetyl CoA

available for amino acid degradation, and an

takes place in two steps (not shown). First,

overview of these is presented here. Further

acetoacetate and succinyl CoA are converted

details are given on pp. 414 and 415.

into acetoacetyl CoA and succinate (enzyme:

3-oxoacid-CoA transferase 2.8.3.5). Acetoacetyl

CoA is then broken down by β-oxidation into

A. Amino acid degradation : overview

two molecules of acetyl CoA (see p. 164),

During the degradation of most amino acids,

while succinate can be further metabolized

the α-amino group is initially removed by

via the tricarboxylic acid cycle.

transamination or deamination. Various

mechanisms are available for this, and these

B. Deamination

are discussed in greater detail in B. The carbon

skeletons that are left over after deamination

There are various ways of releasing ammonia

undergo further degradation in various ways.

(NH₃) from amino acids, and these are illus-

During degradation, the 20 proteinogenic

trated here using the example of the amino

amino acids produce only seven different

acids glutamine, glutamate, alanine, and ser-

degradation products

(highlighted in pink

ine.

and violet). Five of these metabolites (2-oxo-

[1] In the branched-chain amino acids (Val,

glutarate, succinyl CoA, fumarate, oxaloace-

Leu, Ile) and also tyrosine and ornithine, deg-

tate, and pyruvate) are precursors for gluco-

radation starts with a transamination. For ala-

neogenesis and can therefore be converted

nine and aspartate, this is actually the only

into glucose by the liver and kidneys (see

degradation step. The mechanism of transa-

p. 154). Amino acids whose degradation sup-

mination is discussed in detail on p. 178.

plies one of these five metabolites are there-

[2] Oxidative deamination, with the forma-

fore referred to as glucogenic amino acids.

tion of NADH+H⁺, only applies to glutamate in

The first four degradation products listed are

animal metabolism. The reaction mainly takes

already intermediates in the tricarboxylic acid

place in the liver and releases NH₃ for urea

cycle, while pyruvate can be converted into

formation (see p. 178).

oxaloacetate by pyruvate carboxylase and thus

[3] Two amino acids—asparagine and glu-

made available for gluconeogenesis (green

tamine—contain acid-amide groups in the

arrow).

side chains, from which NH₃ can be released

With two exceptions (lysine and leucine;

by hydrolysis (hydrolytic deamination). In the

see below), all of the proteinogenic amino

blood, glutamine is the most important trans-

acids are also glucogenic. Quantitatively,

port molecule for amino nitrogen. Hydrolytic

they represent the most important precursors

deamination of glutamine in the liver also

for gluconeogenesis. At the same time, they

supplies the urea cycle with NH₃.

also have an anaplerotic effect—i. e., they re-

[4] Eliminating deamination takes place in

plenish the tricarboxylic acid cycle in order to

the degradation of histidine and serine. H₂O is

feed the anabolic reactions that originate in it

first eliminated here, yielding an unsaturated

(see p. 138).

intermediate. In the case of serine, this inter-

Two additional degradation products (ace-

mediate is first rearranged into an imine (not

toacetate and acetyl CoA) cannot be chan-

shown), which is hydrolyzed in the second

neled into gluconeogenesis in animal metab-

step into NH₃ and pyruvate, with H₂O being

olism, as there is no means of converting

taken up. H₂O does not therefore appear in

them into precursors of gluconeogenesis.

the reaction equation.

However, they can be used to synthesize ke-

tone bodies, fatty acids, and isoprenoids.

Amino acids that supply acetyl CoA or aceto-

acetate are therefore known as ketogenic

amino acids. Only leucine and lysine are

purely ketogenic. Several amino acids yield

degradation products that are both glucogenic

Protein Metabolism

181

A. Amino acid degradation: overview

Several

Alanine

Threonine

pathways

Glucose

Cysteine

Pyruvate

Serine

Glycine

Asparagine

Acetyl

Aceto-

CoA

acetate

Aspartate

Oxalo-

Ketone

acetate

body

Phenyl-

alanine

Pyruvate

Tricarboxylic

Fuma-

Tyrosine

rate

acid cycle

Leucine

Lysine

Iso-

2-Oxo-

leucine

Succinyl

glutarate

Tryptophan

Alanine

CoA

Valine

Acetyl

Glutamate

Histidine

CoA

Glutamine

Proline

Propionyl

CoA

Cysteine

Pyruvate

Methionine

Serine

Arginine

Glucogenic

Transamination

Hydrolytic deamination

Glucogenic

Ketogenic

and ketogenic

Oxidative deamination

Eliminating deamination

B. Deamination

COO

NADH+H

NAD

COO

H3N C H

(CH₂)

COO

CONH₂

2-OG

Glu

Gln

NH₄

H₂O

COO

H₃N C

H₃N

Ala

Pyr

Ser

H₃

H₂C

COO

O C

H₃

Alanine transaminase [PLP] 2.6.1.2

Glutaminase 3.5.1.2

Glutamate dehydrogenase 1.4.1.2

Serine dehydratase [PLP] 4.2.1.13

182

Metabolism

[1] In the first step, carbamoyl phosphate is

Urea cycle

formed in the mitochondria from hydrogen

Amino acids are mainly broken down in the

carbonate (HCO_3-) and NH₄₊, with two ATP

liver. Ammonia is released either directly or

molecules being consumed. In this com-

indirectly in the process (see p. 178). The deg-

pound, the carbamoyl residue (-O-CO-NH₂)

radation of nucleobases also provides signifi-

is at a high chemical potential. In hepatic

cant amounts of ammonia (see p. 186).

mitochondria, enzyme [1] makes up about

Ammonia (NH₃) is a relatively strong base,

20% of the matrix proteins.

and at physiological pH values it is mainly

[2] In the next step, the carbamoyl residue

present in the form of the ammonium ion

is transferred to the non-proteinogenic amino

NH₄₊ (see p. 30). NH₃ and NH₄₊ are toxic, and

acid ornithine, converting it into citrulline,

at higher concentrations cause brain damage

which is also non-proteinogenic. This is

in particular. Ammonia therefore has to be

passed into the cytoplasm via a transporter.

effectively inactivated and excreted. This can

[3] The second NH₂ group of the later urea

be carried out in various ways. Aquatic ani-

molecule is provided by aspartate, which

mals can excrete NH₄₊ directly. For example,

condenses with citrulline into argininosucci-

fish excrete NH₄₊ via the gills (ammonotelic

nate. ATP is cleaved into AMP and diphos-

animals). Terrestrial vertebrates, including

phate (PP_i) for this endergonic reaction. To

humans, hardly excrete any NH₃, and instead,

shift the equilibrium of the reaction to the

most ammonia is converted into urea before

side of the product, diphosphate is removed

excretion (ureotelic animals). Birds and rep-

from the equilibrium by hydrolysis.

tiles, by contrast, form uric acid, which is

[4] Cleavage of fumarate from argininosuc-

mainly excreted as a solid in order to save

cinate leads to the proteinogenic amino acid

water (uricotelic animals).

arginine, which is synthesized in this way in

The reasons for the neurotoxic effects of

animal metabolism.

ammonia have not yet been explained. It

[5] In the final step, isourea is released

may disturb the metabolism of glutamate

from the guanidinium group of the arginine

and its precursor glutamine in the brain (see

by hydrolysis (not shown), and is immedi-

p. 356).

ately rearranged into urea. In addition, orni-

thine is regenerated and returns via the orni-

thine transporter into the mitochondria,

A. Urea cycle

where it becomes available for the cycle

Urea (H₂N-CO-NH₂) is the diamide of car-

once again.

bonic acid. In contrast to ammonia, it is neu-

The fumarate produced in step [4] is con-

tral and therefore relatively non-toxic. The

verted via malate to oxaloacetate [6, 7], from

reason for the lack of basicity is the molecule’s

which aspartate is formed again by transami-

mesomeric characteristics. The free electron

nation [9]. The glutamate required for reac-

pairs of the two nitrogen atoms are delocal-

tion [9] is derived from the glutamate dehy-

ized over the whole structure, and are there-

drogenase reaction [8], which fixes the sec-

fore no longer able to bind protons. As a small,

ond NH₄₊ in an organic bond. Reactions [6]

uncharged molecule, urea is able to cross bio-

and [7] also occur in the tricarboxylic acid

logical membranes easily. In addition, it is

cycle. However, in urea formation they take

easily transported in the blood and excreted

place in the cytoplasm, where the appropriate

in the urine.

isoenzymes are available.

Urea is produced only in the liver, in a cyclic

The rate of urea formation is mainly con-

sequence of reactions (the urea cycle) that

trolled by reaction [1]. N-acetyl glutamate, as

starts in the mitochondria and continues in

an allosteric effector, activates carbamoyl-

the cytoplasm. The two nitrogen atoms are

phosphate synthase. In turn, the concentration

derived from NH₄₊ (the second has previously

of acetyl glutamate depends on arginine and

been incorporated into aspartate; see below).

ATP levels, as well as other factors.

The keto group comes from hydrogen carbo-

nate (HCO_3-), or CO₂ that is in equilibrium

with HCO_3-.

Protein Metabolism

183

A. Urea cycle

Carbamoyl phosphate synthase (NH₃)

Argininosuccinate synthase 6.3.4.5

6.3.4.16

Ornithine carbamoyltransferase 2.1.3.3

Argininosuccinate lyase 4.3.2.1

N-Acetyl

Arginase 3.5.3.1

glutamate

P P

Fumarate hydratase 4.2.1.2

Malate dehydrogenase 1.1.1.37

Carbamoyl

phosphate

Glutamate dehydrogenase 1.4.1.2

NH₂

Aspartate transaminase [PLP]

COO

H₃N C

COO

HCO₃

H₃N

CH₂

Ornithine

CH₂

Citrulline

CH₂

H N

CH₂

Transporter

NH₂

Urea

NH₂

COO

H₃N

COO

H₂N

CH₂

H₃N

CH₂

H₂O

Arginine

CH₂

Arginino-

CH₂

succinate

COO

CH₂

NH₂

H₂O

NH₂

H₂N

COO

OOC

COO

Fumarate

COO

CH₂

H₂O

COO

NH₄

C NH₃

COO

Aspartate

COO

C O

COO

CH₂

COO

CH₂

COO

2-Oxo-

CH₂

glutarate

CH₂

C NH₃

COO

Malate

COO

Glutamate

Oxaloacetate

184

Metabolism

have to be supplied in food. For example,

Amino acid biosynthesis

animal metabolism is no longer capable of

carrying out de-novo synthesis of the aro-

A. Symbiotic nitrogen fixation

matic amino acids (tyrosine is only non-es-

Practically unlimited quantities of elementary

sential because it can be formed from phenyl-

nitrogen (N₂) are present in the atmosphere.

alanine when there is an adequate supply

However, before it can enter the natural nitro-

available). The branched-chain amino acids

gen cycle, it has to be reduced to NH₃ and

(valine, leucine, isoleucine, and threonine) as

incorporated into amino acids (“fixed”). Only

well as methionine and lysine, also belong to

a few species of bacteria and bluegreen algae

the essential amino acids. Histidine and argi-

are capable of fixing atmospheric nitrogen.

nine are essential in rats; whether the same

These exist freely in the soil, or in symbiosis

applies in humans is still a matter of debate. A

with plants. The symbiosis between bacteria

supply of these amino acids in food appears to

of the genus Rhizobium and legumes

be essential at least during growth.

(Fabales)—such as clover, beans, and peas—is

The nutritional value of proteins

(see

of particular economic importance. These

p. 360) is decisively dependent on their es-

plants are high in protein and are therefore

sential amino acid content. Vegetable pro-

nutritionally valuable.

teins—e. g., those from cereals—are low in ly-

In symbiosis with Fabales, bacteria live as

sine and methionine, while animal proteins

bacteroids in root nodules inside the plant

contain all the amino acids in balanced pro-

cells. The plant supplies the bacteroids with

portions. As mentioned earlier, however,

nutrients, but it also benefits from the fixed

there are also plants that provide high-value

nitrogen that the symbionts make available.

protein. These include the soy bean, one of the

The N₂-fixing enzyme used by the bacteria

plants that is supplied with NH₃ by symbiotic

is nitrogenase. It consists of two components:

N₂ fixers (A).

an Fe protein that contains an [Fe₄S₄] cluster

Non-essential amino acids are those that

as a redox system (see p. 106), accepts elec-

arise by transamination from 2-oxoacids in

trons from ferredoxin, and donates them to

the intermediary metabolism. These belong

the second component, the Fe-Mo protein.

to the glutamate family (Glu, Gln, Pro, Arg,

This molybdenum-containing protein trans-

derived from 2-oxoglutarate), the aspartate

fers the electrons to N₂ and thus, via various

family (only Asp and Asn in this group, de-

intermediate steps, produces ammonia (NH₃).

rived from oxaloacetate), and alanine, which

Some of the reducing equivalents are trans-

can be formed by transamination from pyru-

ferred in a side-reaction to H⁺. In addition to

vate. The amino acids in the serine family (Ser,

NH₃, hydrogen is therefore always produced

Gly, Cys) and histidine, which arise from in-

as well.

termediates of glycolysis, can also be synthe-

sized by the human body.

B. Amino acid biosynthesis: overview

The proteinogenic amino acids (see p. 60) can

be divided into five families in relation to

their biosynthesis. The members of each fam-

ily are derived from common precursors,

which are all produced in the tricarboxylic

acid cycle or in catabolic carbohydrate metab-

olism. An overview of the biosynthetic path-

ways is shown here; further details are given

on pp. 412 and 413.

Plants and microorganisms are able to syn-

thesize all of the amino acids from scratch, but

during the course of evolution, mammals

have lost the ability to synthesize approxi-

mately half of the 20 proteinogenic amino

acids. These essential amino acids therefore

Protein Metabolism

185

A. Symbiotic nitrogen fixation

Bacteroids

Ferredoxin

Fe-Protein

P P P

[Fe₄S₄]

per

Host cell

P P

Air

Root

nodule

FeMo-Protein

N₂

[Fe₄S₄], [FeMoCo]

8 H

Iron-molyb-

denum

cofactor

H₂

2 NH₃

Soil

Nitrogenase

Vascular bundle

1.18.6.1

Ammonia

B. Amino acid biosynthesis: overview

Serine family

Cysteine

Glucose 6-

Ribose 5-

phosphate

Pentose phos-

phate pathway

3-Phospho-

glycerate

Erythrose

Glycine

Serine

Glyco-

4-phosphate

lysis

Phospho-

enolpyruvate

Pyruvate family

Histidine

Valine

Alanine

Leucine

Pyruvate

Serine

Lysine

Asparagine

NH₃

Trypto-

phan

Oxalo-

Tricarboxylic

Phenyl-

Tyrosine

Threo-

Aspar-

acetate

acid cycle

alanine

nine

tate

Synthesized from

Aromatic

phenylalanine

2-Oxo-

family

glutarat

Iso-

leucine

Methionine

2 NH₃

Ornithine

Aspartate family

Urea cycle

Glutamine

Glutamate

Essential amino acid

NH₃

Transamination

Proline

Arginine

Reductive amination

Glutamate family

186

Metabolism

species. The same applies to birds and many

Nucleotide degradation

reptiles. Most other animals continue purine

The nucleotides are among the most complex

degradation to reach allantoic acid or urea

metabolites. Nucleotide biosynthesis is elab-

and glyoxylate.

orate and requires a high energy input (see

Pyrimidine (right). In the degradation of

p. 188). Understandably, therefore, bases and

pyrimidine nucleotides (2), the free bases ura-

nucleotides are not completely degraded, but

cil

(Ura) and thymine (Thy) are initially re-

instead mostly recycled. This is particularly

leased as important intermediates. Both are

true of the purine bases adenine and guanine.

further metabolized in similar ways. The pyri-

In the animal organism, some 90% of these

midine ring is first reduced and then hydro-

bases are converted back into nucleoside

lytically cleaved. In the next step, E-alanine

monophosphates by linkage with phosphori-

arises by cleavage of CO₂ and NH₃ as the

bosyl diphosphate (PRPP) (enzymes [1] and

degradation product of uracil. When there is

[2]). The proportion of pyrimidine bases that

further degradation, E-alanine is broken

are recycled is much smaller.

down to yield acetate, CO₂, and NH₃. Propio-

nate, CO₂, and NH₃ arise in a similar way from

b-aminoisobutyrate, the degradation product

A. Degradation of nucleotides

of thymine (see p. 419).

The principles underlying the degradation of

purines (1) and pyrimidines (2) differ. In the

B. Hyperuricemia

human organism, purines are degraded into

uric acid and excreted in this form. The purine

The fact that purine degradation in humans

ring remains intact in this process. In contrast,

already stops at the uric acid stage can lead to

the ring of the pyrimidine bases (uracil, thy-

problems, since—in contrast to allantoin—uric

mine, and cytosine) is broken down into small

acid is poorly soluble in water. When large

fragments, which can be returned to the me-

amounts of uric acid are formed or uric acid

tabolism or excreted (for further details, see

processing is disturbed, excessive concentra-

p. 419).

tions of uric acid can develop in the blood

Purine (left). The purine nucleotide guano-

(hyperuricemia). This can result in the accu-

sine monophosphate (GMP, 1) is degraded in

mulation of uric acid crystals in the body.

two steps—first to the guanosine and then to

Deposition of these crystals in the joints can

guanine (Gua). Guanine is converted by de-

cause very painful attacks of gout.

amination into another purine base, xanthine.

Most cases of hyperuricemia are due to

In the most important degradative path-

disturbed uric acid excretion via the kidneys

way for adenosine monophosphate (AMP), it

(1). A high-purine diet (e. g., meat) may also

is the nucleotide that deaminated, and inosine

have unfavorable effects (2). A rare hereditary

monophosphate (IMP) arises. In the same way

disease, Lesch-Nyhan syndrome, results from

as in GMP, the purine base hypoxanthine is

a defect in hypoxanthine phosphoribosyl-

released from IMP. A single enzyme, xanthine

transferase (A, enzyme [1]). The impaired re-

oxidase [3], then both converts hypoxanthine

cycling of the purine bases caused by this

into xanthine and xanthine into uric acid. An

leads to hyperuricemia and severe neurolog-

oxo group is introduced into the substrate in

ical disorders.

each of these reaction steps. The oxo group is

Hyperuricemia can be treated with

derived from molecular oxygen; another reac-

allopurinol, a competitive inhibitor of xan-

tion product is hydrogen peroxide

(H₂O₂),

thine oxidase. This substrate analogue differs

which is toxic and has to be removed by

from the substrate hypoxanthine only in the

peroxidases.

arrangement of the atoms in the 5-ring.

Almost all mammals carry out further deg-

radation of uric acid with the help of uricase,

with further opening of the ring to allantoin,

which is then excreted. However, the pri-

mates, including humans, are not capable of

synthesizing allantoin. Uric acid is therefore

the form of the purines excreted in these

Nucleotide Metabolism

187

A. Degradation of nucleotides

Purine nucleotides

Pyrimidine nucleotides

GMP

AMP

UMP

CMP

dTMP

PRPP

P P

H₂O

NH₃

Uracil

Thymine

Free

Ade

IMP

Ura

Thy

bases

Adenine

Rib

PRPP

Dihydro-

HN C

Dihydro-

uracil

thymine

Gua

Guanine

(R = H)

(R = CH

Phospho-

H₂O

ribosyl

H₂O

diphos-

phate

PRPP

COO

NH₃

Rib P

H₂N

N-Carbamoyl

O₂

β-amino-

H₂O₂

β-alanine

isobutyrate

(R = H)

(R = CH

H₂O

COO

NH₃,

CO₂

Xanthine (Xan)

Hypoxanthine (Hyp)

O₂

CH₂

β-Amino-

H₂O

β-Alanine

isobutyrate

(R = H)

NH₃

(R = CH

H₂O₂

Excreted

by primates,

B. Hyperuricemia (gout)

birds, and

reptiles

Causes:

Disturbed uric

C O

acid excretion

Uric acid

GMP

AMP

Elevated uric acid

formation

Excreted

a) Unbalanced

by most

a) nutrition

mammals

b) Impaired

H₂N

Gua

Ade

IMP

b) recycling of

b) purine bases

Allantoin

Hypo-

Recycling

Xanthine

xanthine

reactions

2 Urea +

Allantoic acid

glyoxylate

Allopurinol

Hypoxanthine phosphoribosyl-

transferase 2.4.2.8

Uric

Adenine phosphoribosyl-

acid

transferase 2.4.2.7

Xanthine oxidase [Fe, Mo, FAD] 1.1.3.22

Allopurinol

188

Metabolism

(1b) and then converted into dihydroorotate

Purine and pyrimidine biosynthesis

by closure of the ring (1c). In mammals, steps

The bases occurring in nucleic acids are de-

1a to 1c take place in the cytoplasm, and are

rivatives of the aromatic heterocyclic com-

catalyzed by a single multifunctional enzyme.

pounds purine and pyrimidine (see p. 80).

In the next step (1d), dihydroorotate is oxi-

The biosynthesis of these molecules is com-

dized to orotate by an FMN-dependent dehy-

plex, but is vital for almost all cells. The syn-

drogenase. Orotate is then linked with phos-

thesis of the nucleobases is illustrated here

phoribosyl diphosphate (PRPP) to form the

schematically. Complete reaction schemes

nucleotide orotidine

5 -monophosphate

are given on pp. 417 and 418.

(OMP). Finally, decarboxylation yields uridine

5 -monophosphate (UMP).

Purine biosynthesis starts with PRPP (the

A. Components of nucleobases

names of the individual intermediates are

The pyrimidine ring is made up of three com-

given on p. 417). Formation of the ring starts

ponents: the nitrogen atom N-1 and carbons

with transfer of an amino group, from which

C-4 to C-6 are derived from aspartate, carbon

the later N-9 is derived (2a). Glycine and a

C-2 comes from HCO_3-, and the second nitro-

formyl group from N^10-formyl-THF then sup-

gen (N-3) is taken from the amide group of

ply the remaining atoms of the five-mem-

glutamine.

bered ring (2b, 2c). Before the five-membered

The synthesis of the purine ring is more

ring is closed (in step 2f), atoms N-3 and C-6

complex. The only major component is gly-

of the later six-membered ring are attached

cine, which donates C-4 and C-5, as well as N-

(2d, 2e). Synthesis of the ring then continues

7. All of the other atoms in the ring are in-

with N-1 and C-2 (2g, 2i). In the final step (2j),

corporated individually. C-6

comes from

the six-membered ring is closed, and inosine

HCO_3-. Amide groups from glutamine provide

5 -monophosphate arises. However, the IMP

the atoms N-3 and N-9. The amino group

formed does not accumulate, but is rapidly

donor for the inclusion of N-1 is aspartate,

converted into AMP and GMP. These reactions

which is converted into fumarate in the proc-

and the synthesis of the other nucleotides are

ess, in the same way as in the urea cycle (see

discussed on p. 190.

p. 182). Finally, the carbon atoms C-2 and C-8

are derived from formyl groups in N¹⁰-

Further information

formyl-tetrahydrofolate (see p. 108).

The regulation of bacterial aspartate

carbamoyltransferase by ATP and CTP has

B. Pyrimidine and purine synthesis

been particularly well studied, and is dis-

The major intermediates in the biosynthesis

cussed on p. 116. In animals, in contrast to

of nucleic acid components are the

prokaryotes, it is not ACTase but carbamoyl-

mononucleotides uridine monophosphate

phosphate synthase that is the key enzyme in

(UMP) in the pyrimidine series and inosine

pyrimidine synthesis. It is activated by ATP

monophosphate (IMP, base: hypoxanthine) in

and PRPP and inhibited by UTP.

the purines. The synthetic pathways for pyri-

The biosynthesis of the purines is also

midines and purines are fundamentally dif-

regulated by feedback inhibition. ADP and

ferent. For the pyrimidines, the pyrimidine

GDP inhibit the formation of PRRPP from ri-

ring is first constructed and then linked to

bose-5 -phosphate. Similarly, step 2a is in-

ribose 5 -phosphate to form a nucleotide. By

hibited by AMP and GMP.

contrast, synthesis of the purines starts di-

rectly from ribose 5 -phosphate. The ring is

then built up step by step on this carrier mol-

ecule.

The precursors for the synthesis of the

pyrimidine ring are carbamoyl phosphate,

which arises from glutamate and HCO_3- (1a)

and the amino acid aspartate. These two com-

ponents are linked to N-carbamoyl aspartate

Nucleotide Metabolism

189

A. Components of nucleobases

Glu

Fumarate

Glycine

HCO₃

NH₃

H₂C

COO

[NH₂]

Gln

Asp

THF

[CHO]

OHC

HCO₃

N10

OOC

THF

CHO

N10

[NH₂]

THF

H₃N H COO

Aspartate

Gln

Glu

Gln

Glu

Pyrimidine

Purine

B. Pyrimidine and purine synthesis

[NH

Carbamoyl

Phosphoribosyl

P P

phosphate

diphosphate

O P

HCO₃

N-Carbamoyl

Dihydro-

Orotate 5'-mono- Uridine 5'-mono-

aspartate

orotate

phosphate

phosphate (UMP)

Aspartate

UMP

1. Pyrimidines

CH₂

Phosphoribosyl

H H

diphosphate

P P

OH OH

CH₂

5'-Phosphoribosyl residue

Glycine

H H

OH OH

IMP

2e,

2g,

CH₂

H H

Inosine 5'-mono-

phosphate (IMP)

2. Purines

OH OH

190

Metabolism

side diphosphates. This reduction is a com-

Nucleotide biosynthesis

plex process in which several proteins are

De novo synthesis of purines and pyrimidines

involved. The reducing equivalents needed

yields the monophosphates IMP and UMP,

come from NADPH+H⁺. However, they are

respectively (see p. 188). All other nucleotides

not transferred directly from the coenzyme

and deoxynucleotides are synthesized from

to the substrate, but first pass through a redox

these two precursors. An overview of the

series that has several steps (1).

pathways involved is presented here; further

In the first step, thioredoxin reductase re-

details are given on p. 417. Nucleotide syn-

duces a small redox protein, thioredoxin, via

thesis by recycling of bases (the salvage path-

enzyme-bound FAD. This involves cleavage of

way) is discussed on p. 186.

a disulfide bond in thioredoxin. The resulting

SH groups in turn reduce a catalytically active

disulfide bond in nucleoside diphosphate

A. Nucleotide synthesis: overview

reductase

(“ribonucleotide reductase”). The

The synthesis of purine nucleotides (1) starts

free SH groups formed in this way are the

from IMP. The base it contains, hypoxanthine,

actual electron donors for the reduction of

is converted in two steps each into adenine or

ribonucleotide diphosphates.

guanine. The nucleoside monophosphates

In eukaryotes, ribonucleotide reductase is a

AMP and GMP that are formed are then phos-

tetramer consisting of two R1 and two R2

phorylated by nucleoside phosphate kinases to

subunits. In addition to the disulfide bond

yield the diphosphates ADP and GDP, and

mentioned, a tyrosine radical in the enzyme

these are finally phosphorylated into the

also participates in the reaction (2). It initially

triphosphates ATP and GTP. The nucleoside

produces a substrate radical (3). This cleaves a

triphosphates serve as components for RNA,

water molecule and thereby becomes radical

or function as coenzymes (see p. 106). Con-

cation. Finally, the deoxyribose residue is pro-

version of the ribonucleotides into deoxyribo-

duced by reduction, and the tyrosine radical is

nucleotides occurs at the level of the diphos-

regenerated.

phates and is catalyzed by nucleoside diphos-

The regulation of ribonucleotide reductase

phate reductase (B).

is complex. The substrate-specificity and ac-

The biosynthetic pathways for the pyrimi-

tivity of the enzyme are controlled by two

dine nucleotides (2) are more complicated.

allosteric binding sites (a and b) in the R1

The first product, UMP, is phosphorylated first

subunits. ATP and dATP increase or reduce

to the diphosphate and then to the

the activity of the reductase by binding at

triphosphate, UTP. CTP synthase then converts

site a. Other nucleotides interact with site b,

UTP into CTP. Since pyrimidine nucleotides

and thereby alter the enzyme’s specificity.

are also reduced to deoxyribonucleotides at

the diphosphate level, CTP first has to be hy-

drolyzed by a phosphatase to yield CDP before

dCDP and dCTP can be produced.

The DNA component deoxythymidine tri-

phosphate (dTTP) is synthesized from UDP in

several steps. The base thymine, which only

occurs in DNA (see p. 80), is formed by meth-

ylation of dUMP at the nucleoside monophos-

phate level. Thymidylate synthase and its

helper enzyme dihydrofolate reductase are

important target enzymes for cytostatic drugs

(see p. 402).

B. Ribonucleotide reduction

2 -Deoxyribose, a component of DNA, is not

synthesized as a free sugar, but arises at the

diphosphate level by reduction of ribonucleo-

Nucleotide Metabolism

191

A. Nucleotide synthesis: overview

1. Purine

Precursors

2. Pyrimidine

Precursors

1. nucleotides

2. nucleotides

De novo synthesis

AMP

IMP

GMP

UMP

dUMP

dTMP

dADP

ADP

GDP

dGDP

dCDP

CDP

UDP

dUDP

dTDP

dATP

ATP

GTP

dGTP

dCTP

CTP

UTP

dTTP

DNA

RNA

DNA

RNA

DNA

Ribonucleoside

CTP synthase 6.3.4.2

Nucleoside phosphate kinase 2.7.4.4

diphosphate

reductase 1.17.4.1

Thymidylate synthase 2.1.1.45

Nucleoside diphosphate kinase 2.7.4.6

B. Ribonucleotide reduction

NADPH

NADP

NTP

ATP

dATP

S S

Substrate

Thio-

(NDP)

redoxin

(oxidized)

(reduced)

Tyrosine

radical

2. Ribonucleotide reductase

CH₂

HS SH

S S

Base

OH OH

H2O

NDP

Radical

P P

Base

O Base

H H

NDP

HO OH

HO H

dNDP

H₂O

Nucleoside

Deoxyribonucleoside

diphosphate

CH₂

Base

Ribonucleoside diphosphate reductase 1.17.4.1

OH H

Thioredoxin reductase [FAD] 1.6.4.5

2e , H

dNDP

1. Overview

3. Reaction mechanism

192

Metabolism

chains have to be converted into less polar

Heme biosynthesis

groups.

Heme, an iron-containing tetrapyrrole pig-

[5] Initially, the four acetate residues (R₁)

ment, is a component of O₂-binding proteins

are decarboxylated into methyl groups. The

(see p. 106) and a coenzyme of various oxi-

resulting coproporphyrinogen III returns to

doreductases (see p. 32). Around 85% of heme

the mitochondria again. The subsequent steps

biosynthesis occurs in the bone marrow, and a

are catalyzed by enzymes located either on or

much smaller percentage is formed in the

inside the inner mitochondrial membrane.

liver. Both mitochondria and cytoplasm are

[6] An oxidase first converts two of the

involved in heme synthesis.

propionate groups (R₂) into vinyl residues.

The formation of protoporphyrinogen IX com-

pletes the modification of the side chains.

A. Biosynthesis of heme

[7] In the next step, another oxidation pro-

Synthesis of the tetrapyrrole ring starts in the

duces the conjugated π-electron system of

mitochondria.

protoporphyrin IX.

[1] Succinyl CoA (upper left), an intermedi-

[8] Finally, a divalent iron is incorporated

ate in the tricarboxylic acid cycle, undergoes

into the ring. This step also requires a specific

condensation with glycine and subsequent

enzyme, ferrochelatase. The heme b or Fe-pro-

decarboxylation to yield

5-aminolevulinate

toporphyrin IX formed in this way is found in

(ALA). The ALA synthase responsible for this

hemoglobin and myoglobin, for example (see

step is the key enzyme of the whole pathway.

p. 280), where it is noncovalently bound, and

Synthesis of ALA synthase is repressed and

also in various oxidoreductases (see p. 106).

existing enzyme is inhibited by heme, the

end product of the pathway. This is a typical

Further information

example of end-product or feedback inhibi-

tion.

There are a large number of hereditary or

[2] 5-Aminolevulinate now leaves the mi-

acquired disturbances of porphyrin synthesis,

tochondria. In the cytoplasm, two molecules

known as porphyrias, some of which can

condense to form porphobilinogen, a com-

cause severe clinical pictures. Several of these

pound that already contains the pyrrole ring.

diseases lead to the excretion of heme pre-

Porphobilinogen synthase is inhibited by lead

cursors in feces or urine, giving them a dark

ions. This is why acute lead poisoning is asso-

red color. Accumulation of porphyrins in the

ciated with increased concentrations of ALA

skin can also occur, and exposure to light then

in the blood and urine.

causes disfiguring, poorly healing blisters.

[3] The tetrapyrrole structure characteristic

Neurological disturbances are also common

of the porphyrins is produced in the next

in the porphyrias.

steps of the synthetic pathway. Hydroxyme-

It is possible that the medieval legends

thylbilane synthase catalyzes the linkage of

about human vampires (“Dracula”) originated

four porphobilinogen molecules and cleavage

in the behavior of porphyria sufferers (avoid-

of an NH₂ group to yield uroporphyrinogen III.

ance of light, behavioral disturbances, and

[4] Formation of this intermediate step re-

drinking of blood in order to obtain heme—

quires a second enzyme, uroporphyrinogen III

which markedly improves some forms of por-

synthase. If this enzyme is lacking, the

phyria).

“wrong” isomer, uroporphyrinogen I, is

formed.

The tetrapyrrole structure of uroporphyri-

nogen III is still very different from that of

heme. For example, the central iron atom is

missing, and the ring contains only eight of

the 11 double bonds. In addition, the ring

system only carries charged R side chains

(four acetate and four propionate residues).

As heme groups have to act in the apolar

interior of proteins, most of the polar side

Porphyrin Metabolism

193

A. Heme biosynthesis

Tricarboxylic

acid cycle

R₂

R₁

Succinyl

COO

R₁

R₂

CoA

CH₂

Heme

Fe²⁺

CH₂

R₁

C O

R₃

Vinyl

H₂C COO

Glycine

residue

NH₃

Fe²

COO

CH₂

Protoporphyrin IX

CH₃

CH₂

CO₂

6[H]

R₁

R₂

R₃

1COO

Protoporphyrinogen IX

COO

CH₂

5-Amino-

2 CO₂

Mitochondrion

levulinate

CH₂

(ALA)

CH₂

O₂

H₂C

CH₂

Cytoplasm

NH₃

Coproporphyrinogen III

COO

CH₂

CH₃

CH₂

4 CO₂

R₁

R₂

R₃

2 H₂O

COO

R₂

R₁

OOC CH₂

COO COO

R₁

R₂

CH₂

COO

CH₂

NH HN

Pyrrole

CH₂

ring

NH HN

H₂C

R₁

R₂

R₃

4 NH₄

H₂O

NH₃

R₃

Porphobilinogen

Uroporphyrinogen III

5-Aminolevulinate synthase

Porphobilinogen synthase

Hydroxymethylbilane synthase

[PLP] 2.3.1.37

4.2.1.24

4.3.1.8

Uroporphyrinogen-III synthase

4.2.1.75

194

Metabolism

Some of the bilirubin conjugates are bro-

Heme degradation

ken down further in the intestine by bacterial

b-glucuronidases. The bilirubin released is

A. Degradation of heme groups

then reduced further via intermediate steps

Heme is mainly found in the human organism

into colorless stercobilinogen, some of which

as a prosthetic group in erythrocyte hemoglo-

is oxidized again into orange to yellow-col-

bin. Around 100-200 million aged erythro-

ored stercobilin. The end products of bile pig-

cytes per hour are broken down in the human

ment metabolism in the intestine are mostly

organism. The degradation process starts in

excreted in feces, but a small proportion is

reticuloendothelial cells in the spleen, liver,

resorbed

(enterohepatic circulation; see

and bone marrow.

p. 314). When high levels of heme degrada-

[1] After the protein part (globin) has been

tion are taking place, stercobilinogen appears

removed, the tetrapyrrole ring of heme is

as urobilinogen in the urine, where oxidative

oxidatively cleaved between rings A and B

processes darken it to form urobilin.

by heme oxygenase. This reaction requires

In addition to hemoglobin, other heme pro-

molecular oxygen and NADPH+H⁺, and pro-

teins (myoglobin, cytochromes, catalases, and

duces green biliverdin, as well as CO (carbon

peroxidases; see p. 32) also supply heme

monoxide) and Fe²⁺, which remains available

groups that are degraded via the same path-

for further use (see p. 286).

way. However, these contribute only about

[2] In another redox reaction, biliverdin is

10-15% to a total of ca. 250 mg of bile pig-

reduced by biliverdin reductase to the orange-

ment formed per day.

colored bilirubin. The color change from pur-

ple to green to yellow can be easily observed

Further information

in vivo in a bruise or hematoma.

The color of heme and the other porphyrin

Hyperbilirubinemias. An elevated bilirubin

systems (see p. 106) results from their numer-

level (> 10 mg L^-1) is known as hyperbiliru-

ous conjugated double bonds. Heme contains

binemia. When this is present, bilirubin dif-

a cyclic conjugation (highlighted in pink) that

fuses from the blood into peripheral tissue

is removed by reaction

[1]. Reaction

[2]

and gives it a yellow color (jaundice). The

breaks the π system down into two smaller

easiest way of observing this is in the white

separate systems (highlighted in yellow).

conjunctiva of the eyes.

For further degradation, bilirubin is trans-

Jaundice can have various causes. If in-

ported to the liver via the blood. As bilirubin is

creased erythrocyte degradation (hemolysis)

poorly soluble, it is bound to albumin for

produces more bilirubin, it causes hemolytic

transport. Some drugs that also bind to albu-

jaundice. If bilirubin conjugation in the liver is

min can lead to an increase in free bilirubin.

impaired—e. g., due to hepatitis or liver cir-

[3] The hepatocytes take up bilirubin from

rhosis—it leads to hepatocellular jaundice,

the blood and conjugate it in the endoplasmic

which is associated with an increase in un-

reticulum with the help of UDP-glucuronic

conjugated (“indirect”) bilirubin in the blood.

acid into the more easily soluble bilirubin

By contrast, if there is a disturbance of bile

monoglucuronides and diglucuronides. To do

drainage (obstructive jaundice, due to gall-

this, UDP-glucuronosyltransferase forms ester-

stones or pancreatic tumors), then conjugated

type bonds between the OH group at C-1 of

(“direct”) bilirubin in the blood increases. Neo-

glucuronic acid and the carboxyl groups in

natal jaundice (physiologic jaundice) usually

bilirubin (see p. 316). The glucuronides are

resolves after a few days by itself. In severe

then excreted by active transport into the

cases, however, unconjugated bilirubin can

bile, where they form what are known as

cross the blood-brain barrier and lead to

the bile pigments.

brain damage (kernicterus).

Glucuronide synthesis is the rate-deter-

mining step in hepatic bilirubin metabolism.

Drugs such as phenobarbital, for example, can

induce both conjugate formation and the

transport process.

Porphyrin Metabolism

195

A. Degradation of heme groups

Heme

Cleavage by

R₂

CH₃

H₃C

R₃

Fe²

3 O₂

3 H₂O

Fe²

CH₃

Heme

Reused

for heme

synthesis

COO

Biliverdin

CH₂

OOC

CH₂

H₂C COO

CH₂

CH₃

CH₂

CH₃

O N

N O

H₂

Bilirubin

RES

Bilirubin

Urine

diglucuronide

P P

GlcUA

2 UDP

Slowest

Blood

step in

Albumin

hepatic

metabo-

lism

Gallbladder

Entero-

Albumin

hepatic

Bile

circulation

Bilirubin

pigments

Intestine

Binding

site for

bilirubin

Bilirubin

Bacterial

and drugs

diglucuronide

metabolism

2 GlcUA

Heme oxygenase

Stercobilinogen

Bilirubin

(decyclizing) 1.14.99.3

Urobilinogen

Biliverdin reductase

1.3.1.24

Stercobilin

Glucuronosyl

Urobilin

transferase 2.4.1.17

196

Organelles

B. Structure of an animal cell

Structure of cells

In the human body alone, there are at least

A. Comparison of prokaryotes and

200 different cell types. The illustration out-

eukaryotes

lines the basic structures of an animal cell in

an extremely simplified way. The details

Present-day living organisms can be divided

given regarding the proportion of the com-

into two large groups—the prokaryotes and

partments relative to cell volume (highlighted

eukaryotes. The prokaryotes are represented

in yellow) and their numbers per cell fre-

by bacteria (eubacteria and archaebacteria).

quency (blue) refer to mammalian hepato-

These are almost all small unicellular organ-

cytes (liver cells). The figures can vary widely

isms only a few microns (10^-6 m) in size. The

from cell type to cell type.

eukaryotes include fungi, plants, and animals

The eukaryotic cell is subdivided by mem-

and comprise both unicellular and multicel-

branes. On the outside, it is enclosed by a

lular organisms. Multicellular eukaryotes are

plasma membrane. Inside the cell, there is a

made up of a wide variety of cell types that are

large space containing numerous components

specialized for different tasks. Eukaryotic cells

in solution—the cytoplasm. Additional mem-

are much larger than prokaryotic ones (vol-

branes divide the internal space into

ume ratio approximately 2000 : 1). The most

compartments

(confined reaction spaces).

important distinguishing feature of these cells

Welldefined compartments of this type are

in comparison with the prokaryotes is the fact

known as organelles.

that they have a nucleus

(karyon in

The largest organelle is the nucleus (see

Greek—hence the term).

p. 208). It is easily recognized using the light

In comparison with the prokaryotes, eu-

microscope. The endoplasmic reticulum (ER),

karyotic cells have greater specialization and

a closed network of shallow sacs and tubules

complexity in their structure and functioning.

(see pp. 226ff.), is linked with the outer mem-

Eukaryotic cells are structured into compart-

brane of the nucleus. Another membrane-

ments (see below). The metabolism and syn-

bound organelle is the Golgi apparatus (see

thesis of macromolecules are distributed

p. 228), which resembles a bundle of layered

through these reaction spaces and are sepa-

slices. The endosomes and exosomes are bub-

rately regulated. In prokaryotes, these func-

ble-shaped compartments ( vesicles) that are

tions are organized in a simpler fashion and

involved in the exchange of substances be-

are spatially closely related.

tween the cell and its surroundings. Probably

Although the storage and transfer of ge-

the most important organelles in the cell’s

netic information function according to the

metabolism are the mitochondria, which are

same principle in the prokaryotes and euka-

around the same size as bacteria

(see

ryotes, there are also differences. Eukaryotic

pp. 210ff.). The lysosomes and peroxisomes

DNA consists of very long, linear molecules

are small, globular organelles that carry out

with a total of 10⁷ to more than 10¹⁰ base pairs

specific tasks. The whole cell is traversed by a

(bp), only a small fraction of which are used

framework of proteins known as the cytoske-

for genetic information. In eukaryotes, the

leton (see pp. 204ff.).

genes (20 000-50 000 per genome) are usu-

In addition to these organelles, plant cells

ally interrupted by non-coding regions (in-

(see p. 43) also have plastids—eg., chloro-

trons). Eukaryotic DNA is located in the nu-

plasts, in which photosynthesis takes place

cleus, where together with histones and other

(see p. 128). In their interior, there is a large,

proteins it forms the chromatin (see p. 238).

fluid-filled vacuole. Like bacteria and fungi,

In prokaryotes, by contrast, DNA is ring-

plant cells have a rigid cell wall consisting of

shaped, much shorter (up to 5

10⁶ bp), and

polysaccharides and proteins.

located in the cytoplasm. Almost all of it is

used for information storage, and it does not

contain any introns.

Basics

197

A. Comparison of prokaryotes and eukaryotes

Prokaryotes

Eukaryotes

Organisms

Eubacteria

Fungi

1-10 µm

Archaebacteria

Plants

Animals

Form

Single-celled

Single or multi-cellular

Organelles, cytoskeleton, cell division apparatus

10-100 µm

Missing

Present, complicated, specialized

Small, circular, no

DNA

introns, plasmids

Large, in nucleus, many introns

RNA: Synthesis and maturation

Simple, in cytoplasm

Complicated, in nucleus

Protein: Synthesis and maturation

Simple, coupled with

Complicated, in the cytoplasm

RNA synthesis

and the rough endoplasmic reticulum

Metabolism

Anaerobic or aerobic

very flexible

Mostly aerobic, compartmented

Endocytosis

and Exocytosis

yes

B. Structure of an animal cell

Golgi complex

Plasma

membrane

Nucleus

Lysosome

300

Rough

endoplasmic

Endosome

reticulum

200

Free

Mitochondrion

ribosomes

22%

~2000

Peroxisome

Cytoplasm

400

54%

Number per cell

Proportion of

10-30 µm

cell volume

198

Organelles

Particles that are smaller and less dense

Cell fractionation

than the nuclei can be obtained by step-by-

step acceleration of the gravity on the super-

A. Isolation of cell organelles

natant left over from the first centrifugation.

To investigate the individual compartments of

However, this requires very powerful centri-

the cell (see p. 196), various procedures have

fuges (high-speed centrifuges and ultracentri-

been developed to enrich and isolate cell or-

fuges). The sequence in which the fractions

ganelles. These are mainly based on the size

are obtained is: mitochondria, membrane

and density of the various organelles.

vesicles, and ribosomes. Finally, the superna-

The isolation of cell components starts

tant from the last centrifugation contains the

with disruption of the tissue being examined

cytosol with the cell’s soluble components, in

and subsequent homogenization of it (break-

addition to the buffer.

ing down the cells) in a suitable buffer (see

The isolation steps are carried out at low

below). Homogenization using the “Potter”

temperatures on principle (usually 0-5 °C), to

(the Potter-Elvehjem homogenizer, a rotating

slow down degradation reactions—e. g., due

Teflon pestle in a glass cylinder) is particularly

to released enzymes and other influencing

suitable for animal tissue. This method is very

factors. The addition of thiols and chelating

gentle and is therefore used to isolate fragile

agents protects functional SH groups from

structures and molecules. Other cell disrup-

oxidation. Isolated cell organelles quickly

tion procedures include enzymatic lysis with

lose their biological activity despite these pre-

the help of enzymes that break down the cell

cautions. Nevertheless, it is possible by work-

wall, mechanical disruption by grinding fro-

ing carefully to isolate mitochondria that will

zen tissue, cutting or smashing with rotating

still take up substrates for a few hours in the

knives, large pressure changes, osmotic

test tube and produce ATP via oxidative phos-

shock, and repeated freezing and thawing.

phorylation.

To isolate intact organelles, it is important

for the homogenization solution to be iso-

B. Marker molecules

tonic—i. e., the osmotic value of the buffer

has to be the same as that of the interior of

During cell fractionation, it is very important

the cell. If hypotonic solutions were used, the

to analyze the purity of the fractions obtained.

organelles would take up water and burst,

Whether or not the intended organelle is

while in hypertonic solutions they would

present in a particular fraction, and whether

shrink.

or not the fraction contains other compo-

Homogenization is followed by coarse fil-

nents, can be determined by analyzing

tration through gauze to remove intact cells

characteristic marker molecules. These are

and connective-tissue fragments. The actual

molecules that occur exclusively or predom-

fractionation of cellular components is then

inantly in one type of organelle. For example,

carried out by centrifugation steps, in which

the activity of organelle-specific enzymes

the gravitational force (given as multiples of

(marker enzymes) is often assessed. The dis-

the earth’s gravity, g

= 9.81 m s^-2) is gradu-

tribution of marker enzymes in the cell re-

ally increased (differential centrifugation; see

flects the compartmentation of the processes

p. 200). Due to the different shapes and den-

they catalyze. These reactions are discussed in

sities of the organelles, this leads to succes-

greater detail here under the specific organ-

sive sedimentation of each type out of the

elles.

suspension.

Nuclei already sediment at low accelera-

tions that can be achieved with bench-top

centrifuges. Decanting the residue

(the

“supernatant”) and carefully suspending the

sediment (or “pellet”) in an isotonic medium

yields a fraction that is enriched with nuclei.

However, this fraction may still contain other

cellular components as contaminants—e. g.,

fragments of the cytoskeleton.

Basics

199

A. Isolation of cell organelles

Homo-

Filter

genize

Gauze

Slice

Whole

Tissue

cells,

connective

tissue

Potter

homo-

Buffer

genizer

Centrifuge

g = 300 000

g = 100 000

g = 15 000

g = 600

120'

60'

15'

10'

Cytosol

Super-

natant

Centrifuge

tube

Pellet

Ribosomes

Plasma membrane

Mitochondria

Nucleus

Viruses

ER fragments

Lysosomes

Cytoskeleton

Macromolecules

Small vesicles

Peroxisomes

Microsomal

(Plants:

fraction

chloroplasts)

B. Marker molecules

Golgi complex

Nucleus

Ribosomes

Plasma membrane

α-Mannosidase II

DNA

rRNA

Na+/K+ ATPase

3.2.1.24

3.6.1.37

Phosphodiesterase I

3.1.4.1

Endoplasmic

reticulum

Lysosome

β-N-Acetylhexos-

Glucose 6-phospha-

tase 3.1.3.9

aminidase 3.2.1.52

RNA

β-Galactosidase

3.2.1.23

Mitochondrion

Succinate dehydro-

Endosome

genase 1.3.5.1

Uptake of

Cytochrome-c

peroxidase

oxidase

1.11.1.7

1.9.3.1

Cytosol

Peroxisome

L-Lactate

Catalase

dehydrogenase

1.11.1.6

1.1.1.27

Cell fraction

Marker enzyme

200

Organelles

B. Density gradient centrifugation

Centrifugation

Density gradient centrifugation is used to

A. Principles of centrifugation

separate macromolecules that differ only

slightly in size or density. Two techniques

In a solution, particles whose density is higher

are commonly used.

than that of the solvent sink (sediment), and

In zonal centrifugation, the sample being

particles that are lighter than it float to the

separated (e. g., a cell extract or cells) is placed

top. The greater the difference in density, the

on top of the centrifugation solution as a thin

faster they move. If there is no difference in

layer. During centrifugation, the particles

density (isopyknic conditions), the particles

move through the solution due to their

hover. To take advantage of even tiny differ-

greater density. The rate of movement basi-

ences in density to separate various particles

cally depends on their molecular mass (see A,

in a solution, gravity can be replaced with the

formulae). Centrifugation stops before the

much more powerful “centrifugal force” pro-

particles reach the bottom of the tube. Dril-

vided by a centrifuge.

ling a hole into the centrifugation tube and

Equipment. The acceleration achieved by

allowing the contents to drip out makes it

centrifugation is expressed as a multiple

possible to collect the different particles in

of the earth’s gravitational force

separate fractions. During centrifugation, the

9.81 m s^-2). Bench-top centrifuges can reach

solution tube is stabilized in the tube by a

acceleration values of up to 15 000 g, while

density gradient. This consists of solutions of

highspeed refrigerated centrifuges can reach

carbohydrates or colloidal silica gel, the con-

50000 g and ultracentrifuges, which operate

centration of which increases from the sur-

with refrigeration and in a vacuum, can reach

face of the tube to the bottom. Density gra-

500000 g. Two types of rotor are available in

dients prevent the formation of convection

high-powered centrifuges: fixed angle rotors

currents, which would impair the separation

and swingout rotors that have movable bucket

of the particles.

containers. The tubes or buckets used for cen-

Isopyknic centrifugation, which takes

trifugation are made of plastic and have to be

much longer, starts with a CsCl solution in

very precisely adjusted to avoid any imbalan-

which the sample material (e. g., DNA, RNA,

ces that could lead to accidents.

or viruses) is homogeneously distributed. A

Theory. The velocity (v) of particle sedi-

density gradient only forms during centrifu-

mentation during centrifugation depends on

gation, as a result of sedimentation and dif-

the angular velocity ω of the rotor, its effective

fusion processes. Each particle moves to the

radius (r_eff, the distance from the axis of rota-

region corresponding to its own buoyant den-

tion), and the particle’s sedimentation prop-

sity. Centrifugation stops once equilibrium

erties. These properties are expressed as the

has been reached. The samples are obtained

sedimentation coef•cient S

(1 Svedberg,

by fractionation, and their concentration is

= 10^-13 s). The sedimentation coef cient de-

measured using the appropriate methods.

pends on the mass M of the particle, its shape

(expressed as the coef cient of friction, f), and

its density

(expressed as the reciprocal

density v_, “partial specific volume”).

At the top right, the diagram shows the

densities and sedimentation coef cients for

biomolecules, cell organelles, and viruses.

Proteins and protein-rich structures have

densities of around 1.3 g cm^-3, while nucleic

acids show densities of up to 2 g cm^-3. Equi-

librium sedimentation of nucleic acids there-

fore requires high-density media—e. g., con-

centrated solutions of cesium chloride (CsCl).

To allow comparison of S values measured in

different media, they are usually corrected to

values for water at 20 °C (“S_20W” ).

Basics

201

A. Principles of centrifugation

Centrifuge

bucket

Mitochondria

1.2

Microsomes

Soluble

Nuclei

1.4

proteins

Viruses

reff

Fixed angle rotor

1.6

Glycogen

DNA

Swing-out

centrifuge

bucket

Ribosomes, Polysomes

1.8

RNA

2.0

Axis of rotation

10²

10³

10⁴

10⁵

10⁶

10⁷

Swing-out bucket rotor

Sedimentation coefficient

(Svedberg, S)

Gravitational acceleration

g = ω2 · r_eff

Sedimentation coefficient

(S = 10^-13 s)

Sedimentation velocity

Molecular mass

(cm · s^-1)

v = ω2 · reff · s

v :

Partial specific particle volume

(cm³ · g^-1)

ω:

Angular velocity

r :

Density of the solution

(rad · s^-1)

M · (1 - v · r)

(g · cm³)

s =

r_eff:

Effective radius (cm)

f :

Coefficient of friction

B. Density gradient centrifugation

Particles migrate

Particles distributed

Probe

according to S-value

according to density

Centrifugation

Sucrose

CsCl

density

gradient

After t =

0.5

2 h

8 h

Zonal centrifugation

Isopyknic centrifugation

Sucrose or

CsCl gradient

Fraction

Fractionation

Detection

202

Organelles

tors,

30 aminoacyl-tRNA synthases, 340

Cell components and cytoplasm

tRNA molecules, 2-3 mRNAs (each of which

is 10 times the length of the section shown),

The Gram-negative bacterium Escherichia coli

and six molecules of RNA polymerase.

(E. coli) is a usually harmless symbiont in the

• About 330 other enzyme molecules, includ-

intestine of mammals. The structure and char-

ing 130 glycolytic enzymes and 100 en-

acteristics of this organism have been partic-

zymes from the tricarboxylic acid cycle.

ularly well characterized. E. coli is also fre-

• 30 000

small organic molecules with

quently used in genetic engineering

(see

masses of 100-1000 Da—e. g., metabolites

p. 258).

of the intermediary metabolism and coen-

zymes. These are shown at a magnification

10 times higher in the bottom right corner.

A. Components of a bacterial cell

• And finally, 50 000 inorganic ions. The rest

consists of water.

A single E. coli cell has a volume of about

0.88 µm³. One-sixth of this consists of mem-

The illustration shows that the cytoplasm of

branes and one-sixth is DNA (known as the

cells is a compartment densely packed with

“nucleoid”). The rest of the internal space of

macromolecules and smaller organic mole-

the cell is known as cytoplasm (not “cytosol”;

cules. The distances between organic mole-

see p. 198).

cules are small. They are only separated by a

The main component of E. coli—as in all

few water molecules.

cells—is water (70%). The other components

All of the molecules are in motion. Due to

are macromolecules (proteins, nucleic acids,

constant collisions, however, they do not ad-

polysaccharides), small organic molecules,

vance in a straight path but move in zigzags.

and inorganic ions. The majority of the macro-

Due to their large mass, proteins are particu-

molecules are proteins, which represent ca.

larly slow. However, they do cover an average

55% of the dry mass of the cell. When a num-

of 5 nm in 1 ms—a distance approximately

ber of assumptions are made about the dis-

equal to their own length. Statistically, a pro-

tribution and size (average mass 40 kDa) of

tein is capable of reaching any point in a

proteins, it can be estimated that there are

bacterial cell in less than a second.

approximately 250 000 protein molecules in

the cytoplasm of an E. coli cell. In eukaryotic

C. Biochemical functions of the cytoplasm

cells, which are about a thousand times larger,

it is estimated that the number of protein

In eukaryotes, the cytoplasm, representing

molecules is in the order of several billion.

slightly more than 50% of the cell volume, is

the most important cellular compartment. It

is the central reaction space of the cell. This is

B. Looking inside a bacterial cell

where many important pathways of the inter-

The illustration shows a schematic view in-

mediary metabolism take place—e. g., glycol-

side the cytoplasm of E. coli, magnified ap-

ysis, the pentose phosphate pathway, the ma-

proximately one million times. At this magni-

jority of gluconeogenesis, and fatty acid syn-

fication, a single carbon atom would be the

thesis. Protein biosynthesis (translation; see

size of a grain of salt, and an ATP molecule

p. 250) also takes place in the cytoplasm. By

would be as large as a grain of rice. The detail

contrast, fatty acid degradation, the tricarbox-

shown is

100 nm long, corresponding to

ylic acid cycle, and oxidative phosphorylation

about 1/600th of the volume of a cell in E.

are located in the mitochondria (see p. 210).

coli. To make the macromolecules clearer,

small molecules such as water, cofactors,

and metabolites have all been omitted from

the illustration. The section of the cytoplasm

shown contains:

• Several hundred macromolecules, which

are needed for protein biosynthesis—i. e.,

30 ribosomes, more than 100 protein fac-

204

Organelles

to other cell components (villin, D-actinin,

Cytoskeleton: components

spectrin), or disrupt the helical structure of F

The cytoplasm of eukaryotic cells is traversed

actin (gelsolin). The activity of these proteins

by three-dimensional scaffolding structures

is regulated by protein kinases via Ca²⁺ and

consisting of filaments (long protein fibers),

other second messengers (see p. 386).

which together form the cytoskeleton. These

filaments are divided into three groups, based

B. Intermediate filaments

on their diameters: microfilaments (6-8 nm),

intermediate filaments (ca. 10 nm), and mi-

The components of the intermediate fila-

crotubules (ca. 25 nm). All of these filaments

ments belong to five related protein families.

are polymers assembled from protein compo-

They are specific for particular cell types. Typ-

nents.

ical representatives include the cytokeratins,

desmin, vimentin, glial fibrillary acidic protein

(GFAP), and neurofilament. These proteins all

A. Actin

have a rod-shaped basic structure in the cen-

Actin, the most abundant protein in eukary-

ter, which is known as a superhelix (“coiled

otic cells, is the protein component of the

coil”; see keratin, p. 70). The dimers are ar-

microfilaments (actin filaments). Actin occurs

ranged in an antiparallel fashion to form tet-

in two forms—a monomolecular form (G actin,

ramers. A staggered head-to-head arrange-

globular actin) and a polymer (F actin, fila-

ment produces protofilaments. Eight protofi-

mentous actin). G actin is an asymmetrical

laments ultimately form an intermediary fil-

molecule with a mass of 42 kDa, consisting

ament.

of two domains. As the ionic strength in-

Free protein monomers of intermediate fil-

creases, G actin aggregates reversibly to

aments rarely occur in the cytoplasm, in con-

form F actin, a helical homopolymer. G actin

trast to microfilaments and microtubules.

carries a firmly bound ATP molecule that is

Their polymerization leads to stable polymers

slowly hydrolyzed in F actin to form ADP.

that have no polarity.

Actin therefore also has enzyme properties

(ATPase activity).

C. Tubulins

As individual G actin molecules are always

oriented in the same direction relative to one

The basic components of the tube-shaped mi-

another, F actin consequently has polarity. It

crotubules are α- and β-tubulin (53

and

has two different ends, at which polymeriza-

55 kDa). These form α,β-heterodimers, which

tion takes place at different rates. If the ends

in turn polymerize to form linear protofila-

are not stabilized by special proteins (as in

ments. Thirteen protofilaments form a ring-

muscle cells), then at a critical concentration

shaped complex, which then grows into a

of G actin the (+) end of F actin will constantly

long tube as a result of further polymeriza-

grow, while the (-) end simultaneously de-

tion.

cays. These partial processes can be blocked

Like microfilaments, microtubules are dy-

by fungal toxins experimentally. Phalloidin, a

namic structures with (+) and (-) ends. The

toxin contained in the Amanita phalloides

(-) end is usually stabilized by bonding to the

mushroom, inhibits decay by binding to the

centrosome. The

(+) end shows dynamic

(-) end. By contrast, cytochalasins, mold tox-

instability. It can either grow slowly or

ins with cytostatic effects, block polymeriza-

shorten rapidly. GTP, which is bound by the

tion by binding to the (+) end.

microtubules and gradually hydrolyzed into

Actin-associated proteins. The cytoplasm

GDP, plays a role in this. Various proteins can

contains more than

50 different proteins

also be associated with microtubules.

that bind specifically to G actin and F actin.

Their actin uptake has various different func-

tions. This type of bonding can serve to regu-

late the G actin pool (example: profilin), influ-

ence the polymerization rate of G actin (vil-

lin), stabilize the chain ends of F actin (fragin,

b-actinin), attach filaments to one another or

Cytoskeleton

205

A. Actin

Associates

Dissociates

more easily

ATP

ADP

Polymerization

P_i

Depolymerization

F-actin

ATP

ADP

helical polymer

G-Actin

Slow

P_i

monomers

microfilament (detail)

hydrolysis

42 kDa

Phalloidin

Cytochalasin

(-) End:

dissociation

(+) End:

polymerization

favored

B. Intermediate filaments

IF Proteins:

Cytokeratins

Dimer

Desmin

Vimentin

Glial fibrillary

Superhelical structure

acidic protein

Neurofilaments

Lamins

Tetramer

Protofilament

Intermediate

filament

C. Tubulins

binds GTP and

25 nm

slowly hydrolyzes it

αβ

Protofilament

Tubulin

Microtubule

53 and 55 kDa

(cylindrical polymer)

heterodimer

Plant

alkaloids:

Vinblastine,

vincristine,

colchicine

Taxol

(-) End: stabilized by binding

(+) End: grows

to the centromere

or shortens

206

Organelles

B. Microtubules

Structure and functions

Only the cell’s microtubules are shown here.

The cytoskeleton carries out three major

They radiate out in all directions from a center

tasks:

near the nucleus, the centrosome. The tube-

• It represents the cell’s mechanical scaffold-

shaped microtubules are constantly being

ing, which gives it its typical shape and

synthesized and broken down at their (+)

connects membranes and organelles to

ends. In the centriole, the (-) end is blocked

each other. This scaffolding has dynamic

by associated proteins (see p. 204). The (+)

properties; it is constantly being synthe-

end can also be stabilized by associated pro-

sized and broken down to meet the cell’s

teins—e. g., when the microtubules have

requirements and changing conditions.

reached the cytoplasmic membrane.

• It acts as the motor for movement of animal

The microtubules are involved in defining

cells. Not only muscle cells (see p. 332), but

the shape of the cell and also serve as guiding

also cells of noncontractile tissues contain

tracks for the transport of organelles. To-

many different motor proteins, which they

gether with associated proteins (dynein, kine-

use to achieve coordinated and directed

sin), microtubules are able to carry out me-

movement. Cell movement, shape changes

chanical work—e. g., during the transport of

during growth, cytoplasmic streaming, and

mitochondria, the movement of cilia (hair-

cell division are all made possible by com-

like cell protrusions in the lungs, intestinal

ponents of the cytoskeleton.

epithelium, and oviduct) and the beating of

• It serves as a transport track within the cell.

the flagella of sperm. Microtubules also play a

Organelles and other large protein com-

special role in the mitotic period of cell divi-

plexes can move along the filaments with

sion (see p. 394).

the help of the motor proteins.

C. Architecture

A. Microfilaments and intermediate

The complex structure and net-like density of

filaments

the cytoskeleton is illustrated here using

The illustration schematically shows a detail

three examples in which the cytoskeletal

of the microvilli of an intestinal epithelial cell

components are visualized with the help of

as an example of the structure and function of

antibodies.

the components of the cytoskeleton (see also

1. The border of an intestinal epithelial cell

C1).

is seen here (see also B). There are micro-

Microfilaments of F actin traverse the mi-

filaments (a) passing from the interior of the

crovilli in ordered bundles. The microfila-

cell out into the microvilli. The filaments are

ments are attached to each other by actin-as-

firmly held together by spectrin (b), an asso-

sociated proteins, particularly fimbrin and vil-

ciated protein, and they are anchored to in-

lin. Calmodulin and a myosin-like ATPase con-

termediate filaments (c).

nect the microfilaments laterally to the

2. Only microtubules are seen in this fibro-

plasma membrane. Fodrin, another microfila-

blast cell. They originate from the microtubule

ment-associated protein, anchors the actin

organizing center (centrosome) and radiate

fibers to each other at the base, as well as

out as far as the plasma membrane.

attaching them to the cytoplasmic membrane

3. Keratin filaments are visible here in an

and to a network of intermediate filaments. In

epithelial cell. Keratin fibers belong to the

this example, the microfilaments have a

group of intermediate filaments (see pp. 70,

mainly static function. In other cases, actin is

204; d = nucleus).

also involved in dynamic processes. These in-

clude muscle contraction (see p. 332), cell

movement, phagocytosis by immune cells,

the formation of microspikes and lamellipo-

dia (cellular extensions), and the acrosomal

process during the fusion of sperm with the

egg cell.

208

Organelles

proteins can enter the nucleus without dif -

Nucleus

culty. By contrast, larger proteins

(over

40 kDa) can only pass through the nuclear

A. Nucleus

pores if they carry a nuclear localization se-

The nucleus is the largest organelle in the eu-

quence consisting of four successive basic

karyotic cell. With a diameter of about 10 µm,

amino acids inside their peptide chains (see

it is easily recognizable with the light micro-

p. 228). mRNAs and rRNAs formed in the nu-

scope. This is the location for storage, replica-

cleus cross the pores into the cytoplasm as

tion, and expression of genetic information.

complexes with proteins (see below).

The nucleus is separated from the cyto-

plasm by the nuclear envelope, which consists

C. Relationships between the nucleus and

of the outer and inner nuclear membranes.

cytoplasm

Each of the two nuclear membranes has two

layers, and the membranes are separated

Almost all of the RNA in the cell is synthesized

from each other by the perinuclear space.

in the nucleus. In this process, known as

The outer nuclear membrane is continuous

transcription, the information stored in DNA

with the rough endoplasmic reticulum and

is transcribed into RNA (see p. 242). As men-

is covered with ribosomes. The inner side of

tioned above, ribosomal RNA (rRNA) is mainly

the membrane is covered with a protein layer

produced in the nucleolus, while messenger

(the nuclear lamina), in which the nuclear

and transfer RNA

(mRNA and tRNA) are

structures are anchored.

formed in the region of the euchromatin. En-

The nucleus contains almost all of the cell’s

zymatic duplication of DNA—replication—also

DNA (around 1 % of which is mitochondrial

only takes place in the nucleus (see p. 240).

DNA). Together with histones and structural

The nucleotide components required for

proteins, the nuclear DNA forms the chroma-

transcription and replication have to be im-

tin (see p. 238). It is only during cell division

ported into the nucleus from the cytoplasm.

that chromatin condenses into chromosomes,

Incorporation of these components into RNA

which are also visible with the light micro-

leads to primary products, which are then

scope. During this phase, the nuclear mem-

altered by cleavage, excision of introns, and

brane temporarily disintegrates.

the addition of extra nucleotides (RNA matu-

During the phase between cell divisions,

ration; see p. 242). It is only once these pro-

the interphase, it is possible to distinguish

cess have been completed that the RNA mol-

between the more densely packed hetero-

ecules formed in the nucleus can be exported

chromatin and loose euchromatin using an

into the cytoplasm for protein synthesis

electron microscope. Active transcription of

(translation; see p. 250).

DNA into mRNA takes place in the region of

The nucleus is not capable of synthesizing

the euchromatin. A particularly electron-

proteins. All of the nuclear proteins therefore

dense region is noticeable in many

have to be imported—the histones with which

nuclei—the nucleolus

(several nucleoli are

DNA is associated in chromatin, and also the

sometimes present). The DNA in the nucleolus

so-called non-histone proteins

(DNA poly-

contains numerous copies of the genes for

merases and RNA polymerases, auxiliary and

rRNAs (see p. 242). They are constantly under-

structural proteins, transcription factors, and

going transcription, leading to a high local

ribosomal proteins). Ribosomal RNA (rRNA)

concentration of RNA.

already associates with proteins in the nucle-

olus to form ribosome precursors.

A special metabolic task carried out by the

B. Nuclear pores

nucleus is biosynthesis of NAD⁺. The immedi-

The exchange of substances between the nu-

ate precursor of this coenzyme, nicotinamide

cleus and the cytoplasm is mediated by pore

mononucleotide (NMN⁺), arises in the cyto-

complexes with complicated structures,

plasm and is then transported into the nucle-

which traverse the nuclear membrane. The

olus, where it is enzymatically converted into

nuclear pores consist of numerous proteins

the dinucleotide NAD⁺. Finally, NAD⁺ then re-

that form several connected rings of varying

turns to the cytoplasm.

diameter. Low-molecular structures and small

210

Organelles

Both mitochondrial membranes are very

Structure and functions

rich in proteins. Porins (see p. 214) in the

outer membrane allow small molecules

A. Mitochondrial structure

(< 10 kDa) to be exchanged between the cy-

Mitochondria are bacteria-sized organelles

toplasm and the intermembrane space. By

(about 1 × 2 µm in size), which are found in

contrast, the inner mitochondrial membrane

large numbers in almost all eukaryotic cells.

is completely impermeable even to small

Typically, there are about 2000 mitochondria

molecules (with the exception of O₂, CO₂,

per cell, representing around 25% of the cell

and H₂O). Numerous transporters in the inner

volume. Mitochondria are enclosed by two

membrane ensure the import and export of

membranes—a smooth outer membrane and

important metabolites (see p. 212). The inner

a markedly folded or tubular inner mitochon-

membrane also transports respiratory chain

drial membrane, which has a large surface

complexes, ATP synthase, and other enzymes.

and encloses the matrix space. The folds of

The matrix is also rich in enzymes (see B).

the inner membrane are known as cristae,

and tube-like protrusions are called tubules.

B. Metabolic functions

The intermembrane space is located between

the inner and the outer membranes.

Mitochondria are also described as being the

The number and shape of the mitochon-

cell’s biochemical powerhouse, since—through

dria, as well as the numbers of cristae they

oxidative phosphorylation (see p. 112)—they

have, can differ widely from cell type to cell

produce the majority of cellular ATP. Pyruvate

type. Tissues with intensive oxidative meta-

dehydrogenase (PDH), the tricarboxylic acid

bolism—e. g., heart muscle—have mitochon-

cycle, β-oxidation of fatty acids, and parts of

dria with particularly large numbers of cris-

the urea cycle are located in the matrix. The

tae. Even within one type of tissue, the shape

respiratory chain, ATP synthesis, and enzymes

of the mitochondria can vary depending on

involved in heme biosynthesis (see p. 192) are

their functional status. Mitochondria are mo-

associated with the inner membrane.

bile, plastic organelles.

The inner membrane itself plays an impor-

Mitochondria probably developed during

tant part in oxidative phosphorylation. As it is

an early phase of evolution from aerobic bac-

impermeable to protons, the respiratory

teria that entered into symbiosis with pri-

chain—which pumps protons from the matrix

meval anaerobic eukaryotes. This endosym-

into the intermembrane space via complexes

biont theory is supported by many findings.

I, III, and IV—establishes a proton gradient

For example, mitochondria have a ring-

across the inner membrane, in which the

shaped DNA (four molecules per mitochon-

chemical energy released during NADH oxi-

drion) and have their own ribosomes. The

dation is conserved (see p. 126). ATP synthase

mitochondrial genome became smaller and

then uses the energy stored in the gradient to

smaller during the course of evolution. In hu-

form ATP from ADP and inorganic phosphate.

mans, it still contains

16 569 base pairs,

Several of the transport systems are also de-

which code for two rRNAs, 22 tRNAs, and 13

pendent on the H⁺ gradient.

proteins. Only these 13 proteins (mostly sub-

In addition to the endoplasmic reticulum,

units of respiratory chain complexes) are pro-

the mitochondria also function as an

duced in the mitochondrion. All of the other

intracellular calcium reservoir. The mitochon-

mitochondrial proteins are coded by the nu-

dria also play an important role in

“pro-

clear genome and have to be imported into

grammed cell death”—apoptosis (see p. 396).

the mitochondria after translation in the cy-

toplasm (see p. 228). The mitochondrial en-

velope consisting of two membranes also

supports the endosymbiont theory. The inner

membrane, derived from the former sym-

biont, has a structure reminiscent of proka-

ryotes. It contains the unusual lipid cardioli-

pin (see p. 50), but hardly any cholesterol (see

p. 216).

212

Organelles

B. Malate and glycerophosphate shuttles

Transport systems

Two systems known as “shuttles” are avail-

Mitochondria are surrounded by an inner and

able to allow the import of reducing equiva-

an outer membrane (see p. 210). The outer

lents that arise from glycolysis in the cyto-

membrane contains porins, which allow

plasm in the form of NADH+H⁺. There is no

smaller molecules up to 10 kDa in size to

transporter in the inner membrane for

pass. By contrast, the inner membrane is also

NADH+H⁺ itself.

impermeable to small molecules (with the

In the malate shuttle (left)—which operates

exception of water and the gases O₂, CO₂,

in the heart, liver, and kidneys, for exam-

and NH₃). All of the other substrates of mito-

ple—oxaloacetic acid is reduced to malate by

chondrial metabolism, as well as its products,

malate dehydrogenase (MDH, [2a]) with the

therefore have to be moved through the inner

help of NADH+H⁺. In antiport for 2-oxogluta-

membrane with the help of special transport-

rate, malate is transferred to the matrix,

ers.

where the mitochondrial isoenzyme for

MDH [2b] regenerates oxaloacetic acid and

A. Transport systems

NADH+H⁺. The latter is reoxidized by complex

I of the respiratory chain, while oxaloacetic

The transport systems of the inner mitochon-

acid, for which a transporter is not available in

drial membrane use various mechanisms.

the inner membrane, is first transaminated to

Metabolites or ions can be transported alone

aspartate by aspartate aminotransferase (AST,

(uniport, U), together with a second substance

[3a]). Aspartate leaves the matrix again, and

(symport, S), or in exchange for another mol-

in the cytoplasm once again supplies oxalo-

ecule

(antiport, A). Active transport—i. e.,

acetate for step [2a] and glutamate for return

transport coupled to ATP hydrolysis—does

transport into the matrix [3b]. On balance,

not play an important role in mitochondria.

only NADH+H⁺ is moved from the cytoplasm

The driving force is usually the proton gra-

into the matrix; ATP is not needed for this.

dient across the inner membrane (blue star)

The glycerophosphate shuttle (right) was

or the general membrane potential (red star;

discovered in insect muscle, but is also active

see p. 126).

in the skeletal musculature and brain in

The pyruvate (left) formed by glycolysis in

higher animals. In this shuttle, NADH+H⁺

the cytoplasm is imported into the matrix in

formed in the cytoplasm is used to reduce

antiport with OH^-. The OH^- ions react in the

glycerone 3-phosphate, an intermediate of

intermembrane space with the H⁺ ions abun-

glycolysis

(see p. 150) to glycerol

3-phos-

dantly present there to form H₂O. This main-

phate. Via porins, this enters the intermem-

tains a concentration gradient of OH^-. The

brane space and is oxidized again there on the

import of phosphate (H₂PO_–) is driven in a

exterior side of the inner membrane by the

similar way. The exchange of the ATP formed

flavin enzyme glycerol 3-phosphate dehydro-

in the mitochondrion for ADP via an adenine

genase back into glycerone 3-phosphate. The

nucleotide translocase (center) is also depen-

reducing equivalents are passed on to the

dent on the H⁺ gradient. ATP with a quadruple

respiratory chain via ubiquinone (coenzyme

negative charge is exchanged for ADP with a

Q).

triple negative charge, so that overall one

The carnitine shuttle for transporting acyl

negative charge is transported into the H⁺-

residues into the mitochondrial matrix is dis-

rich intermembrane space. The import of ma-

cussed on p. 164.

late by the tricarboxylate transporter, which is

important for the malate shuttle (see B) is

coupled to the export of citrate, with a net

export of one negative charge to the exterior

again. In the opposite direction, malate can

leave the matrix in antiport for phosphate.

When Ca²⁺ is imported (right), the metal cat-

ion follows the membrane potential. An elec-

troneutral antiport for two H⁺ or two Na⁺

serves for Ca²⁺ export.

Mitochondria

213

A. Transport systems

Driving force:

ATP⁴

2-Oxoglutarate/citrate

Membrane

potential

ADP³

Proton

2-oxo-

Malate^-

gradient

glutarate/

citrate

H₂PO₄

ATP⁴

H₂O

HPO42

Malate^-

ADP³

Citrate export

H₂PO₄

Malate shuttle

HPO₄

H⁺

ATP synthesis

Ca2+

Pyruvate

Ca2+

2⁺ storage

Breakdown

Ca2+

release

Pyruvate

Conversion

(Na + )

Inner mitochondrial membrane

B. Malate and glycerophosphate shuttle

Glyceraldehyde

Malate dehydrogenase 1.1.1.37

Glycerol 3-phosphate dehydrogenase 1.1.1.8

3-phosphate

dehydrogenase

Aspartate transaminase 2.6.1.1

Glyceral 3-phosphate DH (FAD) 1.1.99.5

1.2.1.12

Glucose 6-

NADH + H

phosphate

1,3-Bisphos-

Glyco-

Cyto-

Cytoplasma

phoglycerate

lysis

plasm

Glu

Oxalo-

Fructose 1,6-

acetate

bisphosphate

Glyceral 3-

Glycerone 3-

phosphate

Asp

2-Oxo-

glutarate

Malate

Outer

Glycerophos-

Glycerol 3-

phate shuttle

phosphate

Mitochon-

Malate

drial

membrane

shuttle

Porin

Complex I

Ubiquinone

Inner

2-Oxo-

Malate

Asp

glutarate

Complex III

Oxalo-

Glu

acetate

Complex IV

Matrix

NADH + H

2H+ , O

Mitochondrion

H₂O

214

Organelles

B. Membrane lipids

Structure and components

The illustration shows a model of a small

A. Structure of the plasma membrane

section of a membrane. The phospholipids

are the most important group of membrane

All biological membranes are constructed ac-

lipids. They include phosphatidylcholine

cording to a standard pattern. They consist of

(lecithin), phosphatidylethanolamine, phos-

a continuous bilayer of amphipathic lipids ap-

phatidylserine,

phosphatidylinositol,

and

proximately 5 nm thick, into which proteins

sphingomyelin

(for their structures, see

are embedded. In addition, some membranes

p. 50). In addition, membranes in animal cells

also carry carbohydrates (mono- and oligo-

also contain cholesterol (with the exception

saccharides) on their exterior, which are

of inner mitochondrial membranes). Glycoli-

bound to lipids and proteins. The proportions

pids (a ganglioside is shown here) are mainly

of lipids, proteins, and carbohydrates differ

found on the outside of the plasma mem-

markedly depending on the type of cell and

brane. Together with the glycoproteins, they

membrane (see p. 216).

form the exterior coating of the cell (the gly-

Membrane lipids are strongly amphipathic

cocalyx).

molecules with a polar hydrophilic

“head

group” and an apolar hydrophobic “tail.” In

membranes, they are primarily held together

C. Membrane proteins

by the hydrophobic effect (see p. 28) and

Proteins can be anchored in or on membranes

weak Van der Waals forces, and are therefore

in various ways. Integral membrane proteins

mobile relative to each other. This gives mem-

cross right through the lipid bilayer. The sec-

branes a more or less fluid quality.

tions of the peptide chains that lie within the

The fluidity of membranes primarily de-

bilayer usually consist of 20 to 25 mainly

pends on their lipid composition and on tem-

hydrophobic amino acid residues that form a

perature. At a specific transition temperature,

right-handed α-helix.

membranes pass from a semicrystalline state

Type I and II membrane proteins only

to a more fluid state. The double bonds in the

contain one transmembrane helix of this

alkyl chains of unsaturated acyl residues in

type, while type III proteins contain several.

the membrane lipids disturb the semicrystal-

Rarely, type I and II polypeptides can aggre-

line state. The higher the proportion of unsa-

gate to form a type IV transmembrane pro-

turated lipids present, therefore, the lower the

tein. Several groups of integral membrane

transition temperature. The cholesterol con-

proteins—e. g., the porins (see p. 212)—pene-

tent also influences membrane fluidity. While

trate the membrane with antiparallel β-sheet

cholesterol increases the fluidity of semicrys-

structures. Due to its shape, this tertiary

talline, closely-packed membranes, it stabil-

structure is known as a “β-barrel.”

izes fluid membranes that contain a high pro-

Type V and VI proteins carry lipid anchors.

portion of unsaturated lipids.

These are fatty acids (palmitic acid, myristic

Like lipids, proteins are also mobile within

acid), isoprenoids (e. g., farnesol), or glycoli-

the membrane. If they are not fixed in place

pids such as glycosyl phosphatidylinositol

by special mechanisms, they float within the

(GPI) that are covalently bound to the peptide

lipid layer as if in a two-dimensional liquid;

chain.

biological membranes are therefore also de-

Peripheral membrane proteins are associ-

scribed as being a “fluid mosaic.”

ated with the head groups of phospholipids

Lipids and proteins can shift easily within

or with another integral membrane protein

one layer of a membrane, but switching be-

(not shown).

tween the two layers (“flip/flop”) is not possi-

ble for proteins and is only possible with dif-

ficulty for lipids (with the exception of cho-

lesterol). To move to the other side, phospho-

lipids require special auxiliary proteins

(translocators, “flipases”).

216

Organelles

p. 140) and photosynthesis (see p. 128)—also

Functions and composition

occur in membranes.

The most important membranes in animal

5. Interactions with other cells for the pur-

cells are the plasma membrane, the inner

poses of cell fusion and tissue formation, as

and outer nuclear membranes, the mem-

well as communication with the extracellular

branes of the endoplasmic reticulum (ER) and

matrix.

the Golgi apparatus, and the inner and outer

6. Anchoring of the cytoskeleton

(see

mitochondrial membranes. Lysosomes, peroxi-

p. 204) to maintain the shape of cells and

somes, and various vesicles are also separated

organelles and to provide the basis for move-

from the cytoplasm by membranes. In plants,

ment processes.

additional membranes are seen in the plastids

and vacuoles. All membranes show pola-

B. Composition of membranes

rity—i. e., there is a difference in the composi-

tion of the inner layer (facing toward the

Biological membranes consist of lipids, pro-

cytoplasm) and the outer layer (facing away

teins, and carbohydrates (see p. 214). These

from it).

components occur in varying proportions

(left). Proteins usually account for the largest

proportion, at around half. By contrast, carbo-

A. Functions of membranes

hydrates, which are only found on the side

Membranes and their components have the

facing away from the cytoplasm, make up

following functions:

only a few percent. An extreme composition

is seen in myelin, the insulating material in

1. Enclosure and insulation of cells and or-

nerve cells, three-quarters of which consists

ganelles. The enclosure provided by the

of lipids. By contrast, the inner mitochondrial

plasma membrane protects cells from their

membrane is characterized by a very low pro-

environment both mechanically and chemi-

portion of lipids and a particularly high pro-

cally. The plasma membrane is essential for

portion of proteins.

maintaining differences in the concentration

When the individual proportions of lipids

of many substances between the intracellular

in membranes are examined more closely

and extracellular compartments.

(right part of the illustration), typical patterns

2. Regulated transport of substances,

for particular cells and tissues are also found.

which determines the internal milieu and is

The illustration shows the diversity of the

a precondition for homeostasis—i.e., the

membrane lipids and their approximate

maintenance of constant concentrations of

quantitative composition. Phospholipids are

substances and physiological parameters.

predominant in membrane lipids in compar-

Regulated and selective transport of substan-

ison with glycolipids and cholesterol. Triacyl-

ces through pores, channels, and transporters

glycerols (neutral fats) are not found in mem-

(see p. 218) is necessary because the cells and

branes.

organelles are enclosed by membrane sys-

Cholesterol is found almost exclusively in

tems.

eukaryotic cells. Animal membranes contain

3. Reception of extracellular signals and

substantially more cholesterol than plant

transfer of these signals to the inside of the

membranes, in which cholesterol is usually

cell (see pp. 384 ff.), as well as the production

replaced by other sterols. There is no choles-

of signals.

terol at all in prokaryotes (with a few excep-

4. Enzymatic catalysis of reactions. Impor-

tions). The inner mitochondrial membrane of

tant enzymes are located in membranes at the

eukaryotes is also low in cholesterol, while it

interface between the lipid and aqueous

is the only membrane that contains large

phases. This is where reactions with apolar

amounts of cardiolipin. These facts both sup-

substrates occur. Examples include lipid

port the endosymbiotic theory of the devel-

biosynthesis (see p. 170) and the metabolism

opment of mitochondria (see p. 210).

of apolar xenobiotics (see p. 316). The most

important reactions in energy conver-

sion—i. e., oxidative phosphorylation

(see

218

Organelles

potential also plays a role; the processes are

Transport processes

summed up by the term “electrochemical

gradient” (see p. 126). These processes there-

A. Permeability

fore involve passive transport, which runs

Only small, uncharged molecules such as

“downhill” on the slope of a gradient.

gases, water, ammonia, glycerol, or urea are

By contrast, active transport can also run

able to pass through biological membranes by

“uphill”—i. e., against a concentration or

free diffusion. With increasing size, even com-

charge gradient. It therefore requires an input

pounds of this type are no longer able to pass

of energy, which is usually supplied by the

through. Membranes are impermeable to glu-

hydrolysis of ATP (see p. 124). The transporter

cose and other sugars, for example.

first binds its “cargo” on one side of the mem-

The polarity of a molecule is also impor-

brane. ATP-dependent phosphorylation then

tant. Apolar substances, such as benzene,

causes a conformation change that releases

ethanol, diethyl ether, and many narcotic

the cargo on the other side of the membrane

agents are able to enter biological membranes

(see p. 220). A non-spontaneous transport

easily. By contrast, membranes are imperme-

process can also take place through coupling

able to strongly polar compounds, particu-

to another active transport process (known as

larly those that are electrically charged. To

secondary active transport; see p. 220).

be able to take up or release molecules of

Using the transport systems in the mem-

this type, cells have specialized channels and

branes, cells regulate their volume, internal

transporters in their membranes (see below).

pH value, and ionic environment. They con-

centrate metabolites that are important for

energy metabolism and biosynthesis, and ex-

B. Passive and active transport

clude toxic substances. Transport systems

Free diffusion is the simplest form of mem-

also serve to establish ion gradients, which

brane transport. When it is supported by in-

are required for oxidative phosphorylation

tegral membrane proteins, it is known as fa-

and stimulation of muscle and nerve cells,

cilitated diffusion (or facilitated transport).

for example (see p. 350).

1. Channel proteins have a polar pore

through which ions and other hydrophilic

C. Transport processes

compounds can pass. For example, there are

Another classification of transport processes

channels that allow selected ions to pass (ion

is based on the number of particles trans-

channels; see p. 222) and porins that allow

ported and the direction in which they

molecules below a specific size to pass in a

move. When a single molecule or ion passes

more or less nonspecific fashion (see p. 212).

through the membrane with the help of a

2. Transporters recognize and bind the

channel or transporter, the process is de-

molecules to be transported and help them

scribed as a uniport (example: the transport

to pass through the membrane as a result of a

of glucose into liver cells). Simultaneous

conformational change. These proteins (per-

transport of two different particles can take

meases) are thus comparable with enzy-

place either as a symport (example: the trans-

mes—although with the difference that they

port of amino acids or glucose together with

“catalyze” vectorial transport rather than an

Na⁺ ions into intestinal epithelial cells) or as

enzymatic reaction. Like enzymes, they show

an antiport. Ions are often transported in an

a certain affinity for each molecule trans-

antiport in exchange for another similarly

ported

(expressed as the dissociation

charged ion. This process is electroneutral

constant, K_d in mol L^-1) and a maximum

and therefore more energetically favorable

transport capacity (V).

(example: the exchange of HCO_3- for Cl^- at

Free diffusion and transport processes fa-

the erythrocyte membrane).

cilitated by ion channels and transport pro-

teins always follow a concentration gradient—

i. e., the direction of transport is from the

site of higher concentration to the site of

lower concentration. In ions, the membrane

220

Organelles

C. Aquaporin-1

Transport proteins

Aquaporins help water to pass through bio-

Illustrations B-D show transporters whose

logical membranes. They form hydrophilic

structure has been determined experimen-

pores that allow H₂O molecules, but not hy-

tally or established on analogy with other

drated ions or larger molecules, to pass

known structures. They all belong to group

through. Aquaporins are particularly impor-

III of the α-helical transmembrane proteins

tant in the kidney, where they promote the

(see p. 214).

reuptake of water (see p. 328). Aquaporin-2

in the renal collecting ducts is regulated by

A. Transport mechanisms

antidiuretic hormone

(ADH, vasopressin),

which via cAMP leads to shifting of the chan-

Some cells couple the “pure” transport forms

nels from the ER into the plasma membrane.

discussed on p. 218—i. e., passive transport (1)

Aquaporin-1, shown here, occurs in the

and active transport (2)—and use this mech-

proximal tubule and in Henle’s loop. It con-

anism to take up metabolites. In secondary

tains eight transmembrane helices with dif-

active transport (3), which is used for exam-

ferent lengths and orientations. The yellow-

ple by epithelial cells in the small intestine

colored residues form a narrowing that only

and kidney to take up glucose and amino

H₂O molecules can overcome.

acids, there is a symport (S) located on the

luminal side of the membrane, which takes up

the metabolite M together with an Na⁺ ion.

D. Sarcoplasmic Ca²⁺ pump

An ATP-dependent Na⁺ transporter (Na⁺/K⁺

Transport ATPases transport cations—they are

ATPase; see p. 350) on the other side keeps

“ion pumps.” ATPases of the F type—e. g., mito-

the intracellular Na+ concentration low and

chondrial ATP synthase (see p. 142)—use H⁺

thus indirectly drives the uptake of M. Finally,

transport for ATP synthesis. Enzymes of the V

a uniport (U) releases M into the blood.

type, using up ATP, “pump” protons into lyso-

somes and other acidic cell compartments (see

B. Glucose transporter Glut-1

p. 234). P type transport ATPases are particu-

larly numerous. These are ATP-driven cation

The glucose transporters (Glut) are a family of

transporters that undergo covalent phosphor-

related membrane proteins with varying dis-

ylation during the transport cycle.

tribution in the organs. Glut-1 and Glut-3

The Ca²⁺ ATPase shown also belongs to the

have a relatively high af nity for glucose (K_d

P type. In muscle, its task is to pump the Ca²⁺

= 1 mM). They occur in nearly all cells, and

released into the cytoplasm to trigger muscle

ensure continuous glucose uptake. Glut-2 is

contraction back into the sarcoplasmic retic-

found in the liver and pancreas. This form has

ulum (SR; see p. 334). The molecule (1) con-

a lower af nity (K_d = 15-20 mM). The rate of

sists of a single peptide chain that is folded into

glucose uptake by Glut-2 is therefore strongly

various domains. In the transmembrane part,

dependent on the blood glucose level (nor-

which is formed by numerous α-helices, there

mally 4-8 mM). Transport by Glut-4 (K_d =

are binding sites for two Ca²⁺ ions (blue) ATP

5 mM), which is mainly expressed in muscle

is bound to the cytoplasmic N domain (green).

and fat cells, is controlled by insulin, which

Four different stages can be distinguished

increases the number of transporters on the

in the enzyme’s catalytic cycle (2). First, bind-

cell surface (see p. 388). Glut-5 mediates sec-

ing of ATP to the N domain leads to the uptake

ondary active resorption of glucose in the in-

of two Ca²⁺ into the transmembrane part (a).

testines and kidney (see A).

Phosphorylation of an aspartate residue in the

Glut-1 consists of a single peptide chain

P domain (b) and dissociation of ADP then

that spans the membrane with 12 α-helices

causes a conformation change that releases

of different lengths. The glucose is bound by

the Ca²⁺ ions into the SR (c). Finally, dephos-

the peptide loops that project on each side of

phorylation of the aspartate residue restores

the membrane.

the initial conditions (d).

222

Organelles

tion, the S4 helices are thought to snap up-

Ion channels

wards like springs and thus open the central

Ion channels facilitate the diffusion of ions

pore (b).

through biological membranes. Some ion

channels open and close depending on the

B. Nicotinic acetylcholine receptor

membrane potential (voltage-gated channels,

A) or in response to specific ligands (ligand-

Many receptors for neurotransmitters func-

gated channels, B). Other channels operate

tion as ligand-gated channels for Na⁺, K⁺

passively. In these cases, transport depends

and/or Ca²⁺ ions (see p. 354). The ones that

only on the concentration gradient (C).

have been studied in the greatest detail are

the nicotinic receptors for acetylcholine (see

p. 352). These consist of five separate but

A. Voltage-gated Na⁺ channel

structurally closely related subunits. Each

Voltage-gated Na⁺ channels play a decisive

forms four transmembrane helices, the sec-

part in the conduction of electrical impulses

ond of which is involved in the central pore in

in the nervous system (see p. 350). These

each case. The type of monomer and its ar-

channels open when the membrane potential

rangement in the complex is not identical in

in their environment reverses. Due to the high

all receptors of this type. In the neuromuscu-

equilibrium potential for Na⁺ (see p. 126), an

lar junction

(see p. 334), the arrangement

inflow of Na⁺ ions takes place, resulting in

αβγαδ is found (1).

local depolarization of the membrane, which

In the interior of the structure, acetylcho-

propagates by activation of neighboring volt-

line binds to the two α-subunits and thus

age-dependent Na⁺ channels. A spreading de-

opens the pore for a short time (1-2 ms).

polarization wave of this type is known as an

Negatively charged residues are arranged in

action potential (see p. 350). Externally di-

three groups in a ring shape inside it. They are

rected K⁺ channels are involved in the repola-

responsible for the receptor’s ion specificity. It

rization of the membrane. In their function-

is thought that binding of the neurotransmit-

ing, these resemble the much more simply

ter changes the position of the subunits in

structured K⁺ channels shown in C. The Ca²⁺

such a way that the pore expands (3). The

channels that trigger exocytosis of vesicles

bound acetylcholine dissociates again and is

(see p. 228) are also controlled by the action

hydrolytically inactivated

(see p. 356). The

potential.

receptor is thus able to function again.

The voltage-gated Na⁺ channels in higher

animals are large complexes made up of sev-

C. K⁺ channel in Streptomyces lividans

eral subunits. The α-subunit shown here me-

diates Na⁺ transport. It consists of a very long

The only detailed structures of ion channels

peptide chain (around 2000 amino acid resi-

established so far are those of potassium

dues), which is folded into four domains, each

channels like that of an outwardly directed

with six transmembrane helices (left). The S6

K+ channel in the bacterium Streptomyces liv-

helices of all the domains

(blue) together

idans. It consists of four identical subunits

form a centrally located hydrophilic pore

(blue, yellow, green, and red), each of which

which can be made narrow or wide depend-

contains two long α-helices and one shorter

ing on the channel’s functional status. The six

one. In the interior of the cell (bottom), the K⁺

S4 helices (green) function as voltage sensors.

ions

(violet) enter the structure’s central

The current conception of the way in which

channel. Before they are released to the out-

the opening and closing mechanism functions

side, they have to pass through what is known

is shown in a highly simplified form on the

as a “selectivity filter.” In this part of the

right. For the sake of clarity, only one of the

channel, several C=O groups in the peptide

four domains (domain IV) is shown. The S4

chain form a precisely defined opening that

helices contain several positively charged res-

is only permeable to non-hydrated K⁺ ions.

idues. When the membrane is polarized (a),

the surplus negative charges on the inner side

keep the helix in the membrane. If this attrac-

tion is removed as a result of local depolariza-

224

Organelles

B. Insulin receptor

Membrane receptors

The receptor for the hormone insulin (see

To receive and pass on chemical or physical

p. 76) belongs to the family of 1-helix recep-

signals, cells are equipped with receptor pro-

tors.

teins. Many of these are integral membrane

These molecules span the membrane with

proteins in the plasma membrane, where

only one α-helix. The subunits of the dimeric

they receive signals from their surroundings.

receptor (red and blue) each consist of two

Other receptor proteins are located in inter-

polypeptides (α and β) bound by disulfide

cellular membranes. The receptors for lipo-

bonds. The α-chains together bind the insulin,

philic hormones are among the few that func-

while the β-chains contain the transmem-

tion in a soluble form. They regulate gene

brane helix and, at the C-terminus, domains

transcription in the nucleus (see p. 378).

with tyrosine kinase activity. In the activated

state, the kinase domains phosphorylate

A. Principle of receptor action

themselves and also mediator proteins (re-

ceptor substrates) that set in motion cascades

Membrane-located receptors can be divided

of further phosphorylations (see pp. 120 and

into three parts, which have different tasks.

388).

The receptor domain reacts specifically to a

given signal. Signals of this type can be of a

purely physical nature. For example, many

C. 7-helix receptors

organisms react to light. In this way, plants

A large group of receptors span the mem-

adapt growth and photosynthesis to light

brane with α-helices seven times. These are

conditions, while animals need light recep-

known as 7-helix receptors. Via their effector

tors for visual processing (C; see p. 358). Me-

domains, they bind and activate trimeric pro-

chanoreceptors are involved in hearing and in

teins, which in turn bind and hydrolyze GTP

pressure regulation, among other things.

and are therefore called G proteins. Most G

Channels that react to action potentials (see

proteins, in turn, activate or inhibit enzymes

p. 350) can be regarded as receptors for elec-

that create secondary signaling molecules

trical impulses.

(second messengers; see p. 386). Other G pro-

However, most receptors do not react to

teins regulate ion channels. The illustration

physical stimuli, but rather to signal mole-

shows the complex of the light receptor rho-

cules. Receptors for these chemical signals

dopsin, with the associated G protein trans-

contain binding sites in the receptor domain

ducin (see p. 358). The GTP-binding α-subunit

that are complementary to each ligand. In this

(green) and the γ-subunit (violet) of transdu-

respect, they resemble enzymes (see p. 94).

cin are anchored in the membrane via lipids

As the effector domain of the receptor is usu-

(see p. 214). The β-subunit is shown in detail

ally separated by a membrane, a mechanism

on p. 72.

for signal transfer between the domains is

needed. Little is yet known regarding this. It

is thought that conformation changes in the

D. T-cell receptor

receptor protein play a decisive part. Some

The cells of the immune system communicate

receptors dimerize after binding of the ligand,

with each other particularly intensively. The

thereby bringing the effector domains of two

T-cell receptor plays a central role in the acti-

molecules into contact (see p. 392).

vation of T lymphocytes (see p. 296). The cell

The way in which the effector works differs

at the top has been infected with a virus, and

from case to case. By binding or interconver-

it indicates this by presenting a viral peptide

sion, many receptors activate special media-

(violet) with the help of a class I MHC protein

tor proteins, which then trigger a signal cas-

(yellow and green). The combination of the

cade (signal transduction; see p. 384). Other

two molecules is recognized by the dimeric

receptors function as ion channels. This is

T-cell receptor (blue) and converted into a

particularly widespread in receptors for neu-

signal that activates the T cell (bottom) and

rotransmitters (see p. 354).

thereby enhances the immune response to

the virus.

Biological membranes

225

A. Principle of receptor action

Signal

Chemical signals

Physical signals

Metabolites

Light

Recipient

Hormones

Electrical impulses

Mechanical stimuli

Neurotransmitters

Mediators

Transmitter

Odorants

Tastants

Activator

Other molecules

Protein kinase

Inorganic ions

Effector

Ion channel

Cellular response

Mediator

Cellular response

Protein activated

G-protein

by ions

receptor substrate

B. Insulin receptor

D. T-cell receptor

α2

α1

Antigen-presenting cell

Insulin

Tyrosine

β2

β1

kinase

domain

α2

α1

MHC

β2

β1

protein

(class I)

β₂-

Adaptor

Micro-

protein

globulin

Receptor

Protein kinase

substrate

Protein kinase

C. 7-Helix receptors

Viral

peptide

Lipid

Receptor

anchor

α-Sub-

unit

GTP

G protein

T-cell

β-Sub-

receptor

unit

γ-Sub-

unit

Signaling

G protein

Effector

substance

enzyme

GDP

Activated

Second

receptor

GDP

GTP

Precursor

messenger

T-helper cell

226

Organelles

will take and whether its transport will be

ER: structure and function

constitutive or regulated depends on the sig-

The endoplasmic reticulum (ER) is an exten-

nal sequences or signal structures that pro-

sive closed membrane system consisting of

teins carry with them like address labels (see

tubular and saccular structures. In the area

p. 228). In addition to proteins, the Golgi ap-

of the nucleus, the ER turns into the external

paratus also transports membrane lipids to

nuclear membrane. Morphologically, a dis-

their targets.

tinction is made between the rough ER (rER)

and the smooth ER (sER). Large numbers of

B. Smooth endoplasmic reticulum

ribosomes are found on the membranes of the

rER, which are lacking on the sER. On the

Regions of the ER that have no bound ribo-

other hand, the sER is rich in membrane-

somes are known as the smooth endoplasmic

bound enzymes, which catalyze partial reac-

reticulum (sER). In most cells, the proportion

tions in the lipid metabolism as well as bio-

represented by the sER is small. A marked sER

transformations.

is seen in cells that have an active lipid me-

tabolism, such as hepatocytes and Leydig

cells. The sER is usually made up of branching,

A. Rough endoplasmic reticulum and the

closed tubules.

Golgi apparatus

Membrane-located enzymes in the sER

The rER

(1) is a site of active protein

catalyze lipid synthesis. Phospholipid synthe-

biosynthesis. This is where proteins destined

sis (see p. 170) is located in the sER, for exam-

for membranes, lysosomes, and export from

ple, and several steps in cholesterol biosyn-

the cell are synthesized. The remaining pro-

thesis (see p. 172) also take place there. In

teins are produced in the cytoplasm on ribo-

endocrine cells that form steroid hormones, a

somes that are not bound to membranes.

large proportion of the reaction steps in-

Proteins synthesized at the rER (1) are

volved also take place in the sER (see p. 376).

folded and modified after translation (protein

In the liver’s hepatocytes, the proportion

maturation; see p. 230). They remain either in

represented by the sER is particularly high.

the rER as membrane proteins, or pass with

It contains enzymes that catalyze so-called

the help of transport vesicles (2) to the Golgi

biotransformations. These are reactions in

apparatus (3). Transport vesicles are formed

which apolar foreign substances, as well as

by budding from existing membranes, and

endogenous substances—e. g., steroid hormo-

they disappear again by fusing with them

nes—are chemically altered in order to inacti-

(see p. 228).

vate them and/or prepare them for conjuga-

The Golgi apparatus (3) is a complex net-

tion with polar substances (phase I reactions;

work, also enclosed, consisting of flattened

see p. 316). Numerous cytochrome P450

membrane saccules (“cisterns”), which are

enzymes are involved in these conversions

stacked on top of each other in layers. Pro-

(see p. 318) and can therefore be regarded

teins mature here and are sorted and packed.

as the major molecules of the sER.

A distinction is made between the cis, medial,

The sER also functions as an intracellular

and trans Golgi regions, as well as a trans

calcium store, which normally keeps the Ca²⁺

Golgi network (tGN). The post-translational

level in the cytoplasm low. This function is

modification of proteins, which starts in the

particularly marked in the sarcoplasmic retic-

ER, continues in these sections.

ulum, a specialized form of the sER in muscle

From the Golgi apparatus, the proteins are

cells (see p. 334). For release and uptake of

transported by vesicles to various targets in

Ca²⁺, the membranes of the sER contain sig-

the cells—e. g., to lysosomes (4), the plasma

nal-controlled Ca²⁺ channels and energy-de-

membrane (6), and secretory vesicles (5) that

pendent Ca²⁺ ATPases (see p. 220). In the lu-

release their contents into the extracellular

men of the sER, the high Ca²⁺ concentration is

space by fusion with the plasma membrane

buffered by Ca²⁺-binding proteins.

(exocytosis; see p. 228). Protein transport can

either proceed continuously (constitutive), or

it can be regulated by chemical signals. The

decision regarding which pathway a protein

Endoplasmic reticulum and Golgi apparatus

227

A. Rough endoplasmic reticulum and Golgi apparatus

Morphological

Biochemical

structures

Nucleus

processes

1. Transport

2. Protein synthesis

2. and folding

2. Signal peptide

1. rER

2. cleavage

2. Formation of

2. Transport

2. disulfide bonds

2. vesicle

2. Oligomerization

2. N-Glycosylation

cis

folding

medial

3. Golgi complex

3. cis:

trans

3. Phosphorylation

3. medial:

Membrane

trans-Golgi network

3. Sugar cleavage

protein

3. Addition of GlcNAc

4. Lysosome

3. Addition of

3. Gal and NeuAc

5. Secretory

3. trans-Golgi network:

5. vesicle

3. Sorting

4. Hydrolysis of

4. macromolecules

5. Proteolysis

6. Cytoplasmic

6. membrane

6. Exocytosis

B. Smooth endoplasmic reticulum

Steroid

Phospholipids

Cholesterol

hormones

Outside

Calcium store

Plasma

membrane

Xeno-

Metabolites

Inside

biotics

Ca2+

Enzyme systems

of the lipid metabolism

228

Organelles

organelles (selective protein transfer). Struc-

Protein sorting

tural signals can also activate enzymes that

modify the proteins and thereby determine

A. Protein sorting

their subsequent fate. Examples include lyso-

The biosynthesis of all proteins starts on free

somal proteins (see p. 234) and membrane

ribosomes (top). However, the paths that the

proteins with lipid anchors (see p. 214).

proteins follow soon diverge, depending on

After they have been used, signal peptides

which target they are destined for. Proteins

at the N terminus are cleaved off by specific

that carry a signal peptide for the ER (1) follow

hydrolases (symbol: scissors). In proteins that

the secretory pathway (right). Proteins that do

contain several successive signal sequences,

not have this signal follow the cytoplasmic

this process can expose the subsequent sig-

pathway (left).

nals. By contrast, signal peptides that have to

Secretory pathway. Ribosomes that syn-

be read several times are not cleaved.

thesize a protein with a signal peptide for

the ER settle on the ER (see p. 228). The pep-

C. Exocytosis

tide chain is transferred into the lumen of the

rER. The presence or absence of other signal

Exocytosis is a term referring to processes

sequences and signal regions determines the

that allow cells to expel substances (e. g., hor-

subsequent transport pathway.

mones or neurotransmitters) quickly and in

Proteins that have stop-transfer sequences

large quantities. Using a complex protein ma-

(4) remain as integral membrane proteins in

chinery, secretory vesicles fuse completely or

the ER membrane. They then pass into other

partially with the plasma membrane and re-

membranes via vesicular transport

(see

lease their contents. Exocytosis is usually

p. 226). From the rER, their pathway then

regulated by chemical or electrical signals. As

leads to the Golgi apparatus and then on to

an example, the mechanism by which neuro-

the plasma membrane. Proteins destined to

transmitters are released from synapses (see

remain in the rER—e. g., enzymes—find their

p. 348) is shown here, although only the most

way back from the Golgi apparatus to the rER

important proteins are indicated.

with the help of a retention signal (2). Other

The decisive element in exocytosis is the

proteins move from the Golgi apparatus to

interaction between proteins known as

the lysosomes (3; see p. 234), to the cell

SNAREs that are located on the vesicular

membrane (integral membrane proteins or

membrane (v-SNAREs) and on the plasma

constitutive exocytosis), or are transported

membrane (t-SNAREs). In the resting state

out of the cell (9; signal-regulated exocytosis)

(1), the v-SNARE synaptobrevin is blocked by

by secretory vesicles (8).

the vesicular protein synaptotagmin. When an

Cytoplasmic pathway. Proteins that do not

action potential reaches the presynaptic

have a signal peptide for the ER are synthe-

membrane, voltage-gated Ca²⁺ channels

sized in the cytoplasm on free ribosomes, and

open (see p. 348). Ca²⁺ flows in and triggers

remain in that compartment. Special signals

the machinery by conformational changes in

mediate further transport into the mitochon-

proteins. Contact takes place between synap-

dria (5; see p. 232), the nucleus (6; see p. 208)

tobrevin and the t-SNARE synaptotaxin (2).

or peroxisomes (7).

Additional proteins known as SNAPs bind to

the SNARE complex and allow fusion between

the vesicle and the plasma membrane (3). The

B. Translocation signals

process is supported by the hydrolysis of GTP

Signal peptides are short sections at the N or C

by the auxiliary protein Rab.

terminus, or within the peptide chain. Areas

The toxin of the bacterium Clostridium bot-

on the protein surface that are formed by

ulinum, one of the most poisonous substances

various sections of the chain or by various

there is, destroys components of the exocyto-

chains are known as signal regions. Signal

sis machinery in synapses through enzymatic

peptides and signal regions are structural sig-

hydrolysis, and in this way blocks neurotrans-

nals that are usually recognized by receptors

mission.

on organelles (see A). They move the proteins,

with the help of additional proteins, into the

Endoplasmic reticulum and Golgi apparatus

229

A. Protein sorting

Cytoplasmic pathway

Secretory pathway

Ribosomes

-KDEL

Protein

Rough ER

Retention

Cytoplasm

Retention

-SKL

H2N

Golgi complex

Receptor

Peroxisomes

Mitochondria

Secretory

vesicle

Lysosomes

2 +

Nucleus

Cell membrane

*Standard pathway (without signal)

B. Translocation signals

C. Exocytosis

α-Helix

Transmitter

Vesicle

Rab · GTP

H₂N

Signal peptide

(secretory pathway)

OOC

Synapto-

GTP

brevin

Signal sequence

(v-SNARE)

Synapto-

(ER proteins)

tagmin

...LEDK

Syntaxin

(t-SNARE)

Mannose 6-

Signal group

phosphate

Ca2

(lysosomal proteins)

Synaptic cleft

Channel

Apolar

sequence

GTP

Stop-transfer sequence

(membrane proteins)

Synaptotagmin

+++

releases

Action

Signal peptide

Ca²

v-SNAREs

potential

(mitochondrial

proteins)

Ca²

...KKKRK...

Signal sequence

Rab · GDP

(nuclear proteins)

GDP

Signal sequence

Membrane

(peroxisomes)

...FKS...

fusion

SNAP

+NSF

Signal region

(secretory vesicle)

SNARE complex

230

Organelles

all plasma proteins with the exception of al-

Protein synthesis and maturation

bumin are glycosylated. Together with glyco-

lipids, numerous glycoproteins on the cell

A. Protein synthesis in the rER

surface form the glycocalyx. Inside the ER,

With all proteins, protein biosynthesis

the carbohydrate parts of the glycoproteins

(Translation; for details, see p. 250) starts on

are cotranslationally transferred to the grow-

free ribosomes in the cytoplasm (1). Proteins

ing chain, and are then converted into their

that are exported out of the cell or into lyso-

final form while passing through the ER and

somes, and membrane proteins of the ER and

Golgi apparatus.

the plasma membrane, carry a signal peptide

N-bound oligosaccharides (see p. 44) are

for the ER at their N-terminus. This is a section

always bound to the acid-amide group of as-

of 15-60 amino acids in which one or two

paragine residues. If a glycosylation sequence

strongly basic residues (Lys, Arg) near the N-

(-Asn-X-Ser(Thr)-, where X can be any

terminus are followed by a strongly hydro-

amino acid) appears in the growing peptide

phobic sequence of

10-15

residues

(see

chain, then a transglycosylase in the ER mem-

p. 228).

brane [1] transfers a previously produced core

As soon as the signal peptide (red) appears

oligosaccharide consisting of

hexose

on the surface of the ribosome (2), an RNA-

residues en-bloc from the carrier molecule

containing signal recognition particle

(SRP,

dolichol diphosphate to the peptide.

green) binds to the sequence and initially

Dolichol is a long-chain isoprenoid (see

interrupts translation (3). The SRP then binds

p. 52) consisting of

10-20 isoprene units,

to an SRP receptor in the rER membrane, and

which is embedded in the ER membrane. A

in this way attaches the ribosome to the ER

hydroxyl group at the end of the molecule is

(4). After this, the SRP dissociates from the

bound to diphosphate, on which the nuclear

signal peptide and from the SRP receptor

oligosaccharide is built up in an extended

and is available again for step 3. This ender-

reaction sequence (not shown here in detail).

gonic process is driven by GTP hydrolysis (5).

The core structure consists of two residues of

Translation now resumes. The remainder of

N-acetylglucosamine

(GlcNAc), a branched

the protein, still unfolded, is gradually intro-

group of nine mannose residues (Man) and

duced into a channel (the translocon) in the

three terminal glucose resides (Glc).

lumen of the rER (6), where a signal peptidase

As the proprotein passes through the ER,

located in the inner ER membrane cleaves the

glycosidases [2] remove the glucose residues

signal peptide while translation is still taking

completely and the mannoses partially

place (7). This converts the preprotein into a

(“trimming”), thereby producing the man-

proprotein, from which the mature protein

nose-rich type of oligosaccharide residues.

finally arises after additional post-transla-

Subsequently, various glycosyltransferases [3]

tional modifications (8) in the ER and in the

transfer additional monosaccharides

(e. g.,

Golgi apparatus.

GlcNAc, galactose, fucose, and N-acetylneura-

If the growing polypeptide contains a stop-

minic acid; see p. 38) to the mannose-rich

transfer signal (see p. 228), then this hydro-

intermediate and thereby produce the com-

phobic section of the chain remains stuck in

plex type of oligosaccharide. The structure of

the membrane outside the translocon, and an

the final oligosaccharide depends on the type

integral membrane protein arises. In the

and activity of the glycosyltransferases pre-

course of translation, an additional signal se-

sent in the ER of the cell concerned, and is

quence can re-start the transfer of the chain

therefore genetically determined (although

through the translocon. Several repetitions of

indirectly).

this process produce integral membrane pro-

teins with several transmembrane helices

(see p. 214).

B. Protein glycosylation

Most extracellular proteins contain covalently

bound oligosaccharide residues. For example,

232

Organelles

tible to proteinases. To protect partly folded

Protein maturation

proteins, there are auxiliary proteins called

After translation, proteins destined for the

chaperones because they guard immature

secretory pathway (see p. 228) first have to

proteins against damaging contacts. Chaper-

fold into their native conformation within the

ones are formed increasingly during tempera-

rER (see p. 230). During this process they are

ture stress and are therefore also known as

supported by various auxiliary proteins.

heat-shock proteins (hsp). Several classes of

hsp are distinguished. Chaperones of the

hsp70 type (Dna K in bacteria) are common,

A. Protein folding in the rER

as are type hsp60 chaperonins (GroEL/ES in

To prevent incorrect folding of the growing

bacteria). Class hsp90 chaperones have spe-

protein during protein biosynthesis, chaper-

cial tasks (see p. 378).

ones (see B) in the lumen of the rER bind to

While small proteins can often reach their

the peptide chain and stabilize it until trans-

native conformation without any help (1),

lation has been completed. Binding protein

larger molecules require hsp70 proteins for

(BiP) is an important chaperone in the ER.

protection against aggregation which bind as

Many secretory proteins—e. g., pancreatic

monomers and can dissociate again, depend-

ribonuclease (RNAse; see p. 74)—contain sev-

ent on ATP (3). By contrast, type hsp60 chap-

eral disulfide bonds that are only formed ox-

eronins form large, barrel-shaped complexes

idatively from SH groups after translation.

with 14 subunits in which proteins can fold

The eight cysteine residues of the RNAse can

independently while shielded from their en-

in principle form 105 different pairings, but

vironment (4). The function of hsp60 has been

only the combination of the four disulfide

investigated in detail in the bacterial

bonds shown on p. 75 provides active en-

chaperonin GroEL (right). The barrel has two

zyme. Incorrect pairings can block further

chambers, which are closed with a lid (GroES)

folding or lead to unstable or insoluble con-

during folding of the guest protein. Driven by

formations. The enzyme protein disulfide iso-

ATP hydrolysis, the chambers open and close

merase [1] accelerates the equilibration be-

alternately—i. e., the release of the fully folded

tween paired and unpaired cysteine residues,

protein from one chamber is coupled to the

so that incorrect pairs can be quickly split

uptake of an unfolded peptide in the second

before the protein finds its final conformation.

chamber.

Most peptide bonds in proteins take on the

trans conformation (see p. 66). Only bonds

C. Protein import in mitochondria

with proline residues

(-X-Pro-) can be

present in both cis and trans forms.

Class hsp70 chaperones are also needed for

In the protein’s native conformation, every

translocation of nuclear-coded proteins from

X-Pro bond has to have the correct conforma-

the cytoplasm into the mitochondria (see

tion (cis or trans). As the uncatalyzed transi-

p. 228). As two membranes have to be

tion between the two forms is very slow,

crossed to reach the matrix, there are two

there is a proline cis-trans isomerase [2] in

translocator complexes: TOM

(“transport

the ER that accelerates the conversion.

outer membrane”) and TIM (“transport inner

membrane”). For transport, proteins are un-

folded in the cytoplasm and protected by

B. Chaperones and chaperonins

hsp70. TOM recognizes the positively charged

Most proteins fold spontaneously into their

signal sequence at the protein’s N terminus

native conformation, even in the test tube.

(see p. 228) and with the help of the mem-

In the cell, where there are very high concen-

brane potential threads the chains through

trations of proteins (around 350 g L^-1), this

the central pores of the two complexes. Inside

is more dif cult. In the unfolded state, the

TIM, further hsp70 molecules bind and pull

apolar regions of the peptide chain (yellow)

the chain completely into the matrix. As with

tend to aggregate—due to the hydrophobic

import into the ER, the signal peptide is pro-

effect

(see p. 28)—with other proteins or

teolytically removed by a signal peptidase

with each other to form insoluble products

during translocation.

(2). In addition, unfolded proteins are suscep-

Endoplasmic reticulum and Golgi apparatus

233

A. Protein folding in the rER

Protein disulfide isomerase 5.3.4.1

Cyto-

Peptidyl proline cis-trans-isomerase 5.2.1.8

plasm

gER

S S

BiP (Chaperonin)

Pro (cis)

Pro (trans)

B. Chaperones and chaperonins

GroES

Folded

Small

protein

7 ATP

7 ADP

GroEL

Aggregation

hsp 60

(Chape-

ronin)

7 ADP

7 ATP

hsp 70

(chaperone)

Insoluble

precipitate

or degradation

Folded protein

C. Protein import in mitochondria

Signal peptide

Nuclear-coded

Cytoplasm

for mitochondrial

mitochondrial protein

hsp 70

import

TOM

Outer

mitochondrial

complex

membrane

TIM

Inner

complex

mitochondrial

membrane

Mitochondrial

matrix

Peptidase

hsp 70

234

Organelles

C. Synthesis and transport of lysosomal

Lysosomes

proteins

A. Structure and contents

Primary lysosomes arise in the region of the

Golgi apparatus. Lysosomal proteins are syn-

Animal lysosomes are organelles with a diam-

thesized in the rER and are glycosylated there

eter of 0.2-2.0 µm with various shapes that

as usual (1; see p. 228). The next steps are

are surrounded by a single membrane. There

specific for lysosomal proteins (right part of

are usually several hundred lysosomes per

the illustration). In a two-step reaction, ter-

cell. ATP-driven V-type proton pumps are ac-

minal mannose residues (Man) are phos-

tive in their membranes (see p. 220). As these

phorylated at the C-6 position of the man-

accumulate H⁺ in the lysosomes, the content

nose. First, N-acetylglucosamine 1-phosphate

of lysosomes with pH values of 4.5-5 is much

is transferred to the OH group at C-6 in a

more acidic than the cytoplasm (pH 7-7.3).

terminal mannose residue, and N-acetylglu-

The lysosomes are the cell’s “stomach,”

cosamine is then cleaved again. Lysosomal

serving to break down various cell compo-

proteins therefore carry a terminal mannose

nents. For this purpose, they contain some

6-phosphate (Man6-P; 2).

40 different types of hydrolases, which are

The membranes of the Golgi apparatus

capable of breaking down every type of mac-

contain receptor molecules that bind Man

romolecule. The marker enzyme of lysosomes

6-P. They recognize lysosomal proproteins

is acid phosphatase. The pH optimum of lyso-

by this residue and bind them (3). With the

somal enzymes is adjusted to the acid pH value

help of clathrin, the receptors are concen-

and is also in the range of pH 5. At neutral pH,

trated locally. This allows the appropriate

as in the cytoplasm, lysosomal enzymes only

membrane sections to be pinched off and

have low levels of activity. This appears to be a

transported to the endolysosomes with the

mechanism for protecting the cells from di-

help of transport vesicles (4), from which pri-

gesting themselves in case lysosomal enzymes

mary lysosomes arise through maturation (5).

enter the cytoplasm at any time. In plants and

Finally, the phosphate groups are removed

fungi, the cell vacuoles (see p. 43) have the

from Man 6-P (6).

function of lysosomes.

The Man 6-P receptors are reused. The fall

in the pH value in the endolysosomes releases

B. Functions

the receptors from the bound proteins (7)

which are then transported back to the Golgi

Lysosomes serve for enzymatic degradation of

apparatus with the help of transport vesicles.

macromolecules and cell organelles, which

are supplied in various ways. The example

shows the degradation of an overaged mito-

Further information

chondrion by autophagy. To accomplish this,

Many hereditary diseases are due to genetic

the lysosome encloses the organelle (1). Dur-

defects in lysosomal enzymes. The metabo-

ing this process, the primary lysosome con-

lism of glycogen ( glycogenoses), lipids (

verts into a secondary lysosome, in which the

lipidoses), and proteoglycans ( mucopoly-

hydrolytic degradation takes place (2). Finally,

saccharidoses) is particularly affected. As the

residual bodies contain the indigestible resi-

lysosomal enzymes are indispensable for the

dues of the lysosomal degradation process.

intracellular breakdown of macromolecules,

Lysosomes are also responsible for the degra-

unmetabolized macromolecules or degrada-

dation of macromolecules and particles taken

tion products accumulate in the lysosomes

up by cells via endocytosis and phagocyto-

in these diseases and lead to irreversible cell

sis—e. g., lipoproteins, proteohormones, and

damage over time. In the longer term, en-

bacteria (heterophagy). In the process, lyso-

largement takes place, and in severe cases

somes fuse with the endosomes (3) in which

there may be failure of the organ affected—

the endocytosed substances are supplied.

e. g., the liver.

Lysosomes

235

A. Structure and contents

B. Functions

Overaged

Enzymatic

Approx. 40 different hydrolases

mitochondrion

degradation

with acidic pH optima

Secondary

lysosome

Lysosome

pH = 4.5 - 5.0

Acid

hydrolases

Nucleases

Proteases

Glycosidases

Primary

Lipases

lysosome

Phosphatases

Residual

Sulfatases

body

Phospholipases

Endosome

Secondary

lysosome

Endocytotic

vesicle

Macro-

Cytoplasm

H -transporting

molecules,

pH = 7.0 - 7.3

ATPase

particles

Cell

3.6.1.35

Endocytosis

or phagocytosis

P P P

C. Synthesis and transport of lysosomal proteins

Terminal mannose

rER

Protein

CH₂OH

biosynthesis

N-Glycosy-

O R

lation

cis-Golgi

Glyco-

-GlcNAc

apparatus

protein

Phosphory-

lation

CH₂OH

trans-Golgi

No Man-6-

network

no transport

Binding to

OH H

O P

Receptor

Man-6- P

receptor

Sorting

CH₂

Sealing

Vesicular

CH₃

transport

^H HO

H2O

Endo-

lysosome

Acidification

Dissociation

GlcNAc

of the receptor-

protein

CH₂

complex

Low pH triggers

OHHO

conformational

change

Primary

lysosome

Phosphate

GlcNAc-Phosphotransferase 2.7.8.17

cleavage

GlcNAc-Phosphoglycosidase 3.1.4.45

236

Molecular genetics

mine for uracil—it is identical to that of the

Molecular genetics: overview

sense strand. In this way, the DNA triplet TTC

Nucleic acids (DNA and various RNAs) are of

gives rise in hnRNA to the RNA codon UUC.

central importance in the storage, transmis-

RNA maturation. In eukaryotes, the hnRNA

sion, and expression of genetic information.

initially formed is modified several times be-

The decisive factor involved is their ability to

fore it can leave the nucleus as messenger

enter into specific base pairings with each

RNA (mRNA, 4). During RNA maturation,

other (see p. 84). The individual processes in-

superfluous

(“intervening”) sequences

(in-

volved, which are summed up in an overview

trons) are removed from the molecule, and

here, are discussed in more detail on the fol-

both ends of the transcript are protected by

lowing pages.

the addition of further nucleotides

(see

p. 246).

Translation. Mature mRNA enters the cyto-

A. Expression and transmission of genetic

plasm, where it binds to ribosomes, which

information

convert the RNA information into a peptide

Storage. The genetic information of all cells is

sequence. The ribosomes (see p. 250) consist

stored in the base sequence of their DNA (RNA

of more than 100 proteins and several RNA

only occurs as a genetic material in viruses;

molecules (rRNA; see p. 82). rRNA plays a role

see p. 404). Functional sections of DNA that

as a ribosomal structural element and is also

code for inheritable structures or functions

involved in the binding of mRNA to the ribo-

are referred to as genes. The 30 000-40 000

some and the formation of the peptide bond.

human genes represent only a few percent of

The actual information transfer is based on

the genome, which consists of approximately

the interaction between the mRNA codons

10⁹ base pairs (bp). Most genes code for

and another type of RNA, transfer RNA

proteins—i. e., they contain the information

(tRNA; see p. 82). tRNAs, of which there are

for the sequence of amino acid residues of a

numerous types, always provide the correct

protein (its sequence). Every amino acid res-

amino acid to the ribosome according to the

idue is represented in DNA by a code word (a

sequence information in the mRNA. tRNAs are

codon) consisting of a sequence of three base

loaded with an amino acid residue at the 3

pairs (a triplet). At the level of DNA, codons

end. Approximately in the middle, they

are defined as sequences of the sense strand

present the triplet that is complementary to

read in the 5

3 direction (see p. 84). A DNA

each mRNA codon, known as the anticodon

codon for the amino acid phenylalanine, for

(GAA in the example shown). If the codon UUC

example, is thus TTC (2).

appears on the mRNA, the anticodon binds a

Replication. During cell division, all of the

molecule of Phe-t-RNA^Phe to the mRNA (5)

genetic information has to be passed on to the

and thus brings the phenylalanine residue at

daughter cells. To achieve this, the whole of

the other end of the molecule into a position

the DNA is copied during the S phase of the

in which it can take over the growing poly-

cell cycle (see p. 394). In this process, each

peptide chain from the neighboring tRNA (6).

strand serves as a matrix for the synthesis

Amino acid activation. Before binding to

of a complementary second strand (1; see

the ribosomes, tRNAs are loaded with the

p. 240).

correct amino acids by specific ligases (7;

Transcription. For expression of a gene—i. e.,

see p. 248). It is the amino acid tRNA ligases

synthesis of the coded protein—the DNA se-

that carry out the transfer (translation) of the

quence information has to be converted into a

genetic information from the nucleic acid

protein sequence. As DNA itself is not in-

level to the protein level.

volved in protein synthesis, the information

is transferred from the nucleus to the site of

synthesis in the cytoplasm. To achieve this,

the template strand in the relevant part of

the gene is transcribed into an RNA (hnRNA).

The sequence of this RNA is thus complemen-

tary to that of the template strand (3), but—

with the exception of the exchange of thy-

238

Molecular genetics

The non-histone proteins are very hetero-

Genome

geneous. This group includes structural pro-

teins of the nucleus, as well as many enzymes

A. Chromatin

and transcription factors (see p. 118), which

In the nuclei of eukaryotes (see p. 196), DNA is

selectively bind to specific segments of DNA

closely associated with proteins and RNA.

and regulate gene expression and other pro-

These nucleoprotein complexes, with a DNA

cesses.

proportion of approximately one-third, are

known as chromatin. It is only during cell

B. Histones

division

(see p. 394) that chromatin con-

denses into chromosomes that are visible

The histones are remarkable in several ways.

under light microscopy. During interphase,

With their high proportions of lysine and ar-

most of the chromatin is loose, and in these

ginine (blue shading), they are strongly basic,

conditions a morphological distinction can be

as mentioned above. In addition, their amino

made between tightly packed heterochroma-

acid sequence has hardly changed at all in the

tin and the less dense euchromatin. Euchro-

course of evolution. This becomes clear when

matin is the site of active transcription.

one compares the histone sequences in mam-

The proteins contained in chromatin are

mals, plants, and fungi (yeasts are single-

classified as either histone or non-histone

celled fungi; see p. 148). For example, the

proteins. Histones (B) are small, strongly basic

H4 histones in humans and wheat differ

proteins that are directly associated with

only in a single amino acid residue, and there

DNA. They contribute to the structural organ-

are only a few changes between humans and

ization of chromatin, and their basic amino

yeast. In addition, all of these changes are

acids also neutralize the negatively charged

“conservative”—i. e., the size and polarity

phosphate groups, allowing the dense pack-

barely differ. It can be concluded from this

ing of DNA in the nucleus. This makes it pos-

that the histones were already “optimized”

sible for the 46 DNA molecules of the diploid

when the last common predecessor of ani-

human genome, with their 5

10⁹ base pairs

mals, plants, and fungi was alive on Earth

(bp) and a total length of about 2 m, to be

(more than 700 million years ago). Although

accommodated in a nucleus with a diameter

countless mutations in histone genes have

of only 10 µm. Histones also play a central

taken place since, almost all of these evidently

role in regulating transcription (see p. 244).

led to the extinction of the organisms con-

Two histone molecules each of types H2A

cerned.

(blue), H2B (green), H3 (yellow), and H4 (red)

The histones in the octamer carry N-termi-

form an octameric complex, around which

nal mobile “tails” consisting of some 20 amino

146 bp of DNA are wound in 1.8 turns. These

acid residues that project out of the nucleo-

particles, with a diameter of 7 nm, are re-

somes and are important in the regulation of

ferred to as nucleosomes. Another histone

chromatin structure and in controlling gene

(H1) binds to DNA segments that are not di-

expression (see A2; only two of the eight tails

rectly in contact with the histone octamers

are shown in full length). For example, the

(“linker” DNA). It covers about 20 bp and sup-

condensation of chromatin into chromo-

ports the formation of spirally wound super-

somes is associated with phosphorylation (P)

structures with diameters of 30 nm, known as

of the histones, while the transcription of

solenoids. When chromatin condenses into

genes is initiated by acetylation (A) of lysine

chromosomes, the solenoids form loops about

residues in the N-terminal region (see p. 244).

200 nm long, which already contain about

80 000 bp. The loops are bound to a protein

framework (the nuclear scaffolding), which in

turn organizes some 20 loops to form mini-

bands. A large number of stacked minibands

finally produces a chromosome. In the chro-

mosome, the DNA is so densely packed that

the smallest human chromosome already

contains more than 50 million bp.

Replication

239

A. Chromatin

Solenoid

Nuclear scaffold

200 nm

Loops

30 nm

DNA double helix

Nucleosome

10 nm

Chromosome

2 nm

700 nm

Histone

1. Organization of chromatin

molecules

DNA

N-terminal

tail (H2B)

tail (H3)

H₂A

H₂B

H₃

Histone-Octamer

H₄

(H₂A · H₂B)₂(H₃ · H4)₂

2. Nucleosome

B. Histone

Acetylation

Phosphorylation

Methylation

Animals

G R G

G G A

K R H

V L R D N I

Plants

G R G

G G A

K R H

V L R D N I

Yeast

G R G

G G A

K R H

L R D N I

Q G I

R R

G G V

S G L I Y E

Animals

Plants

Q G I

R R

G G V

S G L I Y E

Yeast

Q G I

R R

G G V

S G L I Y E

E T

V I

D A V

Y T E H A

K R

Animals

Plants

E T

V I

D A V

Y T E H A

Yeast

V I

Y T E H A

K R

100

T V T

K R

Q G

Y G F G G

Animals

Plants

T V T

K R

Q G

Y G F G G

Yeast

T V T

K R

Q G

Y G F G G

Amino acid sequence of histone H4

240

Molecular genetics

the processes taking place in this type of fork,

Replication

and only the most important are shown here.

For genetic information to be passed on dur-

The two strands of the initial DNA (1) are

ing cell division, a complete copy of the ge-

shown in blue and violet, while the newly

nome has to be produced before each mitosis.

formed strands are pink and orange.

This process is known as DNA replication.

Each fork (2) contains two molecules of

DNA polymerase III and a number of helper

proteins. The latter include DNA topoisomer-

A. Mechanism of DNA polymerases

ases and single-strand-binding proteins.

Replication is catalyzed by DNA-dependent

Topoisomerases are enzymes that unwind

DNA polymerases. These enzymes require a

the superhelical DNA double strand (gyrase,

single strand of DNA, known as the tem-

topoisomerase II) and then separate it into the

plate. Beginning at a short starting sequence

two individual strands (helicase, topoisomer-

of RNA (the primer), they synthesize a second

ase I). Since the template strand is always read

complementary strand on the basis of this

from 3

to 5

(see above), only one of the

template, and thus create a complete DNA

strands (known as the leading strand; violet/

double helix again. The substrates of the

pink) can undergo continuous replication. For

DNA polymerases are the four deoxynucleo-

the lagging strand (light blue), the reading

side triphosphates dATP, dGTP, dCTP, and

direction is the opposite of the direction of

dTTP. In each step, base pairing first binds

movement of the fork. In this matrix, the

the nucleotide that is complementary to the

new strand is first synthesized in individual

current base in the template strand. The

pieces, which are known as Okazaki frag-

α-phosphate residue of the newly bound nu-

ments after their discoverer (green/orange).

cleoside triphosphate is then subjected to nu-

Each fragment starts with a short RNA pri-

cleophilic attack by the 3 -OH group of the

mer (green), which is necessary for the func-

nucleotide incorporated immediately previ-

tioning of the DNA polymerase and is synthe-

ously. This is followed by the elimination of

sized by a special RNA polymerase (“primase,”

diphosphate and the formation of a new

not shown). The primer is then extended by

phosphoric acid diester bond. These steps

DNA polymerase III (orange). After 1000-2000

are repeated again for each nucleotide. The

nucleotides have been included, synthesis of

mechanism described means that the matrix

the fragment is interrupted and a new one is

can only be read in the 3

direction. In

begun, starting with another RNA primer that

other words, the newly synthesized strand

has been synthesized in the interim. The in-

always grows in the 5

direction. The

dividual Okazaki fragments are initially not

same mechanism is also used in transcription

bound to one another and still have RNA at

by DNA-dependent RNA polymerases

(see

the 5 end (3). At some distance from the fork,

p. 242). Most DNA and RNA polymerases con-

DNA polymerase I therefore starts to remove

sist of more than 10 subunits, the role of

the RNA primer and replace it with DNA com-

which is still unclear to some extent.

ponents. Finally, the gaps still remaining are

closed by a DNA ligase. In DNA double helices

formed in this way, only one of the strands has

B. Replication in E. coli

been newly synthesized—i. e., replication is

Although replication in prokaryotes is now

semiconservative.

well understood, many details in eukaryotes

In bacteria, some 1000 nucleotides are re-

are still unclear. However, it is certain that the

plicated per second. In eukaryotes, replication

process is in principle similar. A simplified

takes place more slowly (about 50 nucleotides

scheme of replication in the bacterium

s^-1) and the genome is larger. Thousands of

Escherichia coli is shown here.

replication forks are therefore active simulta-

In bacteria, replication starts at a specific

neously in eukaryotes.

point in the circular DNA—the origin of repli-

cation—and proceeds in both directions. This

results in two diverging replication forks, in

which the two strands are replicated simulta-

neously. Numerous proteins are involved in

Replication

241

A. Mechanism of DNA polymerases

Template

G G

Template

strand

H H

Newly synthe-

sized strand

Cyt

O H

Gua

O H₂C

H H

G G

HO H

Thy

DNA poly-

merase

2.7.7.7

Ade

O H₂C

H H

HO H

B. Replication in E. coli

Origin of

Replication fork

Old DNA strands

replication

New DNA strands

RNA primer

DNA polymerase III

Auxiliary proteins

2.7.7.7

DNA helicase 5.99.1.2

DNA gyrase 5.99.1.3

Okazaki

fragments

OF2

Single

strand

Movement of the

OF1

binding

replication fork

proteins

DNA polymerase I

2.7.7.7

OF3

DNA ligase

OF1

6.5.1.1

OF2

Replication is semiconservative

OF3

242

Molecular genetics

3 end of the promoter (“transcription start”)

Transcription

and continues until the polyadenylation se-

For the genetic information stored in DNA to

quence (see below) is reached. The primary

become effective, it has to be rewritten

transcript (hnRNA) still has a length of about

(transcribed) into RNA. DNA only serves as a

6.2 kbp. During RNA maturation, the non-

template and is not altered in any way by the

coding sequences corresponding to the in-

transcription process. Transcribable segments

trons are removed, and the two ends of the

of DNA that code for a defined product are

hnRNA are modified. The translatable mRNA

called genes. It is estimated that the mamma-

still has half the length of the hnRNA and is

lian genome contains 30 000-40 000 genes,

modified at both ends (see p. 246).

which together account for less than 5 % of the

In many eukaryotic genes, the proportion

DNA.

of introns is even higher. For example, the

gene for dihydrofolate reductase (see p. 402)

is over 30 kbp long. The information is dis-

A. Transcription and maturation of RNA:

tributed over six exons, which together have a

overview

length of only about 6 kbp.

Transcription is catalyzed by DNA-dependent

RNA polymerases. These act in a similar way to

C. Transcription process

DNA polymerases (see p. 240), except that

they incorporate ribonucleotides instead of

As mentioned above, RNA polymerase II

deoxyribonucleotides into the newly synthe-

(green) binds to the 3

end of the promoter

sized strand; also, they do not require a pri-

region. A sequence that is important for this

mer. Eukaryotic cells contain at least three

binding is known as the TATA box—a short A-

different types of RNA polymerase. RNA poly-

and T-rich sequence that varies slightly from

merase I synthesizes an RNA with a sedimen-

gene to gene. A typical base sequence (“con-

tation coef cient (see p. 200) of 45 S, which

sensus sequence”) is ...TATAAA... Numerous

serves as precursor for three ribosomal RNAs.

proteins known as basal transcription factors

The products of RNA polymerase II are

are necessary for the interaction of the poly-

hnRNAs, from which mRNAs later develop,

merase with this region. Additional factors

as well as precursors for snRNAs. Finally,

can promote or inhibit the process (transcrip-

RNA polymerase III transcribes genes that

tional control; see p. 244). Together with the

code for tRNAs, 5S rRNA, and certain snRNAs.

polymerase, they form the basal transcription

These precursors give rise to functional RNA

complex.

molecules by a process called RNA maturation

At the end of initiation (2), the polymerase

(see p. 246). Polymerases II and III are inhib-

is repeatedly phosphorylated, frees itself from

ited by D-amanitin, a toxin in the Amanita

the basal complex, and starts moving along

phalloides mushroom.

the DNA in the 3 direction. The enzyme sep-

arates a short stretch of the DNA double helix

into two single strands. The complementary

B. Organization of the PEP-CK gene

nucleoside triphosphates are bound by base

The way in which a typical eukaryotic gene is

pairing in the template strand and are linked

organized is illustrated here using a gene that

step by step to the hnRNA as it grows in the

codes for a key enzyme in gluconeogenesis

direction (3). Shortly after the begin-

(see p. 154)—the phosphoenolpyruvate car-

ning of elongation, the 5 end of the transcript

boxykinase (PEP-CK).

is protected by a “cap” (see p. 246). Once the

In the rat, the PEP-CK gene is nearly 7 kbp

polyadenylation sequence has been reached

(kilobase pairs) long. Only 1863 bp, distrib-

(typical sequence: .. .AATAA...), the transcript

uted over 10 coding segments (exons, dark

is released (4). Shortly after this, the RNA

blue) carry the information for the protein’s

polymerase stops transcribing and dissociates

621 amino acids. The remainder is allotted to

from the DNA.

the promoter (pink) and intervening sequen-

ces (introns, light blue). The gene’s promoter

region (approximately 1 kbp) serves for reg-

ulation (see p. 188). Transcription starts at the

Transcription

243

A. Transcription and maturation of RNA: overview

ATP, GTP, CTP, UTP

Transcription

Maturation

28S rRNA

Polymerase I

45S rRNA

18S rRNA

5.8S rRNA

hnRNA

mRNA

Polymerase II

snRNA-

snRNA

precursors

α-Amanitin

5S rRNA

Polymerase III

Precursors

tRNA

snRNA

DNA

DNA-directed RNA

polymerase 2.7.7.6

B. Organization of the PEP-CK gene

Translation

Transcription

Translation

Exon

Intron

end (TAA)

start

start (ATG)

Transcription

100 Bases

end

DNA

Promoter

region

Transcription

hn RNA

RNA maturation

Poly-A sequence

mRNA

Cap

AUG

UAA

C. Process of transcription

TATA-Box

Transcription start

Polyadenylation

...TATAAA..

..AATAAA..

sequence

Basal transcription complex

RNA Polymerase II

Template strand

Elongation

Cap

Termination

hnRNA

244

Molecular genetics

ent proteins are involved in the basal com-

Transcriptional control

plex. This alone, however, is still not suf cient

Although all cells contain the complete ge-

for transcription to start. In addition, positive

nome, they only use a fraction of the informa-

signals have to be emitted by more distant

tion in it. The genes known as “housekeeping

trans-active factors, integrated by the coacti-

genes,” which code for structural molecules

vator/mediator complex, and passed on to the

and enzymes of intermediate metabolism, are

basal complex (see B).

the only ones that undergo constant tran-

The actual signal for starting elongation

scription. The majority of genes are only ac-

consists of the multiple phosphorylation of a

tive in certain cell types, in specific metabolic

domain in the C-terminal region of the poly-

conditions, or during differentiation. Which

merase. In phosphorylated form, it releases

genes are transcribed and which are not is

itself from the basal complex along with a

regulated by transcriptional control (see also

few TFs and starts to synthesize hnRNA.

p. 118). This involves control elements (cis-

active elements) in the gene’s promoter re-

B. Regulation of PEP-CK transcription

gion and gene-specific regulatory proteins

(transcription factors, trans -active factors),

Phosphoenolpyruvate carboxykinase (PEP-CK),

which bind to the control elements and

a key enzyme in gluconeogenesis, is regulated

thereby activate or inhibit transcription.

by several hormones, all of which affect the

transcription of the PEP-CK gene. Cortisol,

glucagon, and thyroxin induce PEP-CK, while

A. Initiation of transcription

insulin inhibits its induction (see p. 158).

In the higher organisms, DNA is blocked by

More than ten control elements (dark red),

histones (see p. 238) and is therefore not ca-

distributed over approximately 1 kbp, have so

pable of being transcribed without special

far been identified in the promoter of the PEP-

positive regulation. In eukaryotes, it is there-

CK gene (top). These include response ele-

fore histones that play the role of repressors

ments for the glucocorticoid receptor (GRE;

(see p. 118). For transcription to be set in mo-

see p. 378), for the thyroxin receptor (TRE),

tion at all, the chromatin first has to be re-

and for the steroid-like retinoic acid (AF-1).

structured.

Additional control elements (CRE, cAMP-re-

In the resting state, the lysine residues in

sponsive element) bind the transcription fac-

the N-terminal “tail” of the histones

(see

tor C/EBP, which is activated by cAMP-de-

p. 238) are not acetylated. In this state, which

pendent protein kinase A through phosphor-

can be produced by histone deacetylases [1],

ylation. This is the way in which glucagon,

the nucleosomes are stable. It is only the in-

which raises the cAMP level (see p. 158),

teraction of activator and regulator proteins

works. Control element P1 binds the hor-

with their control elements that allows the

mone-independent factor NF-1 (nuclear fac-

binding of coactivator complexes that have

tor-1). All proteins that bind to the control

histone acetylase activity [2]. They acetylate

elements mentioned above are in contact

the histone tails and thereby loosen the nu-

with a coactivator/mediator complex (CBP/

cleosome structure suf ciently for the basal

p300), which integrates their input like a

transcription complex to form.

computer and transmits the result in the

This consists of DNA-dependent RNA poly-

form of stronger or weaker signals to the basal

merase II and basal transcription factors

transcription complex. Inhibition of PEP-CK

(TFIIX, X = A - H). First, the basal factor TFIID

transcription by insulin is mediated by an

binds to the promoter. TFIID, a large complex

insulin-responsive element (IRE) in the vicin-

of numerous proteins, contains TATA box-

ity of the GRE. Binding of an as yet unknown

binding protein

(TBP) and so-called TAFs

factor takes place here, inhibiting the binding

(TBP-associated factors). The polymerase is

of the glucocorticoid receptor to the GRE.

attached to this core with the help of TFIIB.

Before transcription starts, additional TFs

have to bind, including TFIIH, which has heli-

case activity and separates the two strands of

DNA during elongation. In all, some 35 differ-

Transcriptional control

245

A. Initiation of transcription

Enhancer

Histone deacetylase

Activator

Regulator Coactivator complex

(HRE)

protein

(histone acetylase)

TATA-Box

TATA box

Histone “tails”

Nucleosome Upstream promoter element

Coactivator complex

Histone deacetylase n.n.n.n

Mediator complex

TAFs

Histone acetyltransferase 2.3.1.48

RNA polymerase II

RNA polymerase 2.7.7.6

DNA topoisomerase I 5.99.1.2

D F

HRE - hormone response element

TAFs - TBP-associated factors

TBP BE

TBP - TATA box-binding protein

A-H - basal transcription factors

Basal transcription complex

B. Regulation of PEP-CK transcription

Control

AF-1 IRE GRE

TRE

CRE

P1 CRE

TATA-Box

element

Transcription

RAR

? GR

AP-1

C/EBP HNF-1

NF-1 C/EBP

TBP

Tran-

factor

(Fos/Jun)

CREB

scription

start

Receptors for retinoate

cortisol thyroxine

Insulin

PI₃K

Coactivator

Mediator

(CBP/p300)

GRE

Cortisol

NF-1

Thyroxin

TRE

C/EBP

CRE

TATA box

cAMP

Basal transcription complex

Glucagon

PK-A

C/EBP

246

Molecular genetics

are called snRNPs (small nuclear ribonucleo-

RNA maturation

protein particles, pronounced

“snurps”).

Before the hnRNA produced by RNA polymer-

SnRNPs occur in five different forms (U1, U2,

ase II (see p. 242) can leave the nucleus in

U4, U5, and U6). They consist of numerous

order to serve as a template for protein syn-

proteins and one molecule of snRNA each

thesis in the cytoplasm, it has to undergo

(see p. 82).

several modifications first. Even during tran-

To ensure that the RNA message is not

scription, the two ends of the transcript have

destroyed, splicing has to take place in a

additional nucleotides added (A). The sections

very precise fashion. The start and end of

that correspond to the intervening gene se-

the hnRNA introns are recognized by a char-

quences in the DNA (introns) are then cut out

acteristic sequence (...AGGT.. . at the 5

end or

(splicing; see B). Other transcripts—e. g., the

...[C,U]AGG... at the 3

end). Another impor-

45 S precursor of rRNA formed by polymerase

tant structure is the so-called branching point

I (see p. 242)—are broken down into smaller

inside the intron. Its sequence is less con-

fragments by nucleases before export into the

served than the terminal splicing sites, but it

cytoplasm.

always contains one adenosine residue (A).

During splicing, the 2 -OH group of this resi-

due—supported by the spliceosome

(see

A. 5

and 3 modification of mRNA

C)—attacks the phosphoric acid diester bond

Shortly after transcription begins in eukary-

at the 5

end of the intron and cleaves it (b).

otes, the end of the growing RNA is blocked in

Simultaneously, an unusual 2

bond is

several reaction steps by a structure known as

formed inside the intron, which thereby takes

a “cap.” In hnRNAs, this consists of a GTP

on a lasso shape (c; see formula). In the second

residue that is methylated at N-7 of the gua-

step of the splicing process, the free 3 -OH

nine ring. The β-phosphate residue of the cap

group at the end of the 5

terminal exon at-

is linked to the free 5 -OH group of the ter-

tacks the A-G bond at the 3 end of the intron.

minal ribose via an ester bond. After the

As a result, the two exons are linked and the

“polyadenylation signal” has been reached

intron is released, still in a lasso shape (d).

(typical sequence: ...AAUAAA...; see p. 242),

a polyadenylate “tail” consisting of up to 200

C. Spliceosome

AMP nucleotides is also added at the free 3

end of the transcript. This reaction is cata-

As described above, it is residues of the

lyzed by a special polyadenylate polymerase.

hnRNA that carry out bond cleavage and

It is only at this point that the mRNA leaves

bond formation during the splicing process.

the nucleus as a complex with RNA-binding

It is therefore not a protein enzyme that acts

proteins.

as a catalyst here, but rather an RNA. Catalytic

Both the cap and the poly-A tail play a vital

RNAs of this type are called ribozymes (see

part in initiating eukaryotic translation (see

also p. 88). The task of the spliceosomes is to

p. 250). They help position the ribosome cor-

fix and orientate the reacting groups by es-

rectly on the mRNA near to the starting co-

tablishing base pairings between snRNAs and

don. The protection which the additional nu-

segments of the hnRNA. The probable situa-

cleotides provide against premature enzy-

tion before the adenosine attack at the

matic degradation appears to be of lesser im-

branching point on the 5

splicing site (see

portance.

B, Fig. b) is shown schematically on the right

side of the illustration. In this phase, the U1

snRNA fixes the 5

splicing site, U2 fixes the

B. Splicing of hnRNA

branching site, and U5 fixes the ends of the

Immediately after transcription, the hnRNA

two exons.

introns are removed and the exons are linked

to form a continuous coding sequence. This

process, known as splicing, is supported by

complicated RNA-protein complexes in the

nucleus, the so-called spliceosomes. The com-

ponents of these macromolecular machines

RNA maturation

247

A. 5' and 3' modification

B. Splicing of hnRNA: mechanism

of mRNA

5' splicing

Branching

3' splicing

CH₃

site

point

site

...AG

...G

AC...

...CAGG...

H₂N

H₂C O P O

P O

5' exon

Intron

3' exon

P O

HO OH

CH₂

7-methyl guanosine

O OH

...A

..CA

GG...

m⁷Gppp N...

Cap

Lasso

5' end

structure

..CA

GG...

...AG

mRNA

...AG

GG...

...CA

CH₂

Ade

OH O

CH₂

Ade

Gua CH₂

O P

H H

Gua

CH₂

O P O

CH₂

Ade

H H

Poly-A sequence

O OH

Ade CH₂

To the 3' end

C. Spliceosome

Intron

Proteins

snRNA

snRNP

hnRNA

snRNA

U 4/6

5' exon

3' exon

Spliceosome (schematic)

248

Molecular genetics

tortions of the erythrocytes and disturbances

Amino acid activation

of O₂ transport (sickle-cell anemia).

A. The genetic code

B. Amino acid activation

Most of the genetic information stored in the

genome codes for the amino acid sequences

Some 20 different amino acid tRNA ligases in

of proteins. For these proteins to be ex-

the cytoplasm each bind one type of tRNA

pressed, a text in

“nucleic acid language”

(see p. 82) with the corresponding amino

therefore has to be translated into “protein

acid. This reaction, known as amino acid acti-

language.” This is the origin of the use of the

vation, is endergonic and is therefore coupled

term translation to describe protein biosyn-

to ATP cleavage in two steps.

thesis. The dictionary used for the translation

First, the amino acid is bound by the en-

is the genetic code.

zyme and reacts there with ATP to form di-

As there are 20 proteinogenic amino acids

phosphate and an “energy-rich” mixed acid

(see p. 60), the nucleic acid language has to

anhydride (aminoacyl adenylate). In the sec-

contain at least as many words (codons).

ond step, the 3 -OH group (in other ligases it

However, there are only four letters in the

is the 2 -OH group) of the terminal ribose

nucleic acid alphabet (A, G, C, and U or T). To

residue of the tRNA takes over the amino

obtain 20 different words from these, each

acid residue from the aminoacyl adenylate.

word has to be at least three letters long

In aminoacyl tRNAs, the carboxyl group of

(with two letters, there would only be

the amino acid is therefore esterified with

4² = 16 possibilities). And in fact the codons

the ribose residue of the terminal adenosine

do consist of three sequential bases (triplets).

of the sequence .. .CCA-3 .

Figure 1 shows the standard code in “DNA

The accuracy of translation primarily de-

language” (i. e., as a sequence of triplets in the

pends on the specificity of the amino acid

sense strand of DNA, read in the 5

3 direc-

tRNA ligases, as incorrectly incorporated

tion; see p. 84), represented as a circular dia-

amino acid residues are not recognized by

gram. The scheme is read from the inside to

the ribosome later. A “proofreading mecha-

the outside. For example, the triplet CAT codes

nism” in the active center of the ligase there-

for the amino acid histidine. With the excep-

fore ensures that incorrectly incorporated

tion of the exchange of U for T, the DNA co-

amino acid residues are immediately re-

dons are identical to those of mRNA.

moved again. On average, an error only occurs

As the genetic code provides 4³ = 64 co-

once every 1300 amino acid residues. This is a

dons for the 20 amino acids, there are several

surprisingly low rate considering how similar

synonymous codons for most amino acids—

some amino acids are—e. g., leucine and iso-

the code is degenerate. Three triplets do not

leucine.

code for amino acids, but instead signal the

end of translation

(stop codons). Another

C. Asp-tRNA ligase (dimer)

special codon, the start codon, marks the start

of translation. The code shown here is almost

The illustration shows the ligase responsible

universally applicable; only the mitochondria

for the activation of aspartate. Each subunit of

(see p. 210) and a few microorganisms devi-

the dimeric enzyme (protein parts shown in

ate from it slightly.

orange) binds one molecule of tRNA^Asp (blue).

As an example of the way in which the

The active centers can be located by the

code is read, Fig. 2

shows small sections

bound ATP (green). They are associated with

from the normal and a mutated form of the

the 3 end of the tRNA. Another domain in the

β-globin gene (see p. 280), as well as the cor-

protein (upper left) is responsible for “recog-

responding mRNA and protein sequences. The

nition” of the tRNA anticodon.

point mutation shown, which is relatively fre-

quent, leads to replacement of a glutamate

residue in position 6 of the β-chain by valine

(GAG GTG). As a consequence, the mutated

hemoglobin tends to aggregate in the deoxy-

genated form. This leads to sickle-shaped dis-

Genetic code

249

A. The genetic code

2. Normal globin

Sickle-cell globin

Gly

Phe

Leu

gene (β-chain)

Glu

Ser

Asp

C A

C C T

GAG

G AG

C C T

G AG

TCA

Tyr

G G A

C T C

C TC

G G A

C TC

Ala

TCAGTC

GTC

Stop

Transcription

Cys

mRNA

Val

Stop

C C UG AG G AG

C C UG UG G AG

Trp

CUC

C AC

Glu-

Val-

Arg

tRNA

Leu

Ser

Glu

Val

Lys

Pro

Translation

Asn

His

Thr

Gln

Pro Glu Glu

Pro

Val

Glu

Met

Ile

Arg

Start

His

Mutation

Example

B. Amino acid activation

C. Asp-tRNA-Ligase (Dimer)

Amino acid

Anticodon recognition domain

H₃N

R C C O

P O CH₂

tRNAAsp

O Ade

ATP

H H

3' 2'

HO OH

Aminoacyl adenylate

H₃N

P O CH₂

O Ade

H H

ATP

HO OH

Active

CH2 Ade

AMP

center

Active

O OH

center

tRNA

H₃N

H H

O OH

Protein

3' 2'

Cyt

Amino acid-

CH2 Ade

tRNA ligase

O OH

6.1.1.n

Amino

acyl

Asp

3' 2'

tRNA

H H

tRNA

Cyt

250

Molecular genetics

ing a single mRNA molecule simultaneously.

Translation I: initiation

The ribosome first binds near the start codon

Like amino acid activation (see p. 248), pro-

(AUG; see p. 248) at the 5 end of the mRNA

tein biosynthesis (translation) takes place in

(top). During translation, the ribosome moves

the cytoplasm. It is catalyzed by complex

in the direction of the 3 end until it reaches a

nucleoprotein particles, the ribosomes, and

stop codon (UAA, UAG, or UGA). At this point,

mainly requires GTP to cover its energy re-

the newly synthesized chain is released, and

quirements.

the ribosome dissociates again into its two

subunits.

A. Structure of the eukaryotic ribosome

C. Initiation of translation in E. coli

Ribosomes consist of two subunits of different

size, made up of ribosomal RNA (rRNA) and

Protein synthesis in prokaryotes is in princi-

nearly 80 proteins (the number of proteins

ple the same as in eukaryotes. However, as the

applies to rat liver ribosomes). It is customary

process is simpler and has been better studied

to give the sedimentation coef cients (see

in prokaryotes, the details involved in trans-

p. 200) of ribosomes and their components

lation are discussed here and on p. 252 using

instead of their masses. For example, the eu-

the example of the bacterium Escherichia coli.

karyotic ribosome has a sedimentation coef-

The first phase of translation, initiation, in-

ficient of 80 Svedberg units (80 S), while the

volves several steps. First, two proteins, ini-

sedimentation coef cients of its subunits are

tiation factors IF-1 and IF-3, bind to the 30 S

40 S and 60 S (S values are not additive).

subunit (1). Another factor, IF-2, binds as a

The smaller 40 S subunit consists of one

complex with GTP (2). This allows the subunit

molecule of 18 S rRNA and 33 protein mole-

to associate with the mRNA and makes it

cules. The larger 60 S subunit contains three

possible for a special tRNA to bind to the start

types of rRNA with sedimentation coef cients

codon (3). In prokaryotes, this starter tRNA

of 5 S, 5.8 S, and 28 S and 47 proteins. In the

carries the substituted amino acid N-

presence of mRNA, the subunits assemble to

formylmethionine (fMet). In eukaryotes, it car-

form the complete ribosome, with a mass

ries an unsubstituted methionine. Finally, the

about 650 times larger than that of a hemo-

50 S subunit binds to the above complex (4).

globin molecule.

During steps 3 and 4, the initiation factors are

The arrangement of the individual compo-

released again, and the GTP bound to IF-2 is

nents of a ribosome has now been deter-

hydrolyzed to GDP and P_i.

mined for prokaryotic ribosomes. It is known

In the 70 S initiation complex, formylme-

that filamentous mRNA passes through a cleft

thionine tRNA is initially located at a binding

between the two subunits near the charac-

site known as the peptidyl site (P). A second

teristic “horn” on the small subunit. tRNAs

binding site, the acceptor site (A), is not yet

also bind near this site. The illustration shows

occupied during this phase of translation.

the size of a tRNA molecule for comparison.

Sometimes, a third tRNA binding site is de-

Prokaryotic ribosomes have a similar struc-

fined as an exit site (E), from which uncharged

ture, but are somewhat smaller than those of

tRNAs leave the ribosome again (see p. 252;

eukaryotes

(sedimentation coef cient

70 S

not shown).

for the complete ribosome, 30 S and 50 S for

the subunits). Mitochondrial and chloroplast

ribosomes are comparable to prokaryotic

ones.

B. Polysomes

In cells that are carrying out intensive protein

synthesis, ribosomes are often found in a lin-

ear arrangement like a string of pearls; these

are known as polysomes. This arrangement

arises because several ribosomes are translat-

Protein biosynthesis

251

A. Structure of eukaryotic ribosomes

5S-RNA

5.8S-RNA

Large

Ribosome (80S)

(120 nt)

(160 nt)

subunit (60S)

4.2 · 10⁶ Da

2.8 · 10⁶ Da

mRNA

49 Proteins

28S-RNA (4718 nt)

tRNA

Small

subunit (40S)

1.4 · 106 Da

33 Proteins

18S-RNA (1874 nt)

mRNA

Hemoglobin

at the same scale

B. Polysome

C. Initiation of translation in E. coli

GTP

Start

IF-2

IF-1

codon

GTP

(AUG)

IF-2

IF-3

mRNA

IF-3

IF-1

50S

Direction of

subunit

tRNA-

f-Met

IF-3

ribosomal

movement

30S

subunit

GTP

IF-1

IF-2

f-Met

Growing

peptide

chain

Protein

tRNA

Termination

Elongation

70S-

Protein

Initiation

mRNA

complex

rRNA

Stop codon

(16S)

(UAA,UAG

UGA)

IF-1

f-Met

IF-2

Formyl-

60S

methionine

GDP

40S

252

Molecular genetics

[3] After the transfer of the growing pep-

Translation II: elongation and

tide to the A site, the free tRNA at the P site

termination

dissociates and another GTP-containing elon-

gation factor (EF-G GTP) binds to the ribo-

After translation has been initiated

(see

some. Hydrolysis of the GTP in this factor

p. 250), the peptide chain is extended by the

provides the energy for translocation of the

addition of further amino acid residues

ribosome. During this process, the ribosome

(elongation) until the ribosome reaches a

moves three bases along the mRNA in the

stop codon on the mRNA and the process is

direction of the 3

end. The tRNA carrying

interrupted (termination).

the peptide chain is stationary relative to

the mRNA and reaches the ribosome’s P site

A. Elongation and termination of protein

during translocation, while the next mRNA

biosynthesis in E. coli

codon (in this case GUG) appears at the A site.

[4] The uncharged Val-tRNA then dissoci-

Elongation can be divided into four phases:

ates from the E site. The ribosome is now

[1] Binding of aminoacyl tRNA. First, the

ready for the next elongation cycle.

peptidyl site (P) of the ribosome is occupied

When one of the three stop codons (UAA,

by a tRNA that carries at its 3

end the com-

UAG, or UGA) appears at the A site, termi-

plete peptide chain formed up to this point

nation starts.

(top left). A second tRNA, loaded with the

[5] There are no complementary tRNAs for

next amino acid (Val-tRNA^Val in the example

the stop codons. Instead, two releasing factors

shown), then binds via its complementary

bind to the ribosome. One of these factors

anticodon (see p. 82) to the mRNA codon ex-

(RF-1) catalyzes hydrolytic cleavage of the

posed at the acceptor site (in this case GUG).

ester bond between the tRNA and the C-ter-

The tRNA binds as a complex with a GTP-

minus of the peptide chain, thereby releasing

containing protein, the elongation factor Tu

the protein.

(EF-Tu) (1a). It is only after the bound GTP

[6] Hydrolysis of GTP by factor RF-3 sup-

has been hydrolyzed to GDP and phosphate

plies the energy for the dissociation of the

that EF-Tu dissociates again (1b). As the bind-

whole complex into its component parts.

ing of the tRNA to the mRNA is still loose

Energy requirements in protein synthesis

before this, GTP hydrolysis acts as a delaying

are high. Four energy-rich phosphoric acid

factor, making it possible to check whether

anhydride bonds are hydrolyzed for each

the correct tRNA has been bound. A further

amino acid residue. Amino acid activation

protein, the elongation factor Ts (EF-Ts), later

uses up two energy-rich bonds per amino

catalyzes the exchange of GDP for GTP and in

acid (ATP AMP + PP; see p. 248), and two

this way regenerates the EF-Tu GTP com-

GTPs are consumed per elongation cycle. In

plex. EF-Tu is related to the G proteins in-

addition, initiation and termination each re-

volved in signal transduction (see p. 384).

quire one GTP per chain.

[2] Synthesis of the peptide bond takes

place in the next step. Ribosomal peptidyl-

transferase catalyzes (without consumption

Further information

of ATP or GTP) the transfer of the peptide

In eukaryotic cells, the number of initiation

chain from the tRNA at the P site to the NH₂

factors is larger and initiation is therefore

group of the amino acid residue of the tRNA at

more complex than in prokaryotes. The cap

the A site. The ribosome’s peptidyltransferase

at the 5 end of mRNA and the polyA tail (see

activity is not located in one of the ribosomal

p. 246) play important parts in initiation.

proteins, but in the 28 S rRNA. Catalytically

However, the elongation and termination

active RNAs of this type are known as ribo-

processes are similar in all organisms. The

zymes (cf. p. 246). It is thought that the few

individual steps of bacterial translation can

surviving ribozymes are remnants of the “RNA

be inhibited by antibiotics (see p. 254).

world”—an early phase of evolution in which

proteins were not as important as they are

today.

254

Molecular genetics

synthesized by fungi and have a reactive β-

Antibiotics

lactam ring. They are mainly used against

Gram-positive pathogens, in which they in-

A. Antibiotics: overview

hibit cell wall synthesis (C).

Antibiotics are substances which, even at low

The first synthetic antibiotics were the

concentrations, inhibit the growth and repro-

sulfonamides (right). As analogues of p-ami-

duction of bacteria and fungi. The treatment

nobenzoic acid, these affect the synthesis of

of infectious diseases would be inconceivable

folic acid, an essential precursor of the coen-

today without antibiotics. Substances that

zyme THF (see p. 108). Transport antibiotics

only restrict the reproduction of bacteria are

(top center) have the properties of ion chan-

described as having bacteriostatic effects (or

nels (see p. 222). When they are deposited in

fungistatic for fungi). If the target cells are

the plasma membrane, it leads to a loss of ions

killed, then the term bactericidal (or fungici-

that damages the bacterial cells.

dal) is used. Almost all antibiotics are pro-

duced by microorganisms—mainly bacteria

B. Intercalators

of the genus Streptomyces and certain fungi.

However, there are also synthetic antibacte-

The effects of intercalators (see also p. 262)

rial substances, such as sulfonamides and gy-

are illustrated here using the example of the

rase inhibitors.

daunomycin-DNA complex, in which two

A constantly increasing problem in antibi-

daunomycin molecules (red) are inserted in

otic treatment is the development of resistant

the double helix (blue). The antibiotic’s ring

pathogens that no longer respond to the

system inserts itself between G/C base pairs

drugs available. The illustration shows a few

(bottom), while the sugar moiety occupies the

of the therapeutically important antibiotics

minor groove in the DNA (above). This leads

and their sites of action in the bacterial me-

to a localized change of the DNA conforma-

tabolism.

tion that prevents replication and transcrip-

Substances known as intercalators, such as

tion.

rifamycin and actinomycin D (bottom) are de-

posited in the DNA double helix and thereby

C. Penicillin as a “suicide substrate”

interfere with replication and transcription

(B). As DNA is the same in all cells, intercalat-

The site of action in the β-lactam antibiotics is

ing antibiotics are also toxic for eukaryotes,

muramoylpentapeptide carboxypeptidase, an

however. They are therefore only used as cy-

enzyme that is essential for cross-linking of

tostatic agents (see p. 402). Synthetic inhib-

bacterial cell walls. The antibiotic resembles

itors of DNA topoisomerase II (see p. 240),

the substrate of this enzyme (a peptide with

known as gyrase inhibitors (center), restrict

the C-terminal sequence D-Ala-D-Ala) and is

replication and thus bacterial reproduction.

therefore reversibly bound in the active cen-

A large group of antibiotics attack bacterial

ter. This brings the β-lactam ring into prox-

ribosomes. These inhibitors of translation

imity with an essential serine residue of the

(left) include the tetracyclines—broad-spec-

enzyme. Nucleophilic substitution then re-

trum antibiotics that are effective against a

sults in the formation of a stable covalent

large number of different pathogens. The ami-

bond between the enzyme and the inhibitor,

noglycosides, of which streptomycin is the

blocking the active center (see p. 96). In divid-

best-known, affect all phases of translation.

ing bacteria, the loss of activity of the enzyme

Erythromycin impairs the normal functioning

leads to the formation of unstable cell walls

of the large ribosomal subunit. Chlorampheni-

and eventually death.

col, one of the few natural nitro compounds,

inhibits ribosomal peptidyltransferase. Fi-

nally, puromycin mimics an aminoacyl tRNA

and therefore leads to premature interruption

of elongation.

The E-lactam antibiotics (bottom right) are

also frequently used. The members of this

group, the penicillins and cephalosporins, are

Antibiotics

255

A. Antibiotics: overview

H₃C

CH₃

Transport antibiotics

CH₃

H₂N

NH₂

Sulfathiazole

Ion channel

HO O OH O

DNA

Sulfonamides

Tetracycline

Proteins

Folate

Gyrase

synthesis

inhibitors

Aminoglycosides

Tetracyclines

Replication

Erythromycin

Precursors

Puromycin

THF

Translation

Chloramphenicol

Cell wall

synthesis

Transcription

Penicillins

Cephalosporins

mRNA

DNA

Rifamycin

CHCl

Actinomycin D

NH₃

Daunomycin

CH₃

Outer

Inner

Nitro

membrane

Murein

membrane

group

C N

CH₃

NO₂

H COO

Chloramphenicol

Ampicillin

B. Intercalators

C. Penicillin as “suicide substrate”

R''

O OH

R''-D-Ala-

CH₃

D-Ala

(substrate)

H O

H₃CO O OH

Daunomycin

CH₃

H H

H₃N

Penicillin

(inhibitor)

CH₃

C N

CH₃

C HN

CH₃

C/G pair

H COO

G/C pair

Serine residue

Enzyme-inhibitor

Covalent acyl enzyme

Daunomycin-DNA complex

complex

256

Molecular genetics

B. Effects

Mutation and repair

Nitrous acid causes point mutations (1). For

Genetic information is set down in the base

example, C is converted to U, which in the

sequence of DNA. Changes in the DNA bases

next replication pairs with A instead of G.

or their sequence therefore have mutagenic

The alteration thus becomes permanent. Mu-

effects. Mutagens often also damage growth

tations in which a number of nucleotides not

regulation in cells, and they are then also

divisible by three are inserted or removed

carcinogenic

(see p. 400). Gene alterations

lead to reading errors in whole segments of

(mutations) are one of the decisive positive

DNA, as they move the reading frame (frame-

factors in biological evolution. On the other

shift mutations). This is shown in Fig. 2 using

hand, an excessive mutation frequency would

a simple example. From the inserted C on-

threaten the survival of individual organisms

wards, the resulting mRNA is interpreted dif-

or entire species. For this reason, every cell

ferently during translation, producing a com-

has repair mechanisms that eliminate most of

pletely new protein sequence.

the DNA changes arising from mutations (C).

C. Repair mechanisms

A. Mutagenic agents

An important mechanism for the removal of

Mutations can arise as a result of physical or

DNA damage is excision repair (1). In this

chemical effects, or they can be due to acci-

process, a specific excision endonuclease re-

dental errors in DNA replication and recombi-

moves a complete segment of DNA on both

nation.

sides of the error site. Using the sequence of

The principal physical mutagen is ionizing

the opposite strand, the missing segment is

radiation (α, β, and γ radiation, X-rays). In

then replaced by a DNA polymerase. Finally, a

cells, it produces free radicals

(molecules

DNA ligase closes the gaps again.

with unpaired electrons), which are ex-

Thymine dimers can be removed by

tremely reactive and can damage DNA.

photoreactivation (2). A specific photolyase

Short-wavelength ultraviolet light (UV light)

binds at the defect and, when illuminated,

also has mutagenic effects, mainly in skin cells

cleaves the dimer to yield two single bases

(sunburn). The most common chemical

again.

change due to UV exposure is the formation

A third mechanism is recombination repair

of thymine dimers, in which two neighboring

(3, shown in simplified form). In this process,

thymine bases become covalently linked to

the defect is omitted during replication. The

one another (2). This results in errors when the

gap is closed by shifting the corresponding

DNA is read during replication and transcription.

sequence from the correctly replicated second

Only a few examples of the group of chem-

strand. The new gap that results is then filled

ical mutagens are shown here. Nitrous acid

by polymerases and ligases. Finally, the orig-

(HNO₂; salt: nitrite) and hydroxylamine

inal defect is corrected by excision repair as in

(NH₂OH) both deaminate bases; they convert

Fig. 1 (not shown).

cytosine to uracil and adenine to inosine.

Alkylating compounds carry reactive

groups that can form covalent bonds with

DNA bases (see also p. 402). Methylnitro-

samines (3) release the reactive methyl cation

(CH₃₊), which methylates OH and NH₂ groups

in DNA. The dangerous carcinogen benzo

[a]pyrene is an aromatic hydrocarbon that is

only converted into the active form in the

organism (4; see p. 316). Multiple hydroxyla-

tion of one of the rings produces a reactive

epoxide that can react with NH₂ groups in

guanine residues, for example. Free radicals

of benzo[a ]pyrene also contribute to its tox-

icity.

Mutation and repair

257

A. Mutagenic agents

Ionizing

Alkylating

Reactive

radiation

compounds

methyl

group

CH₃

HNO₂

α, β, γ

[CH

3 ]

radi-

ation

CH₃

CHC

Methylnitrosamine

Desami-

Free

CHC

CH₃

Epoxide

nation

radicals

2. Thymine dimer

Deletions

insertions

C H

due to

faulty

recombination

Formation Base

Spon-

Chemical

Mutagenic

exchange

taneous

modificaton

derivative of

pyrimidine

C U

loss of

of bases

benzo(a)pyrene

dimers

A I

bases

B. Effects

C. Repair mechanisms

Thymine dimer

HNO₂

Base

exchange

Excision

endonuclease

Photo-

GTAUC

lyase

CAT

4.1.99.3

Replication

Light

GTA

CAT

Defect-

binding

Normal

Replication

protein

GTAT

2. Photoreactivation

CATAGA

Single-strand

Permanent

binding

DNA poly-

proteins

change

Replication

merase

1. Point mutation

Insertion

CTA

CATGG

DNA ligase

Repaired DNA

·· Val-Pro-

·· -Ala-Thr-X

··

2. Frameshift mutation

1. Excision repair

3. Recombinational repair

258

Molecular genetics

B. DNA cloning

DNA cloning

Most DNA segments—e. g., genes—occur in

The growth of molecular genetics since 1970

very small quantities in the cell. To be able

has mainly been based on the development

to work with them experimentally, a large

and refinement of methods of analyzing and

number of identical copies (“clones”) first

manipulating DNA. Genetic engineering has

have to be produced. The classic procedure

practical applications in many fields. For ex-

for cloning DNA takes advantage of the ability

ample, it has provided new methods of diag-

of bacteria to take up and replicate short,

nosing and treating diseases, and it is now

circular DNA fragments known as plasmids.

also possible to create targeted changes in

The segment to be cloned is first cut out of

specific characteristics of organisms. Since bi-

the original DNA using restriction endonu-

ological risks cannot be completely ruled out

cleases (see above; for the sake of simplicity,

with these procedures, it is particularly im-

cleavage using EcoRI alone is shown here, but

portant to act responsibly when dealing with

in practice two different enzymes are usually

genetic engineering. A short overview of im-

used). As a vehicle (“vector”), a plasmid is

portant methods involved in genetic engi-

needed that has only one EcoRI cleavage site.

neering is provided here and on the following

The plasmid rings are first opened by cleavage

pages.

with EcoRI and then mixed with the isolated

DNA fragments. Since the fragment and the

A. Restriction endonucleases

vector have the same overhanging ends, some

of the molecules will hybridize in such a way

In many genetic engineering procedures, de-

that the fragment is incorporated into the

fined DNA fragments have to be isolated and

vector DNA. When the cleavage sites are

then newly combined with other DNA seg-

now closed again using DNA ligase, a newly

ments. For this purpose, enzymes are used

combined (“recombinant”) plasmid arises.

that can cut DNA and join it together again

By pretreating a large number of host cells,

inside the cell. Of particular importance are

one can cause some of them to take up the

restriction endonucleases—a group of bacterial

plasmid (a process known as transformation)

enzymes that cleave the DNA double strand in

and replicate it along with their own genome

a sequence-specific way. The numerous re-

when reproducing. To ensure that only host

striction enzymes known are named using

bacteria that contain the plasmid replicate,

abbreviations based on the organism from

plasmids are used that give the host resistance

which they originate. The example used

to a particular antibiotic. When the bacteria

here is EcoRI, a nuclease isolated from the

are incubated in the presence of this antibi-

bacterium Escherichia coli.

otic, only the cells containing the plasmid will

Like many other restriction endonucleases,

replicate. The plasmid is then isolated from

EcoRI cleaves DNA at the site of a palin-

these cells, cleaved with EcoRI again, and the

drome—i. e., a short segment of DNA in which

fragments are separated using agarose gel

both the strand and counter-strand have the

electrophoresis (see p. 262). The desired frag-

same sequence (each read in the 5

3 direc-

ment can be identified using its size and then

tion). In this case, the sequence is 5 -GAATTC-

extracted from the gel and used for further

3 . EcoRI, a homodimer, cleaves the phos-

experiments.

phoric acid diester bonds in both strands be-

tween G and A. This results in the formation of

complementary overhanging or “sticky” ends

(AATT), which are held together by base pair-

ing. However, they are easily separated—e. g.

by heating. When the fragments are cooled,

the overhanging ends hybridize again in the

correct arrangement. The cleavage sites can

then be sealed again by a DNA ligase.

260

Molecular genetics

B. Sequencing of DNA

DNA sequencing

The nucleotide sequence of DNA is nowadays

A. Gene libraries

usually determined using the so-called chain

termination method. In single-strand se-

It is often necessary in genetic engineering to

quencing, the DNA fragment (a) is cloned

isolate a DNA segment when its details are not

into the DNA of phage M13 (see p. 404),

fully known—e. g., in order to determine its

from which the coded single strand can be

nucleotide sequence. In this case, one can use

easily isolated. This is hybridized with a pri-

what are known as DNA libraries. A DNA li-

mer—a short, synthetically produced DNA

brary consists of a large number of vector DNA

fragment that binds to 3

end of the intro-

molecules containing different fragments of

duced DNA segment (b).

foreign DNA. For example, it is possible to take

Based on this hybrid, the missing second

all of the mRNA molecules present in a cell and

strand can now be generated in the test tube

transcribe them into DNA. These DNA frag-

by adding the four deoxyribonucleoside tri-

ments (known as copy DNA or cDNA) are then

phosphates (dNTP) and a suitable DNA poly-

randomly introduced into vector molecules.

merase (c). The trick lies in also adding small

A library of genomic DNA can be estab-

amounts of dideoxynucleoside triphosphates

lished by cleaving the total DNA from a cell

(ddNTP). Incorporating a ddNTP leads to the

into small fragments using restriction endo-

termination of second-strand synthesis. This

nucleases (see p. 258), and then incorporating

can occur whenever the corresponding dNTP

these into vector DNA. Suitable vectors for

ought to be incorporated. The illustration

gene libraries include bacteriophages, for ex-

shows this in detail using the example of

ample (“phages” for short). Phages are viruses

ddGTP. In this case, fragments are obtained

that only infect bacteria and are replicated by

that each include the primer plus three, six,

them (see p. 404). Gene libraries have the

eight, 13, or 14 additional nucleotides. Four

advantage that they can be searched for spe-

separate reactions, each with a different

cific DNA segments, using hybridization with

ddNTP, are carried out (c), and the products

oligonucleotides.

are placed side by side on a supporting mate-

The first step is to strongly dilute a small

rial. The fragments are then separated by gel

part of the library (10⁵-10⁶ phages in a small

electrophoresis

(see p. 76), in which they

volume), mix it with host bacteria, and plate

move in relation to their length.

out the mixture onto nutrient medium. The

Following visualization (d), the sequence of

bacteria grow and form a continuous cloudy

the fragments in the individual lanes is simply

layer of cells. Bacteria infected by phages

read from bottom to top (e) to directly obtain

grow more slowly. In their surroundings, the

the nucleotide sequence. A detail from such a

bacterial “lawn” is less dense, and a clearer

sequencing gel and the corresponding protein

circular zone known as a plaque forms. The

sequence are shown in Fig. 2.

bacteria in this type of plaque exclusively

In a more modern procedure, the four

contain the offspring of a single phage from

ddNTPs are covalently marked with fluores-

the library.

cent dyes, which produce a different color for

The next step is to make an impression of

each ddNTP on laser illumination. This allows

the plate on a plastic foil, which is then

the sequence in which the individual frag-

heated. This causes the phage DNA to adhere

ments appear at the lower end of the gel to

to the foil. When the foil is incubated with a

be continuously recorded and directly stored

DNA fragment that hybridizes to the DNA seg-

in digital form.

ment of interest (a gene probe), the probe

binds to the sites on the imprint at which

the desired DNA is attached. Binding of the

gene probe can be detected by prior radio-

active or other labeling of the probe. Phages

from the positive plaques in the original plate

are then isolated and replicated. Restriction

cleavage finally provides large amounts of the

desired DNA.

Genetic engineering

261

A. Gene libraries

Imprint on

Host cell

plastic membrane

Gene library

in phages

Gene probe

Plate

Hybrid-

with phage plaques

ization

Positive plaque

Washing,

detection

of the

gene probe

DNA

Gene

Gene probe

isolation

Phage

Restriction

repli-

Cloned gene

cation

Membrane

B. Sequencing of DNA

G A T C

Protein

sequence

Synthetic primer

Single-stranded preparation

Hybridization

DNA

sequence

Phe

Tyr

+ 4 dNTP

+ ddGTP

+ ddATP

+ ddTTP

+ ddCTP

+ Polymerase

Ala

A T C

Thr

Example:

= ddG

Glu

Gel electrophoresis

Met

Visualization of the fragments

Reading off (

) : ACGATG ...

1. Method

2. Sequence pattern

262

Molecular genetics

on their mass alone. The supporting material

PCR and protein expression

generally used in genetic engineering is a gel

of the polysaccharide agarose

(see p. 40).

A. Polymerase chain reaction (PCR)

Agarose gels are not very stable and are there-

The polymerase chain reaction (PCR) is an

fore poured horizontally into a plastic cham-

important procedure in genetic engineering

ber in which they are used for separation

that allows any DNA segment to be replicated

(top).

(amplified) without the need for restriction

To make the separated fragments visible,

enzymes, vectors, or host cells (see p. 258).

after running the procedure the gels are

However, the nucleotide sequence of the seg-

placed in solutions of ethidium bromide.

ment has to be known. Two oligonucleotides

This is an intercalator (see p. 254) that shows

(primers) are needed, which each hybridize

strong fluorescence in UV light after binding

with one of the strands at each end of the DNA

to DNA, although it barely fluoresces in an

segment to be amplified; also needed are suf-

aqueous solution. The result of separating

ficient quantities of the four deoxyribonucleo-

two PCR amplificates (lanes 1 and 2) is shown

side triphosphates and a special heat-tolerant

in the lower part of the illustration. Compar-

DNA polymerase. The primers are produced

ing their distances with those of poly-

by chemical synthesis, and the polymerase is

nucleotides of known lengths (lane 3; bp =

obtained from thermostable bacteria.

base pairs) yields lengths of approximately

First, the starter is heated to around 90 °C

800 bp for fragment 1 and 1800 bp for frag-

to separate the DNA double helix into single

ment 2. After staining, the bands can be cut

strands

(a; cf. p. 84). The mixture is then

out of the gel and the DNA can be extracted

cooled to allow hybridization of the primers

from them and used for further experiments.

(b). Starting from the primers, complemen-

tary DNA strands are now synthesized in

C. Overexpression of proteins

both directions by the polymerase (c). This

cycle (cycle 1) is repeated 20-30 times with

To treat some diseases, proteins are needed

the same reaction mixture (cycle 2 and sub-

that occur in such small quantities in the or-

sequent cycles). The cyclic heating and cool-

ganism that isolating them on a large scale

ing are carried out by computer-controlled

would not be economically feasible. Proteins

thermostats.

of this type can be obtained by overexpression

After only the third cycle, double strands

in bacteria or eukaryotic cells. To do this, the

start to form with a length equal to the dis-

corresponding gene is isolated from human

tance between the two primers. The propor-

DNA and cloned into an expression plasmid

tion of these approximately doubles during

as described on p. 258. In addition to the gene

each cycle, until almost all of the newly syn-

itself, the plasmid also has to contain DNA

thesized segments have the correct length.

segments that allow replication by the host

cell and transcription of the gene. After trans-

formation and replication of suitable host

B. DNA electrophoresis

cells, induction is used in a targeted fashion

The separation of DNA fragments by electro-

to trigger ef cient transcription of the gene.

phoresis is technically simpler than protein

Translation of the mRNA formed in the host

electrophoresis (see p. 78). The mobility of

cell then gives rise to large amounts of the

molecules in an electrical field of a given

desired protein. Human insulin (see p. 76),

strength depends on the size and shape of

plasminogen activators for dissolving blood

the molecules, as well as their charge. In con-

clots (see p. 292), and the growth hormone

trast to proteins, in which all three factors

somatotropin are among the proteins pro-

vary, the ratio of mass to charge in nucleic

duced in this way.

acids is constant, as all of the nucleotide com-

ponents have similar masses and carry one

negative charge. When electrophoresis is car-

ried out in a wide-meshed support material

that does not separate according to size and

shape, the mobility of the molecules depends

264

Molecular genetics

amplify a segment of this DNA with virus-

Genetic engineering in medicine

specific primers. In this way, an amplificate

Genetic engineering procedures are becom-

with a characteristic length can be obtained

ing more and more important in medicine

for each pathogen and identified using gel

for diagnostic purposes (A-C). New genetic

electrophoresis as described above.

approaches to the treatment of severe dis-

eases are still in the developmental stage

D. Gene therapy

(“gene therapy,” D).

Many diseases, such as hereditary metabolic

defects and tumors, can still not be ad-

A. DNA fingerprinting

equately treated. About 10 years ago, projects

were therefore initiated that aimed to treat

DNA fingerprinting is used to link small

diseases of this type by transferring genes

amounts of biological material—e. g., traces

into the affected cells (gene therapy). The

from the site of a crime—to a specific person.

illustration combines conceivable and already

The procedure now used is based on the fact

implemented approaches to gene therapy for

that the human genome contains non-coding

metabolic defects (left) and tumors (right).

repetitive DNA sequences, the length of which

None of these procedures has yet become

varies from individual to individual. Short

established in clinical practice.

tandem repeats (STRs) thus exist in which

If a mutation leads to failure of an enzyme

dinucleotides (e. g., -T-X-) are frequently re-

E1 (left), its substrate B will no longer be

peated. Each STR can occur in five to 15 differ-

converted into C and will accumulate. This

ent lengths (alleles), of which one individual

can lead to cell damage by B itself or by a

possesses only one or two. When the various

toxic product formed from it. Treatment

allele combinations for several STRs are de-

with intact E1 is not possible, as the proteins

termined after PCR amplification of the DNA

are not capable of passing through the cell

being investigated, a “genetic fingerprint” of

membrane. By contrast, it is in principle pos-

the individual from whom the DNA originates

sible to introduce foreign genes into the cell

is obtained. Using comparative material—e. g.,

using viruses as vectors (adenoviruses or ret-

saliva samples—definite identification is then

roviruses are mainly used). Their gene prod-

possible.

ucts could replace the defective E1 or convert

B into a harmless product. Another approach

B. Diagnosis of sickle-cell anemia using RFLP

uses the so-called antisense DNA (bottom

This example illustrates a procedure for diag-

right). This consists of polynucleotides that

nosing a point mutation in the β-globin gene

hybridize with the mRNA for specific cellular

that leads to sickle-cell anemia (see p. 248).

proteins and thereby prevent their transla-

The mutation in the first exon of the gene

tion. In the case shown, the synthesis of E2

destroys a cleavage site for the restriction

could be blocked, for example.

endonuclease MstII (see p. 258). When the

The main problem in chemotherapy for

DNA of healthy and diseased individuals is

tumors is the lack of tumor-specificity in the

cleaved with MstII, different fragments are

highly toxic cytostatic agents used

(see

produced in the region of the β-globin gene,

p. 402). Attempts are therefore being made

which can be separated by electrophoresis

to introduce into tumor cells genes with prod-

and then demonstrated using specific probes

ucts that are only released from a precursor to

(see p. 260). In addition, heterozygotic car-

form active cytostatics once they have

riers of the sickle-cell gene can be distin-

reached their target (left). Other gene prod-

guished from homozygotic ones.

ucts are meant to force the cells into apoptosis

(see p. 396) or make them more susceptible

C. Identification of viral DNA using RT-PCR

to attack by the immune system. To steer the

In viral infections, it is often dif cult to deter-

viral vectors to the tumor

(targeting), at-

mine the species of the pathogen precisely.

tempts are being made to express proteins

RT-PCR can be used to identify RNA viruses. In

on the virus surface that are bound by tu-

this procedure, reverse transcriptase

(see

mor-specific receptors. Fusion with a tumor-

p. 404) is used to transcribe the viral RNA

specific promoter could also help limit the

into dsDNA, and then PCR is employed to

effect of the foreign gene to the tumor cells.

Genetic engineering

265

A. DNA fingerprinting

B. Diagnosis of sickle-cell anemia using RFLP

STR, z.B.

Mst II

TCTATCTGTCTG

DNA

1200 bp

201 bp

Normal

Extraction

gene

Sickle-cell

gene

1401 bp

Evidence

Mst II

PCR

Mutation

Locus 1

1.4

Locus 2

1 Normal (A/A)

1.2

2 Heterozygotic (A/S)

Locus 3

kbp

3 Homozygotic (S/S)

Amplificate

Comparative

C. Evidence of viral DNA using RT-PCR

fragments

RNA Hy-

ss-

ds-

brid DNA

DNA

Amplificate

Standards

Alleles

Virus

1/3

Locus 1

PCR

1/4

Locus 2

2/4

3/3

Locus 3

Agarose gel

3/5

Reverse

DNA polymerase

Agarose gel

transcriptase

D. Gene therapy

Tumor-

Viral vector

Viral vector with

specific

with foreign DNA

foreign DNA

receptor

Normal

Tumor-

Tumor cell

body cell

specific

DNA

promoter

mRNA

Harmless

product

Immune

Gene

system

product

Gene

product

Accu-

Cytostatic

mulates

agent

Apoptosis

Genome

Toxic

Cell

Antisense

product

Lipo-

proliferation

death

DNA

some

1. For metabolic defects

2. For tumors

266

Tissues and organs

phosphate, and nucleosides (nucleobase pen-

Digestion: overview

tose). These cleavage products are resorbed

Most components of food (see p. 360) cannot

by the intestinal wall in the region of the

be resorbed directly by the organism. It is only

jejunum.

after they have been broken down into

Lipids are a special problem for digestion,

smaller molecules that the organism can

as they are not soluble in water. Before enzy-

take up the essential nutrients. Digestion re-

matic breakdown, they have to be emulsified

fers to the mechanical and enzymatic break-

by bile salts and phospholipids in the bile (see

down of food and the resorption of the result-

p. 314). At the water-lipid interface, pancre-

ing products.

atic lipase then attacks triacylglycerols with

the help of colipase (see p. 270). The cleavage

products include fatty acids, 2-monoacylgly-

A. Hydrolysis and resorption of food

cerols, glycerol, and phosphate from phospho-

components

lipid breakdown. After resorption into the

Following mechanical fragmentation of food

epithelial cells, fats are resynthesized from

during chewing in the mouth, the process of

fatty acids, glycerol and 2-monoacylglycerols

enzymatic degradation starts in the stomach.

and passed into the lymphatic system (see

For this purpose, the chyme is mixed with

p. 272). The lipids in milk are more easily

digestive enzymes that occur in the various

digested, as they are already present in emul-

digestive secretions or in membrane-bound

sion; on cleavage, they mostly provide short-

form on the surface of the intestinal epithe-

chain fatty acids.

lium (see p. 268). Almost all digestive en-

Inorganic components such as water, elec-

zymes are hydrolases (class 3 enzymes; see

trolytes, and vitamins are directly absorbed by

p. 88); they catalyze the cleavage of compo-

the intestine.

site bonds with the uptake of water.

High-molecular-weight indigestible com-

Proteins are first denatured by the

ponents, such as the fibrous components of

stomach’s hydrochloric acid (see p. 270), mak-

plant cell walls, which mainly consist of cel-

ing them more susceptible to attack by the

lulose and lignin, pass through the bowel un-

endopeptidases (proteinases) present in gas-

changed and form the main component of

tric and pancreatic juice. The peptides re-

feces, in addition to cells shed from the intes-

leased by endopeptidases are further de-

tinal mucosa. Dietary fiber makes a positive

graded into amino acids by exopeptidases. Fi-

contribution to digestion as a ballast material

nally, the amino acids are resorbed by the

by binding water and promoting intestinal

intestinal mucosa in cotransport with Na⁺

peristalsis.

ions (see p. 220). There are separate transport

The food components resorbed by the epi-

systems for each of the various groups of

thelial cells of the intestinal wall in the region

amino acids.

of the jejunum and ileum are transported

Carbohydrates mainly occur in food in the

directly to the liver via the portal vein. Fats,

form of polymers (starches and glycogen).

cholesterol, and lipid-soluble vitamins are

They are cleaved by pancreatic amylase into

exceptions. These are first released by the

oligosaccharides and are then hydrolyzed by

enterocytes in the form of chylomicrons (see

glycosidases, which are located on the surface

p. 278) into the lymph system, and only reach

of the intestinal epithelium, to yield mono-

the blood via the thoracic duct.

saccharides. Glucose and galactose are taken

up into the enterocytes by secondary active

cotransport with Na⁺ ions (see p. 220). In ad-

dition, monosaccharides also have passive

transport systems in the intestine.

Nucleic acids are broken down into their

components by nucleases from the pancreas

and small intestine (ribonucleases and deoxy-

ribonucleases). Further breakdown yields the

nucleobases (purine and pyrimidine deriva-

tives), pentoses

(ribose and deoxyribose),

268

Tissues and organs

Elastase mainly cleaves on the C side of the

Digestive secretions

aliphatic amino acids Gly, Ala, Val, and Ile.

Smaller peptides are attacked by carboxy-

A. Digestive juices

peptidases, which as exopeptidases cleave in-

Saliva. The salivary glands produce a slightly

dividual amino acids from the C-terminal end

alkaline secretion which—in addition to water

of the peptides (see p. 176).

and salts—contains glycoproteins (mucins) as

a-Amylase, the most important endoglyco-

lubricants,

antibodies,

and enzymes.

sidase in the pancreas, catalyzes the hydroly-

D-Amylase attacks polysaccharides, and a li-

sis of α1

4 bonds in the polymeric carbohy-

pase hydrolyzes a small proportion of the

drates starch and glycogen. This releases mal-

neutral fats. α-Amylase and lysozyme, a mu-

tose, maltotriose, and a mixture of other oli-

rein-cleaving enzyme (see p. 40), probably

gosaccharides.

serve to regulate the oral bacterial flora rather

Various pancreatic enzymes hydrolyze lip-

than for digestion (see p. 340).

ids, including lipase with its auxiliary protein

Gastric juice. In the stomach, the chyme is

colipase (see p. 270), phospholipase A₂, and

mixed with gastric juice. Due to its hydro-

sterol esterase. Bile salts activate the lipid-

chloric acid content, this secretion of the gas-

cleaving enzymes through micelle formation

tric mucosa is strongly acidic (pH 1-3; see

(see below).

p. 270). It also contains mucus (mainly glyco-

Several hydrolases—particularly ribo-

proteins known as mucins), which protects

nuclease

(RNAse) and deoxyribonuclease

the mucosa from the hydrochloric acid, salts,

(DNAse)—break down the nucleic acids con-

and pepsinogen—the proenzyme (“zymogen”)

tained in food.

of the aspartate proteinase pepsin

(see

Bile. The liver forms a thin secretion (bile)

pp. 176, 270). In addition, the gastric mucosa

that is stored in the gallbladder after water

secretes what is known as “intrinsic factor”—a

and salts have been extracted from it. From

glycoprotein needed for resorption of vitamin

the gallbladder, it is released into the duode-

B₁₂ ( “extrinsic factor”) in the bowel.

num. The most important constituents of bile

In the stomach, pepsin and related en-

are water and inorganic salts, bile acids and

zymes initiate the enzymatic digestion of pro-

bile salts (see p. 314), phospholipids, bile pig-

teins, which takes 1-3 hours. The acidic gas-

ments, and cholesterol. Bile salts, together

tric contents are then released into the duo-

with phospholipids, emulsify insoluble food

denum in batches, where they are neutralized

lipids and activate the lipases. Without bile,

by alkaline pancreatic secretions and mixed

fats would be inadequately cleaved, if at all,

with cystic bile.

resulting in

“fatty stool”

(steatorrhea). Re-

Pancreatic secretions. In the acinar cells,

sorption of fat-soluble vitamins would also

the pancreas forms a secretion that is alkaline

be affected.

due to its HCO_3- content, the buffer capacity

Small-intestinal secretions. The glands of

of which is suf cient to neutralize the stom-

the small intestine (the Lieberkühn and Brun-

ach’s hydrochloric acid. The pancreatic secre-

ner glands) secrete additional digestive en-

tion also contains many enzymes that catalyze

zymes into the bowel. Together with enzymes

the hydrolysis of high-molecular-weight food

on the microvilli of the intestinal epithelium

components. All of these enzymes are hydro-

(peptidases, glycosidases, etc.), these en-

lases with pH optimums in the neutral or

zymes ensure almost complete hydrolysis of

weakly alkaline range. Many of them are

the food components previously broken

formed and secreted as proenzymes and are

down by the endoenzymes.

only activated in the bowel lumen

(see

p. 270).

Trypsin, chymotrypsin, and elastase are en-

dopeptidases that belong to the group of ser-

ine proteinases (see p. 176). Trypsin hydro-

lyzes specific peptide bonds on the C side of

the basic amino acids Arg and Lys, while chy-

motrypsin prefers peptide bonds of the apolar

amino acids Tyr, Trp, Phe, and Leu (see p. 94).

Digestion

269

A. Digestive juices

Saliva

Endoenzyme

Daily secretion 1.0-1.5 l

Exoenzyme

pH 7

Water

Moistens food

Salts

Mucus

Lubricant

Compo-

Function

nents

or substrate

Antibodies

Bind to bacteria

α-Amylases (3.2.1.1)

Cleave starch

Lysozyme (3.2.1.17) Attacks bacterial cell walls

Gastric juice

Daily secretion 2-3 l

pH 1

Bile

Water

Daily secretion 0.6 l

Salts

pH 6.9-7.7

HCl

Denatures proteins,

Water

kills bacteria

HCO₃

Neutralizes gastric juice

Mucus

Protects stomach lining

Bile salts

Facilitate lipid digestion

Pepsins (3.4.23.1-3)

Cleave proteins

Phospholipids

Facilitate lipid digestion

Chymosin (3.4.23.4)

Precipitates casein

Bile pigments

Waste products

Triacylglycerol lipase (3.1.1.3)

Cleaves fats

Cholesterol

Waste product

Intrinsic factor

Protects vitamin B₁₂

Pancreatic secretions

Daily secretion 0.7-2.5 l

pH 7.7 (7.5-8.8)

Water

HCO₃

Neutralizes gastric juice

Trypsin (3.4.21.4)

Proteins

Chymotrypsin (3.4.21.1)

Proteins

Elastase (3.4.21.36)

Proteins

Carboxypeptidases (3.4.n.n)

Peptides

α-Amylase (3.2.1.1)

Starch and glycogen

Triacylglycerol lipase (3.1.1.3)

Fats

Co-Lipase

Cofactor for lipase

Phospholipase A₂ (3.1.1.4)

Phospholipids

Sterol esterase (3.1.1.13)

Cholesterol esters

Ribonuclease (3.1.27.5)

RNA

Deoxyribonuclease I (3.1.21.1)

DNA

Secretions of the small intestine

Daily secretion unknown

pH 6.5-7.8

Aminopeptidases (3.4.11.n)

Peptides

Dipeptidases (3.4.13.n)

Dipeptides

α-Glucosidase (3.2.1.20)

Oligosaccharides

Oligo-1,6-glucosidase (3.2.1.10)

Oligosaccharides

β-Galactosidase (3.2.1.23)

Lactose

Sucrose α-glucosidase (3.2.1.48)

Sucrose

α, α-Trehalase (3.2.1.28)

Trehalose

Alkaline phosphatase (3.1.3.1)

Phosphoric acid esters

Polynucleotidases (3.1.3.n)

Nucleic acids, nucleotides

Nucleosidases (3.2.2.n)

Nucleosides

Phospholipases (3.1.n.n)

Phospholipids

270

Tissues and organs

stimulate pancreatic secretion and bile re-

Digestive processes

lease.

Gastric juice is the product of several cell

types. The parietal cells produce hydrochloric

B. Zymogen activation

acid, chief cells release pepsinogen, and acces-

sory cells form a mucin-containing mucus.

To prevent self-digestion, the pancreas re-

leases most proteolytic enzymes into the du-

odenum in an inactive form as proenzymes

A. Formation of hydrochloric acid

(zymogens). Additional protection from the

The secretion of hydrochloric acid (H⁺ and Cl^-)

effects of premature activation of pancreatic

by the parietal cells is an active process that

proteinases is provided by proteinase inhibi-

uses up ATP and takes place against a concen-

tors in the pancreatic tissue, which inactivate

tration gradient (in the gastric lumen, with a

active enzymes by complex formation (right).

pH of 1, the H⁺ concentration is some 10⁶

Trypsinogen plays a key role among the

times higher than in the parietal cells, which

proenzymes released by the pancreas. In the

have a pH of 7).

bowel, it is proteolytically converted into ac-

The precursors of the exported H⁺ ions are

tive trypsin (see p. 176) by enteropeptidase, a

carbon dioxide (CO₂) and water (H₂O). CO₂

membrane enzyme on the surface of the en-

diffuses from the blood into the parietal cells,

terocytes. Trypsin then autocatalytically acti-

and in a reaction catalyzed by carbonate de-

vates additional trypsinogen molecules and

hydratase (carbonic anhydrase [2]), it reacts

the other proenzymes (left).

with H₂O to form H⁺ and hydrogen carbonate

(HCO_3-). The H⁺ ions are transported into the

C. Fat digestion

gastric lumen in exchange for K⁺ by a mem-

brane-bound H⁺/K⁺-exchanging ATPase [1] (a

Due to the “hydrophobic effect” (see p. 28),

transport ATPase of the P type; see p. 220).

water-insoluble neutral fats in the aqueous

The remaining hydrogen carbonate is re-

environment of the bowel lumen would ag-

leased into the interstitium in electroneutral

gregate into drops of fat in which most of the

antiport in exchange for chloride ions (Cl^-),

molecules would not be accessible to pancre-

and from there into the blood. The Cl^- ions

atic lipase. The amphipathic substances in bile

follow the secreted protons through a chan-

(bile acids, bile salts, phospholipids) create an

nel into the gastric lumen.

emulsion in which they occupy the surface of

The hydrochloric acid in gastric juice is

the droplets and thereby prevent them from

important for digestion. It activates pepsin-

coalescing into large drops. In addition, the

ogen to form pepsin (see below) and creates

bile salts, together with the auxiliary protein

an optimal pH level for it to take effect. It also

colipase, mediate binding of triacylglycerol

denatures food proteins so that they are more

lipase [1] to the emulsified fat droplets. Acti-

easily attacked by proteinases, and it kills

vation of the lipase is triggered by a confor-

micro-organisms.

mation change in the C-terminal domain of

Regulation. HCl secretion is stimulated by

the enzyme, which uncovers the active center.

the peptide hormone gastrin, the mediator

During passage through the intestines, the

histamine (see p. 380), and—via the neuro-

active lipase breaks down the triacylglycerols

transmitter acetylcholine—by the autonomous

in the interior of the droplets into free fatty

nervous system. The peptide somatostatin

acids and amphipathic monoacylglycerols.

and certain prostaglandins (see p. 390) have

Over time, smaller micelles develop

(see

inhibitory effects. Together with cholecysto-

p. 28), in the envelope of which monoacylgly-

kinin, secretin, and other peptides, gastrin

cerols are present in addition to bile salts and

belongs to the group of gastrointestinal hor-

phospholipids. Finally, the components of the

mones (see p. 370). All of these are formed in

micelles are resorbed by the enterocytes in

the gastrointestinal tract and mainly act in the

ways that have not yet been explained.

vicinity of the site where they are formed—

Monoacylglycerols and fatty acids are re-

i. e., they are paracrine hormones (see p. 372).

assembled into fats again (see p. 272), while

While gastrin primarily enhances HCl

the bile acids return to the liver (enterohe-

secretion, cholecystokinin and secretin mainly

patic circulation; see p. 314).

Digestion

271

A. Formation of hydrochloric acid

Interstitial

Parietal cell

Lumen of the stomach

fluid

Peptides

H₂O

Pepsino-

Pepsins

P P

gens

3.4.23.1-3

Native

CO₂

protein

Anion

exchanger

H Cl

P P P

≈ 0.1 mol · l-1

HCO₃

Denatured

Chloride channel

protein

Micro-organism

Carbonate dehydratase 4.2.1.1 [Zn2

]

H /K

-exchanging ATPase 3.6.1.36

B. Zymogen activation

Small bowel

Mucosal cell Entero-

Pancreatic secretion

peptidase

3.4.21.9

Trypsin

3.4.21.4

Various

zymogens

Trypsinogen

Trypsin inhibitor

Premature

Activated digestive

Zymogens:

trypsin

enzymes

Procarboxypeptidases

activation

Proelastase

Chymotrypsinogen

Prophospholipase A₂

Digestion

Trypsinogen

Blocked trypsin

C. Fat digestion

Triacylglycerol lipase 3.1.1.3

Enterocyte

Micelle

Resorption

C-terminal

domain

Monoacyl-

Colipase

glycerol

Bile salt

Phospholipid

Triacylglycerol

272

Tissues and organs

acids. Individual amino acid groups have

Resorption

group-specific amino acid transporters, some

Enzymatic hydrolysis in the digestive tract

of which transport the amino acids into the

breaks down foodstuffs into their resorbable

enterocytes in cotransport with Na⁺ ions (sec-

components. Resorption of the cleavage prod-

ondary active transport), while others trans-

ucts takes place primarily in the small intes-

port them in an Na⁺-independent manner

tine. Only ethanol and short-chain fatty acids

through facilitated diffusion. Small peptides

are already resorbed to some extent in the

can also be taken up.

stomach.

The resorption process is facilitated by the

B. Lipids

large inner surface of the intestine, with its

brush-border cells. Lipophilic molecules pen-

Fats and other lipids are poorly soluble in

etrate the plasma membrane of the mucosal

water. The larger the accessible surface

cells by simple diffusion, whereas polar mol-

is—i. e., the better the fat is emulsified—the

ecules require transporters (facilitated diffu-

easier it is for enzymes to hydrolyze it (see

sion; see p. 218). In many cases, carrier-medi-

p. 270). Due to the special properties of milk,

ated cotransport with Na⁺ ions can be ob-

milk fats already reach the gastrointestinal

served. In this case, the difference in the con-

tract in emulsified form. Digestion of them

centration of the sodium ions (high in the

therefore already starts in the oral cavity

intestinal lumen and low in the mucosal cells)

and stomach, where lipases in the saliva and

drives the import of nutrients against a con-

gastric juice are available. Lipids that are less

centration gradient (secondary active trans-

accessible—e. g., from roast pork—are emulsi-

port; see p. 220). Failure of carrier systems in

fied in the small intestine by bile salts and bile

the gastrointestinal tract can result in dis-

phospholipids. Only then are they capable of

eases.

being attacked by pancreatic lipase [4] (see

p. 270).

Fats (triacylglycerols) are mainly attacked

A. Monosaccharides

by pancreatic lipase at positions 1 and 3 of the

The cleavage of polymeric carbohydrates by

glycerol moiety. Cleavage of two fatty acid

a-amylase

[1] leads to oligosaccharides,

residues gives rise to fatty acids and 2-mono-

which are broken down further by exoglyco-

acylglycerols, which are quantitatively the

sidases

(oligosaccharidases and disacchari-

most important products. However, a certain

dases [2]) on the membrane surface of the

amount of glycerol is also formed by complete

brush border. The monosaccharides released

hydrolysis. These cleavage products are re-

in this way then pass with the help of various

sorbed by a non-ATP-dependent process

sugar-specific transporters into the cells of

that has not yet been explained in detail.

intestinal epithelium. Secondary active

In the mucosal cells, long-chain fatty acids

transport serves for the uptake of glucose

are resynthesized by an ATP-dependent ligase

and galactose, which are transported against

[5] to form acyl-CoA and then triacylglycerols

a concentration gradient in cotransport with

(fats; see p. 170). The fats are released into the

Na⁺. The Na⁺ gradient is maintained on the

lymph in the form of chylomicrons

(see

basal side of the cells by Na⁺/K⁺-ATPase [3].

p. 278) and, bypassing the liver, are deposited

Another passive transporter then releases

in the thoracic duct—i. e., the blood system.

glucose and galactose into the blood.

Cholesterol also follows this route.

Fructose is taken up by a special type of trans-

By contrast, short-chain fatty acids (with

porter using facilitated diffusion.

chain lengths of less than 12 C atoms) pass

directly into the blood and reach the liver via

the portal vein. Resorbed glycerol can also

Amino acids (not illustrated)

take this path.

Protein degradation is initiated by proteina-

ses—by pepsins in the stomach and by trypsin,

chymotrypsin, and elastase in the small intes-

tine. The resulting peptides are then further

hydrolyzed by various peptidases into amino

Digestion

273

A. Monosaccharides

2 K

3 Na

Poly-

saccharides

Na glucose

2 K

Glucose

symporter

ATP

ADP

transporter

Glucose

Galactose

Portal

vein

α-Amylase

Fructose

Other mono-

saccharides

Liver

α-Amylase 3.2.1.1

Disaccharidases

Oligosaccharidases

Na /K -exchanging

ATPase 3.6.1.37

Oligo-

saccharides

Intestinal

Secondary-active transport

epithelial cell

Facilitated diffusion

B. Lipids

Intestinal

Triacyl-

lumen

glycerol

Fat

Lymph

synthesis

Thoracic

Glyco-

duct

Fat

lysis

synthesis

Diacyl-

glycerol

Blood

P P

Short-chain

fatty acids

P P P

Portal

vein

Fatty acids

2-Mono-

acyl-

80%

glycerol

Resorption

Liver

Glycerol

20%

Triacylglycerol

lipase 3.1.1.3

Intestinal

epithelial cell

Fatty acid-CoA ligase 6.2.1.3

Stimulated by bile salts,

phospholipids, colipase and Ca²

274

Tissues and organs

The leukocytes include various types of

Blood: composition and functions

granulocyte, monocyte, and lymphocyte. All

Human blood constitutes about 8 % of the

of these have immune defense functions (see

body’s weight. It consists of cells and cell frag-

p. 294). The neutrophil granulocytes¸ mono-

ments in an aqueous medium, the blood

cytes, and the macrophages derived from

plasma. The proportion of cellular elements,

monocytes are phagocytes. They can ingest

known as hematocrit, in the total volume is

and degrade invading pathogens. The lympho-

approximately 45%.

cytes are divided into two groups, B lympho-

cytes and T lymphocytes. B lymphocytes

produce antibodies, while T lymphocytes reg-

A. Functions of the blood

ulate the immune response and destroy virus-

infected cells and tumor cells. Eosinophilic and

The blood is the most important transport

basophilic granulocytes have special tasks for

medium in the body. It serves to keep the

defense against animal parasites.

“internal milieu” constant (homeostasis) and

Thrombocytes are cell fragments that arise

it plays a decisive role in defending the body

in the bone marrow from large precursor

against pathogens.

cells, the megakaryocytes. Their task is to

Transport. The gases oxygen and carbon

promote hemostasis (see p. 290).

dioxide are transported in the blood. The

blood mediates the exchange of substances

between organs and takes up metabolic end

C. Blood plasma: composition

products from tissues in order to transport

The blood plasma is an aqueous solution of

them to the lungs, liver, and kidney for excre-

electrolytes, nutrients, metabolites, proteins,

tion. The blood also distributes hormones

vitamins, trace elements, and signaling sub-

throughout the organism (see p. 370).

stances. The fluid phase of coagulated blood is

Homeostasis. The blood ensures that a bal-

known as blood serum. It differs from the

anced distribution of water is maintained be-

plasma in that it lacks fibrin and other coag-

tween the vascular system, the cells (intra-

ulation proteins (see p. 290).

cellular space), and the extracellular space.

Laboratory assessment of the composition

The acid-base balance is regulated by the

of the blood plasma is often carried out in

blood in combination with the lungs, liver,

clinical chemistry. Among the electrolytes,

and kidneys (see p. 288). The regulation of

there is a relatively high concentration of

body temperature also depends on the con-

Na⁺, Ca²⁺, and Cl^- ions in the blood in compar-

trolled transport of heat by the blood.

ison with the cytoplasm. By contrast, the con-

Defense. The body uses both non-specific

centrations of K⁺, Mg²⁺, and phosphate ions

and specific mechanisms to defend itself

are higher in the cells. Proteins also have a

against pathogens. The defense system in-

higher intracellular concentration. The elec-

cludes the cells of the immune system and

trolyte composition of blood plasma is similar

certain plasma proteins (see p. 294).

to that of seawater, due to the evolution of

Self-protection. To prevent blood loss

early forms of life in the sea. The solution

when a vessel is injured, the blood has sys-

known as “physiological saline” (NaCl at a con-

tems for stanching blood flow and coagulat-

centration of 0.15 mol L^-1) is almost isotonic

ing the blood (hemostasis; see p. 290). The

with blood plasma.

dissolution of blood clots

(fibrinolysis) is

A list of particularly important metabolites

also managed by the blood itself (see p. 292).

in the blood plasma is given on the right.

B. Cellular elements

The solid elements in the blood are the eryth-

rocytes (red blood cells), leukocytes (white

blood cells), and thrombocytes (platelets).

The erythrocytes provide for gas transport

in the blood. They are discussed in greater

detail on pp. 280-285.

Blood

275

A. Functions of the blood

B. Cellular elements

Blood gases:

O₂

10 µm

CO₂

Erythrocyte

5000 · 10⁹ · l^-1

Nutrients

59%

6.5%

Metabolites

Metabolic

wastes

Neutrophilic

Monocyte

Hormones

granulocyte

31%

Transport

Small

Large

Cell

lymphocyte

Extracellular

H₂O

2.4%

space

0.6%

Water balance

Body

Acid-base

temperature

balance

Homeostasis

Eosinophilic

Basophilic

granulocyte

Blood clotting

Leukocytes

7 · 10⁹ · l^-1

and fibrinolysis

-1

250 · 10⁹ · l

Immune cells

Antibodies

Defense

Self defense

Thrombocytes

C. Blood plasma: composition

Non-electrolytes

Uncharged

Concentration

Metabolite

Concentration (mM)

molecules

200

1.2

H2CO3

Glucose

3.6

- 6.1

Lactate

0.4

- 1.8

HCO

24-28

150

Pyruvate

0.07

- 0.11

Urea

3.5

- 9.0

136-145

100-110

Uric acid

0.18

- 0.54

100

Creatinin

0.06

- 0.13

Amino acids

2.3

- 4.0

HPO

1.1-1.5

Ammonia

0.02

– 0.06

3.5-5.0

0.3-0.6

SO4

Lipids (total)

5.5

- 6.0 g · l^-1

2.1-2.6

Ca2

Organic

acids

Triacylglycerols

1.0

- 1.3 g · l^-1

0.6-1.0

Mg2

Proteins

Cholesterol

1.7

- 2.1 g · l

-1

Cations

Anions

276

Tissues and organs

as plasma cells (see p. 302) and peptide hor-

Plasma proteins

mones, which derive from endocrine gland

Quantitatively, proteins are the most impor-

cells.

tant part of the soluble components of the

With the exception of albumin, almost all

blood plasma. With concentrations of be-

plasma proteins are glycoproteins. They carry

tween 60 and 80 g L^-1, they constitute ap-

oligosaccharides in N-and O-glycosidic bonds

proximately 4% of the body’s total protein.

(see p. 44). N-acetylneuraminic acid

(sialic

Their tasks include transport, regulation of

acid; see p. 38) often occurs as a terminal

the water balance, hemostasis, and defense

carbohydrate among sugar residues.

against pathogens.

Neuraminidases (sialidases) on the surface of

the vascular endothelia gradually cleave the

sialic acid residues and thereby release ga-

A. Plasma proteins

lactose units on the surfaces of the proteins.

Some 100 different proteins occur in human

These asialoglycoproteins (“asialo-” = without

blood plasma. Based on their behavior during

sialic acid) are recognized and bound by gal-

electrophoresis (see below), they are broadly

actose receptors on hepatocytes. In this way,

divided into five fractions: albumins and α₁-,

the liver takes up aged plasma proteins by

α₂-, β- and γ-globulins. Historically, the dis-

endocytosis and breaks them down. The oli-

tinction between the albumins and globulins

gosaccharides on the protein surfaces thus

was based on differences in the proteins’

determine the half-life of plasma proteins,

solubility

-albumins are soluble in pure

which is a period of days to weeks.

water, whereas globulins only dissolve in

In healthy individuals, the concentration of

the presence of salts.

plasma proteins is constant. Diseases in or-

The most frequent protein in the plasma, at

gans that are involved in protein synthesis

around 45 g L^-1, is albumin. Due to its high

and breakdown can shift the protein pattern.

concentration, it plays a crucial role in main-

For example, via cytokines (see p. 392), se-

taining the blood’s colloid osmotic pressure

vere injuries trigger increased synthesis of

and represents an important amino acid re-

acute-phase proteins, which include C-reac-

serve for the body. Albumin has binding sites

tive protein, haptoglobin, fibrinogen, comple-

for apolar substances and therefore functions

ment factor C-3, and others. The concentra-

as a transport protein for long-chain fatty

tions of individual proteins are altered in

acids, bilirubin, drugs, and some steroid hor-

some diseases (known as dysproteinemias).

mones and vitamins. In addition, serum albu-

min binds Ca²⁺ and Mg²⁺ ions. It is the only

B. Carrier electrophoresis

important plasma protein that is not glycosy-

lated.

Proteins and other electrically charged mac-

The albumin fraction also includes trans-

romolecules can be separated using electro-

thyretin (prealbumin), which together with

phoresis (see also pp. 78, 262). Among the

other proteins transports the hormone thy-

various procedures used, carrier electropho-

roxine and its metabolites.

resis on cellulose acetate foil (CAF) is partic-

The table also lists important globulins in

ularly simple. Using this method, serum pro-

blood plasma, with their mass and function.

teins—which at slightly alkaline pH values all

The α- and β-globulins are involved in the

move towards the anode, due to their excess

transport of lipids (lipoproteins; see p. 278),

of negative charges—can be separated into

hormones, vitamins, and metal ions. In addi-

the five fractions mentioned. After the pro-

tion, they provide coagulation factors, pro-

teins have been stained with dyes, the result-

tease inhibitors, and the proteins of the com-

ing bands can be quantitatively assessed us-

plement system (see p. 298). Soluble antibod-

ing densitometry.

ies (immunoglobulins; see p. 300) make up

the γ-globulin fraction.

Synthesis and degradation. Most plasma

proteins are synthesized by the liver. Excep-

tions to this include the immunoglobulins,

which are secreted by B lymphocytes known

Blood

277

A. Plasma proteins

Group

Protein

M_r

in kDa

Function

Albumins:

Transthyretin

50-66

Transport of thyroxin and triiodothyronin

Albumin: 45 g · l^-1

Maintenance of osmotic pressure; transport of

fatty acids, bilirubin, bile acids, steroid hor-

mones, pharmaceuticals and inorganic ions.

Antitrypsin

Inhibition of trypsin and other proteases

^α1-Globulins:

Antichymotrypsin

58-68

Inhibition of chymotrypsin

Lipoprotein (HDL)

200-400

Transport of lipids

Prothrombin

Coagulation factor II, thrombin precursor

(3.4.21.5)

Transcortin

Transport of cortisol, corticosterone and

progesterone

Acid glycoprotein

Transport of progesterone

Thyroxin-binding globulin

Transport of iodothyronins

Ceruloplasmin

135

Transport of copper ions

^α2-Globulins:

Antithrombin III

Inhibition of blood clotting

Haptoglobin

100

Binding of hemoglobin

Cholinesterase (3.1.1.8)

ca. 350

Cleavage of choline esters

Plasminogen

Precursor of plasmin (3.4.21.7), breakdown

of blood clots

Macroglobulin

725

Binding of proteases, transport of zinc ions

Retinol-binding protein

Transport of vitamin A

Vitamin D-binding protein

Transport of calciols

β-Globulins:

Lipoprotein (LDL)

2.000-4.500

Transport of lipids

Transferrin

Transport of iron ions

Fibrinogen

340

Coagulation factor I

Sex hormone-

binding globulin

Transport of testosterone and estradiol

Transcobalamin

Transport of vitamin B₁₂

C-reactive protein

110

Complement activation

γ-Globulins:

IgG

150

Late antibodies

IgA

162

Mucosa-protecting antibodies

IgM

900

Early antibodies

IgD

172

B-lymphocyte receptors

IgE

196

Reagins

B. Electrophoresis

Buffer-saturated strip

Cellulose-acetate sheet

of filter paper

soaked with buffer

–

52-58%

Serum

sample

2.4-4.4%

Anode

Cathode

6.1-10.1%

Electro-

phoresis

8.5-14.5%

10-21%

Staining

Densitometry

Cellulose-acetate sheet

Albumins α1- α2- β- γ-Globulins

278

Tissues and organs

cosa and reach the blood via the lymphatic

Lipoproteins

system (see p. 266). In the peripheral vessel-

Most lipids are barely soluble in water, and

s—particularly in muscle and adipose tis-

many have amphipathic properties. In the

sue—lipoprotein lipase [1] on the surface of

blood, free triacylglycerols would coalesce

the vascular endothelia hydrolyzes most of

into drops that could cause fat embolisms.

the triacylglycerols. Chylomicron breakdown

By contrast, amphipathic lipids would be de-

is activated by the transfer of apoproteins E

posited in the blood cells’ membranes and

and C from HDL. While the fatty acids released

would dissolve them. Special precautions are

and the glycerol are taken up by the cells, the

therefore needed for lipid transport in the

chylomicrons gradually become converted

blood. While long-chain fatty acids are bound

into chylomicron remnants, which are ulti-

to albumin and short-chain ones are dissolved

mately removed from the blood by the liver.

in the plasma (see p. 276), other lipids are

transported in lipoprotein complexes, of

VLDLs, IDLs, and LDLs are closely related to

which there several types in the blood

one another. VLDLs formed in the liver (see

plasma, with different sizes and composition.

p. 312) transport triacylglycerols, cholesterol,

and phospholipids to other tissues. Like chy-

lomicrons, they are gradually converted into

A. Composition of lipoprotein complexes

IDL and LDL under the influence of lipoprotein

Lipoproteins are spherical or discoid aggre-

lipase [1]. This process is also stimulated by

gates of lipids and apoproteins. They consist

HDL. Cells that have a demand for cholesterol

of a nucleus of apolar lipids (triacylglycerols

bind LDL through an interaction between

and cholesterol esters) surrounded by a sin-

their LDL receptor and ApoB-100, and then

gle-layered shell approximately 2 nm thick of

take up the complete particle through recep-

amphipathic lipids (phospholipids and cho-

tor-mediated endocytosis. This type of trans-

lesterol; the example shown here is LDL).

port is mediated by depressions in the mem-

The shell, in which the apoproteins are also

brane (“coated pits”), the interior of which is

deposited, gives the surfaces of the particles

lined with the protein clathrin. After LDL

polar properties and thereby prevents them

binding, clathrin promotes invagination of

from aggregating into large particles. The

the pits and pinching off of vesicles (“coated

larger the lipid nucleus of a lipoprotein

vesicles”). The clathrin then dissociates off and

is—i. e., the larger the number of apolar lipids

is reused. After fusion of the vesicle with ly-

it contains—the lower its density is.

sosomes, the LDL particles are broken down

Lipoproteins are classified into five groups.

(see p. 234), and cholesterol and other lipids

In order of decreasing size and increasing

are used by the cells.

density, these are: chylomicrons, VLDLs

(very-low-density lipoproteins), IDLs (inter-

The HDLs also originate in the liver. They

mediate-density lipoproteins), LDLs

(low-

return the excess cholesterol formed in the

density lipoproteins), and HDLs (high-density

tissues to the liver. While it is being trans-

lipoproteins). The proportions of apoproteins

ported, cholesterol is acylated by lecithin cho-

range from 1% in chylomicrons to over 50% in

lesterol acyltransferase (LCAT). The cholesterol

HDLs. These proteins serve less for solubility

esters formed are no longer amphipathic and

purposes, but rather function as recognition

can be transported in the core of the lipopro-

molecules for the membrane receptors and

teins. In addition, HDLs promote chylomicron

enzymes that are involved in lipid exchange.

and VLDL turnover by exchanging lipids and

apoproteins with them (see above).

B. Transport functions

The classes of lipoproteins differ not only in

their composition, but also in the ways in

which they originate and function.

The chylomicrons take care of the transport

of triacylglycerols from the intestine to the

tissues. They are formed in the intestinal mu-

Blood

279

A. Composition of lipoprotein complexes

Lipoprotein

Composition

coat

core

10 nm

VLDL

Chylomicrons

B-100, C-III, E, C-II

C-III, B-48, C-II,

C-II, E, A-I

LDL

B-100

Apo-B-100

Characteristic

apoproteins

IDL

B-100, E, C-III

HDL

A-I, A-III, C-III

Apoprotein

Lipoprotein

Density (g · cm^-3)

Free cholesterol

Chylomicrons

<0.95

VLDL

0.950

- 1.006

Phospholipid

IDL

1.006

- 1.019

Cholesterol ester

LDL

1.019

- 1.063

Triacylglycerols

HDL

1.063

- 1.210

B. Transport functions

Intestine

Dietary lipids

Endogenous lipids

Extrahepatic

tissues

Receptor-

Liver

mediated

endocytosis

Cholesterol

LDL

Fats

Fatty acids

Chylomicrons

Cholesterol

return

HDL

IDL

Chylomicron

remnants

HDL

VLDL

Muscle

Free

Exchange

fatty

of lipids and

acids

Adipose tissue

apoproteins

Free

HDL

fatty

acids

Free

fatty

Lipoprotein lipase

Lecithin-cholesterol acyltransferase

acids

3.1.1.34

(LCAT) 2.3.1.43

280

Tissues and organs

the R form. The T form (for tense; left) and

Hemoglobin

has a much lower O₂ af nity than the R form

The most important task of the red blood cells

(for relaxed; right).

(erythrocytes) is to transport molecular oxy-

Binding of O₂ to one of the subunits of the T

gen (O₂) from the lungs into the tissues, and

form leads to a local conformational change

carbon dioxide (CO₂) from the tissues back

that weakens the association between the

into the lungs. To achieve this, the higher

subunits. Increasing O₂ partial pressure thus

organisms require a special transport system,

means that more and more molecules convert

since O₂ is poorly soluble in water. For exam-

to the higher-af nity R form. This coopera-

ple, only around 3.2 mL O₂ is soluble in 1 L

tive interaction between the subunits in-

blood plasma. By contrast, the protein hemo-

creases the O₂ af nity of Hb with increasing

globin (Hb), contained in the erythrocytes,

O₂

concentrations—i. e., the O₂

saturation

can bind a maximum of 220 mL O₂

per

curve is sigmoidal (see p. 282).

liter—70 times the physically soluble amount.

Various allosteric effectors influence the

The Hb content of blood, at 140-180 g L^-1

equilibrium between the T and R forms and

in men and 120-160 g L^-1 in women, is

thereby regulate the O₂ binding behavior of

twice as high as that of the plasma proteins

hemoglobin (yellow arrows). The most impor-

(50-80 g L^-1). Hb is therefore also responsi-

tant effectors are CO₂, H⁺, and 2,3-bisphospho-

ble for the majority of the blood proteins’ pH

glycerate (see p. 282).

buffer capacity (see p. 288).

Further information

A. Hemoglobin: structure

As mentioned above, hemoglobin in adults

In adults, hemoglobin (HbA; see below) is a

consists of two α- and two β-chains. In addi-

heterotetramer consisting of two α-chains and

tion to this main form (HbA₁, α₂β₂), adult

two β-chains, each with masses of 16 kDa.

blood also contains small amounts of a second

The α- and β-chains have different sequences,

form with a higher O₂ af nity in which the β-

but are similarly folded. Some 80% of the

chains are replaced by δ-chains (HbA₂, α₂δ₂).

amino acid residues form D-helices, which

Two other forms occur during embryonic and

are identified using the letters A-H.

fetal development. In the first three months,

Each subunit carries a heme group (for-

embryonic hemoglobins are formed, with the

mula on p. 106), with a central bivalent iron

structure ζ₂ε₂ and α₂ε₂. Up to the time of

ion. When O₂

binds to the heme iron

birth, fetal hemoglobin then predominates

(Oxygenation of Hb) and when O₂ is released

(HbF, α₂γ₂), and it is gradually replaced by

(Deoxygenation), the oxidation stage of the

HbA during the first few months of life. Em-

iron does not change. Oxidation of Fe²⁺ to

bryonic and fetal hemoglobins have higher O₂

Fe³⁺ only occurs occasionally. The oxidized

af nities than HbA, as they have to take up

form, methemoglobin, is then no longer able

oxygen from the maternal circulation.

to bind O₂. The proportion of Met-Hb is kept

low by reduction (see p. 284) and usually

amounts to only 1-2%.

Four of the six coordination sites of the iron

in hemoglobin are occupied by the nitrogen

atoms of the pyrrol rings, and another is oc-

cupied by a histidine residue of the globin

(the proximal histidine). The iron’s sixth site

is coordinated with oxygen in oxyhemoglobin

and with H₂O in deoxyhemoglobin.

B. Hemoglobin: allosteric effects

Like aspartate carbamoyltransferase

(see

p. 116), Hb can exist in two different states

(conformations), known as the T form and

282

Tissues and organs

B. Hemoglobin and CO₂ transport

Gas transport

Hemoglobin is also decisively involved in the

Most tissues are constantly dependent on a

transport of carbon dioxide (CO₂) from the

supply of molecular oxygen (O₂) to maintain

tissues to the lungs.

their oxidative metabolism. Due to its poor

Some 5% of the CO₂ arising in the tissues is

solubility, O₂

is bound to hemoglobin for

covalently bound to the N terminus of hemo-

transport in the blood (see p. 280). This not

globin and transported as carbaminohemoglo-

only increases the oxygen transport capacity,

bin (not shown). About 90% of the CO₂ is first

but also allows regulation of O₂ uptake in the

converted in the periphery into hydrogen car-

lungs and O₂ release into tissues.

bonate (HCO_3-), which is more soluble (bot-

tom). In the lungs (top), CO₂ is regenerated

A. Regulation of O₂ transport

again from HCO_3- and can then be exhaled.

These two processes are coupled to the

When an enzyme reacts to effectors (sub-

oxygenation and deoxygenation of Hb.

strates, activators, or inhibitors) with confor-

Deoxy-Hb is a stronger base than oxy-Hb. It

mational changes that increase or reduce its

therefore binds additional protons

(about

activity, it is said to show allosteric behavior

0.7 H⁺ per tetramer), which promotes the for-

(see p. 116). Allosteric enzymes are usually

mation of HCO_3- from CO₂ in the peripheral

oligomers with several subunits that mutually

tissues. The resulting HCO_3- is released into

influence each other.

the plasma via an antiporter in the erythro-

Although hemoglobin is not an enzyme (it

cyte membrane in exchange for Cl^-, and

releases the bound oxygen without changing

passes from the plasma to the lungs. In the

it), it has all the characteristics of an allosteric

lungs, the reactions described above then

protein. Its effectors include oxygen, which as

proceed in reverse order: deoxy-Hb is oxy-

a positive homotropic effector promotes its

genated and releases protons. The protons

own binding. The O₂ saturation curve of he-

shift the HCO₃/CO₂ equilibrium to the left

moglobin is therefore markedly sigmoidal in

and thereby promote CO₂ release.

shape (2, curve 2). The non-sigmoidal satura-

O₂ binding to Hb is regulated by H⁺ ions

tion curve of the muscular protein myoglobin

(i. e., by the pH value) via the same mecha-

is shown for comparison (curve 1). The struc-

nism. High concentrations of CO₂ such as

ture of myoglobin (see p. 336) is similar to

those in tissues with intensive metabolism

that of a subunit of hemoglobin, but as a

locally increase the H⁺ concentration and

monomer it does not exhibit any allosteric

thereby reduce hemoglobin’s O₂

af nity

behavior.

(Bohr effect; see above). This leads to in-

CO₂, H⁺, and a special metabolite of ery-

creased O₂ release and thus to an improved

throcytes—2,3-bisphosphoglycerate

(BPG)—

oxygen supply.

act as heterotropic effectors of hemoglobin.

The adjustment of the equilibrium be-

BPG is synthesized from 1,3-bisphosphogly-

tween CO₂ and HCO_3- is relatively slow in

cerate, an intermediate of glycolysis

(see

the uncatalyzed state. It is therefore acceler-

p. 150), and it can be returned to glycolysis

ated in the erythrocytes by carbonate dehy-

again by breakdown into 2-phosphoglycerate

dratase (carbonic anhydrase) [1])—an enzyme

(1), with loss of an ATP.

that occurs in high concentrations in the

BPG binds selectively to deoxy-Hb, thereby

erythrocytes.

increasing its amount of equilibrium. The re-

sult is increased O₂ release at constant pΟ₂. In

the diagram, this corresponds to a right shift

of the saturation curve (2, curve 3). CO₂ and

H+ act in the same direction as BPG. Their

influence on the position of the curve has

long been known as the Bohr effect.

The effects of CO₂ and BPG are additive. In

the presence of both effectors, the saturation

curve of isolated Hb is similar to that of whole

blood (curve 4).

Blood

283

A. Regulation of O₂ transport

Bisphosphoglycerate

1.0

mutase 5.4.2.4

Bisphosphoglycerate

1,3-Bisphospho-

phosphatase3.1.3.13

0.8

glycerate

ADP

2,3-

0.6

ATP

Bisphospho-

glycerate (BPG)

pH = 7.40

3-Phospho-

glycerate

0.4

Myoglobin

Hemoglobin (Hb)

0.2

Hb + BPG

C O

Hb + CO₂ + BPG

2-Phospho-

glycerate

H₂C

0.0

O2 partial pressure (mmHg)

1. BPG metabolism

2. Saturation curves

D. Hemoglobin and CO₂ transport

Lungs

CO₂

O₂

CO₂

O₂

Lungs

CO₂

H₂O

[H₂CO₃]

HCO₃

H - Hb

Hb -O₂

[H₂CO₃]

pO2

100 mmHg

Blood

Erythrocyte

Heart

HCO₃

+ H - Hb

Hb - O₂

[H₂CO₃]

pO2

CO₂

H₂O

[H₂CO₃]

30-40 mmHg

CO₂

O₂

Veins

Arteries

Tissue

CO₂

O₂

Carbonate dehydratase [Zn²

] 4.2.1.1

284

Tissues and organs

antioxidants include vitamins C and E (see

Erythrocyte metabolism

pp. 364, 368), coenzyme Q (see p. 104), and

Cells living in aerobic conditions are depen-

several carotenoids (see pp. 132, 364). Biliru-

dent on molecular oxygen for energy produc-

bin, which is formed during heme degrada-

tion. On the other hand, O₂ constantly gives

tion (see p. 194), also serves for protection

rise to small quantities of toxic substances

against oxidation.

known as reactive oxygen species

(ROS).

Glutathione, a tripeptide that occurs in

These substances are powerful oxidation

high concentrations in almost all cells, is par-

agents or extremely reactive free radicals

ticularly important. Glutathione (sequence:

(see p. 32), which damage cellular structures

Glu-Cys-Gly) contains an atypical γ-peptide

and functional molecules. Due to their role in

bond between Glu and Cys. The thiol group of

O₂ transport, the erythrocytes are constantly

the cysteine residue is redox-active. Two mol-

exposed to high concentrations of O₂ and are

ecules of the reduced form (GSH, top) are

therefore particularly at risk from ROS.

bound to the disulfide (GSSG, bottom) during

oxidation.

A. Reactive oxygen species

C. Erythrocyte metabolism

The dioxygen molecule (O₂) contains two un-

paired electrons—i. e., it is a diradical. Despite

Erythrocytes also have systems that can in-

this, O₂ is relatively stable due to its special

activate ROS (superoxide dismutase, catalase,

electron arrangement. However, if the mole-

GSH). They are also able to repair damage

cule takes up an extra electron (a), the highly

caused by ROS. This requires products that

reactive superoxide radical ( O_2-) arises. An-

are supplied by the erythrocytes’ mainte-

other reduction step (b) leads to the peroxide

nance metabolism, which basically only in-

anion (O_22-), which easily binds protons and

volves anaerobic glycolysis (see p. 150) and

thus becomes hydrogen peroxide (H₂O₂). In-

the pentose phosphate pathway (PPP; see

clusion of a third electron (c) leads to cleavage

p. 152).

of the molecule into the ions O^2- and O^-.

The ATP formed during glycolysis serves

While O^2- can form water by taking up two

mainly to supply Na⁺/K⁺-ATPase, which main-

protons, protonation of O^- provides the ex-

tains the erythrocytes’ membrane potential.

tremely dangerous hydroxy radical ( OH). A

The allosteric effector 2,3-BPG (see p. 282) is

fourth electron transfer and subsequent pro-

also derived from glycolysis. The PPP supplies

tonation also convert O^- into water.

NADPH+H⁺, which is needed to regenerate

The synthesis of ROS can be catalyzed by

glutathione (GSH) from GSSG with the help

iron ions, for example. Reaction of O₂ with

of glutathione reductase [3]. GSH, the most

FMN or FAD (see p. 32) also constantly pro-

important antioxidant in the erythrocytes,

duces ROS. By contrast, reduction of O₂ by

serves as a coenzyme for glutathione peroxi-

cytochrome c-oxidase (see p. 140) is “clean,”

dase [5]. This selenium-containing enzyme

as the enzyme does not release the intermedi-

detoxifies H₂O₂ and hydroperoxides, which

ates. In addition to antioxidants (B), enzymes

arise during the reaction of ROS with unsatu-

also provide protection against ROS: superox-

rated fatty acids in the erythrocyte mem-

ide dismutase [1] breaks down (“dispropor-

brane. The reduction of methemoglobin

tionates”) two superoxide molecules into O₂

(Hb Fe³⁺) to Hb (Hb Fe²⁺, [4]) is carried out

and the less damaging H₂O₂. The latter is in

by GSH or ascorbate by a non-enzymatic

turn disproportionated into O₂ and H₂O by

pathway; however, there are also NAD(P)H-

heme-containing catalase [2].

dependent Met-Hb reductases.

B. Biological antioxidants

To protect them against ROS and other radi-

cals, all cells contain antioxidants. These are

reducing agents that react easily with oxida-

tive substances and thus protect more impor-

tant molecules from oxidation. Biological

Blood

285

A. Reactive oxygen species

B. Biological antioxidants

Quinols

α-Tocopherol (vitamin E)

Molecular

O₂

and enols

Ubiquinol (coenzyme Q)

oxygen

Ascorbic acid (vitamin C)

Carotenoids

β-Carotin

Dispro-

Lycopin

portionation

Others

Glutathione

Bilirubin

Superoxide

O₂

radical

1. Examples

Glu

Cys

Gly

H O

Hydrogen

peroxide

OOC

(CH₂)₂

C N

C C N CH₂

COO

NH₃

CH₂

O₂

H₂O₂

2 Glutathione

2 (GSH)

Hydroxy

Oxidation

Reduction

radical

H O

H₂O

OOC

(CH₂)₂

C N

C C

N CH₂

COO

Water

Glutathione

disulfide (GSSG)

CH₂

OOC

(CH₂)₂

C N

C C

N CH₂

COO

H O

Superoxide dismutase

Catalase

1.15.1.1

1.11.1.6

2. Glutathione

C. Erythrocyte metabolism

Glutathione reductase

Methemoglobin

Glutathione peroxidase

[FAD] 1.6.4.2

reductase

[Se] 1.11.1.9/12

Glucose 6-

Pentose phosphate pathway

Glucose

phosphate

Glucose

Glycolysis

P P

3 Na

2 K

2 GSH

GSSG

2 GSH

GSSG

Na /K -

O₂

ATPase

P P P

BPG

2 Lactate

R-O-O-R'

R -OH

2 Lactate

R'-OH

Peroxide

Met-Hb

286

Tissues and organs

very tightly. Similar iron transport proteins

Iron metabolism

are found in secretions such as saliva, tears,

and milk; these are known as lactoferrins

A. Distribution of iron

(bottom right). Transferrin and the lactofer-

Iron (Fe) is quantitatively the most important

rins maintain the concentration of free iron in

trace element (see p. 362). The human body

body fluids at values below 10^-10 mol L^-1.

contains 4-5 g iron, which is almost exclusively

This low level prevents bacteria that require

present in protein-bound form. Approximately

free iron as an essential growth factor from

three-quarters of the total amount is found in

proliferating in the body. Like LDLs

(see

heme proteins (see pp. 106, 192), mainly he-

p. 278), transferrin and the lactoferrins are

moglobin and myoglobin. About 1% of the

taken up into cells by receptor-mediated

iron is bound in iron-sulfur clusters

(see

endocytosis.

p. 106), which function as cofactors in the

Excess iron is incorporated into ferritin and

respiratory chain, in photosynthesis, and in

stored in this form in the liver and other

other redox chains. The remainder consists

organs. The ferritin molecule consists of 24

of iron in transport and storage proteins

subunits and has the shape of a hollow sphere

(transferrin, ferritin; see B).

(bottom left). It takes up Fe²⁺ ions, which in

the process are oxidized to Fe³⁺ and then

deposited in the interior of the sphere as fer-

B. Iron metabolism

rihydrate. Each ferritin molecule is capable of

Iron can only be resorbed by the bowel in

storing several thousand iron ions in this way.

bivalent form (i. e., as Fe²⁺). For this reason,

In addition to ferritin, there is another storage

reducing agents in food such as ascorbate

form, hemosiderin, the function of which is

(vitamin C; see p. 368) promote iron uptake.

not yet clear.

Via transporters on the luminal and basal side

of the enterocytes, Fe²⁺ enters the blood,

Further information

where it is bound by transferrin. Part of the

iron that is taken up is stored in the bowel in

Disturbances of the iron metabolism are fre-

the form of ferritin (see below). Heme groups

quent and can lead to severe disease pictures.

can also be resorbed by the small intestine.

Iron deficiency is usually due to blood loss,

Most of the resorbed iron serves for the

or more rarely to inadequate iron uptake.

formation of red blood cells in the bone mar-

During pregnancy, increased demand can

row (erythropoiesis, top). As discussed on

also cause iron deficiency states. In severe

p. 192, it is only in the final step of hem bio-

cases, reduced hemoglobin synthesis can

synthesis that Fe²⁺ is incorporated by ferro-

lead to anemia (“iron-deficiency anemia”). In

chelatase into the previously prepared tetra-

these patients, the erythrocytes are smaller

pyrrol framework.

and have less hemoglobin. As their membrane

In the blood, 2.5-3.0 g of hemoglobin iron

is also altered, they are prematurely elimi-

circulates as a component of the erythrocytes

nated in the spleen.

(top right). Over the course of several months,

Disturbances resulting from raised iron

the flexibility of the red blood cells constantly

concentrations are less frequent. Known as

declines due to damage to the membrane and

hemochromatoses, these conditions can

cytoskeleton. Old erythrocytes of this type are

have genetic causes, or may be due to re-

taken up by macrophages in the spleen and

peated administration of blood transfusions.

other organs and broken down. The organic

As the body has practically no means of ex-

part of the heme is oxidized into bilirubin (see

creting iron, more and more stored iron is

p. 194), while the iron returns to the plasma

deposited in the organs over time in patients

pool. The quantity of heme iron recycled per

with untreated hemochromatosis, ultimately

day is much larger than the amount resorbed

leading to severe disturbances of organ func-

by the intestines.

tion.

Transferrin, a β-globulin with a mass of

80 kDa, serves to transport iron in the blood.

This monomeric protein consists of two sim-

ilar domains, each of which binds an Fe²⁺ ion

288

Tissues and organs

the urine, the H⁺ ions are buffered by NH₃ and

Acid-base balance

phosphate.

A. Hydrogen ion concentration in the blood

plasma

C. Buffer systems in the plasma

The H⁺ concentration in the blood and ex-

The buffering capacity of a buffer system de-

tracellular space is approximately

40 nM

pends on its concentration and its pK_a value.

10^-8 mol L^-1). This corresponds to a pH

The strongest effect is achieved if the pH

of 7.40. The body tries to keep this value con-

value corresponds to the buffer system’s pK_a

stant, as large shifts in pH are incompatible

value (see p. 30). For this reason, weak acids

with life.

with pK_a values of around 7 are best suited for

The pH value is kept constant by buffer

buffering purposes in the blood.

systems that cushion minor disturbances in

The most important buffer in the blood is

the acid-base balance (C). In the longer term,

the CO₂/bicarbonate buffer. This consists of

the decisive aspect is maintaining a balanced

water, carbon dioxide (CO₂, the anhydride of

equilibrium between H⁺ production and up-

carbonic acid H₂CO₃), and hydrogen carbo-

take and H⁺ release. If the blood’s buffering

nate (HCO_3-, bicarbonate). The adjustment

capacity is not suf cient, or if the acid-base

of the balance between CO₂ and HCO_3- is

balance is not in equilibrium—e. g., in kidney

accelerated by the zinc-containing enzyme

disease or during hypoventilation or hyper-

carbonate dehydratase

(carbonic anhydrase

ventilation—shifts in the plasma pH value

[1]; see also p. 282). At the pH value of the

can occur. A reduction by more than 0.03

plasma, HCO_3- and CO₂ are present in a ratio

units is known as acidosis, and an increase is

of about 20 : 1. However, the CO₂ in solution

called alkalosis.

in the blood is in equilibrium with the gaseous

CO₂ in the pulmonary alveoli. The CO₂/HCO_3-

system is therefore a powerful open buffer

B. Acid-base balance

system, despite having a not entirely optimal

Protons are mainly derived from two sour-

pK_a value of 6.1. Faster or slower respiration

ces—free acids in the diet and sulfur-contain-

increases or reduces CO₂ release in the lungs.

ing amino acids. Acids taken up with food—

This shifts the CO₂/HCO_3- ratio and thus the

e. g., citric acid, ascorbic acid, and phosphoric

plasma pH value (respiratory acidosis or alka-

acid—already release protons in the alkaline

losis). In this way, respiration can compensate

pH of the intestinal tract. More important for

to a certain extent for changes in plasma pH

proton balance, however, are the amino acids

values. However, it does not lead to the ex-

methionine and cysteine, which arise from

cretion of protons.

protein degradation in the cells. Their S atoms

Due to their high concentration, plasma

are oxidized in the liver to form sulfuric acid,

proteins—and hemoglobin in the erythro-

which supplies protons by dissociation into

cytes in particular—provide about one-quar-

sulfate.

ter of the blood’s buffering capacity. The buf-

During anaerobic glycolysis in the muscles

fering effect of proteins involves contribu-

and erythrocytes, glucose is converted into

tions from all of the ionizable side chains. At

lactate, releasing protons in the process (see

the pH value of blood, the acidic amino acids

p. 338). The synthesis of the ketone bodies

(Asp, Glu) and histidine are particularly effec-

acetoacetic acid and 3-hydroxybutyric acid

tive.

in the liver (see p. 312) also releases protons.

The second dissociation step in phosphate

Normally, the amounts formed are small and

(H₂PO₄/HPO_42-) also contributes to the buf-

of little influence on the proton balance. If

fering capacity of the blood plasma. Although

acids are formed in large amounts, however

the pK_a value of this system is nearly optimal,

(e. g., during starvation or in diabetes mellitus;

its contribution remains small due to the low

see p. 160), they strain the buffer systems and

total concentration of phosphate in the blood

can lead to a reduction in pH (metabolic

(around 1 mM).

acidoses; lactacidosis or ketoacidosis).

Only the kidney is capable of excreting pro-

tons in exchange for Na⁺ ions (see p. 326). In

Blood

289

A. Hydrogen ion concentration in the blood plasma

pH value of the plasma

Logarithmic scale

]

Linear scale

7.2

7.4

7.6

Acidosis

Alkalosis

Hypoventilation, increased production,

Hyperventilation

decreased excretion of H

increased H

excretion

B. Acid-base balance

Proteins

Thiol groups

Fatty acids

Glucose

Acids

H₂SO₄

Ketone bodies

H + anions

+ SO₄₂

H + anions

H + lactate

CO₂

+ H₂O

HCO₃

Only overproduction leads to acidosis

Lung

Lung influences

pH value by CO₂

excretion

Urine (

/day)

~60 mmol H

C. Buffer systems in the plasma

Carbon dioxide-

CO₂

+ H₂O

H₂CO₃

H + HCO₃

pK_a= 6.1

bicarbonate buffer

1.2 mM

24 mM

Prot · H

Prot + H

Protein buffer

pK_a = 4 - 12

200 - 240 g Protein · l^-1

HCO₃/CO_{2 +}H₂O

75%

Prot/Prot· H

24%

H₂PO₄

HPO

+ H

Phosphate buffer

pK_a = 6.8

1 mM

HPO

/H2PO4

Buffering capacity

Carbonate dehydratase 4.2.1.1

290

Tissues and organs

leads in five steps via factors XIIa, XIa, IXa,

Blood clotting

and Xa to the activation of prothrombin. The

Following injury to blood vessels, hemostasis

significance of this pathway in vivo has been

ensures that blood loss is minimized. Initially,

controversial since it was found that a genetic

thrombocyte activation leads to contraction

deficiency in factor XII does not lead to coag-

of the injured vessel and the formation of

ulation disturbances.

a loose clot consisting of thrombocytes

Both pathways depend on the presence of

(hemostasis). Slightly later, the action of the

activated thrombocytes, on the surface of

enzyme thrombin leads to the formation and

which several reactions take place. For exam-

deposition in the thrombus of polymeric fi-

ple, the prothrombinase complex (left) forms

brin (coagulation, blood clotting). The coagu-

when factors Xa and II, with the help of Va,

lation process is discussed here in detail.

bind via Ca²⁺ ions to anionic phospholipids in

the thrombocyte membrane. For this to hap-

pen, factors II and X have to contain the non-

A. Blood clotting

proteinogenic amino acid J-carboxygluta-

The most important reaction in blood clotting

mate (Gla; see p. 62), which is formed in the

is the conversion, catalyzed by thrombin, of

liver by post-translational carboxylation of

the soluble plasma protein fibrinogen (factor

the factors. The Gla residues are found in

I) into polymeric fibrin, which is deposited as

groups in special domains that create contacts

a fibrous network in the primary thrombus.

to the Ca²⁺ ions. Factors VII and IX are also

Thrombin (factor IIa) is a serine proteinase

linked to membrane phospholipids via Gla

(see p. 176) that cleaves small peptides from

residues.

fibrinogen. This exposes binding sites that

Substances that bind Ca²⁺ ions (e. g., citrate)

spontaneously allow the fibrin molecules to

prevent Gla-containing factors from attaching

aggregate into polymers. Subsequent covalent

to the membrane and therefore inhibit

cross-linking of fibrin by a transglutaminase

coagulation. Antagonists of vitamin K, which

(factor XIII) further stabilizes the thrombus.

is needed for synthesis of the Gla residues

Normally, thrombin is present in the blood

(see p. 364) also have anticoagulatory effects.

as an inactive proenzyme (see p. 270). Pro-

These include dicumarol, for example.

thrombin is activated in two different ways,

Active thrombin not only converts fibrino-

both of which represent cascades of enzy-

gen into fibrin, but also indirectly promotes

matic reactions in which inactive proenzymes

its own synthesis by catalyzing the activation

(zymogens, symbol: circle) are proteolytically

of factors V and VIII. In addition, it catalyzes

converted into active proteinases (symbol:

the activation of factor XIII and thereby trig-

sector of a circle). The proteinases activate

gers the cross-linking of the fibrin.

the next proenzyme in turn, and so on. Sev-

Regulation of blood clotting (not shown).

eral steps in the cascade require additional

To prevent the coagulation reaction from be-

protein factors (factors III, Va and VIIIa) as

coming excessive, the blood contains a num-

well as anionic phospholipids (PL; see below)

ber of anticoagulant substances, including

and Ca²⁺ ions. Both pathways are activated by

highly effective proteinase inhibitors. For

injuries to the vessel wall.

example, antithrombin III binds to various ser-

In the extravascular pathway (right), tissue

ine proteinases in the cascade and thereby

thromboplastin (factor III), a membrane pro-

inactivates them. Heparin, an anticoagulant

tein in the deeper layers of the vascular wall,

glycosaminoglycan (see p. 346), potentiates

activates coagulation factor VII. The activated

the effect of antithrombin III. Thrombomodu-

form of this (VIIa) autocatalytically promotes

lin, which is located on the vascular endothe-

its own synthesis and also generates the ac-

lia, also inactivates thrombin. A glycoprotein

tive factors IXa and Xa from their precursors.

known as Protein C ensures proteolytic deg-

With the aid of factor VIIIa, PL, and Ca²⁺, factor

radation of factors V and VIII. As it is activated

IXa produces additional Xa, which finally—

by thrombin, coagulation is shut down in this

with the support of Va, PL, and Ca²⁺—releases

way.

active thrombin.

The intravascular pathway (left) is prob-

ably also triggered by vascular injuries. It

Blood

291

A. Blood clotting

Kallikrein

Intravascular pathway

Extravascular pathway

~3 min

~10 s

Endothelium

Deeper

wall

XII

XIIa

layers

III

Function

unclear

Thromboplastin

XIa

IXa

VIIa

VII

VIII

VIIIa

IIa

Thrombin

Fibrinogen

Fibrin

Prothrombinase complex

Fibrin

polymer

Thrombin

IIa

XIII

XIIIa

K₂

EGF₂

K₁

EGF₁

Gla domain

Ca²

Thrombocyte

Polymeric

membrane

fibrin network

Coagulation factors

l Fibrinogen

lX Christmas factor* 3.4.21.22

ll Prothrombin* 3.4.21.5

X Stuart-Prower factor* 3.4.21.6

lll Tissue factor/thromboplastin

Xl Plasma thromboplastin antecedent* (PTA) 3.4.21.27

lV Ca²

Xll Hageman factor* 3.4.21.38

V Proaccelerin

Xlll Fibrin-stabilizing factor* 2.3.2.13

Vl Synonym for Va

Vll Proconvertin* 3.4.21.21

Proenzyme

Vlll Antihemophilic factor A

Contains γ-carboxyglutamate

292

Tissues and organs

possess. For example, carriers of blood group

Fibrinolysis, blood groups

A form antibodies against antigen B (“anti-B”),

while carriers of group B form antibodies

A. Fibrinolysis

against antigen A (“anti-A”). Individuals with

The fibrin thrombus resulting from blood

blood group 0 form both types, and those

clotting

(see p. 290) is dissolved again by

with blood group AB do not form any of these

plasmin, a serine proteinase found in the

antibodies.

blood plasma. For this purpose, the pre-

If blood from blood group A is transfused

cursor plasminogen first has to be proteolyti-

into the circulation of an individual with

cally activated by enzymes from various tis-

blood group B, for example, then the anti-A

sues. This group includes the plasminogen

present there binds to the A antigens. The

activator from the kidney (urokinase) and tis-

donor erythrocytes marked in this way are

sue plasminogen activator (t-PA) from vascular

recognized and destroyed by the complement

endothelia. By contrast, the plasma protein

system (see p. 298). In the test tube, aggluti-

α₂-antiplasmin, which binds to active plasmin

nation of the erythrocytes can be observed

and thereby inactivates it, inhibits fibrinoly-

when donor and recipient blood are incom-

sis.

patible.

Urokinase, t-PA, and streptokinase, a bac-

The recipient’s serum should not contain

terial proteinase with similar activity, are

any antibodies against the donor erythro-

used clinically to dissolve thrombi following

cytes, and the donor serum should not con-

heart attacks. All of these proteins are ex-

tain any antibodies against the recipient’s

pressed recombinantly in bacteria

(see

erythrocytes. Donor blood from blood group

p. 262).

0 is unproblematic, as its erythrocytes do not

possess any antibodies and therefore do not

react with anti-A or anti-B in the recipient’s

B. Blood groups: the ABO system

blood. Conversely, blood from the AB group

During blood transfusions, immune reactions

can only be administered to recipients with

can occur that destroy the erythrocytes trans-

the AB group, as these are the only ones with-

fused from the donor. These reactions result

out antibodies.

from the formation of antibodies (see p. 300)

In the Rh system (not shown), proteins on

directed to certain surface structures on the

the surface of the erythrocytes act as antigens.

erythrocytes. Known as blood group antigens,

These are known as “rhesus factors,” as the

these are proteins or oligosaccharides that can

system was first discovered in rhesus mon-

differ from individual to individual. More than

keys.

20 different blood group systems are now

The rhesus D antigen occurs in 84% of all

known. The ABO system and the Rh system

white individuals, who are therefore “Rh-pos-

are of particular clinical importance.

itive.” If an Rh-positive child is born to an Rh-

In the ABO system, the carbohydrate parts

negative mother, fetal erythrocytes can enter

of glycoproteins or glycolipids act as antigens.

the mother’s circulation during birth and lead

In this relatively simple system, there are four

to the formation of antibodies (IgG) against

blood groups (A, B, AB, and 0). In individuals

the D antigen. This initially has no acute ef-

with blood groups A and B, the antigens con-

fects on the mother or child. Complications

sist of tetrasaccharides that only differ in their

only arise when there is a second pregnancy

terminal sugar (galactose or N-acetylgalactos-

with an Rh-positive child, as maternal anti-D

amine). Carriers of the AB blood group have

antibodies cross the placenta to the fetus even

both antigens (A and B). Blood group 0 arises

before birth and can trigger destruction of the

from an oligosaccharide (the H antigen) that

child’s Rh-positive erythrocytes (fetal erythro-

lacks the terminal residue of antigens A and B.

blastosis).

The molecular causes for the differences be-

tween blood groups are mutations in the gly-

cosyl transferases that transfer the terminal

sugar to the core oligosaccharide.

Antibodies are only formed against anti-

gens that the individual concerned does not

Blood

293

A. Fibrinolysis

Plasminogen

Tissue

activator

plasminogen

3.4.21.73

activator

3.4.21.68

Plasmin

Soluble

Fibrin

3.4.21.7

proteins

thrombus

Inactive plasmin

α₂-antiplasmin

B. Blood groups: the AB0 system

Blood group

Genotypes

AA and A0

BB and B0

A A

Antigens

Antibodies

anti-B

anti-A

in blood

anti-B

Frequency in

40%

16%

40%

central Europe

Erythrocyte

Oligosaccharide

Glycoprotein with oligosaccharide

N-acetyl-D-glucosamine

Glyco-

lipid

D-Galactose

Membrane

D-Fucose

protein

N-acetyl-D-galactosamine

Fucosyltransferase 2.4.1.69/152

N-acetyl-galactosaminyl

GDP

transferase 2.4.1.40

Galactosyltransferase 2.4.1.37

GDP

UDP

B antigen

H antigen (blood group 0)

A antigen

294

Tissues and organs

A. Simplified diagram of the immune

Immune response

response

Viruses, bacteria, fungi, and parasites that en-

Pathogens that have entered the body—e. g.,

ter the body of vertebrates of are recognized

viruses (top)—are taken up by antigen-pre-

and attacked by the immune system. Endog-

senting cells (APCs) and proteolytically de-

enous cells that have undergone alterations—

graded (1). The viral fragments produced in

e. g., tumor cells—are also usually recognized

this way are then presented on the surfaces of

as foreign and destroyed. The immune system

these cells with the help of special membrane

is supported by physiological changes in

proteins (MHC proteins; see p. 296) (2). The

infected tissue, known as inflammation. This

APCs include B lymphocytes, macrophages,

reaction makes it easier for the immune cells

and dendritic cells such as the skin’s Langer-

to reach the site of infection.

hans cells.

Two different systems are involved in the

The complexes of MHC proteins and viral

immune response. The innate immune system

fragments displayed on the APCs are recog-

is based on receptors that can distinguish

nized by T cells that carry a receptor that

between bacterial and viral surface structures

matches the antigen (“T-cell receptors”; see

or foreign proteins (known as antigens) and

p. 296) (3). Binding leads to activation of the T

those that are endogenous. With the help of

cell concerned and selective replication of it

these receptors, phagocytes bind to the patho-

(4, “clonal selection”). The proliferation of im-

gens, absorb them by endocytosis, and break

mune cells is stimulated by interleukins (IL).

them down. The complement system (see

These are a group of more than 20 signaling

p. 298) is also part of the innate system.

substances belonging to the cytokine family

The acquired (adaptive) immune system is

(see p. 392), with the help of which immune

based on the ability of the lymphocytes to

cells communicate with each other. For exam-

form highly specific antigen receptors “on

ple, activated macrophages release IL-1 (5),

suspicion,” without ever having met the cor-

while T cells stimulate their own replication

responding antigen. In humans, there are sev-

and that of other immune cells by releasing

eral billion different lymphocytes, each of

IL-2 (6).

which carries a different antigen receptor. If

Depending on their type, activated T cells

this type of receptor recognizes “its” cognate

have different functions. Cytotoxic T cells

antigen, the lymphocyte carrying it is acti-

(green) are able to recognize and bind virus-

vated and then plays its special role in the

infected body cells or tumor cells (7). They

immune response.

then drive the infected cells into apoptosis

In addition, a distinction is made between

(see p. 396) or kill them with perforin, a pro-

cellular and humoral immune responses. The

tein that perforates the target cell’s plasma

T lymphocytes (T cells) are responsible for cel-

membrane (8).

lular immunity. They are named after the thy-

B lymphocytes, which as APCs present viral

mus, in which the decisive steps in their dif-

fragments on their surfaces, are recognized by

ferentiation take place. Depending on their

helper T cells (blue) or their T cell receptors

function, another distinction is made be-

(9). Stimulated by interleukins, selective clo-

tween cytotoxic T cells (green) and helper T

nal replication then takes place of B cells that

cells

(blue). Humoral immunity is based on

carry antigen receptors matching those of the

the activity of the B lymphocytes (B cells, light

pathogen (10). These mature into plasma cells

brown), which mature in the bone marrow.

(11) and finally secrete large amounts of

After activation by T cells, B cells are able to

soluble antibodies (12).

release soluble forms of their specific antigen

receptors, known as antibodies (see p. 300),

into the blood plasma. The immune system’s

“memory” is represented by memory cells.

These are particularly long-lived cells that

can arise from any of the lymphocyte types

described.

296

Tissues and organs

that any two individuals carry the same set of

T-cell activation

MHC proteins—except for monozygotic twins.

For the selectivity of the immune response

Class I MHC proteins occur in almost all

(see p. 294), the cells involved must be able

nucleated cells. They mainly interact with cy-

to recognize foreign antigens and proteins on

totoxic T cells and are the reason for the re-

other immune cells safely and reliably. To do

jection of transplanted organs. Class I MHC

this, they have antigen receptors on their cell

proteins are heterodimers (αβ). The β subunit

surfaces and co-receptors that support recog-

is also known as β₂-microglobulin.

nition.

Class II MHC proteins also consist of two

peptide chains, which are related to each

other. MHC II molecules are found on all anti-

A. Antigen receptors

gen-presenting cells in the immune system.

Many antigen receptors belong to the immu-

They serve for interaction between these cells

noglobulin superfamily. The common charac-

and CD4-carrying T helper cells.

teristic of these proteins is that they are made

up from “immunoglobulin domains.” These

B. T-cell activation

are characteristically folded substructures

consisting of 70-110 amino acids, which are

The illustration shows an interaction between

also found in soluble immunoglobulins (Ig;

a virus-infected body cell (bottom) and a CD8-

see p. 300). The illustration shows schemati-

carrying cytotoxic T lymphocyte (top). The

cally a few of the important proteins in the Ig

infected cell breaks down viral proteins in

superfamily. They consist of constant regions

its cytoplasm (1) and transports the peptide

(brown or green) and variable regions (or-

fragments into the endoplasmic reticulum

ange). Homologous domains are shown in

with the help of a special transporter (TAP)

the same colors in each case. All of the recep-

(2). Newly synthesized class I MHC proteins

tors have transmembrane helices at the C

on the endoplasmic reticulum are loaded

terminus, which anchor them to the mem-

with one of the peptides (3) and then trans-

branes. Intramolecular and intermolecular di-

ferred to the cell surface by vesicular trans-

sulfide bonds are also usually found in pro-

port (4). The viral peptides are bound on the

teins belonging to the Ig family.

surface of the α₂ domain of the MHC protein

Immunoglobulin M (IgM), a membrane

in a depression formed by an insertion as a

protein on the surface of B lymphocytes,

“floor” and two helices as “walls” (see smaller

serves to bind free antigens to the B cells. By

illustration).

contrast, T cell receptors only bind antigens

Supported by CD8 and other co-receptors,

when they are presented by another cell as a

a T cell with a matching T cell receptor binds

complex with an MHC protein (see below).

to the MHC peptide complex (5; cf. p. 224).

Interaction between MHC-bound antigens

This binding activates protein kinases in the

and T cell receptors is supported by co-recep-

interior of the T cell, which trigger a chain of

tors. This group includes CD8, a membrane

additional reactions (signal transduction; see

protein that is typical in cytotoxic T cells. T

p. 388). Finally, destruction of the virus-in-

helper cells use CD4 as a co-receptor instead

fected cell by the cytotoxic T lymphocytes

(not shown). The abbreviation “CD” stands for

takes place.

“cluster of differentiation.” It is the term for a

large group of proteins that are all located on

the cell surface and can therefore be identi-

fied by antibodies. In addition to CD4 and

CD8, there are many other co-receptors on

immune cells (not shown).

The MHC proteins are named after the

“major histocompatibility complex”—the DNA

segment that codes for them. Human MHC

proteins are also known as HLA antigens (“hu-

man leukocyte-associated” antigens). Their

polymorphism is so large that it is unlikely

Immune response

297

A. Antigen receptors

Variable part

H chain

Constant part

L chain

Disulfide bond

Characteristic

domain of the

superfamily

Ig domain

•

α Chain

β Chain

α Chain

β Chain

•

44 kDa

37 kDa

44 kDa

33 kDa

28 kDa

•

α₂

•

α₁

•

β₂ Micro-

•

globulin

•

12 kDa

α₃

C terminus

T cell receptor

IgM

MHC protein

CD8

(class I)

(class II)

B. T cell activation

Viral peptide

Cytotoxic T cell

T cell activity

CD8

T cell

receptor

Virus

Presented

MHC

viral peptide

protein

(class I)

Endoplasmic

ATP

ADP + P

Vesicular

reticulum

transport

Proteo-

lysis

TAP Viral peptides

Virus-infected body cell

298

Tissues and organs

The classic pathway is triggered by the for-

Complement system

mation of factor C1 at IgG or IgM on the sur-

The complement system is part of the innate

face of microorganisms (left). C1 is an 18-part

immune system (see p. 294). It supports non-

molecular complex with three different com-

specific defense against microorganisms. The

ponents (C1q, C1r, and C1s). C1q is shaped like

system consists of some 30 different proteins,

a bunch of tulips, the “flowers” of which bind

the “complement factors,” which are found in

to the F_c region of antibodies (left). This acti-

the blood and represent about

4% of all

vates C1r, a serine proteinase that initiates the

plasma proteins there. When inflammatory

cascade of the classic pathway. First, C4 is

reactions occur, the complement factors enter

proteolytically activated into C4b, which in

the infected tissue and take effect there.

turn cleaves C2 into C2a and C2b. C4B and

The complement system works in three

C2a together form C3 convertase [1], which

different ways:

finally catalyzes the cleavage of C3 into C3a

Chemotaxis. Various complement factors

and C3b. Small amounts of C3b also arise from

attract immune cells that can attack and

non-enzymatic hydrolysis of C3.

phagocytose pathogens.

The alternative pathway starts with the

Opsonization. Certain complement factors

binding of factors C3b and B to bacterial lipo-

(“opsonins”) bind to the pathogens and

polysaccharides (endotoxins). The formation

thereby mark them as targets for phagocytos-

of this complex allows cleavage of B by factor

ing cells (e. g., macrophages).

D, giving rise to a second form of C3 conver-

Membrane attack. Other complement fac-

tase (C3bBb).

tors are deposited in the bacterial membrane,

Proteolytic cleavage of factor C3 provides

where they create pores that lyse the patho-

two components with different effects. The

gen (see below).

reaction exposes a highly reactive thioester

group in C3b, which reacts with hydroxyl or

amino groups. This allows C3b to bind cova-

A. Complement activation

lently to molecules on the bacterial surface

The reactions that take place in the comple-

(opsonization, right). In addition, C3b initiates

ment system can be initiated in several ways.

a chain of reactions leading to the formation

During the early phase of infection, lipopoly-

of the membrane attack complex (see below).

saccharides and other structures on the sur-

Together with C4a and C5a (see below), the

face of the pathogens trigger the alternative

smaller product C3a promotes the inflamma-

pathway

(right). If antibodies against the

tory reaction and has chemotactic effects.

pathogens become available later, the anti-

The “late” factors C5 to C9 are responsible

gen-antibody complexes formed activate the

for the development of the membrane attack

classic pathway (left). Acute-phase proteins

complex (bottom). They create an ion-perme-

(see p. 276) are also able to start the comple-

able pore in the bacterial membrane, which

ment cascade (lectin pathway, not shown).

leads to lysis of the pathogen. This reaction is

Factors C1 to C4 (for “complement”) belong

triggered by C5 convertase [2]. Depending on

to the classic pathway, while factors B and D

the type of complement activation, this en-

form the reactive components of the alterna-

zyme has the structure C4b2a3b or C3bBb3b,

tive pathway. Factors C5 to C9 are responsible

and it cleaves C5 into C5a and C5b. The com-

for membrane attack. Other components not

plex of C5b and C6 allows deposition of C7 in

shown here regulate the system.

the bacterial membrane. C8 and numerous C9

As in blood coagulation (see p. 290), the

molecules—which form the actual pore—then

early components in the complement system

bind to this core.

are serine proteinases, which mutually acti-

vate each other through limited proteolysis.

They create a self-reinforcing enzyme cas-

cade. Factor C3, the products of which are

involved in several functions, is central to

the complement system.

300

Tissues and organs

Disulfide bonds link the two heavy chains to

Antibodies

each other and also link the heavy chains to

Soluble antigen receptors, which are formed

the light chains. Inside the domains, there are

by activated B cells (plasma cells; see p. 294)

also disulfide bonds that stabilize the tertiary

and released into the blood, are known as

structure. The domains are approximately 110

antibodies. They are also members of the im-

amino acids (AA) long and are homologous

munoglobulin family (Ig; see p. 296). Anti-

with each other. The antibody structure evi-

bodies are an important part of the humoral

dently developed as a result of gene duplica-

immune defense system. They have no anti-

tion. In its central region, known as the

microbial properties themselves, but support

“hinge” region, the antibodies are highly mo-

the cellular immune system in various ways:

bile.

1. They bind to antigens on the surface of

pathogens and thereby prevent them from

B. Classes of immunoglobulins

interacting with body cells

(neutralization;

see p. 404, for example).

Human immunoglobulins are divided into

2. They link single-celled pathogens into

five classes. IgA (with two subgroups), IgD,

aggregates (immune complexes), which are

IgE, IgG (with four subgroups), and IgM are

more easily taken up by phagocytes (aggluti-

defined by their H chains, which are desig-

nation).

nated by the Greek letters α, δ, ε, γ, and µ. By

3. They activate the complement system

contrast, there are only two types of L chain

(see p. 298) and thereby promote the innate

(κ and λ). IgD and IgE (like IgG) are tetramers

immune defense system (opsonization).

with the structure H₂L₂. By contrast, soluble

In addition, antibodies have become indis-

IgA and IgM are multimers that are held

pensable aids in medical and biological diag-

together by disulfide bonds and additional

nosis (see p. 304).

J peptides (joining peptides).

The antibodies have different tasks. IgMs

are the first immunoglobulins formed after

A. Domain structure of immunoglobulin G

contact with a foreign antigen. Their early

Type G immunoglobulins (IgG) are quantita-

forms are located on the surface of B cells

tively the most important antibodies in the

(see p. 296), while the later forms are se-

blood, where they form the fraction of γ-glob-

creted from plasma cells as pentamers. Their

ulins (see p. 276). IgGs (mass 150 kDa) are

action targets microorganisms in particular.

tetramers with two heavy chains (H chains;

Quantitatively, IgGs are the most important

red or orange) and two light chains (L chains;

immunoglobulins (see the table showing se-

yellow). Both H chains are glycosylated (vio-

rum concentrations). They occur in the blood

let; see also p. 43).

and interstitial fluid. As they can pass the

The proteinase papain cleaves IgG into two

placenta with the help of receptors, they can

Fab fragments and one Fc fragment. The Fab

be transferred from mother to fetus. IgAs

(“antigen-binding”) fragments, which each

mainly occur in the intestinal tract and in

consist of one L chain and the N-terminal

body secretions. IgEs are found in low con-

part of an H chain, are able to bind antigens.

centrations in the blood. As they can trigger

The F_c (“crystallizable”) fragment is made up

degranulation of mast cells (see p. 380), they

of the C-terminal halves of the two H chains.

play an important role in allergic reactions.

This segment serves to bind IgG to cell sur-

The function of IgDs is still unexplained. Their

faces, for interaction with the complement

plasma concentration is also very low.

system and antibody transport.

Immunoglobulins are constructed in a

modular fashion from several immunoglobu-

lin domains (shown in the diagram on the

right in Ω form). The H chains of IgG contain

four of these domains (V_H, C_H1, C_H2, and

C_H3) and the L chains containtwo (C_L and V_L).

The letters C and V designate constant or

variable regions.

Immune response

301

A. Domain structure of immunoglobulin G

Antigen-

Heavy

binding

chain

site

“Hinge” region

(450 AA)

Variable

domain

Light

chain

C_H1

(212 AA)

F_ab fragment

V_L

C_L

Fab

Cleavage site

Oligo-

for papain

saccharide

C_H2

3.4.22.2

Light chain

Oligo-

saccharide

Disulfide

C_H3

bond

C-terminal end

Heavy chain

B. Classes of immunoglobulins

IgA

IgD

IgE

IgG

IgM

360-720 kDa

172 kDa

196 kDa

150 kDa

935 kDa

IgG

IgA

13.5

3.5

IgM

IgD

IgE

1.5

0.03

0.00005

Serum concentration (g · l-1)

Chain:

κ or λ

Structure:

(α₂κ2)

δ₂κ₂

ε₂κ₂

γ₂κ₂

(µ₂κ₂)₅J

(α₂λ2)

δ₂λ₂

ε₂λ₂

γ₂λ₂

(µ₂λ₂)₅J

n =1, 2 or 3

302

Tissues and organs

maturation give rise to randomly combined

Antibody biosynthesis

new genes (“mosaic genes”).

3. Somatic mutation. During differentiation

The acquired (adaptive) immune system (see

of B cells into plasma cells, the coding genes

p. 294) is based on the ability of the lympho-

mutate. In this way, the “primordial” germ-

cytes to keep an extremely large repertoire of

line genes can become different somatic genes

antigen receptors and soluble antibodies

in the individual B cell clones.

ready for use, so that even infections involv-

ing new types of pathogen can be combated.

The wide range of immunoglobulins (Ig) are

C. Biosynthesis of a light chain

produced by genetic recombination and addi-

We can look at the basic features of the ge-

tional mutations during the development and

netic organization and synthesis of immuno-

maturation of the individual lymphocytes.

globulins using the biosynthesis of a mouse κ

chain as an example. The gene segments for

this light chain are designated L, V, J, and C.

A. Variability of immunoglobulins

They are located on chromosome 6 in the

germ-line DNA (on chromosome 2 in humans)

It is estimated that more than 10⁸ different

and are separated from one another by in-

antibody variants occur in every human

trons (see p. 242) of different lengths.

being. This variability affects both the heavy

Some 150 identical L segments code for the

and the light chains of immunoglobulins.

signal peptide

(“leader sequence,”

17-20

There are five different types of heavy (H)

amino acids) for secretion of the product

chain, according to which the antibody classes

(see p. 230). The V segments, of which there

are defined (α, δ, ε, γ, µ), and two types of light

are 150 different variants, code for most of the

(L) chain (κ and λ; see p. 300). The various Ig

variable domains (95 of the 108 amino acids).

types that arise from combinations of these

L and V segments always occur in pairs—in

chains are known as isotypes. During immu-

tandem, so to speak. By contrast, there are

noglobulin biosynthesis, plasma cells can

only five variants of the J segments (joining

switch from one isotype to another (“gene

segments) at most. These code for a peptide

switch”). Allotypic variation is based on the

with 13 amino acids that links the variable

existence of various alleles of the same

part of the κ chains to the constant part. A

gene—i. e., genetic differences between indi-

single C segment codes for the constant part

viduals. The term idiotypic variation refers to

of the light chain (84 amino acids).

the fact that the antigen binding sites in the

During the differentiation of B lympho-

Fab fragments can be highly variable. Idiotypic

cytes, individual V/J combinations arise in

variation affects the variable domains (shown

each B cell. One of the 150 L/V tandem seg-

here in pink) of the light and heavy chains. At

ments is selected and linked to one of the five

certain sites—known as the hypervariable re-

J segments. This gives rise to a somatic gene

gions (shown here in red)—variation is partic-

that is much smaller than the germline gene.

ularly wide; these sequences are directly in-

Transcription of this gene leads to the forma-

volved in the binding of the antigen.

tion of the hnRNA for the κ chain, from which

introns and surplus J segments are removed

by splicing (see p. 246). Finally, the completed

B. Causes of antibody variety

mRNA still contains one each of the L-V-J-C

There are three reasons for the extremely

segments and after being transported into the

wide variability of antibodies:

cytoplasm is available for translation. The

1. Multiple genes. Various genes are avail-

subsequent steps in Ig biosynthesis follow

able to code for the variable protein domains.

the rules for the synthesis of membrane-

Only one gene from among these is selected

bound or secretory proteins (see p. 230).

and expressed.

2. Somatic recombination. The genes are

divided into several segments, of which there

are various versions. Various (“untidy”) com-

binations of the segments during lymphocyte

Immune response

303

A. Variability of immunoglobulins

Constant

Variable

domain

Hyper-

κ or λ

variable

regions

α,δ,ε,γ

or µ

Constant

domain

Isotypic

Allotypic

Idiotypic

B. Origins of antibody variety

C. Biosynthesis of a light chain

DNA

Intro

Is removed

Germ

line

DNA

V/J Recombination

Protein

1. Multiple genes

Germ line

B cell

Point mutations

DNA

during B cell

maturation

Somatic

DNA

Transcription

in B cell

AAA

Protein

hnRNA

2. Somatic recombination

Splicing

Germ line

DNA

Selection and

linkage of

gene segments

Somatic

AAA

DNA

mRNA

Translation

V3 J

H3N

Protein

3. Somatic mutation

COO

304

Tissues and organs

or in vivo by producing ascites fluid in mice

Monoclonal antibodies,

(6).

immunoassay

B. Immunoassay

A. Monoclonal antibodies

Immunoassays are semiquantitative proce-

Monoclonal antibodies (MABs) are secreted

dures for assessing substances with low con-

by immune cells that derive from a single

centrations. In principle, immunoassays can

antibody-forming cell

(from a single cell

be used to assess any compound against

clone). This is why each MAB is directed

which antibodies are formed.

against only one specific epitope of an immu-

The basis for this procedure is the anti-

nogenic substance, known as an “antigenic

gen-antibody “reaction”—i. e., specific binding

determinant.” Large molecules contain several

of an antibody to the molecule being assayed.

epitopes, against which various antibodies are

Among the many different immunoassay

formed by various B cells. An antiserum con-

techniques that have been developed—e. g.,

taining a mixture of all of these antibodies is

radioimmunoassay (RIA), and chemolumines-

described as being polyclonal.

cence immunoassay (CIA)—a version of the

To obtain MABs, lymphocytes isolated from

enzyme-linked immunoassay (EIA) is shown

the spleen of immunized mice (1) are fused

here.

with mouse tumor cells (myeloma cells, 2).

The substance to be assayed—e. g., the hor-

This is necessary because antibody-secreting

mone thyroxine in a serum sample—is pipet-

lymphocytes in culture have a lifespan of only

ted into a microtiter plate (1), the walls of

a few weeks. Fusion of lymphocytes with tu-

which are coated with antibodies that specif-

mor cells gives rise to cell hybrids, known as

ically bind the hormone. At the same time, a

hybridomas, which are potentially immortal.

small amount of thyroxine is added to the

Successful fusion (2) is a rare event, but the

incubation to which an enzyme known as

frequency can be improved by adding poly-

the “tracer” (1) has been chemically coupled.

ethylene glycol (PEG). To obtain only success-

The tracer and the hormone being assayed

fully fused cells, incubation is required for an

compete for the small number of antibody

extended period in a primary culture with

binding sites available. After binding has

HAT medium (3), which contains hypoxan-

taken place (2), all of the unbound molecules

thine, aminopterin, and thymidine. Amino-

are rinsed out. The addition of a substrate

pterin, an analogue of dihydrofolic acid, com-

solution for the enzyme (a chromogenic solu-

petitively inhibits dihydrofolate reductase and

tion) then triggers an indicator reaction (3),

thus inhibits the synthesis of dTMP

(see

the products of which can be assessed using

p. 402). As dTMP is essential for DNA synthe-

photometry (4).

sis, myeloma cells cannot survive in the pres-

The larger the amount of enzyme that can

ence of aminopterin. Although spleen cells

bind to the antibodies on the container’s

are able to circumvent the inhibitory effect

walls, the larger the amount of dye that is

of aminopterin by using hypoxanthine and

produced. Conversely, the larger the amount

thymidine, they have a limited lifespan and

of the substance being assayed that is present

die. Only hybridomas survive culture in HAT

in the sample, the smaller the amount of

medium, because they possess both the im-

tracer that can be bound by the antibodies.

mortality of the myeloma cells and the spleen

Quantitative analysis can be carried out

cells’ metabolic side pathway.

through parallel measurement using stan-

Only a few fused cells actually produce

dards with a known concentration.

antibodies. To identify these cells, the hybrid-

omas have to be isolated and replicated by

cloning (4). After the clones have been tested

for antibody formation, positive cultures are

picked out and selected by further cloning (5).

This results in hybridomas that synthesize

monoclonal antibodies. Finally, MAB produc-

tion is carried out in vitro using a bioreactor,

Immune response

305

A. Monoclonal antibodies

Immunized

Antigen

Hybridoma cells

Antibody test:

mouse

Positive

cultures

A B C

A B

With

HAT

PEG

medium

Immunization

Spleen cells

Fusion

Primary culture

Myeloma cells

Cell culture

Mouse with

ascites

Subcloning

Cloning

C C

Production of

monoclonal

antibodies

Culture of

Selection

a selected

of positive

clone

clones

Clone

Cell culture

B. Immunoassay

Enzyme:

peroxidase

Sample

Tracer

Antibodies

Incubate

Microtiter plate

Absorption

Working range

10-6-10-12 M

Read

Wash

absorption

Substrate: H₂O₂

Concentration

Chromogen: C

Incubate

Peroxidase

Chromogen + H₂O₂

Dye

+ H₂O

1.11.1.7

306

Tissues and organs

the form of the polysaccharide glycogen or

Liver: functions

converted into fatty acids. When there is a

Weighing 1.5 kg, the liver is one of the largest

drop in the blood glucose level, the liver re-

organs in the human body. Although it only

leases glucose again by breaking down glyco-

represents 2-3% of the body’s mass, it ac-

gen. If the glycogen store is exhausted, glu-

counts for 25-30% of oxygen consumption.

cose can also be synthesized by gluconeogen-

esis from lactate, glycerol, or the carbon skel-

eton of amino acids (see p. 310).

A. Diagram of a hepatocyte

Lipid metabolism. The liver synthesizes

The 3

10¹¹ cells in the liver—particularly the

fatty acids from acetate units. The fatty acids

hepatocytes, which make up 90% of the cell

formed are then used to synthesize fats and

mass—are the central location for the body’s

phospholipids, which are released into the

intermediary metabolism. They are in close

blood in the form of lipoproteins. The liver’s

contact with the blood, which enters the liver

special ability to convert fatty acids into ke-

from the portal vein and the hepatic arteries,

tone bodies and to release these again is also

flows through capillary vessels known as si-

important (see p. 312).

nusoids, and is collected again in the central

Like other organs, the liver also synthesizes

veins of the hepatic lobes. Hepatocytes are

cholesterol, which is transported to other tis-

particularly rich in endoplasmic reticulum,

sues as a component of lipoproteins. Excess

as they carry out intensive protein and lipid

cholesterol is converted into bile acids in the

synthesis. The cytoplasm contains granules of

liver or directly excreted with the bile (see

insoluble glycogen. Between the hepatocytes,

p. 314).

there are bile capillaries through which bile

Amino acid and protein metabolism. The

components are excreted.

liver controls the plasma levels of the amino

acids. Excess amino acids are broken down.

With the help of the urea cycle (see p. 182),

B. Functions of the liver

the nitrogen from the amino acids is con-

The most important functions of the liver are:

verted into urea and excreted via the kidneys.

1. Uptake of nutrients supplied by the in-

The carbon skeleton of the amino acids enters

testines via the portal vein.

the intermediary metabolism and serves for

2. Biosynthesis of endogenous compounds

glucose synthesis or energy production. In

and storage, conversion, and degradation of

addition, most of the plasma proteins are syn-

them into excretable molecules (metabolism).

thesized or broken down in the liver (see

In particular, the liver is responsible for the

p. 276).

biosynthesis and degradation of almost all

Biotransformation. Steroid hormones and

plasma proteins.

bilirubin, as well as drugs, ethanol, and other

3. Supply of the body with metabolites and

xenobiotics are taken up by the liver and in-

nutrients.

activated and converted into highly polar me-

4. Detoxification of toxic compounds by

tabolites by conversion reactions (see p. 316).

biotransformation.

Storage. The liver not only stores energy

5. Excretion of substances with the bile.

reserves and nutrients for the body, but also

certain mineral substances, trace elements,

and vitamins, including iron, retinol, and vi-

C. Hepatic metabolism

tamins A, D, K, folic acid, and B₁₂.

The liver is involved in the metabolism of

practically all groups of metabolites. Its func-

tions primarily serve to cushion fluctuations

in the concentration of these substances in

the blood, in order to ensure a constant sup-

ply to the peripheral tissues (homeostasis).

Carbohydrate metabolism. The liver takes

up glucose and other monosaccharides from

the plasma. Glucose is then either stored in

Liver

307

A. Diagram of a hepatocyte

Erythrocyte

Disse

Sinusoid

space

Lipoproteins

Glycogen

***

Golgi

complex

Nucleus

Rough ER

Smooth ER

Microbody

Mitochondrion

Lysosome

Desmosome

Biliary capillary

B. Functions of the liver

Vena cava

Supply

Metabolism

Detoxifica-

tion

Biosynthesis

Biotrans-

Storage

formation

Conversion

and

Degradation

Portal vein

Uptake

Excretion

Gallbladder

From the gastrointestinal

Bile duct

tract, pancreas, spleen

Intestine

C. Liver metabolism

Carbohydrate

Lipid

Amino acid

Biotrans-

metabolism

formation

Glucose

BSC

Fatty acids

Amino acids

Steroid hormones

Galactose

Fats

Urea

Bile pigments

Fructose

Ketone bodies

Ethanol

Mannose

Cholesterol

BEC

Drugs

Pentoses

Bile acids

Plasma

Lactate

Vitamins

proteins

Glycerol

Glycogen

BSC

Lipoproteins

Albumin

Biosynthesis

Coagulation

Conversion and

factors

degradation

Hormones

Excretion

Enzymes

Storage

308

Tissues and organs

acids, ketone bodies). By contrast, the central

Buffer function in organ meta-

nervous system (CNS) is dependent on glu-

bolism

cose. It is only able to utilize ketone bodies

after a prolonged phase of hunger (B).

All of the body’s tissues have a constant re-

quirement for energy substrates and nu-

trients. The body receives these metabolites

B. Postabsorptive state

with food, but the supply is irregular and in

When the food supply is interrupted, the

varying amounts. The liver acts here along

postabsorbtive state quickly sets in. The pan-

with other organs, particularly adipose tissue,

creatic A cells now release increased amounts

as a balancing buffer and storage organ.

of glucagon, while the B cells reduce the

In the metabolism, a distinction is made

amount of insulin they secrete. The reduced

between the absorptive state (well-fed state)

insulin/glucagon quotient leads to switching

immediately after a meal and the postabsorb-

of the intermediary metabolism. The body

tive state

(state of starvation), which starts

now falls back on its energy reserves. To do

later and can merge into hunger. The switch-

this, it breaks down storage substances (gly-

ing of the organ metabolism between the two

cogen, fats, and proteins) and shifts energy-

phases depends on the concentration of en-

supplying metabolites between the organs.

ergy-bearing metabolites in the blood (plas-

The liver first empties its glycogen store

ma level). This is regulated jointly by hor-

(glycogenolysis; see p. 156). It does not use

mones and by the autonomic nervous system.

the released glucose itself, however, but sup-

plies the other tissues with it. In particular,

the brain, adrenal gland medulla, and eryth-

A. Absorptive state

rocytes depend on a constant supply of glu-

The absorptive state continues for 2-4 hours

cose, as they have no substantial glucose re-

after food intake. As a result of food digestion,

serves themselves. When the liver’s glycogen

the plasma levels of glucose, amino acids, and

reserves are exhausted after

12-24 hours,

fats (triacylglycerols) temporarily increase.

gluconeogenesis begins (see p. 154). The pre-

The endocrine pancreas responds to this by

cursors for this are derived from the muscu-

altering its hormone release—there is an in-

lature (amino acids) and adipose tissue (glyc-

crease in insulin secretion and a reduction in

erol from fat degradation). From the fatty

glucagon secretion. The increase in the insu-

acids that are released (see below), the liver

lin/glucagon quotient and the availability of

starts to form ketone bodies (ketogenesis; see

substrates trigger an anabolic phase in the

p. 312). These are released into the blood and

tissues—particularly liver, muscle, and adi-

serve as important energy suppliers during

pose tissues.

the hunger phase. After 1-2 weeks, the CNS

The liver forms increased amounts of gly-

also starts to use ketone bodies to supply part

cogen and fats from the substrates supplied.

of its energy requirements, in order to save

Glycogen is stored, and the fat is released into

glucose.

the blood in very low density lipoproteins

In muscle, the extensive glycogen reserves

(VLDLs).

are exclusively used for the muscles’ own

Muscle also refills its glycogen store and

requirements (see p. 320). The slowly initi-

synthesizes proteins from the amino acids

ated protein breakdown in muscle supplies

supplied.

amino acids for gluconeogenesis in the liver.

Adipose tissue removes free fatty acids

In adipose tissue, glucagon triggers lipoly-

from the lipoproteins, synthesizes triacylgly-

sis, releasing fatty acids and glycerol. The fatty

cerols from them again, and stores these in

acids are used as energy suppliers by many

the form of insoluble droplets.

types of tissue (with the exception of brain

During the absorptive state, the heart and

and erythrocytes). An important recipient of

neural tissue mainly use glucose as an energy

the fatty acids is the liver, which uses them for

source, but they are unable to establish any

ketogenesis.

substantial energy stores. Heart muscle cells

are in a sense “omnivorous,” as they can also

use other substances to produce energy (fatty

310

Tissues and organs

and therefore cannot be converted into oxalo-

Carbohydrate metabolism

acetic acid, the precursor for gluconeogenesis.

Besides fatty acids and ketone bodies, glucose

is the body’s most important energy supplier.

B. Fructose and galactose metabolism

The concentration of glucose in the blood (the

“blood glucose level”) is maintained at

Fructose is mainly metabolized by the liver,

4-6 mM (0.8-1.0 g L^-1) by precise regula-

which channels it into glycolysis (left half of

tion of glucosesupplying and glucose-utilizing

the illustration).

processes. Glucose suppliers include the in-

A special ketohexokinase [1] initially phos-

testines (glucose from food), liver, and kid-

phorylates fructose into fructose

1-phos-

neys. The liver plays the role of a “glucostat”

phate. This is then cleaved by an aldolase

(see p. 308).

[2], which is also fructose-specific, to yield

The liver is also capable of forming glucose

glycerone

3-phosphate

(dihydroxyacetone

by converting other sugars—e. g., fructose and

phosphate) and glyceraldehyde. Glycerone

galactose—or by synthesizing from other me-

3-phosphate is already an intermediate of

tabolites. The conversion of lactate to glucose

glycolysis

(center), while glyceraldehyde

in the Cori cycle (see p. 338) and the conver-

can be phosphorylated into glyceraldehyde

sion of alanine to glucose with the help of the

3-phosphate by triokinase [3].

alanine cycle (see p. 338) are particularly im-

To a smaller extent, glyceraldehyde is also

portant for the supply of erythrocytes and

reduced to glycerol [4] or oxidized to glycer-

muscle cells.

ate, which can be channeled into glycolysis

Transporters in the plasma membrane of

following phosphorylation (not shown). The

hepatocytes allow insulin-independent trans-

reduction of glyceraldehyde

[4] uses up

port of glucose and other sugars in both di-

NADH. As the rate of degradation of alcohol

rections. In contrast to muscle, the liver pos-

in the hepatocytes is limited by the supply of

sesses the enzyme glucose-6-phosphatase,

NAD⁺, fructose degradation accelerates alco-

which can release glucose from glucose-6-

hol degradation (see p. 320).

phosphate.

Outside of the liver, fructose is channeled

into the sugar metabolism by reduction at C-2

to yield sorbitol and subsequent dehydration

A. Gluconeogenesis: overview

at C-1 to yield glucose (the polyol pathway;

Regeneration of glucose (up to 250 g per day)

not shown).

mainly takes place in the liver. The tubule

Galactose is also broken down in the liver

cells of the kidney are also capable of carrying

(right side of the illustration). As is usual with

out gluconeogenesis, but due to their much

sugars, the metabolism of galactose starts

smaller mass, their contribution only repre-

with a phosphorylation to yield galactose

sents around 10% of total glucose formation.

1-phosphate [5]. The connection to the glu-

Gluconeogenesis is regulated by hormones.

cose metabolism is established by C-4 epime-

Cortisol, glucagon, and epinephrine promote

rization to form glucose 1-phosphate. How-

gluconeogenesis, while insulin inhibits it

ever, this does not take place directly. Instead,

(see pp. 158, 244).

a transferase [6] transfers a uridine 5 -mono-

The main precursors of gluconeogenesis in

phosphate (UMP) residue from uridine di-

the liver are lactate from anaerobically work-

phosphoglucose

(UDPglucose) to galactose

ing muscle cells and from erythrocytes,

1-phosphate. This releases glucose 1-phos-

glucogenic amino acids from the digestive

phate, while galactose 1-phosphate is con-

tract and muscles

(mainly alanine), and

verted into uridine diphosphogalactose (UDP-

glycerol from adipose tissue. The kidney

galactose). This then is isomerized into UDP-

mainly uses amino acids for gluconeogenesis

glucose. The biosynthesis of galactose also fol-

(Glu, Gln; see p. 328).

lows this reaction pathway, which is freely

In mammals, fatty acids and other suppli-

reversible up to reaction [5]. Genetic defects

ers of acetyl CoA are not capable of being used

of enzymes [5] or [6] can lead to the clinical

for gluconeogenesis, as the acetyl residues

picture of galactosemia.

formed during β-oxidation in the tricarbox-

ylic acid cycle (see p. 132) are oxidized to CO₂

Liver

311

A. Gluconeogenesis: overview

Gluco-

Amino acids

neogenesis

Muscle

Liver

Kidney

Cortisol

Glucagon

Epinephrine

Insulin

Lactate

Glycogen

10%

Amino acids

Gluco-

Fructose

Glucose

neogenesis

90%

Galactose

Conversion

Glycerol

Plasma

concentration

4 - 6 mM

Fatty acids

Not possible

in mammals

Adipose tissue

B. Fructose and galactose metabolism

HOCH₂

Fructose

Glucose

Galactose

ATP

ADP

Fructose 1-

Glucose 6-

Glucose 1-

Galactose 1-

Fructose 6-

UDP-Glucose

UDP-Galactose

Fructose 1,6-bis-

Glycer-

Glycerone 3-

aldehyde

aldehyde 3-

Glycolysis

NADH+H +

Pyruvate

NAD

ATP

ADP

Glycerol

Ketohexokinase

Triokinase

Galactokinase

UDPglucose

2.7.1.3

2.7.1.28

2.7.1.6

4-epimerase

5.1.3.2

Fructose-bisphosphate

Aldehyde reductase

Hexose-1-phosphate

aldolase 4.1.2.13

1.1.1.21

uridyltransferase

2.7.7.12

312

Tissues and organs

B. Biosynthesis of ketone bodies

Lipid metabolism

At high concentrations of acetyl-CoA in the

The liver is the most important site for the

liver mitochondria, two molecules condense

formation of fatty acids, fats (triacylglycerols),

to form acetoacetyl CoA [1]. The transfer of

ketone bodies, and cholesterol. Most of these

another acetyl group

[2] gives rise to

products are released into the blood. In con-

3-hydroxy-3-methylglutaryl-CoA (HMG CoA),

trast, the triacylglycerols synthesized in adi-

which after release of acetyl CoA [3] yields

pose tissue are also stored there.

free acetoacetate (Lynen cycle). Acetoacetate

can be converted to 3-hydroxybutyrate by

A. Lipid metabolism

reduction [4], or can pass into acetone by

nonenzymatic decarboxylation

[5]. These

Lipid metabolism in the liver is closely linked

three compounds are together referred to as

to the carbohydrate and amino acid metabo-

“ketone bodies,” although in fact 3-hydroxy-

lism. When there is a good supply of nutrients

butyrate is not actually a ketone. As reaction

in the resorptive (wellfed) state (see p. 308),

[3] releases an H⁺ ion, metabolic acidosis can

the liver converts glucose via acetyl CoA into

occur as a result of increased ketone body

fatty acids. The liver can also take up fatty

synthesis (see p. 288).

acids from chylomicrons, which are supplied

The ketone bodies are released by the liver

by the intestine, or from fatty acid-albumin

into the blood, in which they are easily solu-

complexes (see p. 162). Fatty acids from both

ble. Blood levels of ketone bodies therefore

sources are converted into fats and phospho-

rise during periods of hunger. Together with

lipids. Together with apoproteins, they are

free fatty acids, 3-hydroxybutyrate and ace-

packed into very-low-density lipoproteins

toacetate are then the most important energy

(VLDLs; see p. 278) and then released into

suppliers in many tissues (including heart

the blood by exocytosis. The VLDLs supply

muscle). Acetone cannot be metabolized and

extrahepatic tissue, particularly adipose tis-

is exhaled via the lungs or excreted with

sue and muscle.

urine.

In the postresorptive state (see p. 292)—

To channel ketone bodies into the energy

particularly during fasting and starva-

metabolism, acetoacetate is converted with

tion—the lipid metabolism is readjusted and

the help of succinyl CoA into succinic acid

the organism falls back on its own reserves. In

and acetoacetyl CoA, which is broken down

these conditions, adipose tissue releases fatty

by β-oxidation into acetyl CoA (not shown;

acids. They are taken up by the liver and are

see p. 180).

mainly converted into ketone bodies (B).

If the production of ketone bodies exceeds

Cholesterol can be derived from two sour-

the demand for them outside the liver, there

ces—food or endogenous synthesis from ace-

is an increase in the concentration of ketone

tyl-CoA. A substantial percentage of endo-

bodies in the plasma (ketonemia) and they are

genous cholesterol synthesis takes place in

also eventually excreted in the urine (ketonu-

the liver. Some cholesterol is required for

ria). Both phenomena are observed after pro-

the synthesis of bile acids (see p. 314). In ad-

longed starvation and in inadequately treated

dition, it serves as a building block for cell

diabetes mellitus. Severe ketonuria with ke-

membranes (see p. 216), or can be esterified

toacidosis can cause electrolyte shifts and

with fatty acids and stored in lipid droplets.

loss of consciousness, and is therefore life-

The rest is released together into the blood in

threatening (ketoacidotic coma).

the form of lipoprotein complexes (VLDLs)

and supplies other tissues. The liver also con-

tributes to the cholesterol metabolism by tak-

ing up from the blood and breaking down

lipoproteins that contain cholesterol and cho-

lesterol esters (HDLs, IDLs, LDLs; see p. 278).

Liver

313

A. Lipid metabolism

Intestine

Adipose tissue

Muscle

Glucose

Fatty acids

Acetyl CoA

Ketone bodies

Ketone

bodies

Apolipo-

Fats

proteins

Fats

Fatty acids

Phospholipids

VLDL

Cholesterol

Chylomicron

residues

HDL

Cholesterol

Bile

IDL

esters

acids

LDL

Bile

Peripheral

tissues

Absorptive state

Postabsorptive state

A. Biosynthesis of ketone bodies

H O

H OH H

C C

COO

3-Hydroxy-

Acetyl CoA

Acetacetyl CoA

3-methyl-

glutaryl CoA

Acetyl CoA

CoA

Acetyl CoA CoA

H OH H

H O H

H +

C C

COO

C C

COO

H H

3-Hydroxybutyrate

Acetacetate

Acetone

CO₂

Acetyl-CoA-C-acyltransferase 2.3.1.16

Hydroxymethylglutaryl-CoA lyase 4.1.3.4

Hydroxymethylglutaryl-CoA synthase 4.1.3.5

3-Hydroxybutyrate dehydrogenase 1.1.1.30

Nonenzymatic reaction

314

Tissues and organs

cleavage of the OH group at C-7 (see B).

Bile acids

They are therefore referred to as secondary

Bile is an important product released by the

bile acids.

hepatocytes. It promotes the digestion of fats

from food by emulsifying them in the small

B. Metabolism of bile salts

intestine (see p. 2770). The emulsifying com-

ponents of bile, apart from phospholipids,

Bile salts are exclusively synthesized in the

mainly consist of bile acids and bile salts

liver (see A). The slowest step in their biosyn-

(see below). The bile also contains free cho-

thesis is hydroxylation at position 7 by a 7-D-

lesterol, which is excreted in this way (see

hydroxylase. Cholic acid and other bile acids

p. 312).

inhibit this reaction (end-product inhibition).

In this way, the bile acids present in the liver

regulate the rate of cholesterol utilization.

A. Bile acids and bile salts

Before leaving the liver, a large proportion

Bile acids are steroids consisting of 24 C atoms

of the bile acids are activated with CoA and

carrying one carboxylate group and several

then conjugated with the amino acids glycine

hydroxyl groups. They are formed from cho-

or taurine (2; cf. A). In this way, cholic acid

lesterol in the liver via an extensive reaction

gives rise to glycocholic acid and taurocholic

pathway (top). Cytochrome P450 enzymes in

acid. The liver bile secreted by the liver be-

the sER of hepatocytes are involved in many

comes denser in the gallbladder as a result of

of the steps (seep. 318). Initially, the choles-

the removal of water (bladder bile; 3).

terol double bond is removed. Monooxyge-

Intestinal bacteria produce enzymes that

nases then introduce one or two additional

can chemically alter the bile salts (4). The

OH groups into the sterane framework. Fi-

acid amide bond in the bile salts is cleaved,

nally, the side chain is shortened by three C

and dehydroxylation at C-7 yields the corre-

atoms, and the terminal C atom is oxidized to

sponding secondary bile acids from the pri-

a carboxylate group.

mary bile acids (5). Most of the intestinal bile

It is important that the arrangement of the

acids are resorbed again in the ileum (6) and

A and B rings is altered from trans to cis dur-

returned to the liver via the portal vein (en-

ing bile acid synthesis (see p. 54). The result

terohepatic circulation). In the liver, the sec-

of this is that all of the hydrophilic groups in

ondary bile acids give rise to primary bile

the bile acids lie on one side of the molecule.

acids again, from which bile salts are again

Cholesterol, which is weakly amphipathic

produced. Of the 15-30 g bile salts that are

(top), has a small polar “head” and an ex-

released with the bile per day, only around

tended apolar “tail.” By contrast, the much

0.5g therefore appears in the feces. This ap-

more strongly amphipathic bile acid mole-

proximately corresponds to the amount of

cules (bottom) resemble disks with polar top

daily de novo synthesis of cholesterol.

sides and apolar bottom sides. At physiolog-

ical pH values, the carboxyl groups are almost

Further information

completely dissociated and therefore nega-

tively charged.

The cholesterol excreted with the bile is

Cholic acid and chenodeoxycholic acid,

poorly water-soluble. Together with phos-

known as the primary bile acids, are quanti-

pholipids and bile acids, it forms micelles

tatively the most important metabolites of

(see p. 270), which keep it in solution. If the

cholesterol. After being biosynthesized, they

proportions of phospholipids, bile acids and

are mostly activated with coenzyme A and

cholesterol shift, gallstones can arise. These

then conjugated with glycine or the non-pro-

mainly consist of precipitated cholesterol

teinogenic amino acid taurine (see p. 62). The

(cholesterol stones), but can also contain

acid amides formed in this way are known as

Ca²⁺ salts of bile acids and bile pigments (pig-

conjugated bile acids or bile salts. They are

ment stones).

even more amphipathic than the primary

products.

Deoxycholic acid and lithocholic acid are

only formed in the intestine by enzymatic

Liver

315

A. Bile acids and bile salts

Cholesterol

Bile acids

HO- in position

Primary bile acids

— Cholic acid

C-3

C-7

C-12

— Chenodeoxycholic

C-3

C-7

acid

Secondary bile acids

— Deoxycholic acid

C-3

C-12

— Lithocholic acid

C-3

Bile salts

14 steps

N COO

Cholic acid

COO

Glycine

Glycocholic acid

SO₃

Taurine

Taurocholic acid

Bile salts = conjugated bile acids

B. Metabolism of bile salts

Primary

Cholesterol

bile acids

Intestine

Glycine, taurine

Bile salts

15 - 30 g

Gallbladder

Bile

Bile salts

Breakdown of bile salts

Glycine,

by intestinal bacteria

taurine

Secondary

Primary

bile acids

Resorption

Enterohepatic

circulation

0,5 g

Feces

316

Tissues and organs

Most oxidation reactions are catalyzed by

Biotransformations

cytochrome P450

systems

(see p. 318).

The body is constantly taking up foreign sub-

These monooxygenases are induced by

stances (= xenobiotics) from food or through

their substrates and show wide specificity.

contact with the environment, via the skin

The substrate-specific enzymes of the ste-

and lungs. These substances can be natural

roid metabolism (see p. 376) are exceptions

in origin, or may have been synthetically pro-

to this.

duced by humans. Many of these substances

Phase II reactions (conjugate formation). Type

are toxic, particularly at high concentrations.

II reactions couple their substrates (bilirubin,

However, the body has effective mechanisms

steroid hormones, drugs, and products of

for inactivating and then excreting foreign

phase I reactions) via ester or amide bonds

substances through biotransformations. The

to highly polar negatively charged molecules.

mechanisms of biotransformation are similar

The enzymes involved are transferases, and

to those with which endogenous substances

their products are known as conjugates.

such as bile pigments and steroid hormones

The most common type of conjugate for-

are enzymatically converted. Biotransforma-

mation is coupling with glucuronate (GlcUA)

tions mainly take place in the liver.

as an O-or N-glucuronide. The coenzyme for

the reaction is uridine diphosphate glucuro-

A. Biotransformations

nate, the

“active glucuronate”

(see p. 110).

Phase I reactions (interconversion reactions).

Coupling with the polar glucuronate makes

Type I reactions introduce functional groups

an apolar

(hydrophobic) molecule more

into inert, apolar molecules or alter functional

strongly polar, and it becomes suf ciently

groups that are already present. In many

water-soluble and capable of being excreted.

cases, this is what first makes it possible for

Example (3) shows the glucuronidation of

foreign substances to conjugate with polar

tetrahydrocortisol, a metabolite of the gluco-

molecules via phase II reactions (see below).

corticoid cortisol (see p. 374).

Phase I reactions usually reduce the biological

The biosynthesis of sulfate esters with the

activity or toxicity of a substance (“detoxifica-

help of phosphoadenosine phosphosulfate

tion”). However, some substances only be-

(PAPS), the “active sulfate”, (see p. 110) and

come biologically active as a result of the

amide formation with glycine and glutamine

interconversion reaction (see, for example,

also play a role in conjugation. For example,

benzo[a]pyrene, p. 256) or become more toxic

benzoic acid is conjugated with glycine to

after interconversion than the initial sub-

form the more soluble and less toxic hippuric

stance (“toxification”).

acid (N-benzoylglycine; see p. 324).

Important phase I biotransformation reac-

In contrast with unconjugated compounds,

tions include:

the conjugates are much more water-soluble

and capable of being excreted. The conjugates

• Hydrolytic cleavages of ether, ester, and

are eliminated from the liver either by the

peptide bonds. Example (1) shows hydrol-

biliary route—i. e., by receptor-mediated ex-

ysis of the painkiller acetylsalicylic acid.

cretion into the bile—or by the renal route,

• Oxidations. Hydroxylations, epoxide for-

via the blood and kidneys by filtration.

mation, sulfoxide formation, dealkylation,

deamination. For example, benzene is oxi-

dized into phenol, and toluene (methylben-

Further information

zene) is oxidized into benzoic acid.

To detoxify heavy metals, the liver contains

• Reductions. Reduction of carbonyl, azo-, or

metallothioneins, a group of cysteine-rich pro-

nitro- compounds, dehalogenation.

teins with a high af nity for divalent metal

• Methylations. Example (2) illustrates the

ions such as Cd²⁺, Cu²⁺, Hg²⁺, and Zn²⁺. These

inactivation of the catecholamine norepi-

metal ions also induce the formation of metal-

nephrine by methylation of a phenolic OH

lothioneins via a special metal-regulating el-

group (see p. 334).

ement (MRE) in the gene's promoter (see

• Desulfurations. The reactions take place in

p. 244).

the hepatocytes on the smooth endoplas-

mic reticulum.

Liver

317

A. Biotransformations

Acetic acid

H₂O

CH₃-COOH

Foreign

Endogenous

substances:

substances

Drugs

Steroid hormones

Preservatives

and other low

COO

Plasticizers

molecular weight

Pigments

substances

Acetylsalicylic acid

Salicylate

Pesticides etc.

Bile pigments

1. Hydrolysis of a drug

Poorly

soluble,

biologically

S-adenosyl

S-adenosyl homocysteine

active, some

methionine

toxic

H₃N

CH₂

H₃N

CH₂

Substrate

Transformation

induction

reactions:

Phase I

reactions

Hydrolytic

cleavage,

Epoxide formation

Dealkylation

OCH₃

Deamination

Reduction

Methylation

Desulfuration

Norepinephrine

O-methyl

norepinephrine

2. Methylation

of a hormone/neurotransmitter

Transformation

Tetrahydrocortisol

CH₂OH

product

Conjugate

formation:

Glucuronidation

Phase II

Esterification

Substrate

reactions

with sulfate

Amidation

UDP-GlcUA

induction

with Gly and Glu

CH₂OH

UDP

COO

Water soluble,

Conjugate

inactive,

non-toxic

Tetrahydrocortisol glucuronide

3. Glucuronidation of a hormone

Arylesterase

Catechol O-methyl-

3.1.1.2

transferase 2.1.1.6

Bile

Urine

Glucuronosyltransferase 2.4.1.17

318

Tissues and organs

Only a few examples of the numerous Cyt

Cytochrome P450 systems

P450-dependent reactions are shown here.

During the first phase of biotransformation in

Hydroxylation of aromatic rings (a) plays a

the liver, compounds that are weakly chemi-

central part in the metabolism of medicines

cally reactive are enzymatically hydroxylated

and steroids. Aliphatic methyl groups can also

(see p. 316). This makes it possible for them to

be oxidized to hydroxyl groups (b). Epoxi-

be conjugated with polar substances. The hy-

dation of aromatics (c) by Cyt P450 yields

droxylating enzymes are generally mono-

products that are highly reactive and often

oxygenases that contain a heme as the redox-

toxic. For example, the mutagenic effect of

active coenzyme (see p. 106). In the reduced

benzo[a]pyrene (see p. 244) is based on this

form, the heme can bind carbon monoxide

type of interconversion in the liver. In Cyt

(CO), and it then shows characteristic light

P450 dependent dealkylations (d), alkyl sub-

absorption at 450 nm. This was what led to

stituents of O, N, or S atoms are released as

this enzyme group being termed cytochrome

aldehydes.

P450 (Cyt P450).

Cyt P450 systems are also involved in many

B. Reaction mechanism

other metabolic processes—e. g., the biosyn-

thesis of steroid hormones (see p. 172), bile

The course of Cyt P450 catalysis is in principle

acids

(see p. 314), and eicosanoids

(see

well understood. The most important func-

p. 390), as well as the formation of unsatu-

tion of the heme group consists of converting

rated fatty acids (see p. 409). The liver’s red-

molecular oxygen into an especially reactive

dish-brown color is mainly due to the large

atomic form, which is responsible for all of the

amounts of P450 enzymes it contains.

reactions described above.

[1] In the resting state, the heme iron is

trivalent. Initially, the substrate binds near the

A. Cytochrome P450-dependent mono oxy-

heme group.

genases: reactions

[2] Transfer of an electron from FADH₂ re-

Cyt P450-dependent monooxygenases cata-

duces the iron to the divalent form that is able

lyze reductive cleavage of molecular oxygen

to bind an O₂ molecule (2).

(O₂). One of the two oxygen atoms is trans-

[3] Transfer of a second electron and a

ferred to the substrate, while the other is re-

change in the valence of the iron reduce the

leased as a water molecule. The necessary re-

bound O₂ to the peroxide.

ducing equivalents are transferred to the actual

[4] A hydroxyl ion is now cleaved from this

monooxygenase by an FAD-containing auxili-

intermediate. Uptake of a proton gives rise to

ary enzyme from the coenzyme NADPH+H⁺.

H₂O and the reactive form of oxygen men-

Cyt P450

enzymes occur in numerous

tioned above. In this ferryl radical, the iron

forms in the liver, steroid-producing glands,

is formally tetravalent.

and other organs. The substrate specificity of

[5] The activated oxygen atom inserts itself

liver enzymes is low. Apolar compounds con-

into a C-H bond in the substrate, thereby

taining aliphatic or aromatic rings are partic-

forming an OH group.

ularly easily converted. These include endog-

[6] Dissociation of the product returns the

enous substances such as steroid hormones,

enzyme to its initial state.

as well as medical drugs, which are inacti-

vated by phase I reactions. This is why Cyt

P450 enzymes are of particular interest in

pharmacology. The degradation of ethanol in

the liver is also partly catalyzed by Cyt P450

enzymes (the “microsomal ethanol-oxidizing

system”; see p. 304). As alcohol and drugs are

broken down by the same enzyme system,

the effects of alcoholic drinks and medical

drugs can sometimes be mutually en-

hancing—even sometimes to the extent of

becoming life-threatening.

320

Tissues and organs

The rate of ethanol degradation in the liver

Ethanol metabolism

is limited by alcohol dehydrogenase activity.

The amount of NAD⁺ available is the limiting

A. Blood ethanol level

factor. As the maximum degradation rate is

Ethanol (EtOH, “alcohol”) naturally occurs in

already reached at low concentrations of

fruit in small quantities. Alcoholic drinks

ethanol, the ethanol level therefore declines

contain much higher concentrations. Their

at a constant rate (zero-order kinetics). The

alcohol content is usually given as percent

calorific value of ethanol is 29.4 kJ g^-1. Alco-

by volume. To estimate alcohol uptake and

holic drinks—particularly in alcoholics—can

the blood alcohol level, it is useful to convert

therefore represent a substantial proportion

the amount to grams of ethanol (density

of dietary energy intake.

0.79 kg L^-1). For example, a bottle of beer

(0.5 L at

4% v/v alcohol) contains

C. Liver damage due to alcohol

20 mL = 16 g of ethanol, while a bottle of

wine (0.7 L at

12 % v/v alcohol) contains

Alcohol is a socially accepted drug of abuse in

84 mL = 66 g ethanol.

Western countries. Due to the high potential

Ethanol is membrane-permeable and is

for addiction to develop, however, it is ac-

quickly resorbed. The maximum blood level

tually a “hard” drug and has a much larger

is already reached within 60-90 min after

number of victims than the opiate drugs, for

drinking. The resorption rate depends on var-

example. In the brain, ethanol is deposited in

ious conditions, however. An empty stomach,

membranes due to its amphipathic proper-

a warm drink (e. g., mulled wine), and the

ties, and it influences receptors for neuro-

presence of sugar and carbonic acid (e. g., in

transmitters (see p. 352). The effect of GABA

champagne) promote ethanol resorption,

is enhanced, while that of glutamate declines.

whereas a heavy meal reduces it. Ethanol is

High ethanol consumption over many

rapidly distributed throughout the body. A

years leads to liver damage. For a healthy

large amount is taken up by the muscles and

man, the limit is about 60 g per day, and for

brain, but comparatively little by adipose tis-

a woman about 50 g. However, these values

sue and bones. Roughly 70% of the body is

are strongly dependent on body weight,

accessible to alcohol. Complete resorption of

health status, and other factors.

the ethanol contained in one bottle of beer

Ethanol-related high levels of NADH+H⁺

(16 g) by a person weighing 70 kg (distribu-

and acetyl-CoA in the liver lead to increased

tion in

70 kg

70/100 = 49 kg) leads to a

synthesis of neutral fats and cholesterol.

blood alcohol level of

0.33

per thousand

However, since the export of these in the

(7.2 mM). The lethal concentration of alcohol

form of VLDLs (see p. 278) is reduced due to

is approximately 3.5 per thousand (76 mM).

alcohol, storage of lipids occurs (fatty liver).

This increase in the fat content of the liver

(from less than 5% to more than 50% of the

B. Ethanol metabolism

dry weight) is initially reversible. However, in

The major site of ethanol degradation is the

chronic alcoholism the hepatocytes are in-

liver, although the stomach is also able to me-

creasingly replaced by connective tissue.

tabolize ethanol. Most ethanol is initially oxi-

When liver cirrhosis occurs, the damage to

dized by alcohol dehydrogenase to form etha-

the liver finally reaches an irreversible stage,

nal (acetaldehyde). A further oxidization, cata-

characterized by progressive loss of liver

lyzed by aldehyde dehydrogenase, leads to ace-

functions.

tate. Acetate is then converted with the help

of acetate-CoA ligase to form acetyl CoA, using

ATP and providing a link to the intermediary

metabolism. In addition to cytoplasmic alco-

hol dehydrogenase, catalase and inducible

microsomal alcohol oxidase

(“MEOS”; see

p. 318) also contribute to a lesser extent to etha-

nol degradation. Many of the enzymes men-

tioned above are induced by ethanol.

Liver

321

A. Blood ethanol level

Vol.%

Blood alcohol level

[‰]

Whiskey

Cognac

1,0

Maximum after 60 - 90 min

Corn liquor

Constant decline

Cherry brandy

ca. 0.015 % · h^-1

0,5

Rapid increase

Advocaat

due to easy

resorption

Red wine

White wine

Strong beer

0,0

Beer

6[h]

Water

Vodka (55 Vol.%) 0.75 g EtOH · kg^-1

B. Ethanol metabolism

A c

u m u l a t e s

H C C O

H C

H H

Ethanol

Ethanal

Acetate

P P P

O₂

2 H2O

‚MEOS‘

[Cyt P-450]

P P

H O

Alcohol dehydrogenase 1.1.1.1 [Zn

]

Fatty acid

and

Aldehyde dehydrogenase 1.2.1.3

cholesterol

Tricarboxylic

biosynthesis

acid cycle

Acetyl CoA

Acetate-CoA ligase 6.2.1.1

C. Liver damage due to alcohol

> 50-60 g EtOH

> 160 g EtOH

daily

Healthy

Fatty

Cirrhotic

liver

Abstinence

Death

322

Tissues and organs

transported back into the blood by resorption,

Kidney: functions

to prevent losses of valuable metabolites and

A. Functions of the kidneys

electrolytes. In the proximal tubule, organic

metabolites (e. g., glucose and other sugars,

The kidneys’ main function is excretion of

amino acids, lactate, and ketone bodies) are

water and water-soluble substances (1). This

recovered by secondary active transport (see

is closely associated with their role in regulat-

p. 220). There are several group-specific

ing the body’s electrolyte and acid-base bal-

transport systems for resorbing amino acids,

ance (homeostasis, 2; see pp. 326 and 328).

with which hereditary diseases can be

Both excretion and homeostasis are subject to

associated

(e. g., cystinuria, glycinuria, and

hormonal control. The kidneys are also in-

Hartnup’s disease). HCO_3-, Na⁺, phophate,

volved in synthesizing several hormones (3;

and sulfate are also resorbed by ATP-depend-

see p. 315). Finally, the kidneys also play a role

ent (active) mechanisms in the proximal tu-

in the intermediary metabolism (4), particu-

bule. The later sections of the nephron mainly

larly in amino acid degradation and gluconeo-

serve for additional water recovery and regu-

genesis (see p. 154).

lated resorption of Na⁺ and Cl^- (see pp. 326,

The kidneys are extremely well-perfused

328). These processes are controlled by hor-

organs, with about 1500 L of blood flowing

mones (aldosterone, vasopressin).

through them every day. Approximately 180 L

Secretion. Some excretable substances are

of primary urine is filtered out of this. Re-

released into the urine by active transport in

moval of water leads to extreme concentra-

the renal tubules. These substances include H⁺

tion of the primary urine (to approximately

and K⁺ ions, urea, and creatinine, as well as

one-hundredth of the initial volume). As a

drugs such as penicillin.

result, only a volume of 0.5-2.0 L of final

Clearance. Renalclearanceisusedasaquan-

urine is excreted per day.

titative measure of renal function. It is defined

as the plasma volume cleared of a given sub-

B. Urine formation

stance per unit of time. Inulin, a fructose poly-

The functional unit of the kidney is the neph-

saccharide with a mass of ca. 6 kDa (see p. 40)

ron. It is made up of the Malpighian bodies or

that is neither actively excreted nor resorbed

renal corpuscles (consisting of Bowman’s cap-

but is freely filtered, has a clearance of

sules and the glomerulus), the proximal tu-

120mL min^-1 in healthy individuals.

bule, Henle’s loop, and the distal tubule,

which passes into a collecting duct. The hu-

Further information

man kidney contains around one million

nephrons. The nephrons form urine in the

Concentrating urine and transporting it

following three phases.

through membranes are processes that re-

Ultrafiltration. Ultrafiltration of the blood

quire large amounts of energy. The kidneys

plasma in the glomerulus gives rise to primary

therefore have very high energy demands. In

urine, which is isotonic with plasma. The pores

the proximal tubule, the ATP needed is ob-

in the glomerular basal membrane, which are

tained from oxidative metabolism of fatty

made up of type IV collagen (see p. 344), have

acids, ketone bodies, and several amino acids.

an effective mean diameter of 2.9 nm. This al-

To a lesser extent, lactate, glycerol, and citric

lows all plasma components with a molecular

acid are also used. In the distal tubule and

mass of up to about 15 kDa to pass through

Henle’s loop, glucose is the main substrate

unhindered. At increasing masses, molecules

for the energy metabolism. The endothelial

are progressively held back; at masses greater

cells in the proximal tubule are also capable

than 65 kDa, they are completely unable to

of gluconeogenesis. The substrates for this are

enter the primary urine. This applies to almost

mainly the carbohydrate skeletons of amino

all plasma proteins—which in addition, being

acids. Their amino groups are used as ammo-

anions, are repelled by the negative charge in

nia for buffering urine (see p. 311). Enzymes

the basal membrane.

for peptide degradation and the amino acid

Resorption. All low-molecular weight

metabolism occur in the kidneys at high lev-

plasma components enter the primary urine

els of activity

(e. g., amino acid oxidases,

via glomerular filtration. Most of these are

amine oxidases, glutaminase).

Kidney

323

A. Functions of the kidneys

1. Excretion

3. Hormone synthesis

Water

Salts

Metabolic

wastes

Erythropoietin

Foreign

Calcitriol

substances

4. Metabolism

Glucose

Blood

2. Homeostasis

Acid-base balance

Gluconeo-

Electrolyte balance

Amino

genesis

acids

NH₃

Urine

B. Urine formation

Distal

Resorption

tubule

Afferent

Glomerulus

arteriole

Proximal

Regulated

tubule

secretion

Ultra-

filtration

Final

urine

Collecting

Secretion

duct

Efferent

Bowman’s

arteriole

capsule

Renal corpuscle

Henle’s

loop

Ultrafiltration

Secretion

Resorption

Regulated

resorption

All solute

Glucose

plasma

Lactate

components

smaller

Drugs

2-Oxoacids

of H₂O

than

Amino acids

3 nm = 15 kDaUric acid

Creatinine

Na , K , Ca2 , Mg2

, SO

HCO

4 , HPO4,

Water, etc.

324

Tissues and organs

Modified amino acids, which occur in special

Urine

proteins such as hydroxyproline in collagen

and 3-methylhistidine in actin and myosin,

A. Urine

can be used as indicators of the degradation

Water and water-soluble compounds are ex-

of these proteins.

creted with the urine. The volume and com-

Other components of the urine are conju-

position of urine are subject to wide variation

gates with sulfuric acid, glucuronic acid, gly-

and depend on food intake, body weight, age,

cine, and other polar compounds that are

sex, and living conditions such as tempera-

synthesized in the liver by biotransformation

ture, humidity, physical activity, and health

(see p. 316). In addition, metabolites of many

status. As there is a marked circadian rhythm

hormones (catecholamines, steroids, seroto-

in urine excretion, the amount of urine and its

nin) also appear in the urine and can provide

composition are usually given relative to a 24-

information about hormone production. The

hour period.

proteohormone chorionic gonadotropin (hCG,

A human adult produces 0.5-2.0 L urine

mass ca. 36 kDa), which is formed at the onset

per day, around 95 % of which consists of

of pregnancy, appears in the urine due to its

water. The urine usually has a slightly acidic

relatively small size. Evidence of hCG in the

pH value (around 5.8). However, the pH value

urine provides the basis for an immunological

of urine is strongly affected by metabolic sta-

pregnancy test.

tus. After ingestion of large amounts of plant

The yellow color of urine is due to uro-

food, it can increase to over 7.

chromes, which are related to the bile pig-

ments produced by hemoglobin degradation

(see p. 194). If urine is left to stand long

B. Organic components

enough, oxidation of the urochromes may

Nitrogen-containing compounds are among

lead to a darkening in color.

the most important organic components of

urine. Urea, which is mainly synthesized in

C. Inorganic components

the liver (urea cycle; see p. 182), is the form in

which nitrogen atoms from amino acids are

The main inorganic components of the urine

excreted. Breakdown of pyrimidine bases also

are the cations Na⁺, K⁺, Ca²⁺, Mg²⁺, and NH4

produces a certain amount of urea

(see

and the anions Cl^-, SO_42-, and HPO_42-, as well

p. 190). When the nitrogen balance is con-

as traces of other ions. In total, Na⁺ and Cl^-

stant, as much nitrogen is excreted as is taken

represent about two-thirds of all the electro-

up (see p. 174), and the amount of urea in the

lytes in the final urine. Calcium and magne-

urine therefore reflects protein degradation:

sium occur in the feces in even larger quanti-

70 g protein in food yields approximately

ties. The amounts of the various inorganic

30 g urea in the urine.

components of the urine also depend on the

Uric acid is the end product of the purine

composition of the diet. For example, in

metabolism. When uric acid excretion via the

acidosis there can be a marked increase in

kidneys is disturbed, gout can develop (see

the excretion of ammonia (see p. 326). Excre-

p. 190). Creatinine is derived from the muscle

tion of Na⁺, K⁺, Ca²⁺, and phosphate via the

metabolism, where it arises spontaneously

kidneys is subject to hormonal regulation (see

and irreversibly by cyclization of creatine

p. 330).

and creatine phosphate (see p. 336). Since

the amount of creatinine an individual ex-

Further information

cretes per day is constant (it is directly pro-

portional to muscle mass), creatinine as an

Shifts in the concentrations of the physiolog-

endogenous substance can be used to mea-

ical components of the urine and the appear-

sure the glomerular filtration rate. The

ance of pathological urine components can be

amount of amino acids excreted in free form

used to diagnose diseases. Important exam-

is strongly dependent on the diet and on the

ples are glucose and ketone bodies, which are

ef ciency of liver function. Amino acid deriv-

excreted to a greater extent in diabetes

atives are also found in the urine (e. g., hippu-

mellitus (see p. 160).

rate, a detoxification product of benzoic acid).

326

Tissues and organs

B. Ammonia excretion

Functions in the acid-base balance

Approximately 60 mmol of protons are ex-

Along with the lungs, the kidneys are partic-

creted with the urine every day. Buffering

ularly involved in keeping the pH value of the

systems in the urine catch a large proportion

extracellular fluid constant (see p. 288). The

of the H⁺ ions, so that the urine only becomes

contribution made by the kidneys particularly

weakly acidic (down to about pH 4.8).

involves resorbing HCO_3- and actively excret-

An important buffer in the urine is the

ing protons.

hydrogen phosphate/dihydrogen phosphate

system (HPO_42-/H₂PO_4-). In addition, ammo-

A. Proton excretion

nia also makes a vital contribution to buffer-

ing the secreted protons.

The renal tubule cells are capable of secreting

Since plasma concentrations of free am-

protons (H⁺) from the blood into the urine

monia are low, the kidneys release NH₃ from

against a concentration gradient, despite the

glutamine and other amino acids. At

fact that the H⁺ concentration in the urine is

0.5-0.7 mM, glutamine is the most important

up to a thousand times higher than in the

amino acid in the plasma and is the preferred

blood. To achieve this, carbon dioxide (CO₂)

form for ammonia transport in the blood. The

is taken up from the blood and—together with

kidneys take up glutamine, and with the help

water (H₂O) and with the help of carbonate

of glutaminase [4], initially release NH₃ from

dehydratase (carbonic anhydrase, [1])—con-

the amide bond hydrolytically. From the glu-

verted into hydrogen carbonate (“bicarbo-

tamate formed, a second molecule of NH₃ can

nate,” HCO_3-) and one H⁺. Formally, this yields

be obtained by oxidative deamination with

carbonic acid H₂CO₃ as an intermediate, but it

the help of glutamate dehydrogenase [5] (see

is not released during the reaction.

p. 178). The resulting 2-oxoglutarate is fur-

The hydrogen carbonate formed in car-

ther metabolized in the tricarboxylic acid

bonic anhydrase returns to the plasma, where

cycle. Several other amino acids—alanine in

it contributes to the blood’s base reserve. The

particular, as well as serine, glycine, and

proton is exported into the urine by secondary

aspartate—can also serve as suppliers of am-

active transport in antiport for Na⁺ (bottom

monia.

right). The driving force for proton excretion,

Ammonia can diffuse freely into the urine

as in other secondary active processes, is the

through the tubule membrane, while the am-

Na⁺ gradient established by the ATPase in-

monium ions that are formed in the urine are

volved in the Na⁺/K⁺ exchange (“Na⁺/K⁺ AT-

charged and can no longer return to the cell.

Pase”, see p. 220). This integral membrane

Acidic urine therefore promotes ammonia ex-

protein on the basal side (towards the blood)

cretion, which is normally 30-50 mmol per

of tubule cells keeps the Na⁺ concentration in

day. In metabolic acidosis (e. g., during fasting

the tubule cell low, thereby maintaining Na⁺

or in diabetes mellitus), after a certain time

inflow. In addition to this secondary active H⁺

increased induction of glutaminase occurs in

transport mechanism, there is a V-type H⁺-

the kidneys, resulting in increased NH₃ excre-

transporting ATPase in the distal tubule and

tion. This in turn promotes H⁺ release and

collecting duct (see p. 220).

thus counteracts the acidosis. By contrast,

An important function of the secreted H⁺

when the plasma pH value shifts towards

ions is to promote HCO_3- resorption

(top

alkaline values (alkalosis), renal excretion of

right). Hydrogen carbonate, the most impor-

ammonia is reduced.

tant buffering base in the blood, passes into

the primary urine quantitatively, like all ions.

In the primary urine, HCO_3- reacts with H⁺

ions to form water and CO₂, which returns

by free diffusion to the tubule cells and from

there into the blood. In this way, the kidneys

also influence the CO₂/HCO_3- buffering bal-

ance in the plasma.

328

Tissues and organs

with glucose and amino acids (see p. 322).

Electrolyte and water recycling

These two pathways are responsible for

60-70% of total Na⁺ resorption. In the ascend-

A. Electrolyte and water recycling

ing part of Henle’s loop, there is another

Electrolytes and other plasma components

transporter

(shown at the bottom right),

with low molecular weights enter the primary

which functions electroneutrally and takes

urine by ultrafiltration (right). Most of these

up one Na⁺ ion and one K⁺ ion together with

substances are recovered by energy-depen-

two Cl^- ions. This symport is also dependent

dent resorption (see p. 322). The extent of

on the activity of Na⁺/K⁺ ATPase [2], which

the resorption determines the amount that

pumps the Na⁺ resorbed from the primary

ultimately reaches the final urine and is ex-

urine back into the plasma in exchange for K⁺.

creted. The illustration does not take into ac-

The steroid hormone aldosterone

(see

count the zoning of transport processes in the

p. 55) increases Na⁺ reuptake, particularly in

kidney (physiology textbooks may be referred

the distal tubule, while atrial natriuretic

to for further details).

peptide (ANP) originating from the cardiac

Calcium and phosphate ions. Calcium

atrium reduces it. Among other effects, aldo-

(Ca²⁺) and phosphate ions are almost com-

sterone induces Na⁺/K⁺ ATPase and various

pletely resorbed from the primary urine by

Na⁺ transporters on the luminal side of the

active transport (i. e., in an ATP-dependent

cells.

fashion). The proportion of Ca²⁺ resorbed is

Water. Water resorption in the proximal

over 99%, while for phosphate the figure is

tubule is a passive process in which water

80-90%. The extent to which these two elec-

follows the osmotically active particles, par-

trolytes are resorbed is regulated by the three

ticularly the Na⁺ ions. Fine regulation of water

hormones parathyrin, calcitonin, and calci-

excretion (diuresis) takes place in the collect-

triol.

ing ducts, where the peptide hormone vaso-

The peptide hormone parathyrin (PTH),

pressin (antidiuretic hormone, ADH) operates.

which is produced by the parathyroid gland,

This promotes recovery of water by stimulat-

stimulates Ca²⁺ resorption in the kidneys and

ing the transfer of aquaporins (see p. 220)

at the same time inhibits the resorption of

into the plasma membrane of the tubule cells

phosphate. In conjunction with the effects of

via V₂ receptors. A lack of ADH leads to the

this hormone in the bones and intestines (see

disease picture of diabetes insipidus, in which

p. 344), this leads to an increase in the plasma

up to 30 L of final urine is produced per day.

level of Ca²⁺ and a reduction in the level of

phosphate ions.

B. Gluconeogenesis

Calcitonin, a peptide produced in the C cells

of the thyroid gland, inhibits the resorption of

Apart from the liver, the kidneys are the only

both calcium and phosphate ions. The result is

organs capable of producing glucose by

an overall reduction in the plasma level of both

neosynthesis

(gluconeogenesis; see p. 154).

ions. Calcitonin is thus a parathyrin antago-

The main substrate for gluconeogenesis in

nist relative to Ca²⁺.

the cells of the proximal tubule is glutamine.

The steroid hormone calcitriol, which is

In addition, other amino acids and also lac-

formed in the kidneys (see p. 304), stimulates

tate, glycerol, and fructose can be used as

the resorption of both calcium and phosphate

precursors. As in the liver, the key enzymes

ions and thus increases the plasma level of

for gluconeogenesis are induced by cortisol

both ions.

(see p. 374). Since the kidneys also have a

Sodium ions. Controlled resorption of Na⁺

high level of glucose consumption, they only

from the primary urine is one of the most

release very little glucose into the blood.

important functions of the kidney. Na⁺ resorp-

tion is highly effective, with more than 97%

being resorbed. Several mechanisms are in-

volved: some of the Na⁺ is taken up passively

in the proximal tubule through the junctions

between the cells (paracellularly). In addition,

there is secondary active transport together

330

Tissues and organs

the α₂-globulin group

(see p. 276), which

Renal hormones

like almost all plasma proteins is synthesized

in the liver. The decapeptide cleaved off by

A. Renal hormones

renin is called angiotensin I. Further cleavage

In addition to their involvement in excretion

by peptidyl dipeptidase A (angiotensin-con-

and metabolism, the kidneys also have endo-

verting enzyme, ACE), a membrane enzyme

crine functions. They produce the hormones

located on the vascular endothelium in the

erythropoietin and calcitriol and play a deci-

lungs and other tissues, gives rise to the

sive part in producing the hormone angioten-

octapeptide angiotensin II [3], which acts as

sin II by releasing the enzyme renin. Renal

a hormone and neurotransmitter. The lifespan

prostaglandins (see p. 390) have a local effect

of angiotensin II in the plasma is only a few

on Na⁺ resorption.

minutes, as it is rapidly broken down by other

Calcitriol (vitamin D hormone, 1α,25-dihy-

peptidases (angiotensinases [4]), which occur

droxycholecalciferol) is a hormone closely re-

in many different tissues.

lated to the steroids that is involved in Ca²⁺

The plasma level of angiotensin II is mainly

homeostasis (see p. 342). In the kidney, it is

determined by the rate at which renin is re-

formed from calcidiol by hydroxylation at C-1.

leased by the kidneys. Renin is synthesized by

The activity of calcidiol-1-monooxygenase [1]

juxtaglomerular cells, which release it when

is enhanced by the hormone parathyrin

sodium levels decline or there is a fall in blood

(PTH).

pressure.

Erythropoietin is a peptide hormone that is

Effects of angiotensin II. Angiotensin II has

formed predominantly by the kidneys, but

effects on the kidneys, brain stem, pituitary

also by the liver. Together with other factors

gland, adrenal cortex, blood vessel walls, and

known as “colony-stimulating factors” (CSF;

heart via membrane-located receptors. It in-

see p. 392), it regulates the differentiation of

creases blood pressure by triggering vasocon-

stem cells in the bone marrow.

striction (narrowing of the blood vessels). In

Erythropoietin release is stimulated by hy-

the kidneys, it promotes the retention of Na⁺

poxia (low pO₂). Within hours, the hormone

and water and reduces potassium secretion.

ensures that erythrocyte precursor cells in the

In the brain stem and at nerve endings in the

bone marrow are converted to erythrocytes,

sympathetic nervous system, the effects of

so that their numbers in the blood increase.

angiotensin II lead to increased tonicity (neu-

Renal damage leads to reduced erythropoie-

rotransmitter effect). In addition, it triggers

tin release, which in turn results in anemia.

the sensation of thirst. In the pituitary gland,

Forms of anemia with renal causes can now

angiotensin II stimulates vasopressin release

be successfully treated using erythropoietin

(antidiuretic hormone) and corticotropin

produced by genetic engineering techniques.

(ACTH) release. In the adrenal cortex, it in-

The hormone is also administered to dialysis

creases the biosynthesis and release of aldo-

patients. Among athletes and sports profes-

sterone, which promotes sodium and water

sionals, there have been repeated cases of

retention in the kidneys. All of the effects of

erythropoietin being misused for doping pur-

angiotensin II lead directly or indirectly to

poses.

increased blood pressure, as well as increased

sodium and water retention. This important

hormonal system for blood pressure regula-

B. Renin-angiotensin system

tion can be pharmacologically influenced by

The peptide hormone angiotensin II is not

inhibitors at various points:

synthesized in a hormonal gland, but in the

• Using angiotensinogen analogs that inhibit

blood. The kidneys take part in this process by

renin.

releasing the enzyme renin.

• Using angiotensin I analogs that competi-

Renin [2] is an aspartate proteinase (see

tively inhibit the enzyme ACE [3].

p. 176). It is formed by the kidneys as a pre-

• Using hormone antagonists that block the

cursor

(prorenin), which is proteolytically

binding of angiotensin II to its receptors.

activated into renin and released into the

blood. In the blood plasma, renin acts on

angiotensinogen, a plasma glycoprotein in

Kidney

331

A. Renal hormones

Differentiation

Maturation

Stem cell

Erythrocyte

Calcidiol 1-monooxygenase

[heme P450]1.14.13.13

Renin 3.4.23.15

Erythropoietin

18.4 kDa

Peptidyl-dipeptidase A

[Zn2

]

3.4.15.1 (ACE)

Hormone

CH₂

Blood

Angiotensinogen

57 kDa

Prorenin

Calcitriol

Renin

42 kDa

Parathyrin

Enzyme

Digestive

Angiotensin I

tract

Calcidiol

Kidneys

Bones

Calcidiol

from liver

Angiotensin II

Hormone

B. Renin angiotensin system

Angiotensinogen

Effects

Blood pressure

from liver

Kidneys:

Na retention

O retention

Protein

Residual

protein

Decapeptide

Angiotensin I

Brain:

Release of

corticotropin

ACE inhibitors

and adiuretin,

Thirst

Dipeptide

Octapeptide

Angiotensin II

DRVYIHPF

Adrenals:

Aldosterone

Hormone

production

Blood vessels:

Vasoconstriction

Blood pressure

Peptidases 3.4.n.n

Degradation products

332

Tissues and organs

(64 kDa) attaches to F-actin as a rod-like

Muscle contraction

dimer and connects approximately seven ac-

The musculature is what makes movements

tin units with each other. The heterotrimer

possible. In addition to the skeletal muscles,

troponin (78 kDa) is bound to one end of

which can be contracted voluntarily, there are

tropomyosin.

also the autonomically activated heart muscle

In addition to the above proteins, a number

and smooth muscle, which is also involuntary.

of other proteins are also typical of

In all types of muscle, contraction is based on

muscle—including titin (the largest known

an interplay between the proteins actin and

protein), D- and E-actinin, desmin, and

myosin.

vimentin.

A. Organization of skeletal muscle

B. Mechanism of muscle contraction

Striated muscle consists of parallel bundles of

The sliding filament model describes the

muscle fibers. Each fiber is a single large mul-

mechanism involved in muscle contraction.

tinucleate cell. The cytoplasm in these cells

In this model, sarcomeres become shorter

contains myofibrils 2-3 µm thick that can ex-

when the thin and thick filaments slide along-

tend over the full length of the muscle fiber.

side each other and telescope together, with

The striation of the muscle fibers is charac-

ATP being consumed. During contraction, the

teristic of skeletal muscle. It results from the

following reaction cycle is repeated several

regular arrangement of molecules of differing

times:

density. The repeating contractile units, the

sarcomeres, are bounded by Z lines from

[1 ] In the initial state, the myosin heads are

which thin filaments of F-actin (see p. 204)

attached to actin. When ATP is bound, the

extend on each side. In the A bands, there

heads detach themselves from the actin (the

are also thick parallel filaments of myosin.

“plasticizing” effect of ATP).

The H bands in the middle of the A bands

[2 ] The myosin head hydrolyzes the bound

only contain myosin, while only actin is found

ATP to ADP and P_i, but initially withholds the

on each size of the Z lines.

two reaction products. ATP cleavage leads to

Myosin is quantitatively the most impor-

allosteric tension in the myosin head.

tant protein in the myofibrils, representing

[3 ] The myosin head now forms a new

65% of the total. It is shaped like a golf club

bond with a neighboring actin molecule.

(bottom right). The molecule is a hexamer

[4 ] The actin causes the release of the P_i,

consisting of two identical heavy chains

and shortly afterwards release of the ADP as

(2 × 223 kDa) and four light chains

(each

well. This converts the allosteric tension in

about 20 kDa). Each of the two heavy chains

the myosin head into a conformational

has a globular “head” at its amino end, which

change that acts like a rowing stroke.

extends into a “tail” about 150 nm long in

which the two chains are intertwined to

The cycle can be repeated for as long as ATP

form a superhelix. The small subunits are at-

is available, so that the thick filaments are

tached in the head area. Myosin is present as a

constantly moving along the thin filaments

bundle of several hundred stacked molecules

in the direction of the Z disk. Each rowing

in the form of a “thick myosin filament.” The

stroke of the 500 or so myosin heads in a thick

head portion of the molecule acts as an

filament produces a contraction of about

ATPase, the activity of which is modulated

10 nm. During strong contraction, the process

by the small subunits.

is repeated about five times per second. This

Actin (42 kDa) is the most important com-

leads to the whole complex of thin filaments

ponent of the “thin filaments.” It represents ca.

moving together; the H band becomes shorter

20-25% of the muscle proteins. F-actin is also

and the Z lines slide closer together.

an important component of the cytoskeleton

(see p. 204). This filamentous polymer is held

in equilibrium with its monomer, G-actin. The

other protein components of muscle include

tropomyosin and troponin. Tropomyosin

334

Tissues and organs

enter the sarcoplasm, where they lead to a

Control of muscle contraction

rapid increase in Ca²⁺ concentrations. This in

turn causes the myofibrils to contract (C).

A. Neuromuscular junction

Muscle contraction is triggered by motor

C. Regulation by calcium ions

neurons that release the neurotransmitter

acetylcholine (see p. 352). The transmitter dif-

In relaxed skeletal muscle, the complex con-

fuses through the narrow synaptic cleft and

sisting of troponin and tropomyosin blocks

binds to nicotinic acetylcholine receptors on

the access of the myosin heads to actin (see

the plasma membrane of the muscle cell

p. 332). Troponin consists of three different

(the sarcolemma), thereby opening the ion

subunits (T, C, and I). The rapid increase in

channels integrated into the receptors (see

cytoplasmic Ca²⁺ concentrations caused by

p. 222). This leads to an inflow of Na⁺, which

opening of the calcium channels in the SR

triggers an action potential (see p. 350) in the

leads to binding of Ca²⁺ to the C subunit of

sarcolemma. The action potential propagates

troponin, which closely resembles calmodulin

from the end plate in all directions and con-

(see p. 386). This produces a conformational

stantly stimulates the muscle fiber. With a

change in troponin that causes the whole tro-

delay of a few milliseconds, the contractile

ponin-tropomyosin complex to slip slightly

mechanism responds to this by contracting

and expose a binding site for myosin (red).

the muscle fiber.

This initiates the contraction cycle. After con-

traction, the sarcoplasmic Ca²⁺ concentration

is quickly reduced again by active transport

B. Sarcoplasmic reticulum (SR)

back into the SR. This results in troponin los-

The action potential (A) produced at the neu-

ing the bound Ca²⁺ ions and returning to the

romuscular junction is transferred in the

initial state, in which the binding site for my-

muscle cell into a transient increase in the

osin on actin is blocked. It is not yet clear

Ca²⁺ concentration in the cytoplasm of the

whether the mechanism described above is

muscle fiber (the sarcoplasm).

the only one that triggers binding of myosin

In the resting state, the Ca²⁺ level in the

to actin.

sarcoplasm is very low (less than 10^-7 M). By

When triggering of contraction in striated

contrast, the sarcoplasmic reticulum

(SR),

muscle occurs, the following sequence of

which corresponds to the ER, contains Ca²⁺

processes thus takes place:

ions at a concentration of about 10^-3 M. The

1. The sarcolemma is depolarized.

SR is a branched organelle that surrounds the

2. The action potential is signaled to Ca²⁺

myofibrils like a net stocking inside the

channels in the SR.

muscle fibers (illustrated at the top using

3. The Ca²⁺ channels open and the Ca²⁺ level

the example of a heart muscle cell). The high

in the sarcoplasm increases.

Ca²⁺ level in the SR is maintained by Ca²⁺-

4. Ca²⁺ binds to troponin C and triggers a

transporting ATPases (see p. 220). In addition,

conformational change.

the SR also contains calsequestrin, a protein

5. Troponin causes tropomyosin to slip, and

(55 kDa) that is able to bind numerous Ca²⁺ -

the myosin heads bind to actin.

ions via acidic amino acid residues.

6. The actin-myosin cycle takes place and the

The transfer of the action potential to the SR

muscle fibers contract.

is made possible by transverse tubules (T tu-

bules), which are open to the extracellular space

Conversely, at the end of contraction, the fol-

and establish a close connection with the SR.

lowing processes take place:

There is a structure involved in the contact be-

1. The Ca²⁺ level in the sarcoplasm declines

tween the T tubule and the SR that was formerly

due to transport of Ca²⁺ back into the SR.

known as the “SR foot” (it involves parts of the

2. Troponin C loses Ca²⁺ and tropomyosin re-

ryanodine receptor; see p. 386).

turns to its original position on the actin

At the point of contact with the SR, the

molecule.

action potential triggers the opening of the

3. The actin-myosin cycle stops and the

Ca²⁺ channels on the surface of the sarco-

muscle relaxes.

lemma. Calcium ions then leave the SR and

336

Tissues and organs

maintain glucose degradation and thus ATP

Muscle metabolism I

formation. If there is a lack of O₂, this is

Muscle contraction is associated with a high

achieved by the formation of lactate, which

level of ATP consumption (see p. 332). With-

is released into the blood and is resynthesized

out constant resynthesis, the amount of ATP

into glucose in the liver

(Cori cycle; see

available in the resting state would be used up

p. 338).

in less than 1 s of contraction.

Muscle-specific auxiliary reactions for ATP

synthesis exist in order to provide additional

ATP in case of emergency. Creatine phosphate

A. Energy metabolism in the white and red

(see B) acts as a buffer for the ATP level.

muscle fibers

Another ATP-supplying reaction is catalyzed

Muscles contain two types of fibers, the pro-

by adenylate kinase [1] (see also p. 72). This

portions of which vary from one type of

disproportionates two molecules of ADP into

muscle to another. Red fibers (type I fibers)

ATP and AMP. The AMP is deaminated into

are suitable for prolonged effort. Their metab-

IMP in a subsequent reaction [2] in order to

olism is mainly aerobic and therefore depends

shift the balance of the reversible reaction [1]

on an adequate supply of O₂. White fibers

in the direction of ATP formation.

(type II fibers) are better suited for fast, strong

contractions. These fibers are able to form

B. Creatine metabolism

suf cient ATP even when there is little O₂

available. With appropriate training, athletes

Creatine (N-methylguanidoacetic acid) and its

and sports participants are able to change the

phosphorylated form creatine phosphate

proportions of the two fiber types in the mus-

(a guanidophosphate) serve as an ATP buffer

culature and thereby prepare themselves for

in muscle metabolism. In creatine phosphate,

the physiological demands of their disciplines

the phosphate residue is at a similarly high

in a targeted fashion. The expression of func-

chemical potential as in ATP and is therefore

tional muscle proteins can also change during

easily transferred to ADP. Conversely, when

the course of training.

there is an excess of ATP, creatine phosphate

Red fibers provide for their ATP require-

can arise from ATP and creatine. Both proce-

ments mainly (but not exclusively) from fatty

sses are catalyzed by creatine kinase [5].

acids, which are broken down via β-oxidation,

In resting muscle, creatine phosphate

the tricarboxylic acid cycle, and the respira-

forms due to the high level of ATP. If there is

tory chain (right part of the illustration). The

a risk of a severe drop in the ATP level during

red color in these fibers is due to the mono-

contraction, the level can be maintained for a

meric heme protein myoglobin, which they

short time by synthesis of ATP from creatine

use as an O₂ reserve. Myoglobin has a much

phosphate and ADP. In a nonenzymatic reac-

higher af nity for O₂ than hemoglobin and

tion [6], small amounts of creatine and crea-

therefore only releases its O₂ when there is

tine phosphate cyclize constantly to form cre-

a severe drop in O₂

partial pressure

atinine, which can no longer be phosphory-

(cf. p. 282).

lated and is therefore excreted with the urine

At a high level of muscular effort—e. g.,

(see p. 324).

during weightlifting or in very fast contrac-

Creatine does not derive from the muscles

tions such as those carried out by the eye

themselves, but is synthesized in two steps in

muscles—the O₂

supply from the blood

the kidneys and liver (left part of the illustra-

quickly becomes inadequate to maintain the

tion). Initially, the guanidino group of argi-

aerobic metabolism. White fibers (left part of

nine is transferred to glycine in the kidneys,

the illustration) therefore mainly obtain ATP

yielding guanidino acetate [3]. In the liver,

from anaerobic glycolysis. They have supplies

N-methylation of guanidino acetate leads to

of glycogen from which they can quickly re-

the formation of creatine from this [4]. The

lease glucose-1-phosphate when needed (see

coenzyme in this reaction is S-adenosyl methi-

p. 156). By isomerization, this gives rise to

onine (SAM; see p. 110).

glucose-6-phosphate, the substrate for glycol-

ysis. The NADH+H⁺ formed during glycolysis

has to be reoxidized into NAD⁺ in order to

Muscle

337

A. Energy metabolism in the white and red muscle fibers

White (slow) fibers, anaerobic

Red (fast) fibers, aerobic

Creatine

Glycogen

ADP

Myoglobin

Fatty acids

phosphate

Glucose

O₂

β-Oxidation

Creatine

NAD⁺

Ketone

bodies

ATP

H₂O

P P P

Cori cycle

Glycolysis

Acetyl CoA

(liver)

Contraction

NADH + H⁺

O₂

ADP

Respiratory

chain

Tricarboxylic

Lactate

Pyruvate

acid cycle

NADH + H⁺

Adenylate kinase

2.7.4.3

AMP deaminase

CO₂

3.5.4.6

AMP

NH₃

IMP

CO₂

B. Creatine metabolism

Muscle

S-adenosyl

homocysteine

Liver

S-adenosyl

NH₂

methionine

H₃C

NH₂

H₂C

Creatine

Guanidino

Creatine

acetate

phosphate

H₂C

Blood

Creatinine

Glycine

Guanidino-

amidinotransferase

acetate

2.1.4.1

Orn

H₃C

NH₂

Guanidinoacetate

methyltransferase

H₂C

2.1.1.2

Arg

Creatine

H₂C

kinase 2.7.3.2

Glycine

Not-

enzymatic

Kidney

338

Tissues and organs

B. Protein and amino acid metabolism

Muscle metabolism II

The skeletal muscle is the most important site

A. Cori and alanine cycle

for degradation of the branched-chain amino

acids (Val, Leu, Ile; see p. 414), but other amino

White muscle fibers (see p. 336) mainly ob-

acids are also broken down in the muscles.

tain ATP from anaerobic glycolysis—i. e., they

Alanine and glutamine are resynthesized

convert glucose into lactate. The lactate aris-

from the components and released into the

ing in muscle and, in smaller quantities, its

blood. They transport the nitrogen that arises

precursor pyruvate are released into the

during amino acid breakdown to the liver

blood and transported to the liver, where lac-

(alanine cycle; see above) and to the kidneys

tate and pyruvate are resynthesized into glu-

(see p. 328).

cose again via gluconeogenesis, with ATP being

During periods of hunger, muscle proteins

consumed in the process (see p. 154). The

serve as an energy reserve for the body. They

glucose newly formed by the liver returns

are broken down into amino acids, which are

via the blood to the muscles, where it can be

transported to the liver. In the liver, the car-

used as an energy source again. This circula-

bon skeletons of the amino acids are con-

tion system is called the Cori cycle, after the

verted into intermediates in the tricarboxylic

researchers who first discovered it. There is

acid cycle or into acetoacetyl-CoA (see p. 175).

also a very similar cycle for erythrocytes,

These amphibolic metabolites are then avail-

which do not have mitochondria and there-

able to the energy metabolism and for gluco-

fore produce ATP by anaerobic glycolysis (see

neogenesis. After prolonged starvation, the

p. 284).

brain switches to using ketone bodies in order

The muscles themselves are not capable of

to save muscle protein (see p. 356).

gluconeogenesis. Nor would this be useful, as

The synthesis and degradation of muscle

gluconeogenesis requires much more ATP

proteins are regulated by hormones. Cortisol

than is supplied by glycolysis. As O₂ deficien-

leads to muscle degradation, while testo-

cies do not arise in the liver even during in-

sterone stimulates protein formation. Syn-

tensive muscle work, there is always suf -

thetic anabolics with a testosterone-like ef-

cient energy there available for gluconeogen-

fect have repeatedly been used for doping

esis.

purposes or for intensive muscle-building.

There is also a corresponding circulation

system for the amino acid alanine. The alanine

cycle in the liver not only provides alanine as

Further information

a precursor for gluconeogenesis, but also

transports to the liver the amino nitrogen

Smooth muscle differs from skeletal muscle in

arising in muscles during protein degrada-

various ways. Smooth muscles—which are

tion. In the liver, it is incorporated into urea

found, for example, in blood vessel walls

for excretion.

and in the walls of the intestines—do not

Most of the amino acids that arise in

contain any muscle fibers. In smooth-muscle

muscle during proteolysis are converted into

cells, which are usually spindle-shaped, the

glutamate and 2-oxo acids by transamination

contractile proteins are arranged in a less reg-

(not shown; cf. p. 180). Again by transamina-

ular pattern than in striated muscle. Contrac-

tion, glutamate and pyruvate give rise to ala-

tion in this type of muscle is usually not

nine, which after glutamine is the second im-

stimulated by nerve impulses, but occurs in

portant form of transport for amino nitrogen

a largely spontaneous way. Ca²⁺ (in the form

in the blood. In the liver, alanine and 2-oxo-

of Ca²⁺-calmodulin; see p. 386) also activates

glutarate are resynthesized into pyruvate and

contraction in smooth muscle; in this case,

glutamate (see p. 178). Glutamate supplies

however, it does not affect troponin, but acti-

the urea cycle (see p. 182), while pyruvate is

vates a protein kinase that phosphorylates the

available for gluconeogenesis.

light chains in myosin and thereby increases

myosin’s ATPase activity. Hormones such as

epinephrine and angiotensin II (see p. 330)

are able to influence vascular tonicity in this

way, for example.

Muscle

339

A. Cori and alanine cycle

Liver

Blood

Muscle

Storage

Glucose

3.70-5.18

Glycogen

Glucose 6

Glycogen

6 ATP

2 ATP

Pyruvate

Protein

0.02-0.07

Amino

acids

Lactate

0.74-2.40

Urea

[NH₂]

Alanine

0.33-0.61

NADH/NAD+

quotient low

quotient high

Glycolysis

Alanine cycle

Plasma concentration

Transamination

in adults

Cori cycle

Lactate dehydrogenase

1.1.1.27

Gluconeogenesis

B. Protein and amino acid metabolism

Blood

Muscle

Muscle breaks

Energy

down

reserve in

branched-chain

prolonged

amino acids

Protein

hunger

Testosterone

Anabolic

Cortisol

agents

Val

Leu

Ile

0.25

0.16

0.08

Amino acids

Ala

Gln

Amino acids

[NH₂]

0.42

0.65

Ala, Gln

Synthesis

Degradation

Tri-

carboxylic

Energy gain

acid

Plasma

cycle

concentration

340

Tissues and organs

B. Teeth

Bone and teeth

The illustration shows a longitudinal section

The family of connective-tissue cells includes

through an incisor, one of the 32 permanent

fibroblasts, chondrocytes (cartilage cells), and

teeth in humans. The majority of the tooth

osteoblasts (bone-forming cells). They are spe-

consists of dentine. The crown of the tooth

cialized to secrete extracellular proteins, par-

extends beyond the gums, and it is covered in

ticularly collagens, and mineral substances,

enamel. By contrast, the root of the tooth is

which they use to build up the extracellular

coated in dental cement.

matrix (see p. 346). By contrast, osteoclasts

Cement, dentin, and enamel are bone-like

dissolve bone matter again by secreting H⁺

substances. The high proportion of inorganic

and collagenases (see p. 342).

matter they contain (about 97% in the dental

enamel) gives them their characteristic hard-

A. Bone

ness. The organic components of cement,

dentin, and enamel mainly consist of collagens

Bone is an extremely dense, specialized form

and proteoglycans; their most important min-

of connective tissue. In addition to its suppor-

eral component is apatite, as in bone (see

tive function, it serves to store calcium and

above).

phosphate ions. In addition, blood cells are

A widespread form of dental disease, ca-

formed in the bone marrow. The most impor-

ries, is caused by acids that dissolve the min-

tant mineral component of bone is apatite, a

eral part of the teeth by neutralizing the neg-

form of crystalline calcium phosphate.

atively charged counter-ions in apatite (see

Apatites are complexes of cationic Ca²⁺

A). Acids occur in food, or are produced by

matched by HPO_42-, CO_32-, OH^-, or F^- as

microorganisms that live on the surfaces of

anions. Depending on the counter-ion, apatite

the teeth (e. g., Streptococcus mutans).

can occur in the forms carbonate apatite

The main product of anaerobic degradation

Ca₁₀(PO₄)₆CO₃, as hydroxyapatite Ca₁₀(PO₄)₆

of sugars by these organisms is lactic acid.

(OH)₂, or fluoroapatite Ca₁₀(PO₄)₆F₂. In addi-

Other products of bacterial carbohydrate me-

tion, alkaline earth carbonates also occur in

tabolism include extracellular dextrans (see

bone. In adults, more than 1 kg calcium is

p. 40)—insoluble polymers of glucose that

stored in bone.

help bacteria to protect themselves from their

Osteoblast and osteoclast activity is con-

environment. Bacteria and dextrans are com-

stantly incorporating Ca²⁺ into bone and re-

ponents of dental plaque, which forms on in-

moving it again. There are various hormones

adequately cleaned teeth. When Ca²⁺ salts

that regulate these processes: calcitonin in-

and other minerals are deposited in plaque

creases deposition of Ca²⁺ in the bone matrix,

as well, tartar is formed.

while parathyroid hormone (PTH) promotes

The most important form of protection

the mobilization of Ca²⁺, and calcitriol im-

against caries involves avoiding sweet sub-

proves mineralization (for details, see p. 342).

stances (foods containing saccharose, glucose,

The most important organic components of

and fructose). Small children in particular

bone are collagens (mainly type I; see p. 344)

should not have very sweet drinks freely

and proteoglycans (see p. 346). These form

available to them. Regular removal of plaque

the extracellular matrix into which the apa-

by cleaning the teeth and hardening of the

tite crystals are deposited (biomineralization).

dental enamel by fluoridization are also im-

Various proteins are involved in this not yet

portant. Fluoride has a protective effect be-

fully understood process of bone formation,

cause fluoroapatite (see A) is particularly re-

including collagens and phosphatases. Alka-

sistant to acids.

line phosphatase is found in osteoblasts and

acid phosphatase in osteoclasts. Both of these

enzymes serve as marker enzymes for bone

cells.

Connective tissue

341

A. Bone

Functions:

Composition:

Mechanical support

Inorganic

Organic

Storage for Ca2

Apatite

Type I collagen

and phosphate

Carbonate

Proteoglycans

Synthesis of blood cells

Water

Phosphatases

Maturation of B cells

Hormones

Hydroxyapatite Ca₁₀(PO₄)₆(OH)₂

of the calcium

metabolism

Parathyroid hormone

Ca2

in plasma

Ca2

Calcitonin

Absence leads

to rickets

Calcitriol

B. Teeth

Dental enamel

97%

Hardest substance

Dentin

70%

Dextrans

in the body

Cement

65%

Jawbone

45%

Plaque

Crown

Dental

Inorganic

components

plaque

Dental

Bacterium

enamel

Neck

Sugar

Attack

Dental

Protect

apatite

enamel

bacteria

Saccharose

Glucose

Fructose

Anaerobic

Dextrans

Acids

metabolism

Lactic acid

Propionic acid

Acetic acid

Bacterium

Root

Butyric acid

E.g.,

Streptococcus

De-

Calcium

mineral-

mutans

salts

ization

342

Tissues and organs

tion in estrogen levels. Estrogens normally

Calcium metabolism

inhibit the stimulation of osteoclast differen-

tiation by osteoblasts. If the effects of estrogen

A. Functions of calcium

decline, the osteoclasts predominate and ex-

The human body contains 1-1.5 kg Ca²⁺, most

cess bone removal occurs.

of which (about 98%) is located in the mineral

The effects of the steroid hormone calcitriol

substance of bone (see p. 362).

(see p. 330) in bone are complex. On the one

In addition to its role as a bone component,

hand, it promotes bone formation by stimu-

calcium functions as a signaling substance.

lating osteoblast differentiation (top). This is

Ca²⁺ ions act as second messengers in signal

particularly important in small children, in

transduction pathways

(see p. 386), they

whom calcitriol deficiency can lead to miner-

trigger exocytosis

(see p. 228) and muscle

alization disturbances (rickets; see p. 364). On

contraction (see p. 334), and they are indis-

the other hand, calcitriol increases blood Ca²⁺

pensable as cofactors in blood coagulation (see

levels through increased Ca²⁺ mobilization

p. 290). Many enzymes also require Ca²⁺ for

from bone. An overdose of vitamin D (chole-

their activity. The intracellular and extracel-

calciferol), the precursor of calcitriol, can

lular concentrations of Ca²⁺ are strictly regu-

therefore have unfavorable effects on the

lated in order to make these functions possi-

skeleton similar to those of vitamin deficiency

ble (see B, C, and p. 388).

(hypervitaminosis; see p. 364).

Proteins bind Ca²⁺ via oxygen ligands, par-

ticularly carboxylate groups and carbonyl

C. Calcium homeostasis

groups of peptide bonds. This also applies to

the structure illustrated here, in which a Ca²⁺

Ca²⁺ metabolism is balanced in healthy adults.

ion is coordinated by the oxygen atoms of

Approximately 1g Ca²⁺ is taken up per day,

carboxylate and acid amide groups.

about 300 mg of which is resorbed. The same

amount is also excreted again. The amounts of

Ca²⁺ released from bone and deposited in it

B. Bone remodeling

per day are much smaller. Milk and milk prod-

Deposition of Ca²⁺ in bone (mineralization)

ucts, especially cheese, are particularly rich in

and Ca²⁺ mobilization from bone are regu-

calcium.

lated by at least 15 hormones and hormone-

Calcitriol and parathyroid hormone, on the

like signaling substances. These mainly influ-

one hand, and calcitonin on the other, ensure

ence the maturation and activity of bone cells.

a more or less constant level of Ca²⁺ in the

Osteoblasts (top) deposit collagen, as well

blood plasma and in the extracellular space

as Ca²⁺ and phosphate, and thereby create

(80-110 mg

2.0-2.6 mM). The peptide para-

new bone matter, while osteoclasts (bottom)

thyroid hormone (PTH; 84 AA) and the steroid

secrete H⁺ ions and collagenases that locally

calcitriol (see p. 374) promote direct or indi-

dissolve bone (bone remodeling). Osteoblasts

rect processes that raise the Ca²⁺ level in

and osteoclasts mutually activate each other

blood. Calcitriol increases Ca²⁺ resorption in

by releasing cytokines

(see p. 392) and

the intestines and kidneys by inducing trans-

growth factors. This helps keep bone forma-

porters. Parathyroid hormone supports these

tion and bone breakdown in balance.

processes by stimulating calcitriol biosynthe-

The Ca²⁺-selective hormones calcitriol, par-

sis in the kidneys (see p. 330). In addition, it

athyroid hormone, and calcitonin influence

directly promotes resorption of Ca²⁺ in the

this interaction in the bone cells. Parathyroid

kidneys (see p. 328) and Ca²⁺ release from

hormone promotes Ca²⁺ release by promoting

bone (see B). The PTH antagonist calcitonin

the release of cytokines by osteoblasts. In

(32 AA) counteracts these processes.

turn, the cytokines stimulate the develop-

ment of mature osteoclasts from precursor

cells (bottom). Calcitonin inhibits this process.

At the same time, it promotes the develop-

ment of osteoblasts (top). Osteoporosis, which

mainly occurs in women following the men-

opause, is based (at least in part) on a reduc-

Connective tissue

343

A. Functions of calcium

B. Bone remodeling

Osteoblast

Calcitriol

Calcitonin

Mineralization

Ca²

Muscle

Precursor

con-

cells

traction

Parathyroid

Signal

Hydroxy-

Collagen I

hormone

apatite

transduction

Ca2

Growth

Estrogens

factors

Nerve

conduction

Cyto-

Exocytosis

kines

Precursor

Protein

cells

function

HCO₃

H₂O

CO₂

Ca2

complex

Calcitonin

Osteoclast

C. Calcium homeostasis

Calci-

600 - 900mg

1000000 mg

Stock

Calcitriol

tonin

1000 mg · d-1

oder

Hydroxy-

Parathyroid hormone

500 mg · d-1

apatite

500 mg · d-1

Calcitriol

Bone

Calci-

Parathyroid

tonin

hormone

Filtration

Kidney

300mg · d-1

till 150mg · d-1

10 000 mg · d-1

9 850 mg · d-1

Resorption

Calci-

Parathyroid

850mg · d-1

triol

hormone

Intestine

Blood

150

mg·d^-1

344

Tissues and organs

are seen to have a characteristic banding pat-

Collagens

tern of elements that are repeated every

Collagens are quantitatively the most abun-

64-67 nm.

dant of animal proteins, representing 25 % of

Tropocollagen molecules are firmly linked

the total. They form insoluble tensile fibers

together, particularly at their ends, by cova-

that occur as structural elements of the ex-

lent networks of altered lysine side chains.

tracellular matrix and connective tissue

The number of these links increases with

throughout the body. Their name (which lit-

age. Type IV collagens form networks with a

erally means

“glue-producers”) is derived

defined mesh size. The size-selective filtering

from the gelatins that appear as a decompo-

effect of the basal membranes in the renal

sition product when collagen is boiled.

glomeruli is based on this type of structure

(see p. 322).

A. Structure of collagens

B. Biosynthesis

Nineteen different collagens are now known,

and they are distinguished using roman nu-

The precursor molecule of collagen (prepro-

merals. They mostly consist of a dextro-

collagen), formed in the rER, is subject to

rotatory triple helix made up of three poly-

extensive post-translational modifications

peptides (α-chains) (see p. 70).

(see p. 232) in the ER and Golgi apparatus.

The triplet Gly-X-Y is constantly repeated in

Cleavage of the signal peptide gives rise to

the sequence of the triple-helical regions—

procollagen, which still carries large propep-

i. e., every third amino acid in such sequences

tides at each end [1]. During this phase, most

is a glycine. Proline (Pro) is frequently found in

proline residues and some lysine residues of

positions X or Y; the Y position is often occu-

procollagen are hydroxylated [2]. The procol-

pied by 4-hydroxyproline (4Hyp), although

lagen is then glycosylated at hydroxylysine

3-hydroxyproline (3Hyp) and 5-hydroxylysine

residues [3]. Intramolecular and intermolecu-

(5Hyl) also occur. These hydroxylated amino

lar disulfide bonds form in the propeptides

acids are characteristic components of colla-

[4], allowing correct positioning of the pep-

gen. They are only produced after protein

tide strands to form a triple helix [5]. It is only

biosynthesis by hydroxylation of the amino

after these steps have been completed that

acids in the peptide chain (see p. 62).

procollagen is secreted into the extracellular

The formation of Hyp and Hyl residues in

space by exocytosis. This is where the N- and

procollagen is catalyzed by iron-containing

C-terminal propeptides are removed proteo-

oxygenases

(“proline and lysine hydrox-

lytically [6], allowing the staggered aggrega-

ylase,” EC 1.14.11.1/2). Ascorbate is required

tion of the tropocollagen molecules to form

to maintain their function. Most of the symp-

fibrils [7]. Finally, several ε-amino groups in

toms of the vitamin C deficiency disease

lysine residues are oxidatively converted into

scurvy (see p. 368) are explained by disturbed

aldehyde groups [8]. Covalent links between

collagen biosynthesis.

the molecules then form as a result of con-

The hydroxyproline residues stabilize the

densation [9]. In this way, the fibrils reach

triple helix by forming hydrogen bonds be-

their final structure, which is characterized

tween the α-chains, while the hydroxyl

by its high tensile strength and proteinase re-

groups of hydroxylysine are partly glycosy-

sistance.

lated with a disaccharide (-Glc-Gal).

The various types of collagen consist of

different combinations of α-chains (α1 to α3

and other subtypes). Types I, II, and III repre-

sent 90% of collagens. The type I collagen

shown here has the structure [α1(I)]₂α2(1).

Numerous tropocollagen molecules (mass

285 kDa, length 400 nm) aggregate extracell-

ularly into a defined arrangement, forming

cylindrical fibrils

(20-500 nm in diameter).

Under the electron microscope, these fibrils

Connective tissue

345

A. Structure of collagens

B. Biosynthesis

Special amino acids:

Gene

4-Hydroxyproline (4Hyp)

3-Hydroxyproline (3Hyp)

Transcription

5-Hydroxylysine (5Hyl)

– Gly - X - Y - Gly

- X

Y - Gly - X - Y -

Basic unit

Translation

Primary structure

Pre-procollagen

Hyl

C CH

CH₂

C CH₂

NH₃

C O

Intracellular

H₂

HO C

Hyp = Y

protein

modification

H₂

C O

Exocytosis

H₂

Pro = X

H₂C

Procollagen

H₂

C O

Gly

H₂C

Extracellular

protein

modification

Type I tropocollagen

~285 kDa

Collagen fibril

1 Removal of the prepeptide

Overlap

Gap

Diameter

Hydroxylation of Pro and Lys residues

D=64-67 nm

40 nm

1.5 nm

3 Glycosylation of 5Hyl and Asn

Oxidation of Cys in propeptides

5 Assemblage to form triple helix

Removal of the propeptide

Staggered deposition to form fibrils

Length 400 nm

8 Oxidation of Lys and 5Hyl to aldehydes

9 Cross-linking to form supramolecules

Procollagen-proline 4-dioxygenase 1.14.11.2

[ascorbate, Fe]

Procollagen-lysine 5-dioxygenase 1.14.11.4

[ascorbate, Fe]

Collagen fibril (section)

Protein-lysine 6-oxidase 1.4.3.13 [Cu]

346

Tissues and organs

B. Fibronectins

Extracellular matrix

Fibronectins are typical representatives of

A. Extracellular matrix

adhesive proteins. They are filamentous

dimers consisting of two related peptide

The space between the cells (the interstitium)

chains (each with a mass of 250 kDa) linked

is occupied by a substance with a complex

to each other by disulfide bonds. The fibro-

composition known as the extracellular

nectin molecules are divided into different

matrix (ECM). In many types of tissue—e. g.,

domains, which bind to cell-surface receptors,

muscle and liver—the ECM is only a narrow

collagens, fibrin, and various proteoglycans.

border between the cells, while in others it

This is what gives fibronectins their “molec-

forms a larger space. In connective tissue,

ular glue” characteristics.

cartilage, and bone, the ECM is particularly

The domain structure in fibronectins is

strongly marked and is actually the functional

made up of a few types of peptide module

part of the tissue (see p. 340). The illustration

that are repeated numerous times. Each of

shows the three main constituents of the ex-

the more than 50 modules is coded for by

tracellular matrix in a highly schematic way:

one exon in the fibronectin gene. Alternative

collagen fibers, network-forming adhesive

splicing (see p. 246) of the hnRNA transcript of

proteins, and space-filling proteoglycans.

the fibronectin gene leads to fibronectins with

The ECM has a very wide variety of func-

different compositions. The module that cau-

tions: it establishes mechanical connections

ses adhesion to cells contains the characteristic

between cells; it creates structures with spe-

amino acid sequence -Arg-Gly-Asp-Ser-. It is

cial mechanical properties (as in bone, carti-

these residues that enable fibronectin to bind

lage, tendons, and joints); it creates filters

to cell-surface receptors, known as integrins.

(e. g., in the basal membrane in the renal cor-

puscles; see p. 322); it separates cells and tis-

sues from each other (e. g., to allow the joints

C. Proteoglycans

to move freely); and it provides pathways to

guide migratory cells (important for embry-

Proteoglycans are giant molecule complexes

onic development). The chemical composi-

consisting of carbohydrates (95%) and pro-

tion of the ECM is just as diverse as its func-

teins (5%), with masses of up to 2

10⁶ Da.

tions.

Their bottlebrush-shaped structure is pro-

Collagens (see p. 344), of which there are

duced by an axis consisting of hyaluronate.

at least 19 different varieties, form fibers, fi-

This thread-like polysaccharide

(see p. 44)

brils, networks, and ligaments. Their charac-

has proteins attached to it, from which in

teristic properties are tensile strength and

turn long polysaccharide chains emerge. Like

flexibility. Elastin is a fiber protein with a

the central hyaluronate, these terminal poly-

high degree of elasticity.

saccharides belong to the glycosaminoglycan

Adhesive proteins provide the connections

group (see p. 44).

between the various components of the ex-

The glycosaminoglycans are made up of

tracellular matrix. Important representatives

repeating disaccharide units, each of which

include laminin and fibronectin (see B). These

consists of one uronic acid (glucuronic acid

multifunctional proteins simultaneously bind

or iduronic acid) and one amino sugar (N-

to several other types of matrix component.

acetylglucosamine or N-acetylgalactosamine)

Cells attach to the cell surface receptors in the

(see p. 38). Many of the amino sugars are also

ECM with the help of the adhesive proteins.

esterified with sulfuric acid (sulfated), further

Due to their polarity and negative charge,

increasing their polarity. The proteoglycans

proteoglycans (see C) bind water molecules

bind large amounts of water and fill the

and cations. As a homogeneous “cement,”

gaps between the fibrillar components of

they fill the gaps between the ECM fibers.

the ECM in the form of a hydrated gel. This

inhibits the spread of pathogens in the ECM,

for example.

Connective tissue

347

A. Extracellular matrix

Cell membrane

Collagens

Adhesive

(at least

proteins:

19 different

Elastin, laminin,

types)

fibronectin

Cell surface

Proteoglycans

receptors

and

(Integrins)

hyaluronic acid

B. Fibronectins

Heparan sulfate

Fibrin

Collagens

Integrins

Heparane sulfate Fibrin

Domains

-Arg-Gly-Asp-Ser-

Peptide modules

Variable peptides

C. Proteoglycans

COO

CH₂OH

Disaccharide units

100 nm

O H

- Uronic acid - Amino sugar -

OH H

CH₂OH

O₃S

H HO

COO

O H

CH₃

Dermatan

Hyaluronate

sulfate

C CH₃

IduUA

GalNAc

Core protein

COO

H₂C

O SO₃

Glycosamino-

glycans

OH H

Heparin

GlcUA

GlcNAc

COO

H₂C

O SO₃

Keratan

20 - 40

sulfate

Disaccharide

C CH₃

units

GalUA

GlcNAc

IduUA

= Iduronate

COO

H₂C

SO₃

GlcUA

= Glucuronate

O H

Chondroitin

Ribosome

GalNAc

= N-Acetyl-

OH H

6-sulfate

for

= galactosamine

comparison

C CH₃

GlcNAc

= N-Acetyl-

= glucosamine

GlcUA

GalNAc^O

348

Tissues and organs

only by a narrow synaptic cleft. When an ac-

Signal transmission in the CNS

tion potential (see p. 350) reaches the presyn-

aptic membrane, voltage-gated Ca²⁺ channels

A. Structure of nerve cells

integrated into the membrane open and

Nerve cells (neurons) are easily excitable cells

trigger exocytosis of the neurotransmitter

that produce electrical signals and can react to

stored in the presynaptic cell (for details, see

such signals as well. Their structure is mark-

p. 228).

edly different from that of other types of cell.

Each neuron usually releases only one type

Numerous branching processes project from

of neurotransmitter. Neurons that release

their cell body (soma). Neurons are able to

dopamine are referred to as “dopaminergic,”

receive signals via dendrites and to pass

for example, while those that release acetyl-

them on via axons. The axons, which can be

choline are “cholinergic,” etc. The transmit-

up to 1 m long, are usually surrounded by

ters that are released diffuse through the

Schwann cells, which cover them with a

synaptic cleft and bind on the other side to

lipid-rich myelin sheath to improve their

receptors on the postsynaptic membrane.

electrical insulation.

These receptors are integral membrane pro-

The transfer of stimuli occurs at the

teins that have binding sites for neurotrans-

synapses, which link the individual neurons

mitters on their exterior (see p. 224).

to each other as well as linking neurons func-

The receptors for neurotransmitters are

tionally to muscle fibers. Neurotransmitters

divided into two large groups according to

(see p. 352) are stored in the axonal nerve

the effect produced by binding of the trans-

endings. These signaling substances are re-

mitter (for details, see p. 354).

leased in response to electrical signals in or-

Ionotropic receptors

(bottom left) are

der to excite neighboring neurons (or muscle

ligand-gated ion channels. When they open

cells). It is estimated that each neuron in the

as a result of the transmitter’s influence,

brain is in contact via synapses with approx-

ions flow in due to the membrane potential

imately 10 000 other neurons.

(see p. 126). If the inflowing ions are cations

There is a noticeably high proportion of

(Na⁺, K⁺, Ca²⁺), depolarization of the mem-

lipids in the composition of nerve cells, rep-

brane occurs and an action potential is trig-

resenting about 50% of their dry weight. In

gered on the surface of the postsynaptic cell.

particular, there is a very wide variety of

This is the way in which stimulatory trans-

phospholipids, glycolipids, and sphingolipids

mitters work (e. g., acetylcholine and gluta-

(see p. 216).

mate). By contrast, if anions flow in (mainly

Cl^-), the result is hyperpolarization of the

postsynaptic membrane, which makes the

B. Neurotransmitters and neurohormones

production of a postsynaptic action potential

Neurosecretions are classed into two groups:

more dif cult. The action of inhibitory trans-

neurotransmitters are released into the syn-

mitters such as glycine and GABA is based on

aptic cleft in order to influence neighboring

this effect.

cells (C). They have a short range and a short

A completely different type of effect is ob-

lifespan. By contrast, neurohormones are re-

served in metabotropic receptors (bottom

leased into the blood, allowing them to cover

right). After binding of the transmitter, these

larger distances. However, the distinction be-

interact on the inside of the postsynaptic

tween the two groups is a fluid one; some

membrane with G proteins (see p. 384), which

neurotransmitters simultaneously function

in turn activate or inhibit the synthesis of

as neurohormones.

second messengers. Finally, second messen-

gers activate or inhibit protein kinases, which

phosphorylate cellular proteins and thereby

C. Synaptic signal transmission

alter the behavior of the postsynaptic cells

All chemical synapses function according to a

(signal transduction; see p. 386).

similar principle. In the area of the synapse,

the surface of the signaling cell (presynaptic

membrane) is separated from the surface of

the receiving cell

(postsynaptic membrane)

350

Tissues and organs

uli (or more rarely electrical stimuli). Binding

Resting potential and action

of a neurotransmitter to an ionotropic recep-

potential

tor results in a brief local increase in the

membrane potential from -60 mV to about

A. Resting potential

+30 mV. Although the membrane potential

A characteristic property of living cells is the

quickly returns to the initial value within a

uneven distribution of positively and nega-

few milliseconds (ms) at its site of origin, the

tively charged ions on the inside and outside

depolarization is propagated because neigh-

of the plasma membrane. This gives rise to a

boring membrane areas are activated during

membrane potential (see p. 126)—i. e., there is

this time period.

electrical voltage between the two sides of

[1] The process starts with the opening of

the membrane, which can only balance out

voltage-gated Na⁺ channels (see p. 222). Due

when ion channels allow the unevenly distrib-

to their high equilibrium potential (see A), Na⁺

uted ions to move.

ions flow into the cell and reverse the local

At rest, the membrane potential in most

membrane potential (depolarization).

cells is -60 to -90 mV. It mainly arises from

[2] The Na⁺ channels immediately close

the activity of Na⁺/K⁺ transporting ATPase

again, so that the inflow of positive charges

(“Na⁺/K⁺ ATPase”), which occurs on practically

is only very brief.

all animal cells. Using up ATP, this P-type

[3] Due to the increase in the membrane

enzyme (see p. 220) “pumps” three Na⁺ ions

potential, voltage-dependent K⁺ channels

out of the cell in exchange for two K⁺ ions.

open and K⁺ ions flow out. In addition, Na⁺/

Some of the K⁺ ions, following the concentra-

K+ ATPase (see A) pumps the Na+ ions that

tion gradient, leave the cell again through

have entered back out again. This leads to

potassium channels. As the protein anions

repolarization of the membrane.

that predominate inside the cell cannot fol-

[4] The two processes briefly lead to the

low them, and inflow of Cl^- ions from the

charge even falling below the resting poten-

outside is not possible, the result is an excess

tial (hyperpolarization). The K⁺ channels also

of positive charges outside the cell, while

close after a few milliseconds. The nerve cell

anions predominate inside it.

is then ready for re-stimulation.

An equilibrium potential exists for each of

Generally, it is always only a very small

the ions involved. This is the value of the

part of the membrane that is depolarized dur-

membrane potential at which there is no net

ing an action potential. The process can there-

inflow or outflow of the ions concerned. For

fore be repeated again after a short refractory

K+ ions, the resting potential lies in the range

period, when the nerve cell is stimulated

of the membrane potential, while for Na⁺ ions

again. Conduction of the action potential on

it is much higher at +70 mV. At the first op-

the surface of the nerve cell is based on the

portunity, Na⁺ ions will therefore spontane-

fact that the local increase in the membrane

ously flow into the cell. The occurrence of

potential causes neighboring voltage-gated

action potentials is based on this (see B).

ion channels to open, so that the membrane

Nerve cell membranes contain ion chan-

stimulation spreads over the whole cell in the

nels for Na⁺, K⁺, Cl^-, and Ca²⁺. These channels

form of a depolarization wave.

are usually closed and open only briefly to let

ions pass through. They can be divided into

channels that are regulated by membrane po-

tentials (“voltage-gated”—e. g., fast Na⁺ chan-

nels; see p. 222) and those regulated by

ligands (“ligand-gated”—e. g., nicotinic acetyl-

choline receptors; see p. 222).

B. Action potential

Action potentials are special signals that are

used to transmit information in the nervous

system. They are triggered by chemical stim-

352

Tissues and organs

This provides better protection against break-

Neurotransmitters

down by peptidases.

Neurotransmitters in the strict sense are sub-

Endorphins, dynorphins, and enkephalins

stances that are produced by neurons, stored

are a particularly interesting group of neuro-

in the synapses, and released into the synap-

peptides. They act as “endogenous opiates” by

tic cleft in response to a stimulus. At the post-

producing analgetic, sedative, and euphoriant

synaptic membrane, they bind to special re-

effects in extreme situations. Drugs such as

ceptors and affect their activity.

morphine and heroin activate the receptors

for these peptides (see p. 354).

Purine derivatives with neurotransmitter

A. Important neurotransmitters

function are all derived from adenine-con-

Neurotransmitters can be classified into sev-

taining nucleotides or nucleosides. ATP is re-

eral groups according to their chemical struc-

leased along with acetylcholine and other

ture. The table lists the most important rep-

transmitters, and among other functions it

resentatives of this family, which has more

regulates the emission of transmitters from

than 100 members.

its synapse of origin. The stimulatory effect

Acetylcholine, the acetic acid ester of the

of caffeine is mainly based on the fact that it

cationic alcohol choline (see p. 50) acts at

binds to adenosine receptors.

neuromuscular junctions, where it triggers

muscle contraction (see p. 334), and in certain

B. Biosynthesis of catecholamines

parts of the brain and in the autonomous

nervous system.

The catecholamines are biogenic amines that

Several proteinogenic amino acids

(see

have a catechol group. Their biosynthesis in

p. 60) have neurotransmitter effects. A partic-

the adrenal cortex and CNS starts from tyro-

ularly important one is glutamate, which acts

sine.

as a stimulatory transmitter in the CNS. More

[1] Hydroxylation of the aromatic ring ini-

than half of the synapses in the brain are

tially produces dopa (3,4-dihydroxyphenyl-

glutaminergic. The metabolism of glutamate

alanine). This reaction uses the unusual

and that of the amine GABA synthesized from

coenzyme tetrahydrobiopterin

(THB). Dopa

it (see below) are discussed in more detail on

(cf. p. 6) is also used in the treatment of Par-

p. 356. Glycine is an inhibitory neurotransmit-

kinson’s disease.

ter with effects in the spinal cord and in parts

[2] Decarboxylation of dopa yields dopa-

of the brain.

mine, an important transmitter in the CNS. In

Biogenic amines arise from amino acids by

dopaminergic neurons, catecholamine syn-

decarboxylation (see p. 62). This group in-

thesis stops at this point.

cludes

4-aminobutyrate

(γ-aminobutyric

[3] The adrenal gland and adrenergic neu-

acid, GABA), which is formed from glutamate

rons continue the synthesis by hydroxylating

and is the most important inhibitory trans-

dopamine into norepinephrine (noradrena-

mitter in the CNS. The catecholamines norepi-

line). Ascorbic acid

(vitamin C; see p. 368)

nephrine and epinephrine (see B), serotonin,

acts as a hydrogen-transferring coenzyme

which is derived from tryptophan, and hista-

here.

mine also belong to the biogenic amine group.

[4] Finally, N-methylation of norepineph-

All of them additionally act as hormones or

rine yields epinephrine

(adrenaline). The

mediators (see p. 380).

coenzyme for this reaction is S-adenosylme-

Peptides make up the largest group among

thionine (SAM; see p. 110).

the neurosecretions. Many peptide hormo-

nes—e. g., thyroliberin (TRH) and angiotensin

The physiological effects of the catechol-

II—simultaneously act as transmitters. Most

amines are mediated by a large number of

neuropeptides are small (3-15 AA). At their

different receptors that are of particular inter-

N-terminus, many of them have a glutamate

est in pharmacology. Norepinephrine acts in

residue that has been cyclized to form

the autonomic nervous system and certain

pyroglutamate (5-oxoproline, <G), while the

areas of the brain. Epinephrine is also used

C-terminus is often an acid amide (-NH₂).

as a transmitter by some neurons.

Brain and sensory organs

353

A. Important neurotransmitters

CH₃

Acetyl-

H₃C C O

CH₂

N CH₃

choline

CH₃

COO

Amino

Glutamate

C H

COO

Glycine

acids:

Dopa

(CH

)

H₃N

CH₂

2 2

COO

Glutamate

Glycine

H₃N

CH₂

Biogenic

γ-Aminobutyrate (GABA)

H₃N

CH₂

H₃N

CH₂

amines:

Dopa

CH₂

Dopamine

Norepinephrine

CH₂

Epinephrine

Serotonine

COO

Histamine

GABA

Serotonin

Histamine

Peptides:

β-Endorphin

YGGFMTSEKSQTPLVTLFKNAITKNAYKKGE

Met- and Leu-enkephalin

YGGFM und YGGFL

Thyroliberin (TRH)

<GHP-NH₂

Gonadoliberin (GnRH)

<GHWSYGLRPG-NH

O CH₂

Substance P

RPKPQQFFGLM

Somatostatin

AGCKNFFWKTFTSC

Angiotensin II

DRVYIHPF

Cholecystokinin (CCK-4)

WMDF-NH₂

and many others

Pyroglutamate (<G)

Thyroliberin

Purine

ATP

ADP

P P

derivatives:

P P

AMP

Adenosine

B. Biosynthesis of the catecholamines

Tyrosine 3-monooxygenase [Fe2 ,THB] 1.14.16.2

Dopamine β-monooxygenase[Cu] 1.14.17.1

Aromatic-L-amino-acid decarboxylase

Phenylethanolamine N-methyltransferase 2.1.1.28

(Dopa decarboxylase) [PLP] 4.1.1.28

Dehydro-

S-Adenosyl-

ascorbate

methionine homocysteine

COO

CO₂

CH₃

Ascorbate

THB

H3N CH

H₃N

CH₂

H₃N

CH₂

H₂N

CH₂

O₂

H₂O

O₂

H₂O

Tyrosine

Dopa

Dopamine

Norepinephrine

Epinephrine

354

Tissues and organs

The nicotinic ACh receptor responds to the

Receptors for neurotransmitters

alkaloid nicotine contained in tobacco (many

Like all signaling substances, neurotrans-

of the physiological effects of nicotine are

mitters (see p. 352) act via receptor proteins.

based on this). The nicotinic receptor is iono-

The receptors for neurotransmitters are inte-

tropic. Its properties are discussed in greater

grated into the membrane of the postsynaptic

detail on p. 222.

cell, where they trigger ion inflow or signal

The muscarinic ACh receptors (of which

transduction processes (see p. 348).

there are at least five subtypes) are metabo-

tropic. Their name is derived from the

alkaloid muscarine, which is found in the fly

A. Receptors for neurotransmitters

agaric mushroom (Amanita muscaria), for ex-

A considerable number of receptors for neu-

ample. Like ACh, muscarine is bound at the

rotransmitters are already known and new

receptor, but in contrast to ACh (see C), it is

ones are continuing to be discovered. The

not broken down and therefore causes per-

table only lists the most important examples.

manent stimulation of muscle.

They are classified into two large groups ac-

The muscarinic ACh receptors influence the

cording to their mode of action.

cAMP level in the postsynaptic cells (M₁, M₃

Ionotropic receptors are ligand-gated ion

and M₅ increase it, while subtypes M₂ and M₄

channels (left half of the table). The receptors

reduce it).

for stimulatory transmitters (indicated in the

table by a ⊕) mediate the inflow of cations

C. Metabolism of acetylcholine

(mainly Na⁺). When these open after binding

of the transmitter, local depolarization of the

Acetylcholine is synthesized from acetyl-CoA

postsynaptic membrane occurs. By contrast,

and choline in the cytoplasm of the presynap-

inhibitory neurotransmitters (GABA and gly-

tic axon [1] and is stored in synaptic vesicles,

cine) allow Cl^- to flow in. This increases the

each of which contains around 1000-10 000

membrane’s negative resting potential and

ACh molecules. After it is released by exocy-

hinders the action of stimulatory transmitters

tosis (see p. 228), the transmitter travels by

(hyperpolarization,

-).

diffusion to the receptors on the postsynaptic

Metabotropic receptors (right half of the

membrane. Catalyzed by acetylcholinesterase,

table) are coupled to G proteins (see p. 386),

hydrolysis of ACh to acetate and choline im-

through which they influence the synthesis

mediately starts in the synaptic cleft [2], and

of second messengers. Receptors that work

within a few milliseconds, the ACh released

with type G_s proteins (see p. 386) increase

has been eliminated again. The cleavage

the cAMP level in the postsynaptic cell

products choline and acetate are taken up

([cAMP]

), while those that activate G_i pro-

again by the presynaptic neuron and reused

teins reduce it ([cAMP]

). Via type G_q pro-

for acetylcholine synthesis [3].

teins, other receptors increase the intracellu-

Substances that block the serine residue in

lar Ca²⁺ concentration ([Ca²⁺]

the active center of acetylcholinesterase

There are several receptor subtypes for

[2]—e. g., the neurotoxin E605

and other

most neurotransmitters. These are distin-

organophosphates—prevent ACh degradation

guished numerically (e. g., D₁ to D₅) or are

and thus cause prolonged stimulation of the

named after their agonists—i. e., after mole-

postsynaptic cell. This impairs nerve conduc-

cules experimentally found to activate the

tion and muscle contraction. Curare, a para-

receptor. For example, one specific subtype

lyzing arrow-poison used by South American

of glutamate receptors reacts to NMDA

Indians, competitively inhibits binding of ACh

(N-methyl-D-aspartate), while another sub-

to its receptor.

type reacts to the compound AMPA, etc.

B. Acetylcholine receptors

Acetylcholine (ACh) was the neurotransmitter

first discovered, at the beginning of the last

century. It binds to two types of receptor.

Brain and sensory organs

355

A. Receptors for neurotransmitters

Ionotropic

Metabotropic

Receptor

Transmitter

Ion(s)

Effect

Receptor

Transmitter

Effect

Acetyl-

Acetylcholine

[

]

Ca²

choline

(muscarinic)

[cAMP]

(nicotinic)

M1, M3, M5, M2, M4

5HT3

Serotonin

5HT₁

Serotonin

[

Ca²

]

5HT₂

„

[cAMP]

5HT₄

„

[cAMP]

GABAa

GABA

α₁

Norepinephrine

[

Ca²

]

α₂

„

[cAMP]

„

β₁, β₂, β₃

[cAMP]

Glycine

[cAMP]

D₁, D₅

Dopamine

AMPA

Glutamate

Na K

D₂, D₃, D₄

„

[cAMP]

NMDA

Glutamate

Na K Ca²

Kainate

Glutamate

Opioids

[cAMP]

Na K

δ,κ,µ

B. Acetylcholine receptors

Acetylcholine

Effector enzyme

Receptor G protein

PL-C

Adenylate cyclase

GTP

1. Nicotinic receptor

2. Muscarinic receptors

C. Metabolism of acetylcholine

Acetyl-

Acetylcholine

Choline acetyltransferase

2.3.1.6

Acetylcholinesterase

P P

3.1.1.7

Choline

Packing

Acetate-CoA ligase

6.2.1.1

P P P

Ca2

Acetate

Synaptic

Storage

vesicle

Re-uptake

Release

Presynaptic membrane

Choline

H₂O

Acetate

Acetylcholine

Synaptic

cleft

Curare

Receptor

Neurotoxins

Postsynaptic membrane

356

Tissues and organs

B. Glutamate, glutamine, and GABA

Metabolism

The proteinogenic amino acid glutamate

The brain and other areas of the central ner-

(Glu) and the biogenic amine 4-aminobuty-

vous system (CNS) have high ATP require-

rate derived from it are among the most im-

ments. Although the brain only represents

portant neurotransmitters in the brain (see

about 2% of the body’s mass, it consumes

p. 352). They are both synthesized in the

around 20% of the metabolized oxygen and

brain itself. In addition to the neurons, which

ca. 60% of the glucose. The neurons’ high en-

use Glu or GABA as transmitters, neuroglia are

ergy requirements are mainly due to ATP-de-

also involved in the metabolism of these sub-

pendent ion pumps (particularly Na⁺/K⁺ AT-

stances.

Pase) and other active transport processes

Since glutamate and GABA as transmitters

that are needed for nerve conduction (see

must not appear in the extracellular space in

p. 350).

an unregulated way, the cells of the neuroglia

(center) supply “glutaminergic” and “GABAer-

A. Energy metabolism of the brain

gic” neurons with the precursor glutamine

(Gln), which they produce from glutamate

Glucose is normally the only metabolite from

with the help of glutamine synthetase [1].

which the brain is able to obtain adequate

GABA neurons (left) and glutamate neu-

amounts of ATP through aerobic glycolysis

rons

(right) initially hydrolyze glutamine

and subsequent terminal oxidation to CO₂

with the help of glutaminase [1] to form glu-

and H₂O. Lipids are unable to pass the blood-

tamate again. The glutamate neurons store

brain barrier, and amino acids are also only

this in vesicles and release it when stimu-

available in the brain in limited quantities

lated. The GABA neurons continue the degra-

(see B). As neurons only have minor glycogen

dation process by using glutamate decarbox-

reserves, they are dependent on a constant

ylase [3] to convert glutamate into the trans-

supply of glucose from the blood. A severe

mitter GABA.

drop in the blood glucose level—as can occur

Both types of neuron take up their trans-

after insulin overdosage in diabetics, for ex-

mitter again. Some of it also returns to the

ample—rapidly leads to a drop in the ATP level

neuroglia, where glutamate is amidated back

in the brain. This results in loss of conscious-

into glutamine.

ness and neurological deficits that can lead to

Glutamate can also be produced again from

death. Oxygen deficiency (hypoxia) also fint

GABA. The reaction sequence needed for this,

affects the brain. The effects of a brief period

known as the GABA shunt, is characteristic of

of hypoxia are still reversible, but as time

the CNS. A transaminase

[4] first converts

progresses irreversible damage increasingly

GABA and 2-oxoglutarate into glutamate and

occurs and finally complete loss of function

succinate semialdehyde

(-OOC-CH₂-CH₂-

(“brain death”).

CHO). In an NAD⁺-dependent reaction, the

During periods of starvation, the brain after

aldehyde is oxidized to succinic acid

[5],

a certain time acquires the ability to use ke-

from which 2-oxoglutarate can be regener-

tone bodies (see p. 312) in addition to glucose

ated again via tricarboxylic acid cycle reac-

to form ATP. In the first weeks of a starvation

tions.

period, there is a strong increase in the activ-

The function of glutamate as a stimulatory

ities of the enzymes required for this in the

transmitter in the brain is the cause of what is

brain. The degradation of ketone bodies in the

known as the “Chinese restaurant syndrome.”

CNS saves glucose and thereby reduces the

In sensitive individuals, the monosodium glu-

breakdown of muscle protein that maintains

tamate used as a flavor enhancer in Chinese

gluconeogenesis in the liver during starva-

cooking can raise the glutamate level in the

tion. After a few weeks, the extent of muscle

brain to such an extent that transient mild

breakdown therefore declines to one-third of

neurological disturbances can occur (dizzi-

the initial value.

ness, etc.).

Brain and sensory organs

357

A. Energy metabolism of the brain

Energy suppliers

Constantly

Small amount

Glycogen

during prolonged

required

starvation

Blood glucose

Glucose

Amino acids

Ketone bodies

O₂

P P

Glycolysis

3 Na

Tricarboxylic acid cycle

Respiratory chain

P P P

CO₂ + H₂O

Na /K

-exchanging

ATPase 3.6.1.37

B. Glutamate, glutamine, and GABA

Glutamate

GABA

Glia cell

neuron

Glutamine

P P

H₂O

P P P

NH₄

Glutamate

GABA

2-Oxoglutarate

Succinate

CO₂

semialdehyde

Tricarboxylic

acid cycle

GABA

Exo-

cytosis

Succinic acid

GABA

Glutamate

Glutaminase 3.5.1.2

Glutamine synthetase 6.3.1.2

Glutamate decarboxylase 4.1.1.15

Glutamat-

GABA receptor

4-Aminobutyrate transaminase 2.6.1.19

Glutamate receptor

Rezeptor

Succinic semialdehyde dehydrogenase

1.2.1.24

358

Tissues and organs

contain in such a way that colors can also be

Sight

perceived.

Two types of photoreceptor cell are found in

the human retina—rods and cones. Rods are

B. Signal cascade

sensitive to low levels of light, while the cones

are responsible for color vision at higher light

Dark (bottom left). Rod cells that are not

intensities.

exposed to light contain relatively high con-

Signaling substances and many proteins

centrations (70 µM) of the cyclic nucleotide

are involved in visual processes. Initially, a

cGMP

(3 ,5 -cycloGMP; cf. cAMP, p. 386),

light-induced cis-trans isomerization of the

which is synthesized by a guanylate cyclase

pigment retinal triggers a conformational

([2], see p. 388). The cGMP binds to an ion

change in the membrane protein rhodopsin.

channel in the rod membrane (bottom left)

Via the G protein transducin, which is associ-

and thus keeps it open. The inflow of cations

ated with rhodopsin, an enzyme is activated

(Na⁺, Ca²⁺) depolarizes the membrane and

that breaks down the second messenger

leads to release of the neurotransmitter glu-

cGMP. Finally, the cGMP deficiency leads to

tamate at the synapse (see p. 356).

hyperpolarization of the light-sensitive cell,

Light (bottom right). When the G protein

which is registered by subsequent neurons

transducin binds to light-activated rhodop-

as reduced neurotransmitter release.

sin* (see A, on the structure of the complex;

see p. 224), it leads to the GDP that is bound to

the transducin being exchanged for GTP. In

A. Photoreceptor

transducin* that has been activated in this

The cell illustrated opposite, a rod, has a

way, the GTP-containing α-subunit breaks

structure divided by membrane discs into

off from the rest of the molecule and in turn

which the 7-helix receptor rhodopsin is inte-

activates a membrane cGMP phosphodiester-

grated (see p. 224). In contrast to other recep-

ase [1]. This hydrolyzes cGMP to GMP and

tors in the 7-helix class (see p. 384), rhodop-

thus reduces the level of free cGMP within

sin is a light-sensitive chromoprotein. Its pro-

milliseconds. As a consequence, the cGMP

tein part, opsin, contains the aldehyde retinal

bound at the ion channel dissociates off and

(see p. 364)—an isoprenoid which is bound to

the channel closes. As cations are constantly

the ε-amino group of a lysine residue as an

being pumped out of the cell, the membrane

aldimine.

potential falls and hyperpolarization of the

The light absorption of rhodopsin is in the

cell occurs, which interrupts glutamate re-

visible range, with a maximum at about

lease.

500 nm. The absorption properties of the vis-

Regeneration. After exposure to light, several

ual pigment are thus optimally adjusted to

processes restore the initial conditions:

the spectral distribution of sunlight.

1. The α-subunit of transducin* inactivates

Absorption of a photon triggers isomeriza-

itself by GTP hydrolysis and thus termi-

tion from the 11-cis form of retinal to all-

nates the activation of cGMP esterase.

trans-retinal (top right). Within milliseconds,

2. The reduced Ca²⁺ concentration causes ac-

this photochemical process leads to an allos-

tivation of guanylate cyclase, which in-

teric conformational change in rhodopsin.

creases the cGMP level until the cation

The active conformation (rhodopsin*) binds

channels reopen.

and activates the G protein transducin. The

3. An isomerase [3] transfers all-trans -retinal

signal cascade (B) that now follows causes

to the 11-cis -form, in which it is available

the rod cells to release less neurotransmitter

for the next cycle. A dehydrogenase [4] can

(glutamate) at their synapses. The adjoining

also allow retinal to be supplied from vita-

bipolar neurons register this change and

min A (retinol).

transmit it to the brain as a signal for light.

There are several different rhodopsins in

the cones. All of them contain retinal mole-

cules as light-sensitive components, the ab-

sorption properties of which are modulated

by the different proportions of opsin they

Brain and sensory organs

359

A. Photoreceptor

Light (h · ν)

CH₃

H₃C

CH₃

Cytoplasm

Rhodopsin

Membrane

CH₃

H₃C

discs

11-cis-Retinal

Opsin

Interlamellar

space

The double bond

Cilium

between C-11 and C-

12 is isomerized from

Mitochon-

cis to trans by light

drion

B. Signal cascade

Nucleus

Light

CH₃

H₃C

CH₃

Synapse

Rhodopsin

CH₃

Decreased release

all-trans-Retinal

of neurotransmitter

Rhodopsin*

11-cis-

Transducin

Retinal

GTP

Transducin

GDP

Opsin

GDP

all-trans

Retinal

Retinol

Transducin*

GTP

Vitamin A

cGMP esterase 3.1.4.35

*activates

Guanylate cyclase 4.6.1.2

GTP

GDP

Retinal isomerase 5.2.1.3

Retinol dehydrogenase 1.1.1.105

P P

H₂O

GTP

cGMP

GMP

Light

Dark

Ca²

ATP

ADP P

cGMP

Cytoplasm

Cation channel

Cation pump

Cation channel

Extracellular space

Ca²

Closes due to

lack of cGMP

360

Nutrition

The minimum daily requirement of protein

Organic substances

is 37 g for men and 29 g for women, but the

A balanced human diet needs to contain a

recommended amounts are about twice these

large number of different components. These

values. Requirements in pregnant and breast-

include proteins, carbohydrates, fats, minerals

feeding women are even higher. Not only the

(including water), and vitamins. These sub-

quantity, but also the quality of protein is

stances can occur in widely varying amounts

important. Proteins that lack several essential

and proportions, depending on the type of

amino acids or only contain small quantities

diet. As several components of the diet are

of them are considered to be of low value, and

essential for life, they have to be regularly

larger quantities of them are therefore

ingested with food. Recommended daily min-

needed. For example, pulses only contain

imums for nutrients have been published by

small amounts of methionine, while wheat

the World Health Organization (WHO) and a

and corn proteins are poor in lysine. In con-

number of national expert committees.

trast to vegetable proteins, most animal pro-

teins are high-value (with exceptions such as

collagen and gelatin).

A. Energy requirement

Carbohydrates serve as a general and easily

The amount of energy required by a human is

available energy source. In the diet, they are

expressed in kJ d^-1 (kilojoule per day). An

present as monosaccharides in honey and

older unit is the kilocalorie (kcal; 1 kcal =

fruit, or as disaccharides in milk and in all

4.187 kJ). The figures given are recommended

foods sweetened with sugar (sucrose). Meta-

values for adults with a normal body weight.

bolically usable polysaccharides are found in

However, actual requirements are based on

vegetable products (starch) and animal prod-

age, sex, body weight, and in particular on

ucts (glycogen). Carbohydrates represent a

physical activity. In those involved in compet-

substantial proportion of the body’s energy

itive sports, for example, requirements can

supply, but they are not essential.

increase from 12 000 to 17 000 kJ d^-1.

Fats are primarily important energy suppli-

It is recommended that about half of the

ers in the diet. Per gram, they provide more

energy intake should be in the form of carbo-

than twice as much energy as proteins and

hydrates, a third at most in the form of fat, and

carbohydrates. Fats are essential as suppliers

the rest as protein. The fact that alcoholic bever-

of fat-soluble vitamins (see p. 364) and as

ages can make a major contribution to daily

sources of polyunsaturated fatty acids, which

energy intake is often overlooked. Ethanol has

are needed to biosynthesize eicosanoids (see

a caloric value of about 30 kJ g^-1 (see p. 320).

pp. 48, 390).

Mineral substances and trace elements, a

very heterogeneous group of essential nu-

B. Nutrients

trients, are discussed in more detail on

Proteins provide the body with amino acids,

p. 362. They are usually divided into macro-

which are used for endogenous protein bio-

minerals and microminerals.

synthesis. Excess amino acids are broken

Vitamins are also indispensable compo-

down to provide energy (see p. 174). Most

nents of the diet. The animal body requires

amino acids are glucogenic—i. e., they can be

them in very small quantities in order to syn-

converted into glucose (see p. 180).

thesize coenzymes and signaling substances

Proteins are essential components of the

(see pp. 364-369).

diet, as they provide essential amino acids

that the human body is not capable of pro-

ducing on its own (see the table). Some amino

acids, including cysteine and histidine, are not

absolutely essential, but promote growth in

children. Some amino acids are able to sub-

stitute for each other in the diet. For example,

humans can form tyrosine, which is actually

essential, by hydroxylation from phenylala-

nine, and cysteine from methionine.

Nutrients

361

A. Energy requirement

Daily

Recommended proportion of energy supply:

requirement

(average)

Fats 30%

Proteins

Carbohydrates

15 - 20%

50 - 55%

9 200 kJ

12 600 kJ

(2200 kcal)

000 kcal)

B. Nutrients

Quantity

Energy content

Daily

General function

Essential

in body

kJ · g

-1

requirement (g)

in metabolism

constituents

(kg)

(kcal · g-1)

b c

Supplier of amino acids

Essential

(4.1)

amino acids::

Energy source

Val

(14)

Leu

(16)

Ile

(12)

Lys

(12)

Daily require-

Phe

(16)

Cys and

ment in mg per

Trp

( 3)

His stimu-

Met

(10)

kg body weight

late growth

Thr

( 8)

390

240-

General source

Non-essential

(4.1)

310

of energy (glucose)

nutritional

Energy reserve

constituent

(glycogen)

Roughage (cellulose)

Supporting substances

(bones, cartilage, mucus)

10-15

130

General energy source

Poly-

(9.3)

unsaturated

Most important energy

fatty acids:

reserve

Linoleic acid

Solvent for vitamins

Linolenic acid

Arachidonic acid

Supplier of

essential fatty acids

(together

10 g/day)

35-40

2 400

Solvent

Cellular building block

Dielectric

Reaction partner

Temperature regulator

Building blocks

Macrominerals

Electrolytes

Microminerals

Cofactors of enzymes

(trace elements)

Often precursors

Lipid-soluble vitamins

–

of coenzymes

Water-soluble

vitamins

a: Minimum daily requirement

b: Recommended daily intake

c: Actual daily intake in

c: industrialized nations

362

Nutrition

Ca²⁺, and phosphate (see p. 328), and storage

Minerals and trace elements

of Fe²⁺ and I^-.

Resorption of the required mineral sub-

A. Minerals

stances from food usually depends on the

Water is the most important essential inor-

body’s requirements, and in several cases

ganic nutrient in the diet. In adults, the body

also on the composition of the diet. One ex-

has a daily requirement of 2-3 L of water,

ample of dietary influence is calcium (see

which is supplied from drinks, water con-

p. 342). Its resorption as Ca²⁺ is promoted by

tained in solid foods, and from the oxidation

lactate and citrate, but phosphate, oxalic acid,

water produced in the respiratory chain (see

and phytol inhibit calcium uptake from food

p. 140). The special role of water for living

due to complex formation and the production

processes is discussed in more detail else-

of insoluble salts.

where (see p. 26).

Mineral deficiencies are not uncommon

The elements essential for life can be div-

and can have quite a variety of causes—e. g.,

ided into macroelements (daily requirement

an unbalanced diet, resorption disturbances,

> 100 mg) and microelements (daily require-

and diseases. Calcium deficiency can lead to

ment < 100 mg). The macroelements include

rickets, osteoporosis, and other disturbances.

the electrolytes sodium (Na), potassium (K),

Chloride deficiency is observed as a result of

calcium (Ca), and magnesium (Mg), and the

severe Cl^- losses due to vomiting. Due to the

nonmetals chlorine (Cl), phosphorus (P), sul-

low content of iodine in food in many regions

fur (S), and iodine (I).

of central Europe, iodine deficiency is wides-

The essential microelements are only re-

pread there and can lead to goiter. Magnesium

quired in trace amounts (see also p. 2). This

deficiency can be caused by digestive disor-

group includes iron (Fe), zinc (Zn), manganese

ders or an unbalanced diet—e. g., in alco-

(Mn), copper (Cu), cobalt (Co), chromium (Cr),

holism. Trace element deficiencies often re-

selenium (Se), and molybdenum (Mo). Fluo-

sult in a disturbed blood picture—i. e., forms of

rine (F) is not essential for life, but does pro-

anemia.

mote healthy bones and teeth. It is still a

The last column in the table lists some of

matter of controversy whether vanadium,

the functions of minerals. It should be noted

nickel, tin, boron, and silicon also belong to

that almost all of the macroelements in the

the essential trace elements.

body function either as nutrients or electro-

The second column in the table lists the

lytes. Iodine (as a result of its incorporation

average amounts of mineral substances in

into iodothyronines) and calcium act as sig-

the body of an adult weighing 65 kg. The daily

naling substances. Most trace elements are

requirements listed in the fourth column also

cofactors for proteins, especially for enzymes.

apply to an adult, and are average values.

Particularly important in quantitative terms

Children, pregnant and breast-feeding wo-

are the iron proteins hemoglobin, myoglobin,

men, and those who are ill generally have

and the cytochromes (see p. 286), as well as

higher mineral requirements relative to

more than 300 different zinc proteins.

body weight than men.

As the human body is able to store many

minerals, deviations from the daily ration are

balanced out over a given period of time.

Minerals stored in the body include water,

which is distributed throughout the whole

body; calcium, stored in the form of apatite

in the bones (see p. 340); iodine, stored as

thyroglobulin in the thyroid; and iron, stored

in the form of ferritin and hemosiderin in the

bone marrow, spleen, and liver (see p. 286).

The storage site for many trace elements is

the liver. In many cases, the metabolism of

minerals is regulated by hormones—for exam-

ple, the uptake and excretion of H₂O, Na⁺,

Nutrients

363

A. Minerals

Mineral

Content

Major source

Daily requirement

Functions/Occurrence

(g)

Water

35 000-

Drinks

1200

Solvent, cellular buil-

40 000

Water in solid

ding block, dielectric,

900

foods

coolant, medium for

From metabolism 300g

transport, reaction partner

Macroelements (daily requirement >100 mg)

Osmoregulation,

100

Table salt

1.1-3.3

membrane potential,

mineral metabolism

Vegetables, fruit,

Membrane potential,

150

1.9-5.6

cereals

mineral metabolism

Bone formation,

1 300

Milk, milk products

0.8

blood clotting,

signal molecule

Bone formation,

Green vegetables

0.35

cofactor for enzymes

100

Table salt

1.7-5.1

Mineral metabolism

Bone formation, energy

Meat, milk,

650

0.8

metabolism, nucleic

cereals, vegetables

acid metabolism

S-containing

Lipid and carbohydrate

200

amino acids

0.2

metabolism,

(Cys and Met)

conjugate formation

Microelements (trace elements)

(mg

Meat, liver, eggs,

Hemoglobin, myoglobin,

4-5

vegetables, potatoes,

cytochromes,

cereals

Fe/S clusters

Meat, liver,

2-3

Zinc enzymes

cereals

Found in many

0.02

2-5

Enzymes

foodstuffs

Meat, vegetables,

0.1-0.2

2-3

Oxidases

fruit, fish

<0.01

Meat

Traces

Vitamin B₁₂

<0.01

0.05-0.2

Not clear

Cereals, nuts,

0.02

0.15-0.5

Redox enzymes

legumes

Vegetables, meat

0.05-0.2

Selenium enzymes

Seafood,

0.03

iodized salt,

0.15

Thyroxin

drinking water

Requirement not known

Metals

Non-metals

Drinking water

0.0015-0.004

Bones, dental enamel

(fluoridated), tea, milk

* ^{Content in the body of a 65 kg adult}

364

Nutrition

the chromoprotein rhodopsin

(see p. 358).

Lipid-soluble vitamins

Retinoic acid, like the steroid hormones, in-

Vitamins are essential organic compounds

fluences the transcription of genes in the cell

that the animal organism is not capable of

nucleus. It acts as a differentiation factor in

forming itself, although it requires them in

growth and development processes. Vitamin

small amounts for metabolism. Most vitamins

A deficiency can result in night blindness, vis-

are precursors of coenzymes; in some cases,

ual impairment, and growth disturbances.

they are also precursors of hormones or act as

Vitamin D (calciol, cholecalciferol) is the

antioxidants. Vitamin requirements vary from

precursor of the hormone calcitriol (1α,25-di-

species to species and are influenced by age,

hydroxycholecalciferol; see p. 320). Together

sex, and physiological conditions such as

with two other hormones (parathyrin and

pregnancy, breast-feeding, physical exercise,

calcitonin), calcitriol regulates the calcium

and nutrition.

metabolism (see p. 342). Calciol can be syn-

thesized in the skin from 7-dehydrocholes-

terol, an endogenous steroid, by a photo-

A. Vitamin supply

chemical reaction. Vitamin D deficiencies

A healthy diet usually covers average daily

only occur when the skin receives insuf cient

vitamin requirements. By contrast, malnutri-

exposure to ultraviolet light and vitamin D is

tion, malnourishment (e. g., an unbalanced

lacking in the diet. Deficiency is observed in

diet in older people, malnourishment in alco-

the form of rickets in children and osteomala-

holics, ready meals), or resorption disturban-

cia in adults. In both cases, bone mineraliza-

ces lead to an inadequate supply of vitamins

tion is disturbed.

from which hypovitaminosis, or in extreme

Vitamin E (tocopherol) and related com-

cases avitaminosis, can result. Medical treat-

pounds only occur in plants

(e. g., wheat

ments that kill the intestinal flora—e. g., anti-

germ). They contain what is known as a chro-

biotics—can also lead to vitamin deficiencies

man ring. In the lipid phase, vitamin E is

(K, B₁₂, H) due to the absence of bacterial

mainly located in biological membranes,

vitamin synthesis.

where as an antioxidant it protects unsatu-

Since only a few vitamins can be stored (A,

rated lipids against ROS (see p. 284) and other

D, E, B₁₂), a lack of vitamins quickly leads to

radicals.

deficiency diseases. These often affect the

Vitamin K (phylloquinone) and similar sub-

skin, blood cells, and nervous system. The

stances with modified side chains are in-

causes of vitamin deficiencies can be treated

volved in carboxylating glutamate residues

by improving nutrition and by administering

of coagulation factors in the liver

(see

vitamins in tablet form. An overdose of vita-

p. 290). The form that acts as a cofactor for

mins only leads to hypervitaminoses, with

carboxylase is derived from the vitamin by

toxic symptoms, in the case of vitamins A

enzymatic reduction. Vitamin K antagonists

and D. Normally, excess vitamins are rapidly

(e. g., coumarin derivatives) inhibit this reduc-

excreted with the urine.

tion and consequently carboxylation as well.

This fact is used to inhibit blood coagulation

in prophylactic treatment against thrombosis.

B. Lipid-soluble vitamins

Vitamin K deficiency occurs only rarely, as the

Vitamins are classified as either lipid-soluble

vitamin is formed by bacteria of the intestinal

or water-soluble. The lipid-soluble vitamins

flora.

include vitamins A, D, E, and K, all of which

belong to the isoprenoids (see p. 52).

Vitamin A (retinol) is the parent substance

of the retinoids, which include retinal and

retinoic acid. The retinoids also can be synthe-

sized by cleavage from the provitamin β-car-

otene. Retinoids are found in meat-containing

diets, whereas β-carotene occurs in fruits and

vegetables (particularly carrots). Retinal is in-

volved in visual processes as the pigment of

Vitamins

365

A. Vitamin supply

Healthy

nutrition

Vitamin require-

ment satisfied

Vitamin poisoning

Poor nutrition

Vitamin

Malnutrition

A and D

Antibiotics

Vitamin intake

Disturbed

Hypervitaminosis

resorption

Excess

vitamins

Hypo-

Diseases

vitaminosis

Urine

B. Lipid-soluble vitamins

* Adult daily

Provitamin

Functional form

Important for

* requirement

β-Carotene

Retinal

Sight

Vegetables

CH₃

Visual pigments

H₃C

CH₃

Fruit

CH₂OH

CH₃

Retinol

Sugar

transport

Coenzyme

Milk

Liver

Egg yolk

Development

Retinoic acid

Differentiation

H₃C

Signal molecule

H₃C

CH₃

Cholesterol

Calcium

Calciol

Calcitriol

metabolism

0.01

Hormone

Cod liver oil

Milk

Egg yolk

CH₃

Anti-

Tocopherols

oxidant

H₃C

Reducing agent

Cereals

Liver

Eggs

Seed oil

Blood clotting

Phyllohydro-

Phylloquinones

(carboxylation

quinones

of plasma

0.08

proteins)

CH₃

Intestinal

bacteria

Vegetables

Liver

366

Nutrition

synthesis and the amino acid metabolism are

Water-soluble vitamins I

affected.

The B group of vitamins covers water-soluble

In contrast to animals, microorganisms are

vitamins, all of which serve as precursors for

able to synthesize folate from their own com-

coenzymes. Their numbering sequence is not

ponents. The growth of microorganisms can

continuous, as many substances that were

therefore be inhibited by sulfonamides, which

originally regarded as vitamins were not later

competitively inhibit the incorporation of 4-

confirmed as having vitamin characteristics.

aminobenzoate into folate (see p. 254). Since

folate is not synthesized in the animal organ-

ism, sulfonamides have no effect on animal

A. Water-soluble vitamins I

metabolism.

Vitamin B₁ (thiamine) contains two heterocy-

Nicotinate and nicotinamide, together re-

clic rings—a pyrimidine ring (a six-membered

ferred to as “niacin,” are required for biosyn-

aromatic ring with two Ns) and a thiazole ring

thesis of the coenzymes nicotinamide ad-

(a five-membered aromatic ring with N and

enine dinucleotide (NAD⁺) and nicotinamide

S), which are joined by a methylene group.

adenine dinucleotide phosphate

(NADP⁺).

The active form of vitamin B₁ is thiamine

These both serve in energy and nutrient me-

diphosphate (TPP), which contributes as a

tabolism as carriers of hydride ions

(see

coenzyme to the transfer of hydroxyalkyl res-

pp. 32, 104). The animal organism is able to

idues (active aldehyde groups). The most im-

convert tryptophan into nicotinate, but only

portant reactions of this type are oxidative

with a poor yield. Vitamin deficiency there-

decarboxylation of

2-oxoacids

(see p. 134)

fore only occurs when nicotinate, nicotin-

and the transketolase reaction in the pentose

amide, and tryptophan are all simultaneously

phosphate pathway (see p. 152). Thiamine

are lacking in the diet. It manifests in the form

was the first vitamin to be discovered, around

of skin damage (pellagra), digestive distur-

100 years ago. Vitamin B₁ deficiency leads to

bances, and depression.

beriberi, a disease with symptoms that in-

Pantothenic acid is an acid amide consist-

clude neurological disturbances, cardiac in-

ing of β-alanine and 2,4-dihydroxy-3,3 -di-

suf ciency, and muscular atrophy.

methylbutyrate (pantoic acid). It is a precur-

Vitamin B₂ is a complex of several vita-

sor of coenzyme A, which is required for acti-

mins: riboflavin, folate, nicotinate, and pan-

vation of acyl residues in the lipid metabolism

tothenic acid.

(see pp. 12, 106). Acyl carrier protein (ACP; see

Riboflavin (from the Latin flavus, yellow)

p. 168) also contains pantothenic acid as part

serves in the metabolism as a component of

of its prosthetic group. Due to the widespread

the redox coenzymes flavin mononucleotide

availability of pantothenic acid in food (Greek

(FMN) and flavin adenine dinucleotide (FAD;

pantothen = “from everywhere”), deficiency

see p. 104). As prosthetic groups, FMN and FAD

diseases are rare.

are cofactors for various oxidoreductases (see

p. 32). No specific disease due to a deficiency

Further information

of this vitamin is known.

Folate, the anion of folic acid, is made up of

The requirement for vitamins in humans and

three different components—a pteridine

other animals is the result of mutations in the

derivative,

4-aminobenzoate, and one or

enzymes involved in biosynthetic coenzymes.

more glutamate residues. After reduction to

As intermediates of coenzyme biosynthesis

tetrahydrofolate

(THF), folate serves as a

are available in suf cient amounts in the

coenzyme in the C₁ metabolism (see p. 418).

diet of heterotrophic animals

(see p. 112),

Folate deficiency is relatively common, and

the lack of endogenous synthesis did not

leads to disturbances in nucleotide biosynthe-

have unfavorable effects for them. Microor-

sis and thus cell proliferation. As the precur-

ganisms and plants whose nutrition is mainly

sors for blood cells divide particularly rapidly,

autotrophic have to produce all of these com-

disturbances of the blood picture can occur,

pounds themselves in order to survive.

with increased amounts of abnormal precur-

sors for megalocytes (megaloblastic anemia).

Later, general damage ensues as phospholipid

Vitamins

367

A. Water-soluble vitamins I

* Adult daily

Vitamin

Active form:

Function in

*requirement

coenzyme

metabolism

Transfer of

Thiamine

TPP

hydroxy-

CH₂

CH₂OH

alkyl residues

Thiamine

H₃C

NH₂

1.5 mg *

diphosphate

Grain

Yeast products

Pork

CH₃

FMN

Hydrogen

CH₂

Riboflavin

transfer

FAD

1.8 mg*

Milk

Eggs

CH₂OH

4-Aminobenzoate residue

C₁-

COO

Folate

THF

metabolism

CH₂

Tetrahydro-

0.2 mg*

CH₂

folate

H₂N

CH₂

Fresh green

vegetables

COO

Liver

Pteridine derivative

Glu

Nicotinate

Hydride

COO

Nicotinamide

NADP

transfer

20 mg*

(or 1.2 g tryptophan)

NAD

Nicotinate

Nicotinamide

Meat, yeast products

Fruit and vegetables

H₃C

CH₃O

COO

Activation

Pantothenate

of carboxy-

lic acids

HO OH

7 mg*

CoA

β-Alanine

Pantoinate

Widely

distributed

368

Nutrition

Vitamin C is L-ascorbic acid (chemically:

Water-soluble vitamins II

2-oxogulonolactone). The two hydroxyl

groups have acidic properties. By releasing a

A. Water-soluble vitamins II

proton, ascorbic acid therefore turns into its

Vitamin B₆ consists of three substituted pyr-

anion, ascorbate. Humans, apes, and guinea

idines—pyridoxal, pyridoxol, and pyrid-

pigs require vitamin C because they lack the

oxamine. The illustration shows the structure

enzyme L-gulonolactone oxidase

(1.1.3.8),

of pyridoxal, which carries an aldehyde group

which catalyzes the final step in the conver-

(-CHO) at C-4. Pyridoxol is the corresponding

sion of glucose into ascorbate.

alcohol

(-CH₂OH), and pyridoxamine the

Vitamin C is particularly abundant in fresh

amine (-CH₂NH₂).

fruit and vegetables. Many soft drinks and

The active form of vitamin B₆, pyridoxal

foodstuffs also have synthetic ascorbic acid

phosphate, is the most important coenzyme

added to them as an antioxidant and flavor

in the amino acid metabolism (see p. 106).

enhancer. Boiling slowly destroys vitamin C.

Almost all conversion reactions involving

In the body, ascorbic acid serves as a reducing

amino acids require pyridoxal phosphate, in-

agent in variations reactions (usually hydrox-

cluding transaminations, decarboxylations,

ylations). Among the processes involved are

dehydrogenations, etc. Glycogen phosphory-

collagen synthesis, tyrosine degradation, cate-

lase, the enzyme for glycogen degradation,

cholamine synthesis, and bile acid biosynthesis.

also contains pyridoxal phosphate as a cofac-

The daily requirement for ascorbic acid is

tor. Vitamin B₆ deficiency is rare.

about 60 mg, a comparatively large amount

Vitamin B₁₂ (cobalamine) is one of the most

for a vitamin. Even higher doses of the vita-

complex low-molecular-weight substances

min have a protective effect against infec-

occurring in nature. The core of the molecule

tions. However, the biochemical basis for

consists of a tetrapyrrol system (corrin), with

this effect has not yet been explained. Vitamin

cobalt as the central atom (see p. 108). The

C deficiency only occurs rarely nowadays; it

vitamin is exclusively synthesized by micro-

becomes evident after a few months in the

organisms. It is abundant in liver, meat, eggs,

form of scurvy, with connective-tissue dam-

and milk, but not in plant products. As the

age, bleeding, and tooth loss.

intestinal flora synthesize vitamin B_12, strict

Vitamin H (biotin) is present in liver, egg

vegetarians usually also have an adequate

yolk, and other foods; it is also synthesized by

supply of the vitamin.

the intestinal flora. In the body, biotin is co-

Cobalamine can only be resorbed in the

valently attached via a lysine side chain to

small intestine when the gastric mucosa se-

enzymes that catalyze carboxylation reac-

cretes what is known as intrinsic factor—a

tions. Biotin-dependent carboxylases include

glycoprotein that binds cobalamine (the ex-

pyruvate carboxylase (see p. 154) and acetyl-

trinsic factor) and thereby protects it from

CoA carboxylase (see p. 162). CO₂ binds, using

degradation. In the blood, the vitamin is

up ATP, to one of the two N atoms of biotin,

bound to a special protein known as trans-

from which it is transferred to the acceptor

cobalamin. The liver is able to store vitamin

(see p. 108).

B₁₂ in amounts suf cient to last for several

Biotin

binds with high af nity

months. Vitamin B₁₂

deficiency is usually

(K_d = 10^-15 M) and specificity to avidin, a pro-

due to an absence of intrinsic factor and the

tein found in egg white. Since boiling dena-

resulting resorption disturbance. This leads to

tures avidin, biotin deficiency only occurs

a disturbance in blood formation known as

when egg whites are eaten raw.

pernicious anemia.

In animal metabolism, derivatives of cobal-

amine are mainly involved in rearrangement

reactions. For example, they act as coenzymes

in the conversion of methylmalonyl-CoA to

succinyl-CoA (see p. 166), and in the formation

of methionine from homocysteine (see p. 418).

In prokaryotes, cobalamine derivatives also

play a part in the reduction of ribonucleotides.

Vitamins

369

A. Water-soluble vitamins II

* Adult daily

Vitamin

Active form:

Function in

*requirement

coenzyme

metabolism

Pyridoxal

Activation

CH₂OH

Pyridoxol

PLP

of amino

Pyridoxamine

acids

Pyridoxal

phosphate

H₃C

Pyridoxal

2 mg*

Meat

Vegetables

Grain products

B₁₂

H₂N

5-Deoxy-

Isomerization

Cobalamine

H₃C

adenosyl

e.g.

H₃C

cobalamine

H₂N

NH₂

0.002 mg*

Co²

CH₃

NH₂

H₃C

Meat

H C C C

H₂C

CH₃

Liver

H3C CH

CH₃

Milk

CH₃

H COO

Eggs

H₃C

Methylmalonyl CoA

O NH2

CH₂

H H

C C

COO

Succinyl CoA

Stabilization

of enzyme

Ascorbic acid

Ascorbate

systems,

coenzyme,

60 mg*

antioxidant

CH₂OH

Fruit

Vegetables

Transfer

Biotin

HN NH

carboxyl

groups

0.1 mg*

Biotin

Yeast products

COO

Legumes

Nuts

370

Hormones

subject to hormonal regulation are the up-

Basics

take and degradation of storage substances

Hormones are chemical signaling substances.

(glycogen, fat), metabolic pathways for bio-

They are synthesized in specialized cells that

synthesis and degradation of central me-

are often associated to form endocrine glands.

tabolites

(glucose, fatty acids, etc.), and

Hormones are released into the blood and

the supply of metabolic energy.

transported with the blood to their effector

•

Digestive processes

organs. In the organs, the hormones carry

Digestive processes are usually regulated

out physiological and biochemical regulatory

by locally acting peptides (paracrine; see

functions. In contrast to endocrine hormones,

p. 372), but mediators, biogenic amines,

tissue hormones are only active in the imme-

and neuropeptides are also involved (see

diate vicinity of the cells that secrete them.

p. 270).

The distinctions between hormones and

•

Maintenance of ion concentrations

(ho-

other signaling substances (mediators, neuro-

meostasis)

transmitters, and growth factors) are fluid.

Concentrations of Na⁺, K⁺, and Cl^- in body

Mediators is the term used for signaling sub-

fluids, and the physiological variables de-

stances that do not derive from special hor-

pendent on these (e. g. blood pressure), are

mone-forming cells, but are form by many cell

subject to strict regulation. The principal

types. They have hormone-like effects in their

site of action of the hormones involved is

immediate surroundings. Histamine

(see

the kidneys, where hormones increase or

p. 352) and prostaglandins (see p. 390) are

reduce the resorption of ions and recovery

important examples of these substances.

of water (see pp. 326-331). The concentra-

Neurohormones and neurotransmitters are

tions of Ca²⁺ and phosphate, which form

signaling substances that are produced and

the mineral substance of bone and teeth,

released by nerve cells (see p. 348). Growth

are also precisely regulated.

factors and cytokines mainly promote cell

Many hormones influence the above pro-

proliferation and cell differentiation

(see

cesses only indirectly by regulating the syn-

p. 392).

thesis and release of other hormones (hormo-

nal hierarchy; see p. 372).

A. Hormones: overview

B. Hormonal regulation system

The animal organism contains more than 100

hormones and hormone-like substances,

Each hormone is the center of a hormonal

which can be classified either according to

regulation system. Specialized glandular cells

their structure or according to their function.

synthesize the hormone from precursors,

In chemical terms, most hormones are amino

store it in many cases, and release it into the

acid derivatives, peptides or proteins, or ste-

bloodstream when needed (biosynthesis). For

roids. Hormones regulate the following pro-

transport, the poorly water-soluble lipophilic

cesses:

hormones are bound to plasma proteins

• Growth and differentiation of cells, tissues,

known as hormone carriers. To stop the ef-

and organs

fects of the hormone again, it is inactivated by

These processes include cell proliferation,

enzymatic reactions, most of which take place

embryonic development, and sexual dif-

in the liver (metabolism). Finally, the hor-

ferentiation—i. e., processes that require a

mone and its metabolites are expelled via

prolonged time period and involve proteins

the excretory system, usually in the kidney

de novo synthesis. For this reason, mainly

(excretion). All of these processes affect the

steroid hormones which function via tran-

concentration of the hormone and thus con-

scription regulation are active in this field

tribute to regulation of the hormonal signal.

(see p. 244).

In the effector organs, target cells receive the

• Metabolic pathways

hormone’s message. These cells have hormone

Metabolic regulation requires rapidly act-

receptors for the purpose, which bind the hor-

ing mechanisms. Many of the hormones

mone. Binding of a hormone passes informa-

involved therefore regulate interconversion

tion to the cell and triggers a response (effect).

of enzymes (see p. 120). The main processes

372

Hormones

mone synthesis, release, and degradation al-

Plasma levels and hormone

lows the blood concentrations of hormones to

hierarchy

be precisely adjusted. This is based either on

simple feedback control or on hierarchically

A. Endocrine, paracrine, and autocrine hor-

structured regulatory systems.

mone effects

Hormones transfer signals by migrating from

C. Closed-loop feedback control

their site of synthesis to their site of action.

The biosynthesis and release of insulin by the

They are usually transported in the blood. In

pancreatic B cells (see p. 160) is stimulated by

this case, they are said to have an endocrine

high blood glucose levels (> 5 mM). The in-

effect (1; example: insulin). By contrast, tissue

sulin released then stimulates increased up-

hormones, the target cells for which are in the

take and utilization of glucose by the cells of

immediate vicinity of the glandular cells that

the muscle and adipose tissues. As a result,

produce them, are said to have a paracrine

the blood glucose level falls back to its normal

effect (2; example: gastrointestinal tract hor-

value, and further release of insulin stops.

mones). When signal substances also pass ef-

fects back to the cells that synthesize them,

they are said to have an autocrine effect (3;

D. Hormone hierarchy

example: prostaglandins). Autocrine effects

Hormone systems are often linked to each

are often found in tumor cells (see p. 400),

another, giving rise in some cases to a hier-

which stimulate their own proliferation in

archy of higher-order and lower-order hor-

this way.

mones. A particularly important example is

Insulin, which is formed in the B cells of the

the pituitary-hypothalamic axis, which is con-

pancreas, has both endocrine and paracrine

trolled by the central nervous system (CNS).

effects. As a hormone with endocrine effects,

Nerve cells in the hypothalamus react to

it regulates glucose and fat metabolism. Via a

stimulatory or inhibitory signals from the CNS

paracrine mechanism, it inhibits the synthesis

by releasing activating or inhibiting factors,

and release of glucagon from the neighboring

which are known as liberins (“releasing hor-

A cells.

mones”) and statins (“inhibiting hormones”).

These neurohormones reach the adenohy-

pophysis by short routes through the blood-

B. Dynamics of the plasma level

stream. In the adenohypophysis, they stimu-

Hormones circulate as signaling substances in

late

(liberins) or inhibit

(statins) the bio-

the blood at very low concentrations (10^-12 to

synthesis and release of tropines. Tropines

between 10^-7 mol L^-1). These values change

(glandotropic hormones) in turn stimulate pe-

periodically in rhythms that depend on the

ripheral glands to synthesize glandular hor-

time of day, month, or year, or on physiolog-

mones. Finally, the glandular hormone acts on

ical cycles.

its target cells in the organism. In addition, it

The first example shows the circadian

passes effects back to the higher-order hormone

rhythm of the cortisol level. As an activator

systems. This (usually negative) feedback influ-

of gluconeogenesis (see p. 158), cortisol is

ences the concentrations of the higher-order hor-

mainly released in the early morning, when

mones, creating a feedback loop.

the liver’s glycogen stores are declining. Dur-

Many steroid hormones are regulated by

ing the day, the plasma cortisol level declines.

this type of axis—e. g., thyroxin, cortisol, es-

Many hormones are released into the blood

tradiol, progesterone, and testosterone. In the

in a spasmodic and irregular manner. In this

case of the glucocorticoids, the hypothalamus

case, their concentrations change in an

releases corticotropin-releasing hormone

episodic or pulsatile fashion. This applies, for

(CRH or corticoliberin, a peptide consisting

instance, to luteinizing hormone (LH, lutropin).

of 41 amino acids), which in turn releases

Concentrations of other hormones are

corticotropin (ACTH, 39 AAs) in the pituitary

event-regulated. For example, the body re-

gland. Corticotropin stimulates synthesis and

sponds to increased blood sugar levels after

release of the glandular steroid hormone cor-

meals by releasing insulin. Regulation of hor-

tisol in the adrenal cortex.

Hormonal system

373

A. Endocrine, paracrine and autocrine hormone effects

Gland cell

Target

Hormone receptor

cell

Gland and target cell

Blood

Hormone

stream

1. Endocrine

2. Paracrine

3. Autocrine

B. Plasma level dynamics

D. Hormone hierarchy

mg · l^-1

CNS

Periodic

200

Precursors

100

Cortisol

Hypo-

Time of day

mU · ml^-1

thalamus

Lutropin

Episodic, pulsatile

Liberin

Statin

(releasing

(inhibiting

hormone)

Time of day

Precursors

mU · ml^-1

Event-dependent

Pituitary

Insulin

Meals

Negative

Tropin

feed-

Time of day

back

C. Regulatory circuit

Precursors

Pancreatic B cell

Peripheral

gland

Glandular

hormone

Glucose

H Insulin

Glucose

Metabolite

Muscle cell, fat cell

Response

Target cell

374

Hormones

Testosterone is the most important of the

Lipophilic hormones

male sexual steroids (androgens). It is synthe-

Classifying hormones into hydrophilic and

sized in the Leydig intersitial cells of the

lipophilic molecules indicates the chemical

testes, and controls the development and

properties of the two groups of hormones

functioning of the male gonads. It also deter-

and also reflects differences in their mode of

mines secondary sexual characteristics in

action (see p. 120).

men (muscles, hair, etc.).

Cortisol, the most important glucocorticoid,

is synthesized by the adrenal cortex. It is in-

A. Lipophilic hormones

volved in regulating protein and carbohydrate

Lipophilic hormones, which include steroid

metabolism by promoting protein degrada-

hormones, iodothyronines, and retinoic acid,

tion and the conversion of amino acids into

are relatively small molecules (300-800 Da)

glucose. As a result, the blood glucose level

that are poorly soluble in aqueous media.

rises

(see p. 152). Synthetic glucocorticoids

With the exception of the iodothyronines,

(e. g., dexamethasone) are used in drugs due

they are not stored by hormone-forming cells,

to their anti-inflammatory and immunosup-

but are released immediately after being syn-

pressant effects.

thesized. During transport in the blood, they

Aldosterone, a mineralocorticoid, is also

are bound to specific carriers. Via intracellular

synthesized in the adrenal gland. In the kid-

receptors, they mainly act on transcription

neys, it promotes Na⁺ resorption by inducing

(see p. 358). Other effects of steroid hor-

Na⁺/K⁺ ATPase and Na⁺ channels (see p. 328).

mones—e. g., on the immune system—are

At the same time, it leads to increased K⁺

not based on transcriptional control. Their

excretion. In this way, aldosterone indirectly

details have not yet been explained.

increases blood pressure.

Calcitriol is a derivative of vitamin D (see

p. 364). On exposure to ultraviolet light, a

Steroid hormones

precursor of the hormone can also arise in

The most important steroid hormones in ver-

the skin. Calcitriol itself is synthesized in the

tebrates are listed on p. 57. Calcitriol (vitamin

kidneys (see p. 330). Calcitriol promotes the

D hormone) is also included in this group,

resorption of calcium in the intestine and in-

although it has a modified steroid structure.

creases the Ca²⁺ level in the blood.

The most important steroid hormone in in-

vertebrates is ecdysone.

Iodothyronines

Progesterone is a female sexual steroid be-

longing to the progestin (gestagen) family. It is

The thyroid hormone thyroxine (tetraiodo-

synthesized in the corpus luteum of the ova-

thyronine, T₄) and its active form triiodo-

ries. The blood level of progesterone varies

thyronine (T₃) are derived from the amino

with the menstrual cycle. The hormone pre-

acid tyrosine. The iodine atoms at positions 3

pares the uterus for a possible pregnancy.

and 5 of the two phenol rings are character-

Following fertilization, the placenta also starts

istic of them. Post-translational synthesis of

to synthesize progesterone in order to main-

thyroxine takes place in the thyroid gland

tain the pregnant state. The development of

from tyrosine residues of the protein thyro-

the mammary glands is also stimulated by

globulin, from which it is proteolytically

progesterone.

cleaved before being released. Iodothyronines

Estradiol is the most important of the

are the only organic molecules in the animal

estrogens. Like progesterone, it is synthesized

organism that contain iodine. They increase

by the ovaries and, during pregnancy, by the

the basal metabolic rate, partly by regulating

placenta as well. Estradiol controls the men-

mitochondrial ATP synthesis. In addition, they

strual cycle. It promotes proliferation of the

promote embryonic development.

uterine mucosa, and is also responsible for the

development of the female secondary sexual

characteristics (breast, fat distribution, etc.).

Lipophilic hormones

375

A. Lipophilic hormones

Hormone

Site of formation

Sites of action

Actions

Prepares uterus

Maintenance of

for pregnancy

pregnancy

Ovaries

Promotes implantation

Development of

of fertilized egg

mammary glands

Progesterone

Uterus

Menstrual cycle

Bone development

Stimulates proliferation

of endometrium

Development of

secondary female

Ovaries

sex characteristics

e.g., fat distribution,

Estradiol

Uterus and other organs

breasts, body hair

Causes:

Development of

Testes

secondary male

Sexual differentiation

sex characteristics

to male phenotype

e.g., skeleton,

Formation of ejaculate

muscles, body hair

Testosterone

Spermatogenesis

Protein synthesis

Proteolysis

Amino

Protein synthesis

Proteins

Glucose

acids

Gluconeogenese

Adrenal glands

Blut-Glucose

(cortex)

Activity of the immune

Cortisol

system

ATP

3Na

Na retention

Adrenal glands

K excretion

(cortex)

Aldosterone

Kidneys

Blood pressure

ADP+P_i

Bones

Ca2

- and phosphate

Kidneys

resorption

Ca2 metabolism

Ca2

Calcitriol

Gut

of bones

Thyroid gland

O₂

H₂O

Fetal development,

growth, and maturation

CO₂

Basal metabolic rate

ADP+P_i

ATP, Heat

Heat generation

Thyroxine

Embryo

O₂ consumption

Intermediary

metabolism

376

Hormones

thesis of the androgen testosterone from pro-

Metabolism of steroid hormones

gesterone, the side chain is completely re-

moved. Aromatization of the A ring, as men-

A. Biosynthesis of steroid hormones

tioned above, finally leads to estradiol.

All steroid hormones are synthesized from

On the way to calcitriol (vitamin D hor-

cholesterol. The gonane core of cholesterol

mone; see p. 342), another double bond in

consists of

19 carbon atoms in four rings

the B ring of cholesterol is first introduced.

(A-D). The D ring carries a side chain of eight

Under the influence of UV light on the skin,

C atoms (see p. 54).

the B ring is then photochemically cleaved,

The cholesterol required for biosynthesis of

and the secosteroid cholecalciferol arises (vi-

the steroid hormones is obtained from vari-

tamin D₃; see p. 364). Two Cyt P450-depen-

ous sources. It is either taken up as a constit-

dent hydroxylations in the liver and kidneys

uent of LDL lipoproteins (see p. 278) into the

produce the active vitamin D hormone (see

hormone-synthesizing glandular cells, or syn-

p. 330).

thesized by glandular cells themselves from

acetyl-CoA (see p. 172). Excess cholesterol is

B. Inactivation of steroid hormones

stored in the form of fatty acid esters in lipid

droplets. Hydrolysis allows rapid mobilization

The steroid hormones are mainly inactivated

of the cholesterol from this reserve again.

in the liver, where they are either reduced or

Biosynthetic pathways. Only an overview

further hydroxylated and then conjugated

of the synthesis pathways that lead to the

with glucuronic acid or sulfate for excretion

individual hormones is shown here. Further

(see p. 316). The reduction reactions attack

details are given on p. 410.

oxo groups and the double bond in ring A. A

Among the reactions involved, hydroxyla-

combination of several inactivation reactions

tions (H) are particularly numerous. These are

gives rise to many different steroid metabo-

catalyzed by specific monooxygenases (“hy-

lites that have lost most of their hormonal

droxylases”) of the cytochrome P450 family

activity. Finally, they are excreted with the

(see p. 318). In addition, there are NADPH-

urine and also partly via the bile. Evidence of

dependent and NADP⁺-dependent hydrogena-

steroids and steroid metabolites in the urine

tions (Y) and dehydrogenations (D), as well as

is used to investigate the hormone metabo-

cleavage and isomerization reactions (S, I). The

lism.

estrogens have a special place among the ste-

roid hormones, as they are the only ones that

Further information

contain an aromatic A ring. When this is

formed, catalyzed by aromatase, the angular

Congenital defects in the biosynthesis of ste-

methyl group (C-19) is lost.

roid hormones can lead to severe develop-

Pregnenolone is an important intermedi-

mental disturbances. In the adrenogenital

ate in the biosynthesis of most steroid hor-

syndrome (AGS), which is relatively common,

mones. It is identical to cholesterol with the

there is usually a defect in 21-hydroxylase,

exception of a shortened and oxidized side

which is needed for synthesis of cortisol and

chain. Pregnenolone is produced in three

aldosterone from progesterone. Reduced syn-

steps by hydroxylation and cleavage in the

thesis of this hormone leads to increased for-

side chain. Subsequent dehydrogenation of

mation of testosterone, resulting in masculin-

the hydroxyl group at C-3 (b) and shifting of

ization of female fetuses. With early diagno-

the double bond from C-5 to C-4 results in the

sis, this condition can be avoided by providing

gestagen progesterone.

the mother with hormone treatment before

With the exception of calcitriol, all steroid

birth.

hormones are derived from progesterone. Hy-

droxylations of progesterone at C atoms 17,

21, and 11 lead to the glucocorticoid cortisol.

Hydroxylation at C-17 is omitted during syn-

thesis of the mineralocorticoid aldosterone.

Instead, the angular methyl group (C-18) is

oxidized to the aldehyde group. During syn-

Lipophilic hormones

377

A. Biosynthesis of steroid hormones

DSHH

CH₂

Cholesterol

Calcitriol

H/S

CH₃

Cholesterol

HYDHH

Pregnenolone

Cortisol

CH₃

C21

CH₃

CH₂OH

HHH

OHCCO

HHHD

Progesterone

Aldosterone

C19

Hydroxylation

Dehydrogenation

Progesterone

Isomerization

Hydrogenation

Cleavage

Aromatization

Androstenedione

C18

Estradiol

B. Inactivation of steroid hormones

Oxidative cleavage

Conjugate

Oxidation

formation

CH₂OH

Conjugate

Oxidation

formation

Hydroxylation

Reduction

Conjugate

formation

Conjugate formation

Reduction

Cortisol

Estradiol

378

Hormones

“n” stands for any nucleotide). Each hormone

Mechanism of action

receptor only recognizes its “own” HRE and

therefore only influences the transcription of

A. Mechanism of action of lipophilic

genes containing that HRE. Recognition be-

hormones

tween the receptor and HRE is based on in-

Lipophilic signaling substances include the

teraction between the amino acid residues in

steroid hormones, calcitriol, the iodothy-

the DNA-binding domain (B) and the relevant

ronines (T₃ and T₄), and retinoic acid. These

bases in the HRE (emphasized in color in the

hormones mainly act in the nucleus of the

structure illustrated).

target cells, where they regulate gene tran-

As discussed on p.244, the hormone recep-

scription in collaboration with their receptors

tor does not interact directly with the RNA

and with the support of additional proteins

polymerase, but rather—along with other

(known as coactivators and mediators; see

transcription factors—with a coactivator/me-

p. 244). There are several effects of steroid

diator complex that processes all of the sig-

hormones that are not mediated by transcrip-

nals and passes them on to the polymerase. In

tion control. These alternative pathways for

this way, hormonal effects lead within a pe-

steroid effects have not yet been fully ex-

riod of minutes to hours to altered levels of

plained.

mRNAs for key proteins in cellular processes

In the blood, there are a number of trans-

(“cellular response”).

port proteins for lipophilic hormones (see

p. 276). Only the free hormone is able to pen-

B. Steroid receptors

etrate the membrane and enter the cell. The

hormone encounters its receptor in the nu-

The receptors for lipophilic signaling substan-

cleus (and sometimes also in the cytoplasm).

ces all belong to one protein superfamily. They

The receptors for lipophilic hormones are

are constructed in a modular fashion from

rare proteins. They occur in small numbers

domains with various lengths and functions.

(10³-10⁴

molecules per cell) and show

Starting from the N terminal, these are: the

marked specificity and high affinity for the

regulatory domain, the DNA-binding domain, a

hormone (K_d = 10^-8-10^-10 M). After binding

nuclear localization sequence (see p. 228), and

to the hormone, the steroid receptors are able

the hormone-binding domain (see p. 73D).

to bind as homodimers or heterodimers to

The homology among receptors is particu-

control elements in the promoters of specific

larly great in the area of the DNA-binding

genes, from where they can influence the

domain. The proteins have cysteine-rich se-

transcription of the affected genes—i. e., they

quences here that coordinatively bind zinc

act as transcription factors.

ions (A, Cys shown in yellow, Zn²⁺ in light

The illustration shows the particularly

blue). These centers, known as “zinc fingers”

well-investigated mechanism of action for

or “zinc clusters,” stabilize the domains and

cortisol, which is unusual to the extent that

support their dimerization, but do not take

the hormone-receptor complex already

part in DNA binding directly. As in other tran-

arises in the cytoplasm. The free receptor is

scription factors

(see p. 118),

“recognition

present in the cytoplasm as a monomer in

helices” are responsible for that.

complex with the chaperone hsp90

(see

In addition to the receptors mentioned in

p. 232). Binding of cortisol to the complex

A, the family of steroid receptors also includes

leads to an allosteric conformational change

the product of the oncogene erb-A

(see

in the receptor, which is then released from

p. 398), the receptor for the environmental

the hsp90 and becomes capable of DNA bind-

toxin dioxin, and other proteins for which a

ing as a result of dimerization.

distinct hormone ligand has not been identi-

In the nucleus, the hormone-receptor

fied (known as “orphan receptors”). Several

complex binds to nucleotide sequences

steroid receptors—e. g., the retinoic acid re-

known as hormone response elements

ceptor—form functional heterodimers with

(HREs). These are short palindromic DNA seg-

orphan receptors.

ments that usually promote transcription as

enhancer elements (see p. 244). The illustra-

tion shows the HRE for glucocorticoids (GRE;

Lipophilic hormones

379

A. Mechanism of action of lipophilic hormones

Hormone

Target cell

Hormone

receptor

hsp

Heat-shock

protein

Nucleus

Glucocorticoid receptor/DNA complex

DNA-binding

Hormone-receptor

domain (dimer)

bound to DNA

dimer

RNA

polymerase Gene

DNA

mRNA

Steroid

hormone

DNA

T₃, T₄

Calcitriol

Translation

Retinoic acid

Hormone response element (HRE)

Protein

Cell response

B. Receptors of lipophilic hormones

Variable length

Domains

Receptor

A/B

gene

Regulatory

DNA-

Nuclear-

Hormone-

domain

binding

targeting

binding

domain

sequence

domain

Binds ligand

Interaction with other

nuclear components

Domain E

Receptor protein

with a total of

~250 aa

Domain A/B

400 - 1000 aa

100 - 600 aa

Domain C

Binds to DNA

Domain D

~70 aa

380

Hormones

B. Examples of peptide hormones and

Hydrophilic hormones

proteohormones

The hydrophilic hormones are derived from

Numerically the largest group of signaling

amino acids, or are peptides and proteins

substances, these arise by protein biosynthe-

composed of amino acids. Hormones with

sis

(see p. 382). The smallest peptide hor-

endocrine effects are synthesized in glandular

mone, thyroliberin (362 Da), is a tripeptide.

cells and stored there in vesicles until they are

Proteohormones can reach masses of more

released. As they are easily soluble, they do

than 20 kDa—e. g., thyrotropin (28 kDa). Sim-

not need carrier proteins for transport in the

ilarities in the primary structures of many

blood. They bind on the plasma membrane of

peptide hormones and proteohormones

the target cells to receptors that pass the hor-

show that they are related to one another.

monal signal on

(signal transduction; see

They probably arose from common predeces-

p. 384). Several hormones in this group have

sors in the course of evolution.

paracrine effects—i. e., they only act in the

Thyroliberin

(thyrotropin-releasing hor-

immediate vicinity of their site of synthesis

mone, TRH) is one of the neurohormones of

(see p. 372).

the hypothalamus (see p. 330). It stimulates

pituitary gland cells to secrete thyrotropin

A. Signaling substances derived from amino

(TSH). TRH consists of three amino acids,

acids

which are modified in characteristic ways

(see p. 353).

Histamine, serotonin, melatonin, and the cat-

Thyrotropin

(thyroid-stimulating hor-

echolamines dopa, dopamine, norepineph-

mone, TSH) and the related hormones

rine, and epinephrine are known as “biogenic

lutropin

(luteinizing hormone, LH) and

amines.” They are produced from amino acids

follitropin

(follicle-stimulating hormone,

by decarboxylation and usually act not only as

FSH) originate in the adenohypophysis. They

hormones, but also as neurotransmitters.

are all dimeric glycoproteins with masses of

Histamine, an important mediator (local

around 28 kDa. Thyrotropin stimulates the

signaling substance) and neurotransmitter, is

synthesis and secretion of thyroxin by the

mainly stored in tissue mast cells and baso-

thyroid gland.

philic granulocytes in the blood. It is involved

Insulin (for the structure, see p. 70) is pro-

in inflammatory and allergic reactions. “His-

duced and released by the B cells of the pan-

tamine liberators” such as tissue hormones,

creas and is released when the glucose level

type E immunoglobulins (see p. 300), and

rises. Insulin reduces the blood sugar level by

drugs can release it. Histamine acts via vari-

promoting processes that consume glu-

ous types of receptor. Binding to H₁ receptors

cose—e. g., glycolysis, glycogen synthesis,

promotes contraction of smooth muscle in the

and conversion of glucose into fatty acids. By

bronchia, and dilates the capillary vessels and

contrast, it inhibits gluconeogenesis and gly-

increases their permeability. Via H₂ receptors,

cogen degradation. The transmission of the

histamine slows down the heart rate and pro-

insulin signal in the target cells is discussed

motes the formation of HCl in the gastric mu-

in greater detail on p. 388.

cosa. In the brain, histamine acts as a neuro-

Glucagon, a peptide of 29 amino acids, is a

transmitter.

product of the A cells of the pancreas. It is the

Epinephrine is a hormone synthesized in

antagonist of insulin and, like insulin, mainly

the adrenal glands from tyrosine

(see

influences carbohydrate and lipid metabo-

p. 352). Its release is subject to neuronal con-

lism. Its effects are each opposite to those of

trol. This “emergency hormone” mainly acts

insulin. Glucagon mainly acts via the second

on the blood vessels, heart, and metabolism. It

messenger cAMP (see p. 384).

constricts the blood vessels and thereby in-

creases blood pressure (via α₁ and α₂ recep-

tors); it increases cardiac function (via β₂ re-

ceptors); it promotes the degradation of gly-

cogen into glucose in the liver and muscles

(via β₂ receptors); and it dilates the bronchia

(also via β₂ receptors).

Hydrophilic hormones

381

A. Signaling substances derived from amino acids

Hormone

Sites of formation

Sites of action

Actions

Width of bronchi

Histamine

H₃N

CH₂

stores

Capillaries:

CH₂

width

Mast cell

Lungs

permeability

HCl

Gastric acid

secretion

Basophilic

by parietal cells

Histamine

granulocyte

Stomach

Cardiac output

CH₃

H₂N

CH₂

Width of

Adrenal glands

Heart

blood vessels

HO CH

(medulla)

Blood pressure

Metabolism:

Glycogenolysis

Liver

Blood glucose

Adipose

Epinephrine

tissue

Muscle

Lipolysis

B. Examples of peptide hormones and proteohormones

Hypothalamus

Pituitary

Thyrotropin

secretion

Thyroliberin

(TRH)

Neurotransmitter

3 AA

action

Brain

TSH

Thyrotropin

(TSH)

Synthesis and

secretion of thyroxine

α chain 92 AA

Thyroid

β chain 112 AAAdeno-

hypophysis

gland

Thyroxine

Insulin

Glucose

A chain 21 AA

uptake by cells

B chain 30 AA

Blood glucose

B cells

Glycogen

Proteins

Fats

Pancreas

Storage compounds:

formation

Glucose

Amino

Fatty

degradation

acids

Glycogen

Fats

Glycogenolysis

Glucagon

Gluconeogenesis

29 AA

Glucose

Amino

Fatty

Blood glucose

A cells

acids

Pancreas

Ketone body

Ketone

formation

bodies

382

Hormones

arises, which is modified at both ends (see

Metabolism of peptide hormones

p. 246). This mRNA codes for prepro-POMC—

Hydrophilic hormones and other water-solu-

i. e., a POMC protein that still has a signal

ble signaling substances have a variety of bio-

peptide for the ER at the N terminus (see

synthetic pathways. Amino acid derivatives

p. 230).

arise in special metabolic pathways

(see

[2] Prepro-POMC arises through translation

p. 352) or through post-translational modi-

in the rough endoplasmic reticulum (rER).

fication (see p. 374). Proteohormones, like all

The growing peptide chain is introduced

proteins, result from translation in the ribo-

into the ER with the help of a signal peptide.

some (see p. 250). Small peptide hormones

[3] Cleavage of the signal peptide and other

and neuropeptides, most of which only con-

modifications in the ER (formation of disulfide

sist of 3-30 amino acids, are released from

bonds, glycosylation, phosphorylation) give

precursor proteins by proteolytic degradation.

rise to the mature prohormone (“pro-POMC”).

[4] The neuropeptides and hormones men-

tioned are now formed by limited proteolysis

A. Biosynthesis

and stored in vesicles. Release from these

The illustration shows the synthesis and pro-

vesicles takes place by exocytosis when

cessing of the precursor protein proopiome-

needed.

lanocortin (POMC) as an example of the bio-

The biosynthesis of peptide hormones and

synthesis of small peptides with signaling

proteohormones, as well as their secretion, is

functions. POMC arises in cells of the adeno-

controlled by higher-order regulatory sys-

hypophysis, and after processing in the rER

tems (see p. 372). Calcium ions are among

and Golgi apparatus, it supplies the opiate-

the substances involved in this regulation as

like peptides met-enkephalin and E-endor-

second messengers; an increase in calcium

phin

(implying

“opio-”; see p. 352), three

ions stimulates synthesis and secretion.

melanocyte-stimulating hormones (α-, β- and

γ-MSH, implying “melano-”), and the glan-

B. Degradation and inactivation

dotropic hormone corticotropin (ACTH, im-

plying

“-cortin”). Additional products of

Degradation of peptide hormones often starts

POMC degradation include two lipotropins

in the blood plasma or on the vascular walls;

with catabolic effects in the adipose tissue

it is particularly intensive in the kidneys.

(β- and γ-LPH).

Several peptides that contain disulfide

Some of the peptides mentioned are over-

bonds (e. g., insulin) can be inactivated by

lapping in the POMC sequence. For example,

reductive cleavage of the disulfide bonds (1).

additional cleavage of ACTH gives rise to α-

Peptides and proteins are also cleaved by

MSH and corticotropin-like intermediary

peptidases, starting from one end of the pep-

peptide (CLIP). Proteolytic degradation of β-

tide by exopeptidases (2), or in the middle of it

LPH provides γ-LPH and β-endorphin. The

by proteinases (endopeptidases, 3). Proteoly-

latter can be further broken down to yield

sis gives rise to a variety of hormone frag-

met-enkephalin, while γ-LPH can still give

ments, several of which are still biologically

rise to β-MSH (not shown). Due to the numer-

active. Some peptide hormones and proteo-

ous derivative products with biological activ-

hormones are removed from the blood by

ity that it has, POMC is also known as a poly-

binding to their receptors with subsequent

protein. Which end product is formed and in

endocytosis of the hormone-receptor com-

what amounts depends on the activity of the

plex (4). They are then broken down in the

proteinases in the ER that catalyze the indi-

lysosomes. All of the degradation reactions

vidual cleavages.

lead to amino acids, which become available

The principles underlying protein synthe-

to the metabolism again.

sis and protein maturation (see pp. 230-233)

can be summed up once again using the ex-

ample of POMC:

[1] As a result of transcription of the POMC

gene and maturation of the hnRNA, a mature

mRNA consisting of some 1100 nucleotides

Hydrophilic hormones

383

A. Biosynthesis

Chromosome

DNA

Human

chromosome

with

POMC gene

Transcription

87~3 900

151

~2 800

834 Base pairs

Splicing

Intron

Exon

TATA-

Box

~1100 Nucleotides

POMC-

mRNA

meGppp

AAAA---

mRNA

Kappe

Poly(A)

Translation

sequence

Translation

start

stop

γ-MSH

ACTH

β-LPH

Peptides

encoded

50-6

112-150

153-236

POMC gene

α-MSH CLIP

γ-LPH

β-Endorphin

Cleavage of

signal peptide

112-124

129-150

153-207

220-236

β-MSH

Met-Enke-

phalin

190-207

210-214

Signal peptide

for secretion

Prohormone

Pro-ACTH

Limited

proteolysis

ACTH

β-LPH

Protein

modification

Storage

Secretion

ACTH

Hormone

ACTH

(Cortico-

tropin)

β-En-

γ-MSH

α-MSH-CLIP

γ-LPH

dorphin

β-Endorphin

and other

peptides

B. Degradation and inactivation

Extracellular degradation:

Intracellular degradation:

1. Cleavage of

4. Binding to

1. disulfide bonds

4. membrane

1. by reductases

receptors

4. Endocytosis

4. Degradation

2. Degradation by

in lysosomes

2. exopeptidases

3. Degradation by

3. proteinases

Disulfide bond

384

Hormones

B. Signal transduction by G proteins

Mechanisms of action

G proteins transfer signals from 7-helix re-

The messages transmitted by hydrophilic sig-

ceptors to effector proteins (see above). G

naling substances (see p. 380) are sent to the

protein are heterotrimers consisting of three

interior of the cell by membrane receptors.

different types of subunit (α, β, and γ; see

These bind the hormone on the outside of

p. 224). The α-subunit can bind GDP or GTP

the cell and trigger a new second signal on

(hence the name “G protein”) and has GTPase

the inside by altering their conformation. In

activity. Receptor-coupled G proteins are re-

the interior of the cell, this secondary signal

lated to other GTP-binding proteins such as

influences the activity of enzymes or ion

Ras (see pp. 388, 398) and EF-Tu (see p. 252).

channels. Via further steps, switching of the

G proteins are divided into several types,

metabolism, changes in the cytoskeleton, and

depending on their effects. Stimulatory G pro-

activation or inhibition of transcription factors

teins (G_s) are widespread. They activate ad-

can occur (“signal transduction”) can occur.

enylate cyclases (see below) or influence ion

channels. Inhibitory G proteins (G_i) inhibit ad-

A. Mechanisms of action

enylate cyclase. G proteins in the G_q family

activate another effector enzyme—phospholi-

Receptors are classified into three different

pase c (see p. 386).

types according to their structure (see also

Binding of the signaling substance to a 7-

p. 224):

helix receptor alters the receptor conforma-

1. 1-Helix receptors (left) are proteins that

tion in such a way that the corresponding G

span the membrane with only one α-helix. On

protein can attach on the inside of the cell.

their inner (cytoplasmic) side, they have do-

This causes the α-subunit of the G protein to

mains with allosterically activatable enzyme

exchange bound GDP for GTP (1). The G pro-

activity. In most cases, these are tyrosine

tein then separates from the receptor and

kinases.

dissociates into an α-subunit and a βγ-unit.

Insulins (see p. 388), growth factors, and

Both of these components bind to other mem-

cytokines (see p. 392), for example, act via 1-

brane proteins and alter their activity; ion

helix receptors. Binding of the signaling sub-

channels are opened or closed, and enzymes

stance leads to activation of internal kinase

are activated or inactivated.

activity (in some cases, dimerization of the

In the case of the β₂-catecholamine recep-

receptor is needed for this). The activated

tor (illustrated here), the α-subunit of the G_s

kinase phosphorylates itself using ATP (auto-

protein, by binding to adenylate cyclase, leads

phosphorylation), and also phosphorylates ty-

to the synthesis of the second messenger

rosine residues of other proteins (known as

cAMP. cAMP activates protein kinase A, which

receptor substrates). Adaptor proteins that

in turn activates or inhibits other proteins (2;

recognize the phosphotyrosine residues bind

see p. 120).

to the phosphorylated proteins (see pp. 388,

The βγ-unit of the G protein stimulates a

392). They pass the signal on to other protein

kinase (βARK, not shown), which phosphory-

kinases.

lates the receptor. This reduces its af nity for

2. Ion channels (center). These receptors

the hormone and leads to binding of the

contain ligand-gated ion channels. Binding of

blocking protein arrestin. The internal GTPase

the signaling substance opens the channels

activity of the α-subunit hydrolyzes the

for ions such as Na⁺, K⁺, Ca²⁺, and Cl^-. This

bound GTP to GDP within a period of seconds

mechanism is mainly used by neurotrans-

to minutes, and thereby terminates the action

mitters such as acetylcholine (nicotinic recep-

of the G protein on the adenylate cyclase (3).

tor; see p. 224) and GABA (A receptor; see

p. 354).

3. 7-Helix receptors (serpentine receptors,

right) represent a large group of membrane pro-

teins that transfer the hormone or transmitter

signal, with the help of G proteins (see below), to

effector proteins that alter the concentrations

of ions and second messengers (see B).

Hydrophilic hormones

385

A. Mechanisms of action

1. 1-Helix receptor

2. Ion channel

3. 7-Helix

Effector enzyme

receptor

Hydro-

Adenylate cyclase

philic

Pore for

Phospholipase C

signaling

ions

and A2

substance

Guanylate cyclase

Cytoplasm

G protein

7 Trans-

G protein

membrane

Tyrosine

increases

helices

forms

kinase

Ion concentration

Second messenger

Receptor

Ca²

cAMP

Ca2

substrate

cGMP

DAG

u.a.

ATP ADP

InsP₃

Protein kinases (PKs)

Other

phosphorylate

Protein phosphatases

modify

enzymes

Enzymes

PK-A

and many

PK-G

others

PK-C

Transcription factors

modulate

Nucleus

Transcription

Metabolism

Cytoskeleton

B. Signal transduction by G proteins

Signaling

G protein

Active

Inactive

substance

(G_s)

α-unit

GDP

ATP

GTP

GDP

GDP GTP

β, γ-unit

cAMP

Arrestin

Activated 7-helix receptor

Second

messenger

Adenylate cyclase 4.6.1.1

386

Hormones

phosphate (InsP3), which is soluble, and diac-

Second messengers

ylglycerol (DAG). InsP₃ migrates to the endo-

Second messengers are intracellular chemical

plasmic reticulum (ER), where it opens Ca²⁺

signals, the concentration of which is regu-

channels that allow Ca²⁺ to flow into the cy-

lated by hormones, neurotransmitters, and

toplasm (see C). By contrast, DAG, which is

other extracellular signals (see p. 384). They

lipophilic, remains in the membrane, where

arise from easily available substrates and only

it activates type C protein kinases, which

have a short half-life. The most important

phosphorylate proteins in the presence of

second messengers are cAMP, cGMP, Ca²⁺, in-

Ca²⁺ ions and thereby pass the signal on.

ositol triphosphate

(InsP₃), diacylglycerol

(DAG), and nitrogen monoxide (NO).

C. Calcium ions

Calcium level. Ca²⁺ (see p. 342) is a signaling

A. Cyclic AMP

substance. The concentration of Ca²⁺ ions

Metabolism. The nucleotide cAMP (adenosine

in the cytoplasm is normally very low

3 ,5 -cyclic monophosphate) is synthesized

(10-100 nM), as it is kept down by ATP-

by membrane-bound adenylate cyclases [1]

driven Ca²⁺ pumps and Na⁺/Ca²⁺ exchangers.

on the inside of the plasma membrane. The

In addition, many proteins in the cytoplasm

adenylate cyclases are a family of enzymes

and organelles bind calcium and thus act as

that cyclize ATP to cAMP by cleaving diphos-

Ca²⁺ buffers.

phate (PP_i). The degradation of cAMP to AMP

Specific signals (e. g., an action potential or

is catalyzed by phosphodiesterases [2], which

second messenger such as InsP₃ or cAMP) can

are inhibited by methylxanthines such as caf-

trigger a sudden increase in the cytoplasmic

feine, for example. By contrast, insulin acti-

Ca²⁺ level to

500-1000 nM by opening

vates the esterase and thereby reduces the

Ca²⁺ channels in the plasma membrane or in

cAMP level (see p. 388).

the membranes of the endoplasmic or sarco-

Adenylate cyclase activity is regulated by G

plasmic reticulum. Ryanodine, a plant sub-

proteins (G_s and G_i), which in turn are con-

stance, acts in this way on a specific channel

trolled by extracellular signals via 7-helix re-

in the ER. In the cytoplasm, the Ca²⁺ level

ceptors (see p. 384). Ca²⁺-calmodulin (see be-

always only rises very briefly (Ca²⁺ “spikes”),

low) also activates specific adenylate cyclases.

as prolonged high concentrations in the cyto-

Action. cAMP is an allosteric effector of

plasm have cytotoxic effects.

protein kinase A (PK-A, [3]). In the inactive

Calcium effects. The biochemical effects of

state, PK-A is a heterotetramer (C₂R₂), the

Ca²⁺ in the cytoplasm are mediated by special

catalytic subunits of which (C) are blocked

Ca²⁺-binding proteins

(“calcium sensors”).

by regulatory units

(R; autoinhibition).

These include the annexins, calmodulin, and

When cAMP binds to the regulatory units,

troponin C in muscle (see p. 334). Calmodulin

the C units separate from the R units and

is a relatively small protein (17 kDa) that oc-

become enzymatically active. Active PK-A

curs in all animal cells. Binding of four Ca²⁺

phosphorylates serine and threonine residues

ions (light blue) converts it into a regulatory

of more than 100 different proteins, enzymes,

element. Via a dramatic conformational

and transcription factors. In addition to cAMP,

change (cf. 2a and 2b), Ca²⁺-calmodulin enters

cGMP also acts as a second messenger. It is

into interaction with other proteins and mod-

involved in sight (see p. 358) and in the signal

ulates their properties. Using this mechanism,

transduction of NO (see p. 388).

Ca²⁺ ions regulate the activity of enzymes, ion

pumps, and components of the cytoskeleton.

B. Inositol 1,4,5-trisphosphate and

diacylglycerol

Type G_q G proteins activate phospholipase C

[4]. This enzyme creates two second messen-

gers from the double-phosphorylated mem-

brane phospholipid phosphatidylinositol

bisphosphate (PInsP₂), i. e., inositol 1,4,5-tris-

Hydrophilic hormones

387

A. Cyclic AMP

7 Helix receptors

Adenylate cyclase 4.6.1.1

cAMP

Phosphodiesterase 3.1.4.17

CH₂

Protein kinase A 2.7.1.37

H H

G proteins

Caffeine

G_i

O OH

Enzymes

ATP

cAMP

AMP

Transcription

ATP

factors

PP_i

H₂O

Ion channels

Protein kinase A

ADP

B. Inositol 1,4,5-trisphosphate and diacylglycerol

7 Helix

DAG (Diacylglycerol)

receptors

Phospholipid

Protein

kinase C

G protein (G_q)

Acyl residue 1

H₂O

Acyl residue 2

Intracellular

Inositol

Ca²

P P

release

PlnsP₂

Phospholipase C 3.1.4.3

InsP₃

C. Calcium ions

Ca2

ATP

ER/SR

Ca2

10-100 nM

ADP

P_i

Ca2

InsP₃

Ryanodine

Ca2

Calcium-

cAMP

500-1000 nM

binding

protein

Depolarization

Glutamate

Ca2

1. Calcium transport

ATP

2. Calmodulin

ca. 2 500 000 nM

388

Hormones

pids from the phosphatidylinositol group (see

Signal cascades

p. 50) at position

3. Protein kinase PDK-1

The signal transduction pathways that medi-

binds to these reaction products, becoming

ate the effects of the metabolic hormone in-

activated itself and in turn activating protein

sulin are of particular medical interest (see A).

kinase B (PK-B).

The mediator nitrogen monoxide (NO) is also

This has several effects. In a manner not yet

clinically important, as it regulates vascular

fully understood, PK-B leads to the fusion

caliber and thus the body’s perfusion with

with the plasma membrane of vesicles that

blood (see B).

contain the glucose transporter Glut-4. This

results in inclusion of Glut-4 in the membrane

and thus to increased glucose uptake into the

A. Insulin: signal transduction

muscles and adipose tissue (see p. 160). In

The diverse effects of insulin (see p. 160) are

addition, PK-B inhibits glycogen synthase kin-

mediated by protein kinases that mutually

ase 3 (GSK-3) by phosphorylation. As GSK-3 in

activate each other in the form of enzyme

turn inhibits glycogen synthase by phosphor-

cascades. At the end of this chain there are

ylation

(see p. 120), its inhibition by PK-B

kinases that influence gene transcription in

leads to increased glycogen synthesis. Protein

the nucleus by phosphorylating target pro-

phosphatase-1 (PP-1) converts glycogen syn-

teins, or promote the uptake of glucose and

thase into its active form by dephosphoryla-

its conversion into glycogen. The signal trans-

tion (see p. 120). PP-1 is also activated by

duction pathways involved have not yet been

insulin.

fully explained. They are presented here in a

simplified form.

B. Nitrogen monoxide (NO) as a mediator

The insulin receptor (top) is a dimer with

subunits that have activatable tyrosine kinase

Nitrogen monoxide (NO) is a short-lived rad-

domains in the interior of the cell (see p. 224).

ical that functions as a locally acting mediator

Binding of the hormone increases the tyrosine

(see p. 370).

kinase activity of the receptor, which then

In a complex reaction, NO arises from argi-

phosphorylates itself and other proteins

nine in the endothelial cells of the blood ves-

(receptor substrates) at various tyrosine re-

sels [1]. The trigger for this is Ca²⁺-calmodulin

sidues. Adaptor proteins, which conduct the

(see p. 386), which forms when there is an

signal further, bind to the phosphotyrosine

increase in the cytoplasmic Ca²⁺ level.

residues.

NO diffuses from the endothelium into the

The effects of insulin on transcription are

underlying vascular muscle cells, where it

shown on the left of the illustration. Adaptor

leads, as a result of activation of guanylate

proteins Grb-2 and SOS (“son of sevenless”)

cyclase [2], to the formation of the second

bind to the phosphorylated IRS (insulin-re-

messenger cGMP (see pp. 358, 384). Finally,

ceptor substrate) and activate the G protein

by activating a special protein kinase (PK-G),

Ras (named after its gene, the oncogene ras;

cGMP triggers relaxation of the smooth

see p. 398). Ras activates the protein kinase

muscle and thus dilation of the vessels. The

Raf (another oncogene product). Raf sets in

effects of atrionatriuretic peptide (ANP; see

motion a phosphorylation cascade that leads

p. 328) in reducing blood pressure are also

via the kinases MEK and ERK (also known as

mediated by cGMP-induced vasodilation. In

MAPK, “mitogen-activated protein kinase”) to

this case, cGMP is formed by the guanylate

the phosphorylation of transcription factors

cyclase activity of the ANP receptor.

in the nucleus.

Some of the effects of insulin on the carbo-

Further information

hydrate metabolism (right part of the illustra-

tion) are possible without protein synthesis.

The drug nitroglycerin

(glyceryl trinitrate),

In addition to Grb-2, another dimeric adaptor

which is used in the treatment of angina

protein can also bind to phosphorylated IRS.

pectoris, releases NO in the bloodstream and

This adaptor protein thereby acquires phos-

thereby leads to better perfusion of cardiac

phatidylinositol-3-kinase activity (PI₃K) and,

muscle.

in the membrane, phosphorylates phospholi-

Hydrophilic hormones

389

A. Insulin: signal transduction

Insulin

Phosphatidyl-

Glucose

receptor

inositols

Phosphatidyl-

inositol

3-phosphate

PI-3-

Kinase

SOS

Ras

Glut-4

Grb-2

IRS-1

PDK-1

Glucose

uptake

Raf

MEK

PK-B

(MAPKK)

Glut-4

PP-1

MAPK

(ERK)

GSK-3

Intracellular

Transcription

vesicle

factors

Glycogen synthase

Glycogen

(active)

synthesis

Activated

transcription

DNA

factors

Protein kinase

Inactive

Nucleus

Protein phosphatase

Active

Promoter

Transcription

B. Nitrogen monoxide (NO) as a mediator

Ca2

Physiological effects

PK-G

Signaling

substance

Guanine

ANP

²O

InsP₃

P P

H H

Arginine

GTP

2 O₂

O OH

cGMP

Ca2

3/2

Ca2

3/2

Calmodulin

2 H₂O

Citrulline

NO·

P P P

GTP

Endothelial cell

Vascular muscle cell

NO synthase 1.14.13.39

Guanylate cyclase 4.6.1.2

ANF receptor 4.6.1.2

390

Hormones

The eicosanoids have a very wide range of

Eicosanoids

physiological effects. As they can stimulate or

The eicosanoids are a group of signaling sub-

inhibit smooth-muscle contraction, depend-

stances that arise from the C-20 fatty acid

ing on the substance concerned, they affect

arachidonic acid and therefore usually contain

blood pressure, respiration, and intestinal and

20 C atoms (Greek eicosa = 20). As mediators,

uterine activity, among other properties. In

they influence a large number of physiological

the stomach, prostaglandins inhibit HCl se-

processes (see below). Eicosanoid metabolism

cretion via G_i proteins (see p. 270). At the

is therefore an important drug target. As

same time, they promote mucus secretion,

short-lived substances, eicosanoids only act

which protects the gastric mucosa against

in the vicinity of their site of synthesis (para-

the acid. In addition, prostaglandins are in-

crine effect; see p. 372).

volved in bone metabolism and in the activity

of the sympathetic nervous system. In the

immune system, prostaglandins are impor-

A. Eicosanoids

tant in the inflammatory reaction. Among

Biosynthesis. Almost all of the body’s cells

other things, they attract leukocytes to the

form eicosanoids. Membrane phospholipids

site of infection. Eicosanoids are also deci-

that contain the polyunsaturated fatty acid

sively involved in the development of pain

arachidonic acid (20:4; see p. 48) provide the

and fever. The thromboxanes promote throm-

starting material.

bocyte aggregation and other processes in-

Initially, phospholipase A₂ [1] releases the

volved in hemostasis (see p. 290).

arachidonate moiety from these phospholi-

Metabolism. Eicosanoids are inactivated

pids. The activity of phospholipase A₂ is strictly

within a period of seconds to minutes. This

regulated. It is activated by hormones and

takes place by enzymatic reduction of double

other signals via G proteins. The arachidonate

bonds and dehydrogenation of hydroxyl

released is a signaling substance itself. How-

groups. As a result of this rapid degradation,

ever, its metabolites are even more important.

their range is very limited.

Two different pathways lead from arachi-

donate to prostaglandins, prostacyclins, and

Further information

thromboxanes, on the one hand, or leuko-

trienes on the other. The key enzyme for the

Acetylsalicylic acid and related non-steroidal

first pathway is prostaglandin synthase [2].

anti-inflammatory drugs (NSAIDs) selectively

Using up O₂, it catalyzes in a two-step reac-

inhibit the cyclooxygenase activity of prosta-

tion the cyclization of arachidonate to prosta-

glandin synthase [2] and consequently the

glandin H₂, the parent substance for the pros-

synthesis of most eicosanoids. This explains

taglandins, prostacyclins, and thromboxanes.

their analgesic, antipyretic, and antirheumatic

Acetylsalicylic acid (aspirin) irreversibly ace-

effects. Frequent side effects of NSAIDs also

tylates a serine residue near the active center

result from inhibition of eicosanoid synthesis.

of prostaglandin synthase, so that access for

For example, they impair hemostasis because

substrates is blocked (see below).

the synthesis of thromboxanes by thrombo-

As a result of the action of lipoxygenases [3],

cytes is inhibited. In the stomach, NSAIDs in-

hydroxyfatty acids and hydroperoxyfatty acids

crease HCl secretion and at the same time

are formed from arachidonate, from which

inhibit the formation of protective mucus.

elimination of water and various conversion

Long-term NSAID use can therefore damage

reactions give rise to the leukotrienes. The for-

the gastric mucosa.

mulae only show one representative from each

of the various groups of eicosanoids.

Effects. Eicosanoids act via membrane re-

ceptors in the immediate vicinity of their site

of synthesis, both on the synthesizing cell

itself (autocrine action) and on neighboring

cells (paracrine action). Many of their effects

are mediated by the second messengers cAMP

and cGMP.

Other signaling substances

391

A. Eicosanoids

Essential

Phospholipid

fatty acids:

Linoleic acid

Hormones and

Inclusion in

other signals

Linolenic acid

Lysophospholipid

Arachidonic acid

COO

Prostaglandin

Peroxidase

Arachidonate

CH₃

synthase

center

Heme

Prosta-

Lipoxygenase

glandin

Cyclooxy-

Ser

synthase

genase

Acetylsalicylic

channel

acid

Hydroxy- and

Hydroperoxy fatty acids

Arachidonate

Prostaglandin H₂

Leukotrienes

S Cys

Gly

COO

CH₃

H OH

Prostaglandin H₂

Leukotriene D₄

Prostacyclins

Prostaglandins

Thromboxanes

COO

CH₃

HO O

H OH

Prostacyclin I₂

Prostaglandin F2α

Thromboxane B₂

Effects: Stimulation of

Hormone-controlled lipases

Contraction of smooth muscle

Thrombocyte aggregation

Biosynthesis of steroid hormones

Pain production

Gastric juice secretion

Inflammatory response

Prostaglandin H-synthase [heme]

Phospholipase A₂ 3.1.1.4

(dioxygenase + peroxidase) 1.14.99.1

Arachidonate lipoxygenases 1.13.11. n

392

Hormones

STPs (2). Class I cytokine receptors interact

Cytokines

with three different STPs (gp130, β_c, and γ_c).

The STPs themselves do not bind cytokines,

A. Cytokines

but conduct the signal to tyrosine kinases (3).

Cytokines are hormone-like peptides and pro-

The fact that different cytokines can activate

teins with signaling functions, which are syn-

the same STP via their receptors explains the

thesized and released by cells of the immune

overlapping biological activity of some cyto-

system and other cell types. Their numerous

kines.

biological functions operate in three areas:

As an example of the signal transduction

they regulate the development and homeosta-

pathway in cytokines, the illustration shows

sis of the immune system; they control the

the way in which the IL-6 receptor, after bind-

hematopoietic system; and they are involved

ing its ligand IL-6 (1), induces the dimeriza-

in non-specific defense, influencing inflamma-

tion of the STP gp130 (2). The dimeric gp130

tory processes, blood coagulation, and blood

binds cytoplasmic tyrosine kinases from the

pressure. In general, cytokines regulate the

Jak family (“Janus kinases,” with two kinase

growth, differentiation, and survival of cells.

centers) and activates them (3). The Janus

They are also involved in regulating apoptosis

kinases phosphorylate cytokine receptors,

(see p. 396).

STPs, and various cytoplasmic proteins that

There is an extremely large number of cy-

conduct the signal further. In addition, they

tokines; only the most important representa-

phosphorylate transcription factors known as

tives are listed opposite. The cytokines

STATs (“signal transducers and activators of

include interleukins (IL), lymphokines, mono-

transcription”). STATs are among the proteins

kines, chemokines, interferons (IFN), and col-

that have an SH2 domain and are able to bind

ony-stimulating factors (CSF). Via interleukins,

phosphotyrosine residues (see p. 388). They

immune cells stimulate the proliferation and

therefore bind to cytokine receptors that have

activity of other immune cells (see p. 294).

been phosphorylated by Janus kinases. When

Interferons are used medically in the treat-

STATs are then also phosphorylated them-

ment of viral infections and other diseases.

selves (4), they are converted into their active

Although cytokines rarely show structural

form and become dimers (5). After transfer to

homologies with each other, their effects are

the nucleus, they bind—along with auxiliary

often very similar. The cytokines differ from

proteins as transcription factors—to the pro-

hormones (see p. 370) only in certain re-

moters of inducible genes and in this way

spects: they are released by many different

regulate their transcription (6).

cells, rather than being secreted by defined

The activity of the cytokine receptors is

glands, and they regulate a wider variety of

terminated by protein phosphatases, which

target cells than the hormones.

hydrolytically cleave the phosphotyrosine

residues. Several cytokine receptors are able

to lose their ligand-binding extracellular do-

B. Signal transduction in the cytokines

main by proteolysis (not shown). The extra-

As peptides or proteins, the cytokines are hy-

cellular domain then appears in the blood,

drophilic signaling substances that act by

where it competes for cytokines. This reduces

binding to receptors on the cell surface (see

the effective cytokine concentration.

p. 380). Binding of a cytokine to its receptor

(1) leads via several intermediate steps (2 -5)

to the activation of transcription of specific

genes (6).

In contrast to the receptors for insulin and

growth factors (see p. 388), the cytokine re-

ceptors (with a few exceptions) have no ty-

rosine kinase activity. After binding of cyto-

kine (1), they associate with one another to

form homodimers, join together with other

signal transduction proteins (STPs) to form

dimers, or promote dimerization of other

Other signaling substances

393

A. Cytokines

IL-1

Interleukin 1

G-CSF

Granulocyte colony-stimulating factor

IL-2

Interleukin 2

GM-CSF

Granulocyte/macrophage colony-stimulating

IL-3

Interleukin 3

factor

IL-4

Interleukin 4

MIF

Macrophage migration inhibitory factor

IL-5

Interleukin 5

M-CSF

Monocyte colony-stimulating factor

IL-6

Interleukin 6

TNFα

Tumor necrosis factor- α

IFN-α

Interferon α

TNFβ

Tumor necrosis factor- β

IFN-β

Interferon β

IFN-γ

Interferon γ

and others

Immune system

Hematopoietic system

Cytokine

Nonspecific defense

Secretion by

Signal peptide

Effects on many

individual cells

or signal protein

cell types

B. Signal transduction in the cytokines

gp 130

Phosphorylation of STAT

ATP

ADP

Janus

kinase

STAT

ADP

IL-6

gp 130

Dimerization of STAT

STAT

SH2 domain

can bind

Tyr

phospho-

tyrosine

Janus kinase

residues

IL-6

Phosphorylation

Dimerization

receptor

STAT

STAT dimer

Phospho-

STAT

tyrosine

dimer

residue

Nucleus

Transcriptional control

394

Growth and development

The above outline of cell cycle progression

Cell cycle

can be examined here in more detail using the

G₂-M transition as an example.

A. Cell cycle

Entry of animal cells into mitosis is based

Proliferating cells undergo a cycle of division

on the “mitosis-promoting factor” (MPF). MPF

(the cell cycle), which lasts approximately

consists of CDK1 (cdc2) and cyclin B. The in-

24 hours in mammalian cells in cell culture.

tracellular concentration of cyclin B increases

The cycle is divided into four different phases

constantly until mitosis starts, and then de-

(G₁, S, G₂, and M—in that sequence).

clines again rapidly (top left). MPF is initially

Fully differentiated animal cells only divide

inactive, because CDK1 is phosphorylated and

rarely. These cells are in the so-called G₀

cyclin B is dephosphorylated (top center). The

phase, in which they can remain permanently.

M phase is triggered when a protein phos-

Some G₀ cells return to the G₁ phase again

phatase [1] dephosphorylates the CDK while

under the influence of mitogenic signals

cyclin B is phosphorylated by a kinase [2]. In

(growth factors, cytokines, tumor viruses,

its active form, MPF phosphorylates various

etc.), and after crossing a control point (G₁ to

proteins that have functions in mitosis—e. g.,

S), enter a new cycle. DNA is replicated (see

histone H1 (see p. 238), components of the

p. 240) during the S phase, and new chroma-

cytoskeleton such as the laminins in the nu-

tin is formed. Particularly remarkable in mor-

clear membrane, transcription factors, mitotic

phological terms is the actual mitosis

spindle proteins, and various enzymes.

phase), in which the chromosomes separate

When mitosis has been completed, cyclin B

and two daughter cells are formed. The M and

is marked with ubiquitin and broken down

S phases are separated by two segments

proteolytically by proteasomes (see p. 176).

known as the G₁ and G₂ phases (the G stands

Protein phosphatases then regain control

for “gap”). In the G₁ phase, the duration of

and dephosphorylate the proteins involved

which can vary, the cell grows by de novo

in mitosis. This returns the cell to the inter-

synthesis of cell components. Together, the

phase.

G₁, G₀, S, and G₂ phases are referred to as

the interphase, which alternates in the cell

Further information

cycle with the short M phase.

The G₁-S transition (not shown) is particu-

larly important for initiating the cell cycle. It

B. Control of the cell cycle

is triggered by the CDK4-cyclin D complex,

The progression of the cell cycle is regulated

which by phosphorylating the protein pRb

by interconversion processes. In each phase,

releases the transcription factor E2F previ-

special Ser/Thr-specific protein kinases are

ously bound to pRb. This activates the tran-

formed, which are known as cyclin-depen-

scription of genes needed for DNA replication.

dent kinases (CDKs). This term is used be-

If the DNA is damaged by mutagens or ion-

cause they have to bind an activator protein

izing radiation, the protein p53 initially delays

(cyclin) in order to become active. At each

entry into the S phase. If the DNA repair sys-

control point in the cycle, specific CDKs asso-

tem (see p. 256) does not succeed in remov-

ciate with equally phase-specific cyclins. If

ing the DNA damage, p53 forces the cell into

there are no problems (e. g., DNA damage),

apoptosis (see p. 396). The genes coding for

the CDK-cyclin complex is activated by phos-

pRb and p53 belong to the tumor-suppressor

phorylation and/or dephosphorylation. The

genes

(see p. 398). In many tumors

(see

activated complex in turn phosphorylates

p. 400), these genes are in fact damaged by

transcription factors, which finally lead to

mutation.

the formation of the proteins that are re-

quired in the cell cycle phase concerned (en-

zymes, cytoskeleton components, other CDKs,

and cyclins). The activity of the CDK-cyclin

complex is then terminated again by pro-

teolytic cyclin degradation.

Cell proliferation

395

A. Cell cycle

M phase

G₁ phase

0 h

Mitosis

RNA and protein

Chromosome

synthesis

separation

Cell growth

Cell division

G₂ phase

G₀ phase

Preparation

for mitosis

12h

4 h

No cell

division

S phase

DNA replication

Restriction

Histone synthesis

point

Centrosome formed

Chromosome

8 h

duplication

B. Control of the cell cycle

Reactions early

Cyclin B concentration

M = Mitosis

in mitosis

Reactions late

in mitosis

Time

Cyclin-dependent

Cyclin B

protein kinase (CDK1)

Cyclin-

dependent

Catalytic

Regulatory

subunit

protein

subunit

kinases

Cyclin

CDK 1 - 6

P P

fragments

Inactive

protein

Cyclin

kinase

Proteolysis

Cyclins A - E

P P P

P P

Interphase

Mitosis

MPF

Active protein kinase

Protein

Histone H1

Spindle formation

Laminin

Chromosome

Protein kinases

condensation

Transcription

Disappearance of

factors

Phosphoprotein

nuclear membrane

phosphatase

Transcription stop

Other proteins

Cyclin degradation

Protein kinase

396

Growth and development

p. 290). Other enzymes in this group, known

Apoptosis

as effector caspases, cleave cell components

after being activated—e. g., laminin in the nu-

A. Cell proliferation and apoptosis

clear membrane and snRP proteins

(see

The number of cells in any tissue is mainly

p. 246)—or activate special DNases which

regulated by two processes—cell proliferation

then fragment the nuclear DNA.

and physiological cell death, apoptosis. Both of

An important trigger for apoptosis is

these processes are regulated by stimulatory

known as the Fas system. This is used by

and inhibitory factors that act in solute form

cytotoxic T cells, for example, which eliminate

(growth factors and cytokines) or are pre-

infected cells in this way (top left). Most of the

sented in bound form on the surface of neigh-

body’s cells have Fas receptors (CD 95) on

boring cells (see below).

their plasma membrane. If a T cell is activated

Apoptosis is genetically programmed cell

by contact with an MHC presenting a viral

death, which leads to “tidy” breakdown and

peptide

(see p. 296), binding of its Fas

disposal of cells. Morphologically, apoptosis is

ligands occurs on the target cell’s Fas recep-

characterized by changes in the cell mem-

tors. Via the mediator protein FADD (“Fas-

brane (with the formation of small blebs

associated death domain”), this activates cas-

known as “apoptotic bodies”), shrinking of

pase-8 inside the cell, setting in motion the

the nucleus, chromatin condensation, and

apoptotic process.

fragmentation of DNA. Macrophages and

Another trigger is provided by tumor ne-

other phagocytic cells recognize apoptotic

crosis factor-D (TNF-α), which acts via a sim-

cells and remove them by phagocytosis with-

ilar protein (TRADD) and supports the endog-

out inflammatory phenomena developing.

enous defense system against tumors by in-

Cell necrosis (not shown) should be distin-

ducing apoptosis.

guished from apoptosis. In cell necrosis, cell

Caspase-8 activates the effector caspases

death is usually due to physical or chemical

either directly, or indirectly by promoting

damage. Necrosis leads to swelling and burst-

the cytochrome c (see p. 140) from mitochon-

ing of the damaged cells and often triggers an

dria. Once in the cytoplasm, cytochrome c

inflammatory response.

binds to and activates the protein Apaf-1

The growth of tissue (or, more precisely,

(not shown) and thus triggers the caspase

the number of cells) is actually regulated by

cascade. Apoptotic signals can also come

apoptosis. In addition, apoptosis allows the

from the cell nucleus. If irreparable DNA dam-

elimination of unwanted or superfluous

age is present, the p53

protein

(see

cells—e. g., during embryonic development

p. 394)—the product of a tumor suppressor

or in the immune system. The contraction of

gene—promotes apoptosis and thus helps

the uterus after birth is also based on apop-

eliminate the defective cell.

tosis. Diseased cells are also eliminated by

There are also inhibitory factors that op-

apoptosis—e. g., tumor cells, virus-infected

pose the signals that activate apoptosis. These

cells, and cells with irreparably damaged

include bcl-2 and related proteins. The ge-

DNA. An everyday example of this is the peel-

nomes of several viruses include genes for

ing of the skin after sunburn.

this type of protein. The genes are expressed

by the host cell and (to the benefit of the

virus) prevent the host cell from being pre-

B. Regulation of apoptosis

maturely eliminated by apoptosis.

Apoptosis can be triggered by a number of

different signals that use various transmission

pathways. Other signaling pathways prevent

apoptosis.

At the center of the apoptotic process lies a

group of specialized cysteine-containing as-

partate proteinases (see p. 176), known as cas-

pases. These mutually activate one another,

creating an enzyme cascade resembling the

cascade involved in blood coagulation (see

398

Growth and development

usually indicate the origin of the viral gene

Oncogenes

and are printed in italics (e. g., myc for mye-

Oncogenes are cellular genes that can trigger

locytomatosis, a viral disease in birds). Onco-

uncontrolled cell proliferation if their se-

gene products can be classified into the fol-

quence is altered or their expression is incor-

lowing groups according to their functions.

rectly regulated. They were first discovered as

1. Ligands such as growth factors and

viral (v-) oncogenes in retroviruses that cause

cytokines, which promote cell proliferation.

tumors (tumor viruses). Viruses of this type

2. Membrane receptors of the 1-helix type

(see p. 404) sometimes incorporate genes

with tyrosine kinase activity, which can

from the host cell into their own genome. If

bind growth factors and hormones (see

these genes are reincorporated into the host

p. 394).

DNA again during later infection, tumors can

3. GTP-binding proteins. This group includes

then be caused in rare cases. Although virus-

the G proteins in the strict sense and re-

related tumors are rare, research into them

lated proteins such as Ras (see p. 388), the

has made a decisive contribution to our

product of the oncogene c-ras.

understanding of oncogenes and their func-

4. Receptors for lipophilic hormones mediate

tioning.

the effects of steroid hormones and related

signaling substances. They regulate the

A. Proto-oncogenes: biological role

transcription of specific genes

(see

p. 378). The products of several oncogenes

The cellular form of oncogenes (known as c-

(e. g., erbA) belong to this superfamily of

oncogenes or proto-oncogenes) code for pro-

ligand-controlled transcription factors.

teins involved in controlling growth and dif-

5. Nuclear tumor suppressors inhibit return

ferentiation processes. They only become on-

to the cell cycle in fully differentiated cells.

cogenes if their sequence has been altered by

The genes that code for these proteins are

mutations (see p. 256), deletions, and other

referred to as anti-oncogenes due to this

processes, or when excessive amounts of the

function. On the role of p53 and pRb, see

gene products have been produced as a result

p.394.

of overexpression.

6. DNA-binding proteins. A whole series of

Overexpression can occur when amplifica-

oncogenes code for transcription factors.

tion leads to numerous functional copies of

Particularly important for cell proliferation

the respective gene, or when the gene falls

are myc, as well as fos and jun. The protein

under the influence of a highly active pro-

products of the latter two genes form the

moter (see p. 244). If the control of oncogene

transcription factor AP-1 as a heterodimer

expression by tumor suppressor genes (see

(see p. 244).

p. 394) is also disturbed, transformation and

Protein kinases play a central role in intra-

unregulated proliferation of the cells can oc-

cellular signal transduction. By phosphor-

cur. A single activated oncogene does not

ylating proteins, they bring about altera-

usually lead to a loss of growth control. It

tions in biological activity that can only

only occurs when over the course of time

be reversed again by the effects of protein

mutations and regulation defects accumulate

phosphatases. The interplay between pro-

in one and the same cell. If the immune sys-

tein phosphorylation by protein kinases

tem does not succeed in eliminating the

and dephosphorylation by protein phos-

transformed cell, it can over the course of

phatases (interconversion) serves to regu-

months or years grow into a macroscopically

late the cell cycle (see p. 394) and other

visible tumor.

important processes. The protein kinase

Raf is also involved in the signal transduc-

B. Oncogene products:

tion of insulin (see p. 388).

biochemical functions

A feature common to all oncogenes is the fact

that they code for proteins involved in signal

transduction processes. The genes are desig-

nated using three-letter abbreviations that

Cell proliferation

399

A. Proto-oncogenes: biological role

Transformation

Tumor

Altered

formation

Defective

proteins

control

Tumor virus

Altered

control

protein

Oncogene

Defective

suppressor gene

Reverse

transcription

Mutation, deletion,

Tumor

incorporation

amplification,

initiation

altered control

v-Oncogene

Tumor

Proto-oncogene

suppressor

gene

Control protein

e.g., p53 protein

Normal

Rb protein

development

growth and

differentiation

B. Oncogene products: biochemical functions

Oncogene products

(examples)

Effector

Receptor

enzyme

Gene

Ligands

GTP

G protein

sis, hst, int-2, wnt-1

Second

messenger

Receptors

Voltage-

fms, trk, trkB, ros, kit,

Other

Protein

mas, neu, erbB

gated

effects

kinase

ion channel

Ca2

GTP-binding proteins

Ha-ras, Ki-ras, N-ras

Nuclear hormone

receptors

Calmodulin

erbA, NGF1-B

Phospho-

Protein

rylated

Ligand-

Transcription

phospha-

protein

Nuclear tumor

gated

factor

tase

ion channel

suppressors

Rb, p53, wt1, DCC, APC

DNA-binding proteins

jun, fos, myc, N-myc,

Intra-

Hormone

GTP

myb, fra1, egr-1, rel

receptor

cellular

Transcription

G protein

Protein kinases

src, yes, fps, abl, met,

mos, raf

400

Growth and development

tumor cells (group 1) or are induced by them

Tumors

in other cells

(group

2). Group

1 tumor

markers include tumor-associated antigens,

A. Division behavior of cells

secreted hormones, and enzymes. The table

The body’s cells are normally subject to strict

lists a few examples.

“social” control. They only divide until they

The transition from a normal to a trans-

come into contact with neighboring cells; cell

formed state is a process involving several

division then ceases due to contact inhibition.

steps.

Exceptions to this rule include embryonic

1. Tumor initiation. Almost every tumor be-

cells, cells of the intestinal epithelium (where

gins with damage to the DNA of an individual

the cells are constantly being replaced), cells

cell. The genetic defect is almost always caused

in the bone marrow (where formation of

by environmental factors. These can include

blood cells takes place), and tumor cells. Un-

tumor-inducing chemicals (carcinogens—e. g.,

controlled cell proliferation is an important

components of tar from tobacco), physical

indicator of the presence of a tumor. While

processes (e. g., UV light, X-ray radiation; see

normal cells in cell culture only divide 20-60

p. 256), or in rare cases tumor viruses (see

times, tumor cells are potentially immortal

p. 398). Most of the approximately 10¹⁴ cells

and are not subject to contact inhibition.

in the human body probably suffer this type

In medicine, a distinction is made between

of DNA damage during the average lifespan,

benign and malignant tumors. Benign tumors

but it is usually repaired again (see p. 256). It

consist of slowly growing, largely differenti-

is mainly defects in proto-oncogenes

(see

ated cells. By contrast, malignant tumors

p. 398) that are relevant to tumor initiation;

show rapid, invasive growth and tend to

these are the decisive cause of transformation.

form metastases (dissemination of daughter

Loss of an anti-oncogene (a tumor-suppressor

lesions). The approximately

100

different

gene) can also contribute to tumor initiation.

types of tumor that exist are responsible for

2. Tumor promotion is preferential prolif-

more than 20% of deaths in Europe and North

eration of a cell damaged by transformation. It

America.

is a very slow process that can take many

years. Certain substances are able to strongly

accelerate it—e. g., phorbol esters. These occur

B. Transformation

in plants (e. g., Euphorbia species) and act as

The transition of a normal cell into a tumor

activators of protein kinase C (see p. 386).

cell is referred to as transformation.

3. Tumor progression finally leads to a

Normal cells have all the characteristics of

macroscopically visible tumor as a result of

fully differentiated cells specialized for a par-

growth. When solid tumors of this type ex-

ticular function. Their division is inhibited

ceed a certain size, they form their own vas-

and they are usually in the G₀ phase of the

cular network that supplies them with blood

cell cycle (see p. 394). Their external shape is

(angiogenesis). Collagenases (matrix metallo-

variable and is determined by a strongly

proteinases, MMPs) play a special role in the

structured cytoskeleton.

metastatic process, by loosening surrounding

In contrast, tumor cells divide without in-

connective tissue and thereby allowing tumor

hibition and are often de-differentiated—i. e.,

cells to disseminate and enter the blood-

they have acquired some of the properties of

stream. New approaches to combating tumors

embryonic cells. The surface of these cells is

have been aimed at influencing tumor angio-

altered, and this is particularly evident in a

genesis and metastatic processes.

disturbance of contact inhibition by neighbor-

ing cells. The cytoskeleton of tumor cells is

also restructured and often reduced, giving

them a rounded shape. The nuclei of tumor

cells can be atypical in terms of shape, num-

ber, and size.

Tumor markers are clinically important for

detecting certain tumors. These are proteins

that are formed with increasing frequency by

Cell proliferation

401

A. Division behavior of cells

Growth inhibition

Uncontrolled

due to contacts

cell proliferation

with adjacent cells

Nutrient

medium

Normal cells

Tumor cells

B. Transformation

Normal cell

Indicators:

Differentiated

Tumor initiators

Non-dividing

H₃C

Defined form

Viruses

Carcinogenic

chemicals

Tumor initiation:

Genetic damage

Physical processes

Tumor promoters

Tumor progression:

H₃C

CH₃

Preferential propagation

e.g. Esters

CH₃

of phorbol

H₃C

Indicators:

O HO

Hormones

CH₂OH

De-differentiated

Phorbol

Tumor cell

Uncontrolled cell division

Altered cell surface

Altered cytoskeleton

Tumor markers (examples)

and nucleus

Tumor-associated antigens

CEA

Carcinoembryonic

antigen

Tumor progression:

Acquisition of malignancy

AFP

α1-Fetoprotein

Hormones Calcitonin

ACTH

Enzymes Acid phosphatase

402

Growth and development

The cytostatic drugs administered (indi-

Cytostatic drugs

cated by a syringe in the illustration) are often

Tumors (see p. 400) arise from degenerated

not active themselves but are only converted

(transformed) cells that grow in an uncon-

into the actual active agent in the metabolism.

trolled way as a result of genetic defects.

This also applies to the adenine analogue 6-

Most transformed cells are recognized by

mercaptopurine, which is initially converted

the immune system and eliminated

(see

to the mononucleotide tIMP

(thioinosine

p. 294). If endogenous defense is not suf -

monophosphate). Via several intermediate

ciently effective, rapid tumor growth can oc-

steps, tIMP gives rise to tdGTP, which is in-

cur. Attempts are then made to inhibit growth

corporated into the DNA and leads to cross-

by physical or chemical treatment.

links and other anomalies in it. The second

A frequently used procedure is targeted

effective metabolite of 6-mercaptopurine is

irradiation with γ-rays, which block cell re-

S-methylated tIMP, an inhibitor of amidophos-

production due their mutagenic effect (see

phoribosyl transferase (see p. 188).

p. 256). Another approach is to inhibit cell

Hydroxyurea selectively inhibits ribonu-

growth by chemotherapy. The growth-inhib-

cleotide reductase (see p. 190). As a radical

iting substances used are known as cytostatic

scavenger, it removes the tyrosine radicals

drugs. Unfortunately, neither radiotherapy

that are indispensable for the functioning of

nor chemotherapy act selectively—i. e., they

the reductase.

damage normal cells as well, and are there-

Two other important cytostatic agents tar-

fore often associated with severe side effects.

get the synthesis of DNA-typical thymine,

Most cytostatic agents directly or indirectly

which takes place at the level of the deoxy-

inhibit DNA replication in the S phase of the

mononucleotide (see p. 190). The deoxymo-

cell cycle (see p. 394). The first group (A) lead

nonucleotide formed by 5-fluorouracil or the

to chemical changes in cellular DNA that im-

corresponding nucleoside inhibits thymidy-

pede transcription and replication. A second

late synthase. This inhibition is based on the

group of cytostatic agents (B) inhibit the syn-

fact that the fluorine atom in the pyrimidine

thesis of DNA precursors.

ring cannot be substituted by a methyl group.

In addition, the fluorine analogue is also in-

corporated into the DNA.

A. Alkylating agents, anthracyclines

Dihydrofolate reductase acts as an auxiliary

Alkylating agents are compounds capable of

enzyme for thymidylate synthase. It is in-

reacting covalently with DNA bases. If a com-

volved in the regeneration of the coenzyme

pound of this type contains two reactive

N⁵,N¹⁰-methylene-THF, initially reducing DHF

groups, intramolecular or intermolecular

to THF with NADPH as the reductant (see

crosslinking of the DNA double helix and

p. 418). The folic acid analogue methotrexate,

“bending” of the double strand occurs. Exam-

a frequently used cytostatic agent, is an ex-

ples of this type shown here are cyclophos-

tremely effective competitive inhibitor of di-

phamide and the inorganic complex cisplatin.

hydrofolate reductase. It leads to the deple-

Anthracyclines such as doxorubicin (adriamy-

tion of N⁵,N¹⁰-methylene-THF in the cells and

cin) insert themselves non-covalently be-

thus to cessation of DNA synthesis.

tween the bases and thus lead to local alter-

ations in the DNA structure (see p. 254 B).

Further information

To reduce the side effects of cytostatic agents,

B. Antimetabolites

new approaches are currently being devel-

Antimetabolites are enzyme inhibitors

(see

oped on the basis of gene therapy

(see

p. 96) that selectively block metabolic pathways.

p. 264). Attempts are being made, for exam-

The majority of clinically important cytostatic

ple, to administer drugs in the form of pre-

drugs act on nucleotide biosynthesis. Many of

cursors (known as prodrugs), which only be-

these are modified nucleobases or nucleotides

come active in the tumor itself (“tumor tar-

that competitively inhibit their target enzymes

geting”).

(see p. 96). Many are also incorporated into the

DNA, thereby preventing replication.

Cell proliferation

403

A. Alkylating agents, anthracyclines

Cross-linking

“Bending”

of DNA

of the DNA

components

double helix

H₃N

CH₂

CH₂OH

CH₂

H₃N Cl

H O

H₃CO O OH

Cyclophosphamide

Adriamycin

Cisplatin

B. Antimetabolites

CH₃

N C

SAH

SAM

Rib

me-tIMP

tIMP

6-Mercaptopurine

GIn

Glu

P P

tIMP

tGMP

tGDP

tdGDP

Purine

DNA

Phospho-

synthesis

ribosyl

IMP

GMP

GDP

dGDP

PRPP

amine

Hypoxanthine phospho-

Amidophosphoribosyl

ribosyltransferase 2.4.2.8

transferase 2.4.2.14

H₂N

Thiopurine methyl-

Ribonucleoside diphosphate

transferase2.1.1.67

reductase 1.17.4.1

Hydroxyurea

Precursors

H₂N

N⁵,N¹⁰

-methylene-THF

CH₂

dUMP

H₃C

THF

NH2

Rib

5-fluoro-

Methotrexate

deoxyuridine

DHF

(amethopterin)

monophosphate

C O

dTMP

Dihydrofolate

OOC

CH₂

COO

dTTP

5-fluorouracil

5-fluoro-

deoxyuridine

Thymidylate synthase 2.1.1.45

DNA

Dihydrofolate reductase 1.5.1.3

404

Growth and development

other to form pentamers and hexamers. In all,

Viruses

60 protein molecules are involved in the

Viruses are parasitic nucleoprotein complexes.

structure of the capsid.

They often consist of only a single nucleic acid

molecule (DNA or RNA, never both) and a

C. Life cycle of HIV

protein coat. Viruses have no metabolism of

their own, and can therefore only replicate

The human immunodeficiency virus

(HIV)

themselves with the help of host cells. They

causes the immunodeficiency disease known

are therefore not regarded as independent

as AIDS

(acquired immune deficiency syn-

organisms. Viruses that damage the host cell

drome). The structure of this virus is similar

when they replicate are pathogens. Diseases

to that of the influenza virus (A).

caused by viruses include AIDS, rabies, polio-

The HIV genome consists of two molecules

myelitis, measles, German measles, smallpox,

of ssRNA (each 9.2 kb). It is enclosed by a

influenza, and the common cold.

double-layered capsid and a protein-contain-

ing coating membrane. HIV mainly infects T

helper cells (see p. 294) and can thereby lead

A. Viruses: examples

to failure of the immune system in the longer

Only a few examples from the large number

term.

of known viruses are illustrated here. They are

During infection

(1), the virus’s coating

all shown on the same scale.

membrane fuses with the target cell’s plasma

Viruses that only replicate in bacteria are

membrane, and the core of the nucleocapsid

known as bacteriophages (or “phages” for

enters the cytoplasm (2). In the cytoplasm,

short). An example of a phage with a simple

the viral RNA is initially transcribed into an

structure is M13. It consists of a single-

RNA/DNA hybrid (3) and then into dsDNA (4).

stranded DNA molecule (ssDNA) of about

Both of these reactions are catalyzed by re-

7000 bp with a coat made up of 2700 helically

verse transcriptase, an enzyme deriving from

arranged protein subunits. The coat of a virus

the virus. The dsDNA formed is integrated

is referred to as a capsid, and the complete

into the host cell genome (5), where it can

structure as a nucleocapsid. In genetic engi-

remain in an inactive state for a long time.

neering, M13 is important as a vector for for-

When viral replication occurs, the DNA

eign DNA (see p. 258).

segment corresponding to the viral genome

The phage T4 (bottom left), one of the larg-

is first transcribed by host cell enzymes (6).

est viruses known, has a much more complex

This gives rise not only to viral ssRNA, but also

structure with around 170 000 base pairs (bp)

to transcription of mRNAs for precursors of

of double-stranded DNA (dsDNA) contained

the viral proteins (7). These precursors are

within its “head.”

integrated into the plasma membrane (8, 9)

The tobacco mosaic virus (center right), a

before undergoing proteolytic modification

plant pathogen, has a structure similar to that

(10). The cycle is completed by the release of

of M13, but contains ssRNA instead of DNA.

new virus particles (11).

The poliovirus, which causes poliomyelitis, is

The group of RNA viruses to which HIV

also an RNA virus. In the influenza virus, the

belongs are called retroviruses, because DNA

pathogen that causes viral flu, the nucleocap-

is produced from RNA in their replication cy-

sid is additionally surrounded by a coat de-

cle—the reverse of the usual direction of tran-

rived from the plasma membrane of the host

scription (DNA RNA).

cell (C). The coat carries viral proteins that are

involved in the infection process.

B. Capsid of the rhinovirus

Rhinoviruses cause the common cold. In these

viruses, the capsid is shaped like an icosahe-

dron—i. e., an object made up of 20 equilateral

triangles. Its surface is formed from three dif-

ferent proteins, which associate with one an-

Viruses

405

A. Viruses: examples

B. Capsid of the rhinovirus

Phage M13

ssDNA 7 kb

Helical

Coat

T4-Phage

ds DNA

Influenza virus

170 kbp

ssRNA (8 molecules) 3.6 kb

Eicosa-

complex

Nucleocapsid with coat

hedral

structure

head

Tail

1. Structure

Tobacco mosaic virus

ssRNA6.4 kb

Pentamer

Helical

Poliovirus

Phage DNA

ssRNA 7 kb

Bacterial cell

Eicosahedral capsid

30 nm

Hexamer

Capsid

2. Plant and animal

Eicosahedron of

180 monomers

1. Bacteriophages

pathogenic viruses

2. Diagram

C. Life cycle of the human immunodeficiency virus (HIV)

Glycoprotein

Other

GP120

enzymes

Infection

100 nm

Reverse

transcriptase

Core

Viral

RNA

Membrane

Viral

RNA

GP120

Precursors

of core proteins

RNA/

and enzymes

DNA

Translation

hybrid

mRNA

Viral

RNA

Transcription

Mature

DNA

virus

particle

Integration

Reverse transcriptase

2.7.7.49

Cytoplasm

Ribonuclease H

Nucleus

Host DNA

3.1.26.4

406

Metabolic charts

Example

Metabolic charts

On p. 407, the initial step of the dark reactions

Explanations

in plant photosynthesis (in the Calvin cycle) is

shown at the top left.

The following 13 plates (pp. 407-419) provide

a concise schematic overview of the most

important metabolic pathways. Explanatory

text is deliberately omitted from them.

These “charts”:

• Contain details of metabolic pathways that

are only shown in outline in the main text

for reasons of space. This applies in partic-

ular to the synthesis and degradation of the

amino acids and nucleotides, and for some

aspects of carbohydrate and lipid metabo-

lism.

• Offer a quick overview of a specific path-

way, the metabolites that arise in it, and the

enzymes involved.

• Can be used for reference purposes and for

In this reaction, one molecule of ribulose-

revising material previously learned.

1,5-bisphosphate (metabolite 1) and one mol-

ecule of CO₂ (metabolite 2) give rise to two

The most important intermediates are shown

molecules of 3-phosphoglycerate (metabolite

with numbers in the charts. The correspond-

3). The enzyme responsible has the EC

ing compounds can be identified using the

number 4.1.1.39. The annotated enzyme list

table on the same page.

shows that this refers to ribulose bisphosphate

In addition, at each step the four-figure EC

carboxylase (“rubisco” for short). Rubisco be-

number (see p. 88) for the enzyme responsi-

longs to enzyme class 4 (the lyases) and,

ble for a reaction is given in italics. The en-

within that group, to subclass 4.1 (the car-

zyme name and its systematic classification in

boxy-lyases). It contains copper as a cofactor

the system used by the Enzyme Catalogue are

([Cu]).

available in the following annotated enzyme

list (pp. 420-430), in which all of the enzymes

mentioned in this book are listed according to

their EC number. The book’s index is helpful

when looking for a specific enzyme in the

text.

In reactions that involve coenzymes, the

coenzyme names are also given (sometimes

in simplified form). Particularly important

starting, intermediate, or end products are

given with the full name, or as formulae.

Metabolic charts

407

A. Calvin cycle (plant chloroplasts)

6 CO₂ + 18 ATP + 12 NADPH + 12 H

Hexose + 18 ADP + 18 P + 12 NADP

Ribulose 1,5 - bis P

CO₂

5.3.1.1

C₃

4.1.1.39

4.1.2.13

ATP

ADP

2.7.2.3

3.1.3.11

C₆

NADPH

NADP

2.2.1.1

1.2.1.13

C₄

Glucose 6-

Glyceraldehyde 3-

phosphate

Ribulose 1,5-bisphosphate

Carbon dioxide

3-Phosphoglycerate

C₇

3.1.3.37

1,3-Bisphosphoglycerate

Glyceraldehyde 3-phosphate

2.2.1.1

Dihydroxyacetone phosphate

Fructose 1,6-bisphosphate

Fructose 6-phosphate

C₅

Erythrose 4-phosphate

Sedoheptulose 1,7-bisphosphate

5.1.3.4

5.3.1.6

Sedoheptulose 7-phosphate

Xylulose 5-phosphate

C₅

Ribose 5-phosphate

ATP

Ribulose 5-phosphate

ADP

2.7.1.19

Glucose 6-phosphate

408

Metabolic charts

A. Carbohydrate metabolism

5.1.3.1

5.3.1.6

Ribose 5-

Glycogen

phosphate

CO2

NADPH

2.2.1.1

NADP

UDP

H2O

2.2.1.2

P P

UTP

NADPH

5.4.2.2

2.2.1.1

NADP

Glucose

3.1.3.9

5.3.1.9

3.1.3.11

Glucose 6-

2.7.1.1

phosphate

2.7.1.11

ATP

ADP

ATP

ADP

4.1.2.13

5.4.2.1

2.7.2.3

1.2.1.12

5.3.1.1

NADH

ATP

ADP

NADH

NAD

ADP

ATP

H2O

NAD

Pyruvate

2.7.1.40

1.1.1.27

Lactate

CO2

GDP

ADP

ATP

Mitochondrion

GTP

Amino

Glycerol

acids

6.4.1.1

ADP

ATP

Fat

Glycogen

Ribose 5-phosphate

1,3-Bisphosphoglycerate

UDP-Glucose

Xylulose 5-phosphate

3-Phosphoglycerate

Glucose 1-phosphate

Sedoheptulose 7-phosphate

2-Phosphoglycerate

Glucose

Glyceraldehyde 3-phosphate

Phosphoenolpyruvate

Glucose 6-phosphate

Erythrose 4-phosphate

Pyruvate

Lactate

Gluconolactone 6-

Fructose 6-phosphate

Oxaloacetate

Gluconate 6-phosphate

Fructose 1,6-bisphosphate

Glycerol

Ribulose 5-phosphate

Glycerone-3-phosphate

Glycerol 3-phosphate

Metabolic charts

409

A. Biosynthesis of fats and membrane lipids

Glycolysis

ATP

ADP

NAD

NADH

Fatty acid

synthase

Acetyl

CoA

2.7.1.30

1.1.1.8

CoA

1.1.1.101

Ketone bodies

Acyl-CoA

Isoprenoids

NADP

NADPH

CoA

Pyruvate

2.7.7.41

Dihydroxyacetone 3-

Inositol

Acetyl CoA

CTP

CoA

CMP

Glycerol

Fat

Glycerol 3-phosphate

2.3.1.20

Acyl CoA

CMP

1-Acylglycerol 3-phosphate

2.7.1.32

2.7.7.15

1-Acylglycerone 3-phosphate

2.7.8.2

Phosphatidate

ATP

ADP

CTP

CMP

CDP-diacylglycerol

2.7.1.82

2.7.7.14

1,2-Diacylglycerol

2.7.8.1

Phosphatidylinositol

ATP

ADP

CTP

Choline

CDP-choline

Palmitoyl CoA

Phosphatidylcholine

Ethanolamine

Sphingosine

CDP-ethanolamine

UDP-Glc, UDP-Gal

Serine

UDP-GlcNAc

Phosphatidylethanolamine

CMP-NeuAc

Palmitoyl CoA

Ganglio-

Ceramide

sides

Phosphatidylserine

UDP-Gal

Sphingosine

UDP

Serine

Ceramide

Sphingo-

Cere-

Galactosylceramide

myelins

brosides

Sphingomyelin

410

Metabolic charts

A. Synthesis of ketone bodies and steroids

NADH

NAD

Pyruvate

Glycolysis

Glucose

1.1.1.30

NAD

Ketone bodies

CoA

NADH

4.1.3.5

2.3.1.16

Bile

salts

NADPH

Acetyl CoA

NADP

Glycine

Fatty acid

β-Oxi-

CoA

Taurine

synthesis

dation

ATP

2 H₂O

Bile

2 [H]

ADP

CoA

acids

O₂

Fatty acid

ATP

extension

ATP

AMP

ADP

NADP

NADPH

CO₂

Cholesterol

2.5.1.1

2.5.1.10

2.5.1.21

O₂

2 [H]

NADP

NADPH

2 [H] O₂

H₂O

1.14.99.9

1.1.1.51

NADPH

5.3.3.1

Isoprenoids

H₂O

2 [H] O₂

H₂O

2 [H] O₂

NADP

Proge-

Testo-

sterone

1.14.99.10

1.14.99.9

O₂

“Aromatase”

2 [H]

H₂O

Aldosterone

H₂O

Hormone

Estradiol

Cortisol

Pyruvate

Oleyl CoA

Dehydroepiandrosterone

Acetyl CoA

Mevalonate

Androstene-3,17-dione

Acetoacetyl CoA

Mevalonate 5-diphosphate

Testosterone

3-Hydroxy-3-methyl-

Isopentenyl diphosphate

Estradiol

glutaryl CoA

Acetoacetate

Geranyl diphosphate

Progesterone

Acetone

Farnesyl diphosphate

17-OH-Progesterone

3-Hydroxybutyrate

Squalene

11-Deoxycortisol

Palmitate

Cholesterol

Cortisol

Palmitoyl CoA

Pregnenolone

11-Deoxycorticosterone

Stearoyl CoA

17-OH-Pregnenolone

Aldosterone

Metabolic charts

411

A. Degradation of fats and phospholipids

Phospholipases

H₂O

A₁

3.1.1.32

A₂

3.1.1.4

3.1.4.3

ATP

H₂O

3.1.4.4

CoA

H₂O

CoA

A₁

A₂

Adipose tissue

ATP

CoA

From uneven-

numbered fatty acids

ADP

1.3.99.3

6.4.1.3

NAD

H₂O

ETF_ox

ETF_red

Glucose

ATP

CO₂

ADP

NADH

Respiratory chain

β-Oxidation

NAD

Pyruvate

CoA

Respiratory

NADH

chain

2.3.1.16

Triacylglycerol

Free fatty acid

3-Oxoacyl CoA

Diacylglycerol

Acyl CoA

Acetyl CoA

Monoacylglycerol

Shortened acyl CoA

Propionyl CoA

Glycerol

Carnitine

(S)-Methylmalonyl CoA

Glycerol 3-phosphate

Acyl carnitine

(R)-Methylmalonyl CoA

Glycerone 3-phosphate

2,3-Dehydroacyl CoA

Succinyl CoA

Phospholipid

3-Hydroxyacyl CoA

412

Metabolic charts

A. Biosynthesis of the essential amino acids

Isoleucine

Leucin

Valine

2-Oxo-

glutarate

ATP

Glu

Threonine

Glu

Pyruvate

CO₂

4.1.3.18

ATP

ADP

Cysteine

Methionine

2.7.2.4

NADPH

[CH₃]

Aspartate

NADP

1.1.1.3

2.7.1.39

4.2.99.2

Threonine

H₂O

NADPH

NADP

ADP

ATP

Glu

Lysine

Histidine

PEP

Glu

Trypto-

Phenyl-

Serine

phan

alanine

Pyruvate

Phosphoribosyl

Erythrose 4-phosphate

diphosphate

2-Oxo-3-deoxy-

2-Oxobutyrate

Aspartate

arabinoheptulosonate

2-Aceto-

7-phosphate

2-hydroxybutyrate

Aspartyl 4-phosphate

Chorismate

2-Oxo-4-methylvalerate

Aspartate 4-semialdehyde

Phenylpyruvate

2-Acetolactate

Homoserine

Anthranilate

2-Oxoisovalerate

Phosphohomoserine

N-(Phosphoribosyl)-

2-Oxoisocaproate

Phosphoenolpyruvate

anthranilate

Metabolic charts

413

A. Biosynthesis of the non-essential amino acids

1.14.16.1

Phenylalanine

Tyrosine

Glycolysis

Tetra-

THB

DHP

H2O

hydro-

biopterin

2.6.1.52

1.1.1.95

2-Oxoglutarate

Glu

NADH

NAD

5,10

THF

M-THF

Glu

Serine

Methionine

Alanine

2.1.2.1

2.6.1.2

Glycine

Glu

ATP

Gln

Glu

AMP

H2O

4.2.1.22

2.6.1.1

6.3.5.4

H2O

Aspar-

tate

agine

NH3

Tricarboxylic

Cysteine

Proline

acid cycle

NADP

3-Phosphoglycerate

3-Phosphohydroxypyruvate

NADPH

3-Phosphoserine

NH3

NADP

Glycine

NADH

Gluta-

mate

Cystathionine

NAD

NADPH

2.7.2.11

Homocysteine

2-Oxobutyrate

ATP

Pyruvate

ATP

ADP

NH3

Urea

Oxaloacetate

cycle

ADP

Aspartate

Asparagine

Glutamine

Arginine

Acetyl

2-Oxoglutarate

CoA

Ace-

Glutamate

tate

CoA

γ-Glutamyl phosphate

∆¹-Pyrroline-5-carboxylate

ATP

N-Acetylglutamate

N-Acetylglutamate 5-phosphate

ADP

Glu

N-Acetylglutamate semialdehyde

1.2.1.38

N-Acetylornithine

Ornithine

NADPH

NADP

Arginine

414

Metabolic charts

A. Amino acid degradation I

Iso-

1.4.4.2

Valine

Leucine

Glycine

leucine

CO2

2.1.2.10

THF

^5,10M-THF

Glu

4.1.2.5

Threo-

1 a, b, c

Serine

Glycine

2.1.2.1

nine

NAD

Branched-chain

CoA

α-ketoacid

NADH

dehydrogenase

NH3

complex

CO₂

Histi-

2 a, b, c

Glu

dine

[FAD]

CoQ_ox

Alanine

[FADH₂]

CoQ

2.6.1.2

red

NH3

3 a, b, c

ATP

H₂O

CO₂

H₂O

ADP

H₂O

4.2.1.18

Tricarboxylic

H₂O

NAD

H₂O

acid cycle

CoA

NADH

2.1.2.5

NAD

NH3

⁵F-THF

THF

NADH

NH3

H₂O

ATP

CO₂

ADP

NAD

Gluta-

6.4.1.3

mate

3.5.1.2

mine

CoA

2[H

2-Oxoisovalerate

3-Hydroxyisobutyrate

Acetoacetate

2-Oxo-3-methylvalerate

Methylmalonyl-semialdehyde

Acetyl CoA

2-Oxoisocapronate

(S)-Methylmalonyl CoA

Pyruvate

Isobutyryl CoA

(R)-Methylmalonyl CoA

Acetaldehyde

2-Methylbutyryl CoA

Succinyl CoA

Urocanate

Isovaleryl CoA

2-Methyl-3-hydroxybutyryl CoA

Imidazolone-

5-propionate

Methylacrylyl CoA

2-Methylacetoacetyl CoA

Tiglyl CoA

Propionyl CoA

N-Formimino-

glutamate

3-Methylcrotonyl CoA

3-Methylglutaconyl CoA

3-Hydroxyisobutyryl CoA

3-Hydroxy-3-methylglutaryl CoA

2-Oxoglutarate

Metabolic charts

415

A. Amino acid degradation II

Non-enzymatic

Pyru-

reaction

2.6.1.3

1.13.11.20

Cys-

Methionine

Asparagine

vate

teine

ATP

H₂O

SO₂

Glu

O₂

β-Oxidation

NH3

Acetyl

Aspartate

CoA

[CH₃]

Ade-

nosine

H₂O

8 steps

Glu

Serine

H₂O

Several

Trypto-

pathways

phan

H₂O

Tricarboxylic

acid cycle

NH3

O₂

Cysteine

Lysine

See pre-

CO₂

H₂O

vious page

NH3

Ascorbate

CoA

NADH

Dehydroascorbate

O₂

NAD

[2 H]

CO₂

2.6.1.5

1.14.16.1

Tyro-

Phenyl-

Glutamate

sine

alanine

NADH

Glu

H₂O

O₂

NAD

THB

Non-

H₂O

enzymatic

1.5.99.8

reaction

2.6.1.13

3.5.3.1

Argi-

Proline

nine

2[H]

H₂O

Glu

H₂O

Urea

S-Adenosylmethionine

Oxaloacetate

4-Maleylacetoacetate

Homocysteine

Cysteine sulfinate

Fumarylacetoacetate

Cystathionine

3-Sulfinylpyruvate

Acetoacetate

2-Oxobutyrate

2-Oxoadipate

Glutamate 4-semialdehyde

Propionyl CoA

Crotonyl CoA

∆¹-Pyrroline-5-carboxylate

Succinyl CoA

4-Hydroxyphenylpyruvate

Ornithine

Fumarate

Homogentisate

2-Oxoglutarate

Metabolic charts

417

A. Biosynthesis of purine nucleotides

Ribose 5-

PRPP

phosphate

N¹⁰-Formyl-

THF

2.7.6.1

2.4.2.14

6.3.4.13

ATP

AMP

Gln

Glu

P P

Gly

ATP

ADP

F-THF

HCO₃

ADP

ATP

ADP

Glu

ATP

Gln

THF

4.1.1.21

6.3.3.1

6.3.5.3

Asp

ATP

ADP

Fumarate

2.1.2.3

3.5.4.10

N IMP

Rib

¹⁰F-THF

THF

H₂O

Asp

ATP

NAD

Xanthine

Ribose 5-phosphate

mono-

ADP

NADH

phosphate

Phosphoribosyl

XMP

diphosphate (PRPP)

Gln

PR-amine

ATP

PR-glycineamide

ADP

PR-formylglycine-

Fumarate

amide

Glu

PR-formylglycine-

AMP

GMP

amidine

PR-5-aminoimidazole

NADPH

NADP

NADPH

NADP

PR-4-carboxy-5-

aminoimidazole

ADP

dADP

GDP

dGDP

1.17.4.1

PR-5-amino-4-

imidazolecarboxamide

Nucleoside

diphosphate

PR-5-formamido-

reductase

imidazole-4-carbox-

ATP

dATP

GTP

dGTP

amide

Inosine 5'-mono-

phosphate

Adenylosuccinic acid

PR = 5'-Phosphoribosyl-

RNA

DNA

RNA

DNA

418

Metabolic charts

A. Biosynthesis of the pyrimidine nucleotides and C1 metabolism

HCO₃

Carbamoyl

Gln

ATP

ADP

Glu

Asp

H₂O

FMN

FMNH₂

phosphate

Carbamoyl

aspartate

6.3.5.5

2.1.3.2

3.5.2.3

1.3.99.11

Dihydroorotate

Orotate

DHF

^5,10M-THF

P P

Phosphoribosyl

diphosphate

4..1.1.23

dTMP

dUMP

UMP

2.1.1.45

Orotate 5'-mono-

phosphate

Thymidylate

2[H

CO₂

synthase

1.17.4.1

dTDP

dUDP

UDP

CDP

dCDP

1.17.4.1

ADP

ATP

Nucleoside

2[H

[NH

diphosphate

reductase

dTTP

UTP

CTP

dCTP

6.3.4.2

CTP

synthase

DNA

RNA

Tetrahydro-

Histidine

HCO

folate

THF

ATP

N⁵-Formyl-

Methionine

ADP

THF

NADPH

NADP

NADPH

NADP

Homocysteine

H H

THF

1.5.1.5

1.5.1.20

N5,N10-Methenyl-

N⁵,N¹⁰-Methylen-

N⁵-Methyl-

THF

H₂O

dUMP

Glycine

HCO

dTMP

H₂O

THF

Serine

N¹⁰-Formyl-THF

2.1.2.2, 2.1.2.3

1.5.1.3

Dihydro-

THF

DHF

folate

Purine ring (C-2, C-8)

NADP

NADPH

Metabolic charts

419

A. Nucleotide degradation

Ade

AMP

GMP

dTMP

UMP

CMP

H₂O

H₂O H

H₂O

NH₃

3.5.4.5

IMP

H₂O

NH₃ H

Rib

P Rib

NH₃

Inosine

Gua

Thy

Ura

H₂O

NADPH

Rib

NH₃

NADP

1.1.3.22

H₂O

H₂O₂

O₂

Primates,

H₂O

birds, reptiles

Uric

acid

H₂O

O₂

Other mammals,

NH₃,

molluscs

CO₂

H₂O

2-OG

(Pyr)

Glu

Osseous fish

(Ala)

H₂O

CO₂

Cartilaginous fish,

amphibians

Propionate

Acetate

Hypoxanthine (Hyp)

Carbamoyl-β-amino-

isobutyrate

Xanthine (Xan)

β-Aminoisobutyrate

Allantoin

2-Methyl-3-oxopropionate

Allantoic acid

Dihydrouracil

Glyoxylate

Carbamoyl-β-alanine

Urea

β-alanine

Dihydrothymine

3-oxopropionate

420

Annotated enzyme list

Only the enzymes mentioned in this atlas are listed here, from among the more than 2000

enzymes known. The enzyme names are based on the IUBMB’s of cial Enzyme nomenclature

1992. The additions shown in round brackets belong to the enzyme name, while prosthetic

groups and other cofactors are enclosed in square brackets. Common names of enzyme groups

are given in italics, and trivial names are shown in quotation marks.

Class 1: Oxidoreductases (catalyze reduction-oxidation reactions)

Subclass 1.n: What is the electron donor?

Sub-subclass

1.n.n: What is the electron acceptor?

1.1

A -CH-OH group is the donor

1.1.1

NAD(P)⁺ is the acceptor (dehydrogenases, reductases)

1.1.1.1

Alcohol dehydrogenase [Zn²⁺]

1.1.1.3

Homoserine dehydrogenase

1.1.1.8

Glycerol 3-phosphate dehydrogenase (NAD⁺)

1.1.1.21

Aldehyde reductase

1.1.1.27

Lactate dehydrogenase

1.1.1.30

3-Hydroxybutyrate dehydrogenase

1.1.1.31

3-Hydroxyisobutyrate dehydrogenase

1.1.1.34

Hydroxymethylglutaryl-CoA reductase (NADPH)

1.1.1.35

3-Hydroxyacyl-CoA dehydrogenase

1.1.1.37

Malate dehydrogenase

1.1.1.40

Malate dehydrogenase (oxaloacetate-decarboxylating, NADP⁺)—“malic enzyme”

1.1.1.41

Isocitrate dehydrogenase (NAD⁺)

1.1.1.42

Isocitrate dehydrogenase (NADP⁺)

1.1.1.44

Phosphogluconate dehydrogenase (decarboxylating)

1.1.1.49

Glucose 6-phosphate 1-dehydrogenase

1.1.1.51

3(or 17)β-Hydroxysteroid dehydrogenase

1.1.1.95

Phosphoglycerate dehydrogenase

1.1.1.100

3-Oxoacyl-[ACP] reductase

1.1.1.101

Acylglycerone phosphate reductase

1.1.1.105

Retinol dehydrogenase

1.1.1.145

3β-Hydroxy-∆⁵-steroid dehydrogenase

1.1.1.205

IMP dehydrogenase

1.1.3

Molecular oxygen is the acceptor (oxidases)

1.1.3.4

Glucose oxidase [FAD]

1.1.3.8

L-Gulonolactone oxidase

1.1.3.22

Xanthine oxidase [Fe, Mo, FAD]

1.1.99.5

Glycerol-3-phosphate dehydrogenase (FAD)

1.2

An aldehyde or keto group is the donor

1.2.1

NAD(P)⁺ is the acceptor (dehydrogenases)

1.2.1.3

Aldehyde dehydrogenase (NAD⁺)

1.2.1.11

Aspartate semialdehyde dehydrogenase

1.2.1.12

Glyceraldehyde 3-phosphate dehydrogenase

1.2.1.13

Glyceraldehyde 3-phosphate dehydrogenase (NADP⁺) (phosphorylating)

1.2.1.24

Succinate semialdehyde dehydrogenase

1.2.1.25

2-Oxoisovalerate dehydrogenase (acylating)

1.2.1.38

N-Acetyl-γ-glutamylphosphate reductase

1.2.1.41

Glutamylphosphate reductase

Annotated enzyme list

421

1.2.4

A disulfide is the acceptor

1.2.4.1

Pyruvate dehydrogenase (lipoamide) [TPP]

1.2.4.2

Oxoglutarate dehydrogenase (lipoamide) [TPP]

1.2.7

An Fe/S protein is the acceptor

1.2.7.2

2-Oxobutyrate synthase

1.3

A -CH-CH- group is the donor

1.3.1.10

Enoyl-[ACP] reductase (NADPH)

1.3.1.24

Biliverdin reductase

1.3.1.34

2,4-Dienoyl-CoA reductase

1.3.5.1

Succinate dehydrogenase (ubiquinone) [FAD, Fe₂S₂, Fe₄S₄], “complex II”

1.3.99.3

Acyl-CoA dehydrogenase [FAD]

1.3.99.11

Dihydroorotate dehydrogenase [FMN]

1.4

A -CH-NH2 group is the donor

1.4.1.2

Glutamate dehydrogenase

1.4.3.4

Amine oxidase [FAD], “monoamine oxidase (MAO)”

1.4.3.13

Protein lysine 6-oxidase [Cu]

1.4.4.2

Glycine dehydrogenase (decarboxylating) [PLP]

1.5

A -CH-NH group is the donor

1.5.1.2

Pyrroline-5-carboxylate reductase

1.5.1.3

Dihydrofolate reductase

1.5.1.5

Methylenetetrahydrofolate dehydrogenase (NADP⁺)

1.5.1.12

1-Pyrroline-5-carboxylate dehydrogenase

1.5.1.20

Methylenetetrahydrofolate reductase (NADPH) [FAD]

1.5.5.1

Electron-transferring flavoprotein (ETF) dehydrogenase [Fe₄S₄]

1.5.99.8

Proline dehydrogenase [FAD]

1.6

NAD(P)H is the donor

16.4.2

Glutathione reductase (NADPH) [FAD]

1.6.4.5

Thioredoxin reductase (NADPH) [FAD]

1.6.5.3

NADH dehydrogenase (ubiquinone) [FAD, Fe₂S₂, Fe₄S₄]—“complex I”

1.8

A sulfur group is the donor

1.8.1.4

Dihydrolipoamide dehydrogenase [FAD]

1.9

A heme group is the donor

1.9.3.1

Cytochrome c oxidase [heme, Cu, Zn] - “cytochrome oxidase,” “complex IV”

1.10

A diphenol is the donor

1.10.2.2

Ubiquinol cytochrome c reductase [heme, Fe₂S₂]—“complex III”

1.11

A peroxide is the acceptor (peroxidases)

1.11.1.6

Catalase [heme]

1.11.1.7

Peroxidase [heme]

1.11.1.9

Glutathione peroxidase [Se]

1.11.1.12

Lipid hydroperoxide glutathione peroxidase [Se]

1.13

Molecular oxygen is incorporated into the electron donor (oxygenases)

1.13.11

One donor, both O atoms are incorporated (dioxygenases)

1.13.11.5

Homogentisate 1,2-dioxygenase [Fe]

1.13.11.20

Cysteine dioxygenase [Fe]

1.13.11.27

4-Hydroxyphenylpyruvate dioxygenase [ascorbate]

1.13.11.n

Arachidonate lipoxygenases

422

Annotated enzyme list

1.14

Two donors, one O atom is incorporated into both (monooxygenases, hydroxylases)

1.14.11.2

Procollagen proline 4-dioxygenase [Fe, ascorbate]—“proline hydroxylase”

1.14.11.4

Procollagen lysine 5-dioxygenase [Fe, ascorbate]—“lysine hydroxylase”

1.14.13.13

Calcidiol 1-monooxygenase [heme]

1.14.15.4

Steroid 11β-monooxygenase [heme]

1.14.15.6

Cholesterol monooxygenase (side-chain-cleaving) [heme]

1.14.16.1

Phenylalanine 4-monooxygenase [Fe, tetrahydrobiopterin]

1.14.16.2

Tyrosine 3-monooxygenase [Fe, tetrahydrobiopterin]

1.14.17.1

Dopamine β-monooxygenase [Cu]

1.14.99.1

Prostaglandin H-synthase [heme]

1.14.99.3

Heme oxygenase (decyclizing) [heme]

1.14.99.5

Stearoyl-CoA desaturase [heme]

1.14.99.9

Steroid 17α-monooxygenase [heme]

1.14.99.10

Steroid 21-monooxygenase [heme]

1.15

A superoxide radical is the acceptor

1.15.1.1

Superoxide dismutase

1.17

A -CH₂ group is the donor

1.17.4.1

Ribonucleoside diphosphate reductase [Fe]—“ribonucleotide reductase”

1.18

Reduced ferredoxin is the donor

1.18.1.2

Ferredoxin-NADP⁺ reductase [FAD]

1.18.6.1

Nitrogenase [Fe, Mo, Fe₄S₄]

Class 2: Transferases (catalyze the transfer of groups from one molecule to another)

Subclass

2.n: Which group is transferred?

2.1

A C₁ group is transferred

2.1.1

A methyl group

2.1.1.2

Guanidinoacetate N-methyltransferase

2.1.1.6

Catechol O-methyltransferase

2.1.1.13

5-Methyltetrahydrofolate-homocysteine S-methyltransferase

2.1.1.28

Phenylethanolamine N-methyltransferase

2.1.1.45

Thymidylate synthase

2.1.1.67

Thiopurine methyltransferase

2.1.2

A formyl group

2.1.2.1

Glycine hydroxymethyltransferase [PLP]

2.1.2.2

Phosphoribosylglycinamide formyltransferase

2.1.2.3

Phosphoribosylaminoimidazolecarboxamide formyltransferase

2.1.2.5

Glutamate formiminotransferase [PLP]

2.1.2.10

Aminomethyltransferase

2.1.3

A carbamoyl group

2.1.3.2

Aspartate carbamoyltransferase [Zn²⁺]

2.1.3.3

Ornithine carbamoyltransferase

2.1.4

An amidino group

2.1.4.1

Glycine amidinotransferase

2.2

An aldehyde or ketone residue is transferred

2.2.1.1

Transketolase [TPP]

2.2.1.2

Transaldolase

Annotated enzyme list

423

2.3

An acyl group is transferred

2.3.1

With acyl-CoA as donor

2.3.1.1

Amino acid N-acetyltransferase

2.3.1.6

Choline O-acetyltransferase

2.3.1.12

Dihydrolipoamide acetyltransferase [lipoamide]

2.3.1.15

Glycerol 3-phosphate O-acyltransferase

2.3.1.16

Acetyl-CoA acyltransferase

2.3.1.20

Diacylglycerol O-acyltransferase

2.3.1.21

Carnitine O-palmitoyltransferase

2.3.1.22

Acylglycerol O-palmitoyltransferase

2.3.1.24

Sphingosine N-acyltransferase

2.3.1.37

5-Aminolevulinate synthase [PLP]

2.3.1.38

[ACP] S-acetyltransferase

2.3.1.39

[ACP] S-malonyltransferase

2.3.1.41

3-Oxoacyl-[ACP] synthase

2.3.1.42

Glycerone phosphate O-acyltransferase

2.3.1.43

Phosphatidylcholine-sterol acyltransferase—“lecithin-cholesterol acyltransferase

(LCAT)”

2.3.1.51

Acylgylcerol-3-phosphate O-acyltransferase

2.3.1.61

Dihydrolipoamide succinyltransferase

2.3.1.85

Fatty-acid synthase

2.3.2

An aminoacyl group is transferred

2.3.2.2

γ-glutamyltransferase

2.3.2.12

Peptidyltransferase (a ribozyme)

2.3.2.13

Protein-glutamine γ-glutamyltransferase [Ca]—“fibrin-stabilizing factor”

2.4

A glycosyl group is transferred

2.4.1

A hexose residue

2.4.1.1

Phosphorylase [PLP]—“glycogen (starch) phosphorylase”

2.4.1.11

Glycogen (starch) synthase

2.4.1.17

Glucuronosyltransferase

2.4.1.18

1,4-α-Glucan branching enzyme

2.4.1.25

4-α-Glucanotransferase

2.4.1.47

N-Acylsphingosine galactosyltransferase

2.4.1.119

Protein glycotransferase

2.4.2

A pentose residue

2.4.2.7

Adenine phosphoribosyltransferase

2.4.2.8

Hypoxanthine phosphoribosyltransferase

2.4.2.10

Orotate phosphoribosyltransferase

2.4.2.14

Amidophosphoribosyl transferase

2.5

An alkyl or aryl group is transferred

2.5.1.1

Dimethylallyltransferase

2.5.1.6

Methionine adenosyltransferase

2.5.1.10

Geranyltransferase

2.5.1.21

Farnesyl diphosphate farnesyltransferase

2.6

A nitrogen-containing group is transferred

2.6.1

An amino group (transaminases)

2.6.1.1

Aspartate transaminase [PLP]—“GOT”

2.6.1.2

Alanine transaminase [PLP]—“GPT”

424

Annotated enzyme list

2.6.1.3

Cysteine transaminase [PLP]

2.6.1.5

Tyrosine transaminase [PLP]

2.6.1.6

Leucine transaminase (PLP]

2.6.1.11

Acetylornithine transaminase [PLP]

2.6.1.13

Ornithine transaminase [PLP]

2.6.1.19

4-Aminobutyrate transaminase [PLP]

2.6.1.42

Branched-chain amino acid transaminase [PLP]

2.6.1.52

Phosphoserine transaminase [PLP]

2.7

A phosphorus-containing group is transferred (kinases)

2.7.1

With -CH-OH as acceptor

2.7.1.1

Hexokinase

2.7.1.3

Ketohexokinase

2.7.1.6

Galactokinase

2.7.1.11

6-Phosphofructokinase

2.7.1.19

Phosphoribulokinase

2.7.1.28

Triokinase (triosekinase)

2.7.1.30

Glycerol kinase

2.7.1.32

Choline kinase

2.7.1.36

Mevalonate kinase

2.7.1.37

Protein kinase

2.7.1.38

Phosphorylase kinase

2.7.1.39

Homoserine kinase

2.7.1.40

Pyruvate kinase

2.7.1.67

1-Phosphatidylinositol-4-kinase

2.7.1.68

1-Phosphatidylinositol 4-phosphate kinase

2.7.1.82

Ethanolamine kinase

2.7.1.99

[Pyruvate dehydrogenase] kinase

2.7.1.105

6-Phosphofructo-2-kinase

2.7.1.112

Protein tyrosine kinase

2.7.2

With -CO-OH as acceptor

2.7.2.3

Phosphoglycerate kinase

2.7.2.4

Aspartate kinase

2.7.2.8

Acetylglutamate kinase

2.7.2.11

Glutamate 5-kinase

2.7.3

With a nitrogen-containing group as acceptor

2.7.3.2

Creatine kinase

2.7.4

With a phosphate group as acceptor

2.7.4.2

Phosphomevalonate kinase

2.7.4.3

Adenylate kinase

2.7.4.4

Nucleoside phosphate kinase

2.7.4.6

Nucleoside diphosphate kinase

2.7.6

A diphosphate residue is transferred

2.7.6.1

Ribose phosphate pyrophosphokinase

2.7.7

A nucleotide is transferred

2.7.7.6

DNA-directed RNA polymerase—“RNA polymerase”

2.7.7.7

DNA-directed DNA polymerase—“DNA polymerase”

2.7.7.9

UTP-glucose-l-phosphate uridyltransferase

2.7.7.12

Hexose-1-phosphate uridyltransferase

2.7.7.14

Ethanolamine phosphate cytidyltransferase

Annotated enzyme list

425

2.7.7.15

Choline phosphate cytidyltransferase

2.7.7.41

Phosphatidate cytidyltransferase

2.7.7.49

RNA-directed DNA polymerase—“reverse transcriptase”

2.7.8

Another substituted phosphate is transferred

2.7.8.1

Ethanolaminephosphotransferase

2.7.8.2

Diacylglycerol cholinephosphotransferase

2.7.8.11

CDPdiacylglycerol-inositol 3-phosphatidyltransferase

2.7.8.16

1-Alkyl-2-acetylglycerol cholinephosphotransferase

2.7.8.17

N-Acetylglucosaminephosphotransferase

Class 3: Hydrolases (catalyze bond cleavage by hydrolysis)

Subclass

3.n: What kind of bond is hydrolyzed?

3.1

An ester bond is hydrolyzed (esterases)

3.1.1

In carboxylic acid esters

3.1.1.2

Arylesterase

3.1.1.3

Triacylglycerol lipase

3.1.1.4

Phospholipase A₂

3.1.1.7

Acetylcholinesterase

3.1.1.13

Cholesterol esterase

3.1.1.17

Gluconolactonase

3.1.1.32

Phospholipase A₁

3.1.1.34

Lipoprotein lipase, diacylglycerol lipase

3.1.2

In thioesters 3.1.2.4

3-Hydroxyisobutyryl-CoA hydrolase

3.1.2.14

Acyl-[ACP] hydrolase

3.1.3

In phosphoric acid monoesters (phosphatases)

3.1.3.1

Alkaline phosphatase [Zn²⁺]

3.1.3.2

Acid phosphatase

3.1.3.4

Phosphatidate phosphatase

3.1.3.9

Glucose 6-phosphatase

3.1.3.11

Fructose bisphosphatase

3.1.3.13

Bisphosphoglycerate phosphatase

3.1.3.16

Phosphoprotein phosphatase

3.1.3.37

Sedoheptulose bisphosphatase

3.1.3.43

[Pyruvate dehydrogenase] phosphatase

3.1.3.46

Fructose-2,6-bisphosphate 2-phosphatase

3.1.3.n

Polynucleotidases

3.1.4

In phosphoric acid diesters (phosphodiesterases)

3.1.4.1

Phosphodiesterase

3.1.4.3

Phospholipase C

3.1.4.4

Phospholipase D

3.1.4.17

3 ,5 -cNMP phosphodiesterase

3.1.4.35

3 ,5 -cGMP phosphodiesterase

3.1.4.45

N-Acetylglucosaminyl phosphodiesterase

3.1.21

In DNA

3.1.21.1

Deoxyribonuclease I

3.1.21.4

Site-specific deoxyribonuclease (type II)—“restriction endonuclease”

426

Annotated enzyme list

3.10.26-7

In RNA

3.1.26.4

Ribonuclease H

3.1.27.5

Pancreatic ribonuclease

3.2

A glycosidic bond is hydrolyzed (glycosidases)

3.2.1

In O-glycosides

3.2.1.1

α-Amylase

3.2.1.10

Oligo-1,6-glucosidase

3.2.1.17

Lysozyme

3.2.1.18

Neuraminidase

3.2.1.20

α-Glucosidase

3.2.1.23

β-Galactosidase

3.2.1.24

α -Mannosidase

3.2.1.26

β-Fructofuranosidase—“saccharase,” “invertase”

3.2.1.28

α,α-Trehalase

3.2.1.33

Amylo-1,6-glucosidase

3.2.1.48

Sucrose α-glucosidase

3.2.1.52

β-N-Acetylhexosaminidase

3.2.2.n

Nucleosidases

3.3

An ether bond is hydrolyzed

3.3.1.1

Adenosylhomocysteinase

3.4

A peptide bond is hydrolyzed (peptidases)

3.4.11

Aminopeptidases (N-terminal exopeptidases)

3.4.11.n

Various aminopeptidases [Zn²⁺]

3.4.13

Dipeptidases (act on dipeptides only)

3.4.13.n

Various dipeptidases [Zn²⁺]

3.4.15

Peptidyl dipeptidases (C-terminal exopeptidases, releasing dipeptides)

3.4.15.1

Peptidyl-dipeptidase A [Zn²⁺]—“angiotensin-converting enzyme (ACE)”

3.4.17

Carboxypeptidases (C-terminal exopeptidases)

3.4.17.1

Carboxypeptidase A [Zn²⁺]

3.4.17.2

Carboxypeptidase B [Zn²⁺]

3.4.17.8

Muramoylpentapeptide carboxypeptidase

3.4.21

Serine proteinases (endopeptidases)

3.4.21.1

Chymotrypsin

3.4.21.4

Trypsin

3.4.21.5

Thrombin

3.4.21.6

Coagulation factor Xa—“Stuart-Prower factor”

3.4.21.7

Plasmin

3.4.21.9

Enteropeptidase—“enterokinase”

3.4.21.21

Coagulation factor VIIa—“proconvertin”

3.4.21.22

Coagulation factor IXa—“Christmas factor”

3.4.21.27

Coagulation factor XIa—“plasma thromboplastin antecedent”

3.4.21.34

Plasma kallikrein

3.4.21.35

Tissue kallikrein

3.4.21.36

Elastase

3.4.21.38

Coagulation factor XIIa—“Hageman factor”

3.4.21.43

C3/C5 convertase (complement—classical pathway)

3.4.21.47

C3/C5 convertase (complement—alternative pathway)

Annotated enzyme list

427

3.4.21.68

Plasminogen activator (tissue)—“tissue plasminogen activator (t-PA)”

3.4.21.73

Plasminogen activator (urine)—“urokinase”

3.4.22

Cysteine proteinases (endopeptidases)

3.4.22.2

Papain

3.4.23

Aspartate proteinases (endopeptidases)

3.4.23.1

Pepsin A

3.4.23.2

Pepsin B

3.4.23.3

Gastricsin (pepsin C)

3.4.23.4

Chymosin

3.4.23.15

Renin

3.4.24

Metalloproteinases (endopeptidases)

3.4.24.7

Collagenase

3.4.99

Other peptidases

3.4.99.36

Signal peptidase

3.5

Another amide bond is hydrolyzed (amidases)

3.5.1.1

Asparaginase

3.5.1.2

Glutaminase

3.5.1.16

Acetylornithine deacetylase [Zn²⁺]

3.5.2.3

Dihydroorotase

3.5.2.7

Imidazolonepropionase

3.5.3.1

Arginase

3.5.4.6

AMP deaminase

3.5.4.9

Methylenetetrahydrofolate cyclohydrolase

3.5.4.10

IMP cyclohydrolase

3.6

An anhydride bond is hydrolyzed

3.6.1.6

Nucleoside diphosphatase

3.6.1.32

Myosin ATPase

3.6.1.34

H+-transporting ATP synthase—“ATP synthase,” “complex V”

3.6.1.35

H+-transporting ATPase

3.6.1.36

H+/K⁺-exchanging ATPase

3.6.1.37

Na⁺/K⁺-exchanging ATPase—“Na⁺/K⁺-ATPase”

3.6.1.38

Ca²⁺-transporting ATPase

3.7

A C-C bond is hydrolyzed

3.7.1.2

Fumarylacetoacetase

Class 4: Lyases (cleave or form bonds without oxidative or hydrolytic steps)

Subclass 4.n: What kind of bond is formed or cleaved?

4.1

A C-C bond is formed or cleaved

4.1.1

Carboxy-lyases (carboxylases, decarboxylases)

4.1.1.1

Pyruvate decarboxylase [TPP]

4.1.1.15

Glutamate decarboxylase [PLP]

4.1.1.21

Phosphoribosylaminoimidazole carboxylase

4.1.1.23

Orotidine-5 -phosphate decarboxylase

4.1.1.28

Aromatic L-amino acid decarboxylase [PLP]

4.1.1.32

Phosphoenolpyruvate carboxykinase (GTP)

4.1.1.39

Ribulose bisphosphate carboxylase [Cu]—“rubisco”

428

Annotated enzyme list

4.1.2

Acting on aldehydes or ketones

4.1.2.5

Threonine aldolase [PLP]

4.1.2.13

Fructose bisphosphate aldolase—“aldolase”

4.1.3.4

Hydroxymethylglutaryl-CoA lyase

4.1.3.5

Hydroxymethylglutaryl-CoA synthase

4.1.3.7

Citrate synthase

4.1.3.8

ATP-citrate lyase

4.1.3.18

Acetolactate synthase [TPP, flavin]

4.1.99

Other C-C lyases

4.1.99.3

Deoxyribodipyrimidine photolyase [FAD]—“photolyase”

4.2

A C-O bond is formed or cleaved

4.2.1

Hydrolyases (hydratases, dehydratases)

4.2.1.1

Carbonate dehydratase [Zn²⁺]—“carbonic anhydrase”

4.2.1.2

Fumarate hydratase—“fumarase”

4.2.1.3

Aconitate hydratase [Fe₄S₄]—“aconitase”

4.2.1.11

Phosphopyruvate hydratase—“enolase”

4.2.1.13

Serine dehydratase

4.2.1.17

Enoyl-CoA hydratase

4.2.1.18

Methylglutaconyl-CoA hydratase

4.2.1.22

Cystathionine β-synthase [PLP]

4.2.1.24

Porphobilinogen synthase

4.2.1.49

Urocanate hydratase

4.2.1.61

3-Hydroxypalmitoyl-[ACP] dehydratase

4.2.1.75

Uroporphyrinogen III synthase

4.2.99

Other C-O lyases

4.2.99.2

Threonine synthase [PLP]

4.3

A C-N bond is formed or cleaved

4.3.1

Ammonia lyases 4.3.1.3

Histidine ammonia lyase

4.3.1.8

Hydroxymethylbilane synthase

4.3.2

Amidine lyases 4.3.2.1

Argininosuccinate lyase

4.3.2.2

Adenylosuccinate lyase

4.4

A C-S bond is formed or cleaved

4.4.1.1

Cystathionine γ-lyase [PLP]

4.6

A P-O bond is formed or cleaved

4.6.1.1

Adenylate cyclase

4.6.1.2

Guanylate cyclase

Class 5: Isomerases (catalyze changes within one molecule)

Subclass 5.n: What kind of isomerization is taking place?

5.1

A racemization or epimerization (epimerases)

5.1.3.1

Ribulose phosphate 3-epimerase

5.1.3.2

UDPglucose 4-epimerase

5.1.3.4

L-Ribulose phosphate 4-epimerase

5.1.99.1

Methylmalonyl-CoA epimerase

Annotated enzyme list

429

5.2

A cis-trans isomerization

5.2.1.2

Maleylacetoacetate isomerase

5.2.1.3

Retinal isomerase

5.2.1.8

Peptidyl proline cis-trans-isomerase

5.3

An intramolecular electron transfer

5.3.1.1

Triose phosphate isomerase

5.3.1.6

Ribose 5-phosphate isomerase

5.3.1.9

Glucose 6-phosphate isomerase

5.3.3.1

Steroid ∆-isomerase

5.3.3.8

Enoyl-CoA isomerase

5.3.4.1

Protein disulfide isomerase

5.4

An intramolecular group transfer (mutases)

5.4.2.1

Phosphoglycerate mutase

5.4.2.2

Phosphoglucomutase

5.4.2.4

Bisphosphoglycerate mutase

5.4.99.2

Methylmalonyl-CoA mutase [cobamide]

5.99

Another kind of isomerization

5.99.1.2

DNA topoisomerase (type I)—“DNA helicase”

5.99.1.3

DNA topoisomerase (ATP-hydrolyzing, type II)—“DNA gyrase”

Class 6: Ligases (join two molecules with hydrolysis of an “energy-rich” bond)

Subclass

6.n: What kind of bond is formed?

6.1

A C-O bond is formed

6.1.1.n

(Amino acid)-tRNA ligases (aminoacyl-tRNA synthetases)

6.2

A C-S bond is formed

6.2.1.1

Acetate-CoA ligase

6.2.1.3

Long-chain fatty-acid-CoA ligase

6.2.1.4

Succinate-CoA ligase (GDP-forming)—“thiokinase”

6.3

A C-N bond is formed

6.3.1.2

Glutamate-NH₃ ligase—“glutamine synthetase”

6.3.2.6

Phosphoribosylaminoimidazolesuccinocarboxamide synthase (sorry!)

6.3.3.1

Phosphoribosylformylglycinamidine cycloligase

6.3.3.2

5-Formyltetrahydrofolate cycloligase

6.3.4.2

CTP synthase

6.3.4.4

Adenylosuccinate synthase

6.3.4.5

Argininosuccinate synthase

6.3.4.13

Phosphoribosylamine glycine ligase

6.3.4.16

Carbamoylphosphate synthase (NH₃)

6.3.5.2

GMP synthase (glutamine-hydrolyzing)

6.3.5.3

Phosphoribosylformylglycinamidine synthase

6.3.5.4

Asparagine synthase (glutamine-hydrolyzing)

6.3.5.5

Carbamoylphosphate synthase (glutamine-hydrolyzing)

6.4

A C-C bond is formed

6.4.1.1

Pyruvate carboxylase [biotin]

6.4.1.2

Acetyl-CoA carboxylase [biotin]

6.4.1.3

Propionyl-CoA carboxylase [biotin]

6.4.1.4

Methylcrotonyl-CoA carboxylase [biotin]

6.5

A P-O bond is formed

6.5.1.1

DNA ligase (ATP)

Abbreviations

431

Abbreviations

Abbreviations for amino acids, p. 60

For bases and nucleosides, p. 80

For monosaccharides, p. 38

Amino acid

FAD

Flavin adenine dinucleotide

ACE

Angiotensin-converting en-

Ferredoxin

zyme (peptidyl-dipeptidase A)

FFA

Free fatty acid

ACP

Acyl carrier protein

fMet

N-formylmethionine

ACTH

Adrenocorticotropic hormone

FMN

Flavin mononucleotide

(corticotropin)

Flavoprotein (containing FMN

ADH

Antidiuretic hormone (adiure-

or FAD)

tin, vasopressin)

GABA

γ-Aminobutyric acid

ADP

Adenosine 5 -diphosphate

GDP

Guanosine 5 -diphosphate

AIDS

Acquired immunodeficiency

Glut

Glucose transporter

syndrome

GMP

Guanosine 5 -monophosphate

ALA

5-Aminolevulinic acid

GSH

Reduced glutathione

AMP

Adenosine 5 -monophosphate

GSSG

Oxidized glutathione

ANF

Atrial natriuretic factor

GTP

Guanosine 5 -triphosphate

ANP

Atrial natriuretic peptide

hour

(= ANF)

HAT medium Medium containing hypoxan-

ATP

Adenosine 5 -triphosphate

thine, aminopterin, and thymi-

AVP

Arginine vasopressin

dine

Base

Hemoglobin

Base pair

HDL

High-density lipoprotein

BPG

2,3-Bisphosphoglycerate

HIV

Human immunodeficiency

cAMP

3 ,5 -Cyclic AMP

virus

CAP

Catabolite activator protein

HLA

Human leukocyte-associated

CDK

Cyclin-dependent protein

antigen

kinase (in cell cycle)

HMG-CoA

3-Hydroxy-3-methylglutaryl-

cDNA

Complementary DNA

CoA

CDP

Cytidine 5 -diphosphate

HMP

Hexose monophosphate path-

cGMP

3 ,5 -Cyclic GMP

way

CIA

Chemoluminescence immuno-

hnRNA

Heterogeneous nuclear ribo-

assay

nucleic acid

CMP

Cytidine 5 -monophosphate

HPLC

High-performance liquid chro-

CoA

Coenzyme A

matography

CoQ

Coenzyme Q (ubiquinone)

hsp

Heat-shock protein

CSF

colony-stimulating factor

IDL

Intermediate-density lipopro-

CTP

Cytidine 5 -triphosphate

tein

Deoxy-

Intermediary filament

Dalton (atomic mass unit)

IFN

Interferon

DAG

Diacylglycerol

Immunoglobulin

Dideoxy-

Interleukin

Dehydrogenase

InsP₃

Inositol 1,4,5-trisphosphate

DNA

Deoxyribonucleic acid

IPTG

Isopropylthiogalactoside

dsDNA

Double-stranded DNA

IRS

Insulin-receptor substrate

Ethanolamine

kDa

Kilodalton (10³ atomic mass

EIA

Enzyme-linked immunoassay

units)

Endoplasmic reticulum

Michaelis constant

432

Abbreviations

LDH

Lactate dehydrogenase

QH₂

Reduced coenzyme Q (ubiqui-

LDL

Low-density lipoprotein

nol)

Molarity (mol L^-1)

Gas constant

Mab

Monoclonal antibody

rER

Rough endoplasmic reticulum

MAP kinase

Mitogen-activated protein

RES

Reticuloendothelial system

kinase

RFLP

Restriction fragment length

MHC

Major histocompatability

polymorphism

complex

RIA

Radioimmunoassay

MPF

Maturation-promoting factor

RNA

Ribonucleic acid

mRNA

Messenger ribonucleic acid

ROS

Reactive oxygen species

Nucleotide with any base

Reversed phase (of silica gel)

NAD⁺

Oxidized nicotinamide adenine

rRNA

Ribosomal ribonucleic acid

dinucleotide

Svedberg (unit of sedimenta-

NADH

Reduced nicotinamide adenine

tion coef cient)

dinucleotide

SAH

S-adenosyl L-homocysteine

NADP⁺

Oxidized nicotinamide adenine

SAM

S-adenosyl L-methionine

dinucleotide phosphate

SDS

Sodium dodecylsulfate

NADPH

Reduced nicotinamide adenine

sER

Smooth endoplasmic reticulum

dinucleotide phosphate

Stereospecific numbering

NeuAc

N-acetylneuraminic acid

snRNA

Small nuclear ribonucleic acid

Nanometer (10^-9 m)

Sarcoplasmic reticulum

ODH

2-Oxoglutarate dehydrogenase

ssDNA

Single-stranded DNA

PAGE

Polyacrylamide gel electropho-

TBG

Thyroxine-binding globulin

resis

THB

Tetrahydrobiopterin

Pan

Pantetheine

THF

Tetrahydrofolate

PAPS

Phosphoadenosine

TLC

Thin-layer chromatography

phosphosulfate

TPP

Thiamine diphosphate

PCR

Polymerase chain reaction

TRH

Thyrotropin-releasing hor-

PDH

Pyruvate dehydrogenase

mone (thyroliberin)

PEG

Polyethylene glycol

Tris

Tris(hydroxymethyl)aminome-

PEP

Phosphoenolpyruvate

thane

pH value

tRNA

Transfer ribonucleic acid

Inorganic phosphate

TSH

Thyroid-stimulating hormone

Protein kinase

(thyrotropin)

PLP

Pyridoxal phosphate

UDP

Uridine 5 -diphosphate

Protein phosphatase

UMP

Uridine 5 -monophosphate

PPP

Pentose phosphate pathway

UTP

Uridine 5 -triphosphate

Plastoquinone

Ultraviolet radiation

PRPP

5-Phosphoribosyl 1-diphos-

Vmax, V

Maximal velocity (of an

phate

enzyme)

Photosystem

VLDL

Very-low-density lipoprotein

PTH

Parathyroid hormone

Oxidized coenzyme Q (ubiqui-

none)

Quantities and units

433

Quantities and units

1. SI base units

Quantity

SI unit

Symbol

Remarks

Length

Meter

1 yard (yd) = 0.9144 m

1 inch (in) = 0.0254 m

1 Å = 10^-10 m = 0.1 nm

Mass

Kilogram

1 pound (lb) = 0.4536 kg

Time

Second

Current strength

Ampere

Temperature

Kelvin

°C (degree Celsius) = K - 273.2

Fahrenheit: °C = 5/9 (°F - 32)

Light

Candela

Amount of substance

Mol

mol

2 Derived units

Quantity

Unit

Symbol

Derivation

Remarks

Frequency

Hertz

-1

Volume

Liter

10^-3 m³

1 U.S. gallon (gal) = 3.785 L

Force

Newton

kg m s^-2

Pressure

Pascal

N m^-2

1 bar = 10⁵ Pa

1 mmHg = 133.3 Pa

Energy, work, heat

Joule

N m

1 calorie (cal) = 4.1868 J

Power

Watt

J s^-1

Electrical charge

Coulomb

A s

Voltage

Volt

W A^-1

Concentration

Molarity

mol L^-1

Molecular mass

Dalton

1.6605

10^-24

Molar mass

Molecular weight

Nondimensional

Reaction rate

mol s^-1

Catalytic activity

Katal

kat

mol s^-1

1 unit (U) = 1.67

10^-8 kat

Specific activity

kat

(kg

Usually: U

(mg enzyme)^-1

enzyme)^-1

Sedimentation

Svedberg

10^-13 s

coef cient

Radioactivity

Becquerel

Decays s^-1

1 curie (Ci) = 3.7

10¹⁰ Bq

3 Multiples and fractions

4 Important constants

Factor Prefix Sym- Example

General gas

R = 8.314 J mol^-1 K^-1

bol

constant, R

Loschmidt

N = 6.0225

10⁹

Giga G

GHz = 10⁹

hertz

(Avogadro)

10⁶

Mega M

MPa = 10⁶

pascal

number, N

10³

Kilo

kJ = 10³ joule

-1

(number of

10^-3

Milli

mM = 10-3 mol

particles per

10^-6

Micro

µV = 10^-6 volt

mol)

10^-9

Nano

nkat = 10^-9 katal

-1

Faraday constant F F = 96480 C mol

10^-12

Pico

pm = 10^-12 meter

434