Biochemistry and molecular biology:
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| Main Authors: | , |
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| Format: | Book |
| Language: | English |
| Published: |
Oxford [u.a.]
Oxford Univ. Press
2005
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| Edition: | 3. ed. |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XXXIII, 582 S. Ill., graph. Darst. |
| ISBN: | 0199271992 |
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MARC
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| 100 | 1 | |a Elliott, William H. |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Biochemistry and molecular biology |c William H. Elliott ; Daphne C. Elliott |
| 250 | |a 3. ed. | ||
| 264 | 1 | |a Oxford [u.a.] |b Oxford Univ. Press |c 2005 | |
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| _version_ | 1804133115715649536 |
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| adam_text | Brief content
Diseases and medically relevant topics xxix
List of abbreviations xxxi
Part i Basic concepts of life
1 The basic molecularthemes of life 3
2 Cells and viruses 15
3 Energy considerations in biochemistry 27
Part 2 Structure and function of proteins
and membranes
4 The structure of proteins 47
5 Methods in protein investigation 74
6 Enzymes 90
7 The cell membrane and membrane proteins 105
8 Muscle contraction, the cytoskeleton, and
molecular motors 130
Part 3 Metabolism
9 Food digestion, absorption, distribution to
the tissues, and appetite control 151
10 Biochemical mechanisms involved in
transport, storage, and mobilization of
dietary components 168
11 Principles of energy release from food 184
12 Glycolysis, the citric acid cycle, and the
electron transport system: reactions involved
in these pathways 196
13 Energy release from fat 226
14 The synthesis of fat and related compounds 233
15 Synthesis of glucose (gluconeogenesis) 247
s
16 Strategies for metabolic control and their
application to carbohydrate and fat metabolism 255
17 Why should there be an alternative pathway of
glucose oxidation? The pentose phosphate
pathway 279
18 Raising electrons of water back up the energy
scale—photosynthesis 285
19 Amino acid metabolism 295
20 Enzymic protective mechanisms in the body 312
21 Nucleotide synthesis and metabolism 324
Part 4 Information storage and utilization
22 DNA and genomes 341
23 DNA synthesis, repair, and recombination 356
24 Gene transcription and control 380
25 Protein synthesis and controlled protein
breakdown 408
26 Protein targeting—how proteins are delivered
to their cellular destinations 432
27 Signal transduction 452
28 Manipulating DNA and genes 482
Part 5 The immune system, cell cycle,
apoptosis, and cancer
29 The immune system 509
30 Cell cycle control, apoptosis, and cancer 524
Figure acknowledgements 538
Answers to problems 540
Index of diseases and medically relevant topics 567
Index 569
Contents
Preface v
Acknowledgements ix
List of abbreviations xxxi
¦k^ dS Parti Basic concepts of life
Chapter 1 The basic molecular themes of life 3
Unity of life at the molecular level 3
Living cells obey the laws of physics and chemistry: the
energy cycle in life 3
• ATP (adenosine triphosphate) is the universal
energy currency in life 4
Types of molecule found in living cells 4
• Small molecules 5
• The macromolecular constituents of cells 5
Proteins 5
• Catalysis of reactions by enzyme proteins is
central to the existence of life 5
Evolution of proteins 7
• Development of new genes 7
DNA (deoxyribonucleic acid) 7
• DNA can direct its own replication 8
Junk DNA 9
Molecular recognition by proteins io
Noncovalent or weak chemical bonds io
How did it all start? io
• The RNA world n
The new omics phase of biochemistry and
molecular biology 12
Summary 13
Further reading 14
Chapter 2 Cells and viruses 15
Cells are the units of all living systems 15
Classification of organisms 15
• Prokaryotic cells 15
Cell division in prokaryotes 16
• Eukaryotic cells 17
Eukaryotic cell growth and division 2 0
Stem cells 20
• Mitosis and cell division in eukaryotic cells 21
• Meiosis 21
Viruses 23
• Genetic material of viruses 24
• Some examples of viruses of special interest 24
• Retroviruses 25
Summary 25
Further reading 26
Problems 26
Chapter 3 Energy considerations in biochemistry 27
• What determines whether a chemical reaction is
possible? 27
• Reversible and irreversible reactions and AG values 28
• The importance of irreversible reactions in the strategy
of metabolism 29
• Why is this metabolic strategy used in the cell? 29
• How are AG values obtained? 30
• Standard free energy values and equilibrium constants 30
• Given that a reaction has a negative AG value, what
determines whether it actually takes place at
a perceptible rate in the cell? 30
How is food breakdown in cells coupled to drive
energy requiring reactions? 31
• The high energy phosphate compound 32
What is a high energy phosphate compound ? 32
Xvi CONTENTS
• What are the structural features of high energy
phosphate compounds? 33
• What transports the—® around the cell? 35
• How does ATP perform chemical work? 35
Calculation of A6 value 36
• HowdoesATPdriveothertypesofwork? 37
• A note on the relationship between AMP, ADP, and ATP 37
Covalent and noncovatent bonds 37
• What causes weak bond formation and breakage? 39
• The vital role of weak bonds in molecular recognition 39
Appendix: Buffers and pKa values 39
• pKa values and their relationship to buffers 40
Summary 42
Further reading 42
Problems 42
jL^Kf Part 2 Structure and function
%*fc|V of proteins and membranes
Chapter 4 The structure of proteins 47
The primary structure of proteins 47
• What is a native protein? 48
• What are the basic considerations which determine the
folded structure of a protein? 48
• Structures of the 20 amino acids 49
Hydrophobic amino acids 49
Hydrophilic amino acids 50
Amino acids for special purposes 50
lonization of amino acids 51
Symbols foramina acids 51
The different levels of protein structure—primary,
secondary, tertiary, and quaternary 52
• Secondary structure of proteins 52
The a helix 52
The ^ pleated sheet 53
Connecting loops 54
• Tertiary structure of proteins 54
How do the three motifs—the a helix, the ^ pleated sheet, and
connecting loops—make up a protein ? 54
What forces hold the tertiary structure in position? 55
Where do the disulphide orS—S covalent bonds come into
protein structure? 55
• Quaternary structure of proteins 56
Protein homologies and evolution 57
Protein domains 57
• Domain shuffling 57
The problem of protein folding 58
• Membrane proteins 58
• Conjugated proteins 58
Extracellular matrix proteins 58
• Structure of collagens 59
Box4.1 Genetic diseases of collagen 61
• Structure of elastin 61
• Structure of proteoglycans 61
• Adhesion proteins of the extracellular matrix 63
• Integrins are important signalling proteins 64
• Myoglobin and haemoglobin—an illustration of how
protein structure is related to function 64
• Myoglobin 65
• Structure of haemoglobin 65
• Binding of oxygen to haemoglobin 66
How is the sigmoidal oxygen saturation curve achieved? 66
• Theoretical models to explain protein allosterism 67
• Mechanism of the allosteric change in
haemoglobin 67
• The essential role of 2:3 bisphosphoglycerate (BPG) in
haemoglobin function 68
• Effect of pH on oxygen bindingto haemoglobin 69
Role ofpH changes in oxygen and C02 transport 69
Box 4.2 Sickle cell anaemia and thalassaemias 7°
pH buffering in the blood 71
Summary 7*
Further reading 72
Problems T1
Chapter 5 Methods in protein investigation 74
Purification of proteins 74
• Column chromatography 75
• SDSpolyacrylamidegelelectrophoresis 76
Immunological detection of proteins 77
Methods of protein sequencing 78
• The role of databases in protein sequencing 78
• Deduction ofaminoacid sequences of proteins
from the base sequence of genes 79
Determination of the three dimensional
structure of proteins 79
• X ray diffraction 79
• Nuclear magnetic resonance 80
• Homology modelling 80
• An exercise in obtaining a 3 D structure from
a protein database 80
Analysis of proteins by mass spectrometry 80
• Introduction 80
Mass spectrometers consist of three principal components 80
• lonization methods for protein and peptide MS 80
• Types of mass analyser 81
Quadrupole (Q) 81
Time of flight (TOF) 81
Ion trap 81
• Types of mass spectrometer 81
Single analyser mass spectrometers 81
Tandem mass spectrometers (MS/MS) 81
• Identification of proteins using MS for peptide
mass analysis ( fingerprinting ) and database
searching 81
Identification of proteins by limited sequencing and
database searching 82
• Sequencing a protein by MS 83
• Molecular weight determination of proteins 83
• Analysis of posttranslational modification of proteins 83
Proteomics and MS 83
Bioinformatics and databases 84
• A bioinformatics overview 84
Database website addresses 85
Appendix: An example of how the structure of
a protein can be obtained from the protein data bank (PDB) 85
Summary 87
Further reading 88
Problems 89
Chapter 6 Enzymes 90
Enzyme catalysis 90
• The nature of enzyme catalysis 91
• The induced fit mechanism of enzyme catalysis 92
Enzyme kinetics 93
• Hyperbolic kinetics of a classical enzyme 93
• Allosteric enzymes 95
CONTENTS xvi
General properties of enzymes 95
• Nomenclature of enzymes 95
• Isozymes 95
• Enzyme cofactors and activators 95
• Effect of pH on enzymes 96
• Effect of temperature on enzymes 96
• Effect of inhibitorson enzymes 97
Reversible and irreversible inhibitors 97
Competitive and noncompetitive inhibitors 97
What are the structural features of enzyme proteins that
confer catalytic activity on them? 98
• Mechanism of the chymotrypsin reaction 98
• The catalytic triad of the active centre 98
• The reactions at the catalytic centre of
chymotrypsin 99
• What is the function of the aspartate residue of the
catalytic triad? 101
• Other serine proteases 101
• A brief description of othertypes of protease 101
Summary 102
Further reading 103
Problems 104
Chapter 7 The cell membrane and
membrane proteins 105
Basic lipid architecture of membranes 105
• The polar lipid constituents of cell membranes 105
Glycerophospholipids 106
• What are the polar groups attached to
the phosphatidic acid? 107
Sphingolipids 108
• Membrane lipid nomenclature 109
• Why are there so many different types of
membrane lipid? 110
• The fatty acid components of membrane lipids 110
• What is cholesterol doing in membranes? 111
• The self sealing character of the lipid bilayer 111
• Permeability characteristics of the lipid bilayer 112
Membrane proteins and membrane design n2
Structures of integral membrane proteins 112
• Anchoring of peripheral membrane proteins
to membranes n^
• Glycoproteins n^
i CONTENTS
Functions of membranes 5
• Transport of substances in and out of the cell 115
Active transport 115
Calculation of energy required fortransport 115
Mechanism of the Na /K* pump 115
Box 7.1 Cardiac glycosides 116
Sym port systems 117
Antiport systems 117
Uniport systems 117
Passive transport or facilitated diffusion 118
• Gated ion channels 118
• Mechanism of the selectivity of the potassium channel 118
• Nerve impulse transmission 120
Box 7.2 Cholinesterase inhibitors and
Alzheimer s disease 121
The acetykholine gated Na /K channel oracetylcholine receptor 121
How does acetylcholine binding to a membrane receptor
result in a nerve impulse? 121
How is the initial signal propagated along nerve axons? 122
Mechanism for ensuring that the nerve impulse only goes forward 124
Mechanism of control of the voltage gated Na and K* channels 124
• Myelinated neurons permit more rapid
nerve impulse transmission 125
Why doesn t the Na /K pump conflict with the
propagation of action potentials? 125
• Role of the cell membrane in maintainingthe
shape of the cell 125
• Cell cell interactions—tight junctions, gap
junctions, and cellular adhesive proteins 126
Box 7.3 Membrane targeted antibiotics 127
Summary 127
Further reading 128
Problems 129
Chapter 8 Muscle contraction,
the cytoskeleton, and molecular motors 130
Muscle contraction 130
• Areminderofconformationalchangesin proteins 130
Types of muscle cell and their energy supply 130
• Structure of skeletal striated muscle 131
Structure of the myopbril 131
How does the sarcomere shorten? 131
Structure and action of thick and thin filaments 132
• How does the myosin head convert the energy of ATP
hydrolysis into mechanical force on the actin filament? 133
Mechanism of the conformational changes in the myosin head 133
Box 8.1 Muscular dystrophy 134
How is contraction in voluntary striated muscle
controlled? 136
• How does Ca2 trigger contraction? 136
Box 8.2 Malignant hyperthermia 138
How does smooth muscle differ in structure and
control from striated muscle? 138
• Control of smooth muscle contractions 138
HowdoesCa2 control smooth muscle contraction? 138
The cytoskeleton 139
• Molecular motors and movements in cells 139
The role of actin and myosin in nonmuscle cells 139
• Structural role of actin and its involvement in
cell movement 14°
Mechanism of contraction in nonmuscle cells 14°
• The role of actin and myosin in intracellular
transport of vesicles M1
Microtubules, cell movement, and intracellular
transport J4*
• Microtubules and intracellulartransport *42
Molecular motors: kinesins and dyneins *42
Role of microtubules in cell movement *43
Role of microtubules in mitosis *43
Intermediate filaments *43
Box 8.3 Effects of drugs on the cytoskeleton *44
Summary J44
Further reading *45
Problems « 6
»^?S Part 3 Metabolism
Chapter 9 Food digestion, absorption, distribution
to the tissues, and appetite control 151
Chemistry of foodstuffs «*
Digestion and absorption 1 $2
• Anatomy of the digestive tract 152
• What are the energy considerations in digestion
and absorption? 152
• A major problem in digestion—why doesn t the body
digest itself? 153
Zymogen or proenzyme production J
Protection of intestinal epithelial cells by mucous *
Digestion of proteins 153
• HCI production in the stomach 153
• Pepsin, the proteolytic enzyme of the stomach 153
• Completion of protein digestion in the small intestine 154
• Activation of the pancreatic proenzymes 154
• Absorption ofamino acids into the bloodstream 155
Digestion of carbohydrates 155
• Digestion of starch 156
• Digestion of lactose 156
• Absorption of monosaccharides 157
Digestion and absorption of fat 157
• Resynthesis of TAG in intestinal cells 158
• Chylomicrons 158
• Digestion of other components of food 159
• Outline of fuel distribution and utilization by the
different tissues of the body 160
Storage of food com portents i n the body 160
• How are the different food components stored in cells? 160
Glucose storage as glycogen 160
Storage of fat in the body 160
Are amino acids stored by the body? 161
• Characteristics of different tissues in terms of
energy metabolism 161
• Overall control of fuel distribution in the body
by hormones 163
• Postprandial condition 163
• Fasting condition 163
• Prolonged fasting or starvation 163
• The emergency situation—fight or flight 164
Regulation of food intake: appetite control 164
• Hormones which control appetite 164
• How do these hormones control appetite? 164
• Can hormones be used therapeutically to control obesity? 165
Summary 165
Further reading 166
Problems 167
Chapter 10 Biochemical mechanisms involved
in transport, storage, and mobilization of
dietary components 168
Glucose traffic in the body 168
• Mechanism of glycogen synthesis 168
How is energy injected into the process? 169
CONTENTS Xlx
G i P is converted to the activated form, UDPG 170
Adding branches to glycogen 170
• Breakdown of glycogen to release glucose into the blood 171
Removing branches from glycogen 172
• Key issues in the interconversion of glucose and glycogen 173
• Why does liver have glucokinase and the other
tissues hexokinase? 173
• What happens to other sugars absorbed from the
intestine? 173
Galactose metabolism 174
Box 10.1 Uridyl transferase deficiency and galactosaemia 175
Amino acid traffic in the body (in terms of fuel logistics) 176
Fat and cholesterol traffic in the body 176
• Uptake of fat from chylomicrons into cells 176
• Logistics of fat and cholesterol movement in the body 176
• An overview 176
• Utilization of cholesterol in the body 1/7
• Lipoproteins involved in fat and cholesterol
movement in the body 178
• Apolipoproteins 179
• Mechanism of TAG and cholesterol transport from the
liver and the reverse cholesterol transport in the body 179
The role of HDL in cholesterol transport 179
How does cholesterol exit cells to be picked up by HDL ? 179
Cholesterol homeostasis in cells 180
Box 10.2 Inhibitors of cholesterol synthesis 181
• Release of FFA from adipose cells 181
• How are FFA carried in the blood? 181
Summary 182
Further reading 182
Problems 183
Chapter 11 Principles of energy release
from food 184
Biological oxidation and hydrogen transfer systems 184
NAD —an important electron carrier 185
FAD and FMN are also electron carriers 186
Energy release from glucose 186
• The main stages of glucose oxidation 186
• Stage 1 in the release of energy from glucose; glycolysis 186
Anaerobic glycolysis 186
• Stage 2 of glucose oxidation: the citric acid cycle 188
How is pyruvate fed into the citric acid cycle? 188
What is coenzyme A? 188
Oxidative decarboxylation of pyruvate 189
XX CONTENTS
• Stage 3 of glucose oxidation: electron transport to oxygen 189
• The electron transport chain—a hierarchy of electron carriers 189
Redox potentials 189
Determination of redox potentials 190
Electrons are transported in a stepwise fashion 190
Calculation of the relationship between
the AG0 value and the £ o value 191
Energy release from oxidation of fat 191
Energy release from oxidation of amino acids 192
The interconvertibility of fuels 192
Boxll.l A survey of vitamins 194
Summary 194
Problems 195
Chapter 12 Glycolysis, the citric acid cycle, and
the electron transport system: reactions
involved in these pathways 196
Stage 1—glycolysis 196
• Glucose or glycogen? 196
• Why use ATP here at the beginning of glycolysis? 197
Why is glucose 6 phosphate converted to fructose 6 phosphate? 197
Splitting fructose bisphosphate to two C3 compounds 197
• A note on the AG0 and AG values for the aldolase reaction 198
• Interconversion of dihydroxyacetone phosphate and
glyceraldehyde 3 phosphate 199
• Gyceraldehyde 3 phosphate dehydrogenase— an oxidation
linked to ATP synthesis 199
• The final steps in glycolysis 200
• The ATP balance sheet from glycolysis 202
• Reoxidation of cytoplasmic NADH from glycolysis by
electron shuttle systems 202
The glycerolphosphate shuttle 202
The malate aspartate shuttle 202
• Transport of pyruvate into the mitochondria 203
Conversion of pyruvate to acetyl CoA—a preliminary
step before the citric acid cycle 203
• Components involved in the pyruvate
dehydrogenase reaction 204
Stage 2—the citric acid cycle 205
• The citric acid cycle as a water splitting machine 205
• A simplified version of the citric acid cycle 205
• Mechanisms of the citric acid cycle reactions 206
The synthesis of citrate 206
Conversion of citrate to a ketoglutarate 206
Citrate — isocitrate 206
Isocitrate dehydrogenase 207
The C^ part of the cycle 207
Generation of GTP coupled to splitting ofsuccinyl CoA 208
Conversion ofsuccinate to oxaloacetate 208
• What determines the direction of the citric acid cycle? 209
• Stoichiometry of the cycle 209
• Topping up the citric acid cycle 210
Biotin is the cofactor for CO, activation 210
Stage 3—the electron transport chain that
conveys electrons from NADH and FADH2 to oxygen 211
• The electron transport chain 211
Where does it take place? 211
Nature of the electron carriers in the chain 211
Arrangementofthe electron carriers 212
• Oxidative phosphorylation—the generation of ATP
coupled to electron transport 213
The chemiosmotic theory of oxidative phosphorylation 214
• How are protons ejected? 214
TheQ cycle in complex III ejects protons from mitochondria 215
Complex IV also creates a proton gradient 216
• ATP synthesis byATPsynthase is driven by the
proton gradient 2l6
• Structure of ATP synthase 217
TheFi unit and its role in the conversion ofADP+P/toATP 217
Activities of the enzyme catalytic centres on the F, subunit 217
Structure of the Fo unit and its role 219
• Mechanism by which proton flow causes rotation of Fo 219
• Transport of ADP into mitochondria and ATP out 221
• The balance sheet of ATP production by electron
transport 222
• Yield of ATP from the oxidation of a molecule of
glucose to CO2 and H2O 222
• Is ATP production the only use that is made of the
potential energy in the proton motive force? 222
Box 12.1 Inhibitors of oxidative phosphorylation 223
Summary 223
Further reading 22*
Problems *
Chapter 13 Energy release from fat 226
Mechanism of acetyl CoA formation from fatty acids 227
• Activation of fatty acids by formation of fatty
acyl CoA derivatives 227
• Transport of fatty acyl CoA derivatives into
mitochondria 227
• Conversion of fatty acyl CoA to acetyl CoA molecules
inside the mitochondrion by/3 oxidation 228
• Energy yield from fatty acid oxidation 228
Oxidation of unsaturated fat 229
Is the acetyl CoA derived from fat breakdown always
directly fed into the citric acid cycle? 229
• How is acetoacetate made from acetyl CoA? 229
Utilization ofacetoacetate 229
Oxidation of odd numbered carbon chain fatty acids 230
Peroxisomal oxidation of fatty acids 231
• Where to now? 231
Summary 231
Further reading 232
Problems 232
Chapter 14 The synthesis of fat and
related compounds 233
Mechanism of fat synthesis 233
• General principles of the process 233
• Synthesis of malonyl CoA 233
• The acyl carrier protein (ACP) and the /3 ketoacyl synthase 234
• Mechanism of fatty acyl CoA synthesis 234
• Organization of the fatty acid synthesis process 234
• The reductive steps in fatty acid synthesis 235
WhatisNADPM? 236
• Where does fatty acid synthesis take place? 236
Synthesis of unsaturated fatty acids 237
Box 14.1 Omega fatty acids and diet 238
Synthesis of TAG and membrane lipids from fatty acids 238
Synthesis of new membrane lipid bilayer 238
• Synthesis of glycerophospholipids 239
• Synthesis of new membrane lipid bitayer 241
Synthesis of prostaglandins and related compounds 242
• The prostaglandins and thromboxanes 242
Box 14.2 Nonsteroidal anti inflammatory drugs (NSAIDs) 243
• Leukotrienes 244
• Synthesis of cholesterol 244
• Conversion of cholesterol to steroid hormones 244
Summary 245
Further reading 245
Problems 245
CONTENTS XXI
Chapter 15 Synthesis of glucose
(gluconeogenesis) 247
• Mechanism of glucose synthesis from pyruvate 247
• What are the sources of pyruvate used by the liver for
gluconeogenesis? 248
• Synthesis of glucose from glycerol 250
• Effects of ethanol metabolism on gluconeogenesis 251
Effect of ethanol metabolism on the NADH/NAD ratio in the liver cell 251
• Synthesis of glucose via the glyoxylate cycle 252
Summary 253
Further reading 253
Problems 253
Chapter 16 Strategies for metabolic control and
their application to carbohydrate and fat
metabolism 255
Why are controls necessary? 255
• The potential danger of futile cycles in metabolism 256
How are enzyme activities controlled? 257
• Metabolic control by varyingthe amounts of enzymes is
not instantaneous 257
• Metabolic control by regulation of the activities of
enzymes in the cell 257
• Which enzymes in metabolic pathways are regulated? 257
• The nature of control enzymes 258
Allosteric control of enzymes 258
• The mechanism of allosteric control of enzymes 258
What causes the sigmoidal response of reaction velocity to
substrate concentration? 259
• Reversibility of allosteric control 259
• Allosteric control is a tremendously powerful metabolic concept 259
Altosteric enzymes often have multiple allosteric modulators 260
Control of enzyme activity by phosphorylation 260
• Protein kinases and phosphatases 260
• Control by phosphorylation usually depends on chemical
signals from other cells 261
General aspects of the hormonal control of metabolism 261
• How do glucagon, epinephrine, and insulin work? 261
• What is a second messenger? 261
• The second messenger for glucagon and epinephrine is
cyclic AMP (cAMP) 262
XxM CONTENTS
Control of carbohydrate metabolism 263
• Control of glucose uptake into cells 263
• Control of glycogen metabolism 264
Control of glycogen breakdown in muscle 264
• Mechanism of muscle phosphorylase activation bycAMP 265
• Control of glycogen breakdown in the liver 266
• Reversal of phosphorylase activation in muscle and liver 266
• Control of glycogen synthase 267
cAMP causes inactivation of glycogen synthase 267
Mechanism of insulin activation of glycogen synthase 267
How does insulin inactivate GSK3? 267
• Control of glycolysis and gluconeogenesis 268
Allosteric controls 268
Hormonal control of glycolysis and gluconeogenesis 269
Control of glycolysis and gluconeogenesis pathways by
fructose 2:6 bisphosphate (F 2 .6 BP) 269
Control ofpyruvate kinase 270
Glucocorticoid stimulation of gluconeogenesis 271
• Control ofpyruvate dehydrogenase, the citric acid
cycle, and oxidative phosphorylation 271
Controls of fatty acid oxidation and synthesis 272
• Nonhormonal controls 272
• Hormonal controls on fat metabolism 273
• Regulation of the cellular ATP level by AMP activated
protein kinase 273
• Insulin and diabetes 274
• A concluding note on metabolic control analysis 275
Summary 276
Further reading 277
Problems 278
Chapter 17 Why should there be an
alternative pathway of glucose oxidation?
The pentose phosphate pathway 279
The oxidative section produces equal amounts of
ribose 5 phosphate and NADPH 279
• The nonoxidative section and its purpose 279
• Conversion of surplus ribose 5 phosphate to
glucose 6 phosphate 280
• Glucose 6 phosphate to ribose 5 phosphate
production without NADPH generation 281
• Where does the complete oxidation of glucose
come into all of this? 282
Box 17.1 Why do red blood cells have the pentose
phosphate pathway? 283
Summary 283
Further reading 284
Problems 284
Chapter 18 Raising electrons of water back up
the energy scale—photosynthesis 285
• Overview 285
• Site of photosynthesis—the chloroplast 286
The light dependent reactions of photosynthesis 286
• The photosynthetic apparatus and its organization
in the thylakoid membrane 286
• How is light energy captured? 287
• Mechanism of light dependent reduction of NADP+ 288
• Photosystem II 288
• Photosystem I 288
The water splitting centre ofPSII 289
• How is ATP generated? 289
An explanatory note 290
The dark reactions of photosynthesis 290
• How is CO2 converted to carbohydrate? 29°
Getting from 3 phosphoglycerate to glucose 290
3 Phosphoglycerate is formed from ribulose i:; bisphosphate 290
Where does the ribulose i:s bisphosphate come from? 291
• Has evolution slipped up a bit? 29l
• The C4 pathway 292
Summary 293
Further reading 294
Problems 294
Chapter 19 Amino acid metabolism 295
Nitrogen balance of the body 296
General metabolism of amino acids 296
• Aspects of amino acid metabolism 296
• Glutamate dehydrogenase has a central role in the
deamination of amino acids 297
Mechanism oftransamination reactions 29°
Special deamination mechanisms forserine and cysteine 29°
• Fate of the keto acid or carbon skeletons of
deaminated amino acids 299
• Genetic errors in amino acid metabolism cause diseases 300
Phenylketonuria 300
Maple syrup disease 301
Alcaptonuria 301
• Methionineand transfer of methyl groups 301
What ore the methyl groups transferred to? 302
Synthesis of amino acids 302
• Synthesis of glutamic acid 302
• Synthesis of aspartic acid and alanine 302
• Synthesis of serine 302
• Synthesis of glycine 303
Haem and its synthesis from glycine 303
• Destruction of haem 303
Box 19.1 Acute intermittent porphyria 304
• Synthesis of epinephrine and norepinephrine 304
The urea cycle 305
• Mechanism of arginine synthesis 306
• Conversion of citrulline to arginine 307
• How is the amino nitrogen transported from
extrahepatic tissues to the liver to be converted
into urea? 308
Transport of ammonia in the blood as glutamine 308
Transport of amino nitrogen in the blood as alanine 309
• Diseases due to urea cycle deficiencies 309
• Alternatives to urea formation exist in different animals 309
Summary 310
Further reading 310
Problems 311
Chapter 20 Enzymic protective mechanisms
in the body 312
Blood clotting 312
• What are the signals that clot formation is needed? 313
• How does thrombin cause thrombus (clot) formation? 313
• Keeping clotting in check 314
• Rat poison, blood clotting, and vitamin K 315
Protection against ingested foreign chemicals (xenobiotics) 315
• CytochromeP450 316
• Medical significance of P450s 316
• Secondary modification—addition of a polargroupto
products oftheP450 attack 316
The glucuronidation system 316
The glutathione S transferase system 316
• Multidrug resistance 3J7
Protection of the body against its own proteases 317
CONTENTS xxil
Protection against reactive oxygen species 318
• Mopping up oxygen free radicals with vitamins C and E 319
• Enzymic destruction of superoxide by superoxide
dismutase 319
The glutathione peroxidase glutathione reductase
strategy 319
Protection against hypoxia (low oxygen levels) 320
• Mechanism of the hypoxia response 320
Summary 321
Further reading 322
Problems 323
Chapter 21 Nucleotide synthesis and
metabolism 324
Structure and nomenclature of nucleotides 324
• The sugarcomponent of nucleotides 324
• The base component of nucleotides 325
Nomenclature 325
Structure of the bases 325
• Attachment of the bases in nucleotides 325
Synthesis of purine and pyrimidine nucleotides 326
• Purine nucleotides 326
PRPP—the ribotidation agent 326
• The denovo purine nucleotide synthesis pathway 327
The one carbon transfer reaction in purine nucleotide
synthesis 327
Where does the formyl group in N formyl FH,t come from ? 329
How are ATP and GTP produced from AMP and GMP? 329
• The purine salvage pathway 330
What is the physiological role of the purine salvage pathway? 331
• Formation of uric acid from purines 331
• Control of purine nucleotide synthesis 332
• Synthesis of pyrimidine nucleotides 332
• How are deoxyribonucleotides formed? 333
Thymidylate synthesis—conversion ofdUMP to dTMP 333
Medical effects of folate deficiencies 335
• Thymidylate synthesis is targeted by anticancer
agents such as the antifolate, methotrexate 33;
Vitamin B,2 deficiency in cells and the folate methyl trap 335
Summary 336
Further reading 336
Problems 336
;j JCXiv CONTENTS
¦ Part 4 Information storage
and utilization
Chapter 22 DNA and genomes 341
What are nucleic acids? 341
The primary structure of DNA 341
• What are the bases in DNA? 342
• Attachment of the bases to deoxyribose 342
• The physical properties of the polynucleotide
components 342
• Structure of the polynucleotide of DNA 342
• Why deoxyribose? Why not ribose? 343
• The DNA double helix 344
Complementary base pairing 344
• DNA chains are antiparallel; what does this mean? 346
How is the DNA packed into a nucleus? 348
• How does the described structure of DNA correlate
with the compact eukaryotic chromosomes visible in
the light microscope? 349
• The mitochondrial genome 350
What is a gene in molecular terms? 350
• Some variations on the standard gene 351
• Size and organization of genomes 351
Organization of the human genome 351
• Repetitive DNA sequences 351
• Transposon movement 352
• Noncoding RNAs are challengingthe basic dogma
of moleculargenetics 352
Discovery ofmicrogenes (orsmall noncoding RNAs 352
• RNA interference (RNAi) 353
• Where are we now? 353
Summary 353
Further reading 354
Problems 355
Chapter 23 DNA synthesis, repair,
and recombination 356
Overall principle of DNA replication 356
Control of initiation of DNA replication in E. coli 357
Initiation and regulation of DNA replication in
eukaryotes 357
Unwinding the DNA double helix and supercoiling 358
• How are positive supercoils removed ahead of the
replicative fork? 359
The basic enzymic reaction catalysed by DNA
polymerases 361
How does a new strand get started? 362
The polarity problem in DNA replication 362
• Mechanism of Okazaki fragment synthesis 363
• Enzyme complex at the replicative fork in E. coli 364
The DNA sliding clamp and the clamp loading mechanism 364
• Processing the Okazaki fragments 364
How is fidelity achieved in DNA replication? 366
• Exonucleolytic proofreading 368
• Methyl directed mismatch repair 368
Repair of DNA damage in E. coli 369
Repair of double strand breaks 37°
The machinery in the eukaryotic replicative fork 371
• The problem of replicating the ends of eukaryotic
chromosomes 371
How is telomeric DNA synthesized? 373
Telomere shortening correlates with ageing 373
DNA damage repair in eukaryotes 373
Is the mechanism described above the only way in
which DNA is synthesized? 374
• DNA synthesis by reverse transcription 374
Homologous recombination 375
• Mechanism of homologous recombination inf. coli 375
Formation of cross over junctions by single strand invasion 37*
Separation of the duplexes 37^
• Recombination in eukaryotes 377
Summary 377
Further reading 377
Problems 37«
Chapter 24 Gene transcription and control 38°
Messenger RNA 380
• The structure of RNA 380
• How is mRNA synthesized? 380
• Some general properties of mRNA 3Sl
• Some essential terminology 381
• A note on where we go from here 382
Gene transcription in E. coli 382
• Whatdowe mean bythe 5 end of a gene? 383
• Phases of gene transcription 383
Initiation of transcription in E. coli 383
Separating the DNA strands 384
Termination of transcription 384
• The rate of gene transcription initiation in prokaryotes 384
• Control of transcription by different sigma factors 385
• Gene control in f. coli: the lac operon 385
• Structure of the E. colilac operon 386
Gene transcription in eukaryotic cells 387
• Capping the RNA transcribed by RNApolymerase II 387
• Split genes 387
Mechanism of splicing 387
Ribozymes and self splicing of RNA 389
• What is the biological status of introns? 390
What is the origin of split genes? 390
Alternative splicing or two (or more) proteins for the price of one gene 390
Mechanism of initiation of eukaryotic gene
transcription and its control 390
• Unpacking of the DNA for transcription 390
• A general overview of the differences in the initiation
and control of gene transcription in prokaryotes
and eukaryotes 391
• Types of eukaryotic genes and their controlling regions 392
Type II eukaryotic gene promoters 392
Enhancers 393
Transcription factors (activators) 393
• Most transcription factors themselves are regulated 394
• How do transcription factors promote transcriptional
initiation? 394
The role ofchromatin in eukaryotic gene control 394
How do transcription factors open up gene promoters? 394
• How is transcription initiated on the opened promoter? 396
Discovery of the mediator 397
The RNA polymerase II of eukaryotic cells 398
• Termination of transcription in eukaryotic cells 399
• Switching off the gene 399
mRNA stability and the control of gene expression 399
• Determinants of mRNA stability and their role in
gene expression control 399
Role ofthepolyA tail 399
Structural stability determinants ofmRNAs 399
CONTENTS XXV
Gene transcription in mitochondria 400
Genes that do not code for proteins 401
• The structure of DNA binding proteins 401
Helix turn helix proteins 401
Leucine zipper proteins 402
Helix loop helix proteins 402
Zinc finger proteins 403
Summary 403
Further reading 404
Problems 406
Chapter 25 Protein synthesis and controlled
protein breakdown 408
Essential basis of the process of protein synthesis 409
• The genetic code 409
• How are the codons translated? 410
• Transfer RNA 410
• The wobble mechanism 411
• How are amino acids attached to tRNA molecules? 411
Proofreading byaminoocyl tRNA ligases 412
Ribosomes 413
Initiation of translation 414
• Initiation of translation inf. coli 414
Once initiation is achieved, elongation is the next
step 416
• Cytoplasmic elongation factors in E. coli 416
• Mechanism of elongation in E. coli 416
• How is accuracy of translation achieved? 416
Mechanism of transtocation on the £. co// ribosome 418
Box 25.1 Effects of antibiotics and toxins on
protein synthesis 418
Termination of protein synthesis in E. coli 419
• Physical structure of the ribosome 419
• What is a polysome? 420
Protein synthesis in eukaryotes 420
Protein synthesis in mitochondria 420
Folding up of the polypeptide chain 421
• Chaperones (heat shock proteins) 421
Mechanism of action of molecular chaperones 422
• Enzymes involved in protein folding 423
Prion diseases and protein folding 424
XXVI CONTENTS
Translational control mechanisms 424
• Regulation of globin synthesis 424
• Translational control of proteins involved in haem
synthesis and iron metabolism 424
Programmed destruction of protein by proteasomes 425
• The structure of proteasomes 426
• Selection of proteins for destruction—the
ubiquitination system 427
• What determines which proteins are ubiquitinated? 427
• The role of proteasomes in the immune system 427
Summary 428
Further reading 429
Problems 431
Chapter 26 Protein targeting—how proteins
are delivered to their cellular destinations 432
A preliminary overview of the field 432
• Structure and function of the ER and Golgi apparatus 433
The importance of the GTP/GDP switch mechanism in
protein targeting 435
How are proteins translocated through the ER
membrane? 435
• Mechanism of cotranslational transport through
the ER membrane 435
• Folding of the polypeptides inside the ER 437
• Glycosylation of proteins in the ER lumen and
Golgi apparatus 437
• Vesicles involved in protein translocation from
the ER and Golgi 437
Lysosomes and the mechanism of their formation
by receptor mediated endocytosis 438
How are proteins sorted, packaged, and despatched
by the Golgi apparatus? 439
• Proteins to be returned to the ER 439
• Proteins destined for lysosomes 439
• Proteins to be secreted from the cell 439
Box 26.1 Lysosomal storage disorders 439
Mechanism of COP coated vesicle formation 440
• How does a vesicle find its target membrane? 440
Synthesis of integral membrane proteins and
their transport 441
• How is the membrane protein given the
correct orientation? 441
Posttranslational transport of proteins
into organetles 442
• Transport of proteins into mitochondria 442
• Targeting peroxisomal proteins 444
• Nuclear cytoplasmic traffic 444
• Why is there a nuclear membrane? 444
• The nuclear pore complex 444
• Nuclear localization signals 446
• Mechanism of nuclear cytoplasmic transport and
the role of guanine nucleotide binding proteins 446
• Regulation of nuclear transport by cell signals and
its role in gene control 448
Summary 449
Further reading 449
Problems 451
Chapter 27 Signal transduction 452
Overview 452
• Organization of this chapter 454
What are the signalling molecules? 454
• Neurotransmitters 454
• Hormones 454
• Cytokines and growth factors 455
Growth factors/cytokines and the cell cycle 456
• Vitamin D3 and retinoic acid 456
Intracellular receptor mediated responses 456
Box 27.1 Theglucocorticoid receptor and
anti inflammatory drugs 457
Classification of types of membrane receptor signalling
systems 458
• Bindingdomainsof signaltransduction proteins 459
• Terminating signals 460
Examples of signal transduction pathways 460
Signal transduction pathways from tyrosine
kinase receptors 461
• The Ras pathway 461
• Mechanism of the Ras signalling pathway 461
Concept ofthe GTP/GDPswitch mechanism, illustrated by
the Ras pathway 4*1
The MAP kinase cascade in the Ras pathway 4°2
Nomenclature ofthe protein kinases ofthe Ras pathway 4°3
Concept ofthe role of protein phosphatases, illustrated by
the Ras pathway 463
Box 27.2 Some deadly toxins work by increasing or
inhibiting dephosphorylation of proteins 464
• Concept of signal sorting in Ras type pathways 464
• The phosphatidylinositide 3 kinase (PI 3 kinase)
pathway and insulin signalling 465
• TheJAK/STATpathways: anothertype oftyrosine
kinase associated signalling system 466
Negative control of 1AK/STATpathways 467
• The G protein coupled receptors and associated
signal transduction pathways 468
• Overview 468
• Structure of G protein receptors 468
• Epinephrine signalling—a G protein pathway mediated
by cAMP as second messenger 468
Control ofcAMP levels in cells 469
GTPase activating proteins (GAPs) regulate G protein signalling 470
Different types of G protein receptor 470
How does cAMP control gene activities ? 470
Desensitization of the G protein receptors 471
• The phosphatidylinositol cascade: another example
of a G protein coupled receptorwhich works via a
different second messenger 471
• Othercontrolrolesofcalcium 472
• Vision: a process dependent on a G protein coupled
receptor 473
Transduction of the light signal 474
Signal transduction pathways using cGMP as
second messenger 475
• Activation ofaguanylatecyclase by nitric oxide 477
Summary 477
Further reading 478
Problems 480
Chapter 28 Manipulating DNA and genes 482
Basic methodologies 483
• Some preliminary considerations 483
• Cutting DNA with restriction endonucleases 483
• Separating DNA pieces 484
• Visualizing the separated pieces 484
• Detection of specific DNA fragments by nucleic acid
hybridization probes 484
• Southern blotting 484
Sequencing DNA 485
• Outline of the dideoxyDNA sequencing technique 485
How is this interpreted as a base sequence? 486
Automated DNA sequencing 487
CONTENTS XXVI
Amplification of DNA by the polymerase chain
reaction (PCR) 487
Joining DNA to form recombinant molecules 488
Cloning DNA 489
• Cloning in plasmids 489
• Cloning using bacteriophage A as vector 490
• Cloningin cosmids 491
Applications of recombinant DNA technology 492
• Production of human and other proteins 492
• Preparation of a cDNA library 492
• Expressing the cDNA in E. coli 493
• Site directed mutagenesis 494
• PCR in forensic science 494
• Locating disease producing genes 49 ,
• Knockout mice or gene targeting 496
Method of obtaining a ^pecifu qenc knockout 496
• The embryonic stem (E5) cell system 496
• Gene targeting 498
• Gene silencing by RNA interference (RNAi) 499
• Analysis of multiple gene expression in cells using
DNA microarrays 499
• Transgenic animals and plants 500
DNA databases and genomics
Summary 502
Further reading 503
Problems 504
¦ Part5 The immune system,
cell cycle, apoptosis, and
cancer
Chapter 29 The immune system 509
Overview 509
• The problem of autoimmune reactions 510
• The cells involved in the immune system 510
• There are two arms to the adaptive immune response 510
• Where is the immune system located in the body? 511
Antibody based or humoral immunity 511
• Structure of antibodies 511
• What are the functions of antibodies? 511
• The different classes of antibodies 512
• Generation of antibody diversity 512
XXVili CONTENTS
Activation of B cells to produce antibodies 514
• Deletion of potentially self reacting B cells in
the bone marrow 514
• The theory of clonal selection 515
• B cells must be activated before they can develop
into antibody secreting cells 515
Role of helper T cells 515
Activation of helper Tcells 516
Activation ofB cells by activated helper Tcells 516
• Role of the MHC proteins in presenting peptides
on the outside of cells 517
• Affinity maturation of antibodies 517
• Memory cells 517
T cells and cell mediated immunity 517
• Mechanism of action of cytotoxic (killerT) cells 519
CD proteins reinforce the selectivity of Tcell receptors for
the two classes of MHC protein 519
Why does the human immune system reject
transplanted human cells? 5i9
Monoclonal antibodies 520
Summary 521
Further reading 522
Problems 522
Chapter 30 Cell cycle control, apoptosis,
and cancer 524
The eukaryotic cell cycle 524
• Why the cell cycle must have controls 524
Cell cycle controls 52 $
• Cytokines and growth factor control in the cell cycle 525
• Cell cycle checkpoints 525
• Cell cycle controls depend on the synthesis and
destruction of cyclins 525
• Controls in G, are complex 525
• TheGj checkpoint 526
• How is DNA damage detected? 526
• Progression to S phase 526
• Progression to M phase 526
• Mitosis phase 526
Apoptosis 527
• An overview of what initiates apoptosis 527
Mechanism of stress damage induced apoptosis 528
The role ofcaspases in apoptosis 528
Death receptor mediated activation of apoptosis 528
Cancer 528
• General concepts 528
Most normal cells can divide only a limited
numberoftimes 529
Cancer cells have no limitation on the number of
cell divisions they can make 529
Types of abnormal cell multiplication 529
• Malignant Darwinism: cancer development involves
an evolutionary progression of mutations 53°
Development of colorectal cancer 53°
• Mutations cause cancer 53°
• Tumour promoters 531
• The types of genetic change involved in cancer 531
• Oncogenes 531
• How are oncogenes acquired? 532
A note on nomenclature of viral oncogenes 533
• Tumour suppression genes 533
• Mechanism of protection by the p53 gene 533
• Mechanism of protection by the retinoblastoma gene 534
• Molecular biology advances have potential for
development of new cancer therapies 534
Summary 534
Further reading 534
Problems 537
Figure acknowledgements 538
Answers to problems 54°
Index of diseases and medically relevant topics 5* 7
Index 569
Diseases and
relevant topic
Box4.1 Genetic diseases of collagen 61
Box 4.2 Sickle cell anaemia and thalassaemias 70
Box 7.1 Cardiac glycosides 116
Box 7.2 Cholinesterase inhibitors and Alzheimer s disease 121
Box 7.3 Membrane targeted antibiotics 127
Box 8.1 Muscular dystrophy 134
Box8.2 Malignant hyperthermia 138
Box 8.3 Effects of drugs on the cytoskeleton 144
Box 10.1 Uridyltransferase deficiency and galactosaemia 175
Box 10.2 Inhibitors of cholesterol synthesis 181
Box 11.1 A survey of vitamins 194
Box 12.1 Inhibitors of oxidative phosphorylation 223
medically
s
Box 14.1 Omega fatty acids and diet 238
Box 14.2 Nonsteroidal anti inflammatory drugs
(NSAIDs) 243
Box 17.1 Why do red blood cells have the pentose
phosphate pathway? 283
Box 19.1 Acute intermittent porphyria 304
Box 25.1 Effects of antibiotics and toxins on
protein synthesis 418
Box 26.1 Lysosomal storage disorders 439
Box 27.1 The glucocorticoid receptor and
anti inflammatory drugs 457
Box 27.2 Some deadly toxins work by increasing or
inhibiting dephosphorylation of proteins 464
|
| any_adam_object | 1 |
| author | Elliott, William H. Elliott, Daphne C. |
| author_facet | Elliott, William H. Elliott, Daphne C. |
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| author_sort | Elliott, William H. |
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| dewey-full | 572 |
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| dewey-search | 572 |
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| dewey-tens | 570 - Biology |
| discipline | Biologie Chemie |
| edition | 3. ed. |
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| publisher | Oxford Univ. Press |
| record_format | marc |
| spelling | Elliott, William H. Verfasser aut Biochemistry and molecular biology William H. Elliott ; Daphne C. Elliott 3. ed. Oxford [u.a.] Oxford Univ. Press 2005 XXXIII, 582 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Biochemie Molekularbiologie Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Molekularbiologe (DE-588)1023071983 gnd rswk-swf Biochemie (DE-588)4006777-4 gnd rswk-swf 1\p (DE-588)4123623-3 Lehrbuch gnd-content Biochemie (DE-588)4006777-4 s Molekularbiologie (DE-588)4039983-7 s DE-604 Molekularbiologe (DE-588)1023071983 s 2\p DE-604 Elliott, Daphne C. Verfasser aut HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013005712&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk 2\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Elliott, William H. Elliott, Daphne C. Biochemistry and molecular biology Biochemie Molekularbiologie Molekularbiologie (DE-588)4039983-7 gnd Molekularbiologe (DE-588)1023071983 gnd Biochemie (DE-588)4006777-4 gnd |
| subject_GND | (DE-588)4039983-7 (DE-588)1023071983 (DE-588)4006777-4 (DE-588)4123623-3 |
| title | Biochemistry and molecular biology |
| title_auth | Biochemistry and molecular biology |
| title_exact_search | Biochemistry and molecular biology |
| title_full | Biochemistry and molecular biology William H. Elliott ; Daphne C. Elliott |
| title_fullStr | Biochemistry and molecular biology William H. Elliott ; Daphne C. Elliott |
| title_full_unstemmed | Biochemistry and molecular biology William H. Elliott ; Daphne C. Elliott |
| title_short | Biochemistry and molecular biology |
| title_sort | biochemistry and molecular biology |
| topic | Biochemie Molekularbiologie Molekularbiologie (DE-588)4039983-7 gnd Molekularbiologe (DE-588)1023071983 gnd Biochemie (DE-588)4006777-4 gnd |
| topic_facet | Biochemie Molekularbiologie Molekularbiologe Lehrbuch |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013005712&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT elliottwilliamh biochemistryandmolecularbiology AT elliottdaphnec biochemistryandmolecularbiology |