The Biochemistry of the Nucleic Acids

689 Pages·1992·31.53 MB·English

by  Roger L. P. Adams

The Biochemistry of the
Nucleic Acids
The Biochemistry of the
Nucleic Acids
ELEVENTH EDITION
Roger L. P. Adams
Department of Biochemistry
University of Glasgow
John T. Knowler
Department of Biological Sciences
Glasgow Polytechnic
David P. Leader
Department of Biochemistry
University of Glasgow
Springer-Science+B usiness Media, B. V.
ISBN 978-0-412-39940-4 ISBN 978-94-011-2290-0 (eBook)
DOI 10.1007/978-94-011-2290-0
First edition 1950 by Methuen and Co. Ltd
Eleventh edition 1992 by Chapman & Hali Ltd
© 1992 Roger L. P. Adams, John T. Knowler and David P. Leader
Originally published by Chapman & Hali in 1992
10!112!
Typeset in pt Times by Best-set Typesetter Ltd, Hong Kong
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Contents
Preface xvii
Abbreviations and nomenclature xix
1 Introduction 1
References 3
2 The structure of the nucleic acids 5
2.1 Monomeric components 5
2.1.1 Pyrimidine bases 5
2.1.2 Purine bases 5
2.1.3 Pentose and deoxypentose sugars 6
2.1.4 Nucleosides 8
2.1.5 Nucleotides 9
2.2 The primary structure of the nucleic acids 9
2.2.1 Shorthand notation 10
2.2.2 Base composition analysis of DNA 12
2.2.3 Molecular weight of DNA 14
2.3 The secondary structure of DNA 14
2.3.1 The basic structures 14
2.3.2 Variations on the B-form of DNA 19
2.3.3 Z-ONA 21
2.3.4 The dynamic structure of DNA 22
2.4 Denaturation and renaturation 22
2.4.1 DNA denaturation: the helix-coil transition 22
2.4.2 The renaturation of DNA: C0t value analysis 24
2.4.3 The buoyant density of DNA 24
2.5 More complex DNA structures 26
2.5.1 Supercoiling 26
2.5.2 Cruciforms 27
2.5.3 Multi-stranded DNA 29
vi Contents
2.6 The secondary and tertiary structure of RNA 29
2. 7 Chemical reactions of bases, nucleotides and polynucleotides 32
2. 7.1 Reactions of ribose and deoxyribose 32
2.7.2 Reactions ofthe bases 32
2. 7.3 Phosphodiester bond cleavage 34
2. 7.4 Photochemistry 36
References 36
3 Genomes of eukaryotes, bacteria and viruses:
chromosome organization 41
3.1 Eukaryotic chromosomes 41
3.1.1 The nucleus 41
3.1.2 The cell cycle 42
3 .1. 3 Eukaryotic chromosomes 43
3.1.4 The allocation of specific genes to specific chromosomes 45
3.2 The eukaryotic genome 47
3.2.1 Haploid DNA content (C value) 47
3.2.2 Gene frequency 48
3.2.3 Eukaryotic gene structure 52
3.3 Chromatin structure 53
3.3.1 Histones and non-histone proteins 53
3.3.2 The nucleosome 55
3.3.3 Nucleosome phasing 60
3.3.4 Higher orders of chromatin structure 61
3.3.5 Loops, matrix and the chromosome scaffold 61
3.3.6 Lampbrush chromosomes 64
3.3.7 Polytene chromosomes 65
3.4 Extranuclear DNA 65
3.4.1 Mitochondrial DNA 65
3.4.2 Chloroplast DNA 67
3.4.3 Kinetoplast DNA 67
3.5 Bacteria 67
3.5.1 The bacterial chromosome 68
3.5.2 The bacterial division cycle 69
3.5.3 Bacterial transformation 69
3.6 Plasmids 71
3.7 Viruses 73
3.7.1 The structure of viruses 73
3.7.2 Virus classification 75
3.7.3 The life cycle of viruses 76
3.7.4 The Hershey-Chase experiment 78
3.7.5 Virus mutants 79
3.7.6 Virus nucleic acids 79
3.7.7 The information content of viral nucleic acids 83
Contents vii
3.7.8 Lysogeny and transduction 85
3.7.9 Tumour viruses and animal cell transformation 87
3.7.10 Viroids and pathogenic RNAs 88
3.7.11 Prions 88
References 89
4 Degradation and modification of nucleic acids 97
4.1 Introduction and classification of nucleases 97
4.2 Non-specific nucleases 98
4.2.1 Non-specific endonucleases 98
4.2.2 Non-specific exonucleases 99
4.3 Ribonucleases (RNases) 99
4.3.1 Endonucleases which form 3' -phosphate groups 100
4.3.2 Endonucleases which form 5' -phosphate groups 106
4.3.3 RNA exonucleases 106
4.3.4 Ribonucleases which act on RNA:DNA hybrids
(RNaseH) 107
4.3.5 Double-stranded RNA-specific ribonucleases 107
4.3.6 Ribonuclease inhibitors 108
4.4 Polynucleotide phosphorylase (PNPase, EC 2.7.7.8) 108
4.5 Deoxyribonucleases (DNases) 109
4.5.1 Endonucleases 109
4.5.2 Exonucleases 113
4.5.3 Restriction endonucleases 117
4.6 Nucleic acid methylation 121
4.6.1 DNA methylation 121
4.6.2 RNA methylation and other RNA nucleotide
modifications 124
4. 7 Nucleic acid kinases and phosphatases 124
4.7.1 Bacteriophage polynucleotide kinase 124
4.7.2 Eukaryotic DNA and RNA kinases 126
4.8 Base exchange in RNA and DNA 126
References 127
5 The metabolism of nucleotides 135
5.1 Anabolic pathways 135
5.2 The biosynthesis of the purines 135
5.3 Preformed purines as precursors 138
5.4 The biosynthesis of the pyrimidines 139
5.5 The biosynthesis of deoxyribonucleotides and its
control 141
5.6 The biosynthesis of thymine derivatives 143
5.7 Aminopterin in selective media 144
5.8 Formation of nucleoside triphosphates 145
viii Contents
5.9 General aspects of catabolism 145
5.10 Purine catabolism 145
5.11 Pyrimidine catabolism 148
References 149
6 Replication of DNA 153
6.1 Introduction 153
6.2 Semiconservative replication 153
6.3 The replication fork 155
6.3.1 Discontinuous synthesis 155
6.3.2 Okazaki pieces 158
6.3.3 Direction of chain growth 159
6.3.4 Initiation of Okazaki pieces 159
6.3.5 Continuous synthesis 162
6.4 DNA polymerase 162
6.4.1 Introduction 162
6.4.2 Mechanism of action of DNA polymerase 163
6.4.3 E. coli DNA polymerase I 166
6.4.4 E. coli DNA polymerase II 172
6.4.5 E. coli DNA polymerase III 173
6.4.6 DNA polymerases of other prokaryotes 175
6.4.7 DNA polymerases in eukaryotes 176
6.4.8 Reverse transcriptase or RNA-dependent DNA
polymerase 179
6.5 Other proteins involved in replication 181
6.5.1 DNA ligases 181
6.5.2 Single-stranded DNA-binding proteins 183
6.5.3 DNA helicases (DNA-dependent ATPases) 184
6.5.4 Topoisomerases 185
6.5.5 Primase 189
6.6 Fidelity of replication 190
6.6.1 Introduction 190
6.6.2 Fidelity assays and results 190
6.6.3 Frameshift errors 193
6.7 In vitro systems for studying DNA replication 193
6.7.1 dna mutants 193
6.7.2 Permeable cells 193
6.7.3 Celllysates 194
6.7.4 Soluble extracts 195
6.7.5 Reconstruction experiments 196
6.7.6 Synthesis of Okazaki pieces (lagging-strand
synthesis) 196
6.7.7 Leading-strand synthesis 200
6.8 Initiation of replication-simple systems 201
6.8.1 Methods of locating the origin and direction of
replication 201
6.8.2 Initiation of replication of double-stranded DNA
molecules 202
6.9 Rolling circle replication 202
6.10 Initiation of replication using primase 205
6.10.1 E. coli DNA replication 205
6.10.2 Replication of phage lambda DNA 208
6.10.3 Low copy number plasmids 209
6.10.4 Papovavirus DNA replication 210
6.11 Initiation using RNA polymerase 213
6.11.1 Replication of phage T7 DNA 213
6.11.2 Replication of phage T4 DNA 215
6.11.3 Plasmid Col El replication 216
6.11.4 Mitochondrial DNA replication 217
6.12 Terminal initiation 218
6.13 Positive or negative control of initiation 219
6.14 Retrovirus replication 220
6.15 Initiation of replication-complex systems 222
6.15.1 Replicons in eukaryotes 222
6.15.2 Origins of replication in repeated genes 223
6.15.3 ARS elements and yeast plasmids 224
6.15.4 Other methods of identifying origins 225
6.1~.5 Matrix attachment and temporal replication 225
6.15.6 Amplification 227
6.16 Termination of replication 230
6.16.1 Competition between replication and
transcription 230
6.16.2 Replicon fusion 231
6.16.3 Small linear viral chromosomes 231
6.16.4 Telomeres on eukaryotic chromosomes 234
6.17 Chromatin replication 236
References 238
7 Repair, recombination and rearrangement of DNA 257
7.1 Introduction 257
7.2 Mutations and mutagens 257
7 .2.1 Base and nucleoside analogues 259
7 .2.2 Alkylating agents 260
7.2.3 Intercalating agents 261
7.2.4 The effects of ionizing radiations 262
7.2.5 Ultraviolet radiation 263
7.3 Repair mechanisms 263
7. 3.1 Reversal of damage 264
7.3.2 Excision repair 264
7.3.3 Mismatch repair 267
7 .3.4 Bypass synthesis, translesion replication or error-prone
repair 269
Contents
X
7.4 Recombination 270
7. 4.1 Models of general recombination 271
7. 4.2 The E. coli rec system and single-strand invasion 274
7 .4.3 Illegitimate recombination 277
7. 4.4 Site-specific recombination 277
7.5 Genome rearrangements 277
7 .5.1 Integration of phage lambda DNA 277
7.5.2 Nitrogen-fixing genes 279
7.5.3 Pilus phase variation 280
7.5.4 Yeast mating-type locus 280
7.5.5 Variant surface glycoprotein (VSG) genes in
trypanosomes 282
7 .5.6 Macronucleus formation 283
7. 5.7 Immunoglobulin and T-cell receptor genes 284
7.5.8 Chromosomal translocations 289
7.6 Gene duplication and pseudogenes 290
7 .6.1 Multiple related copies of eukaryotic genes 290
7 .6.2 Mechanism of tandem gene duplication 291
7.6.3 Pseudogenes 293
7.6.4 Concerted evolution of duplicated genes 294
7. 7 Transposition of DNA 295
7. 7.1 Transposable elements 295
7.7.2 Prokaryotic transposons 296
7.7.3 Eukaryotic transposons 301
7. 7.4 Other transposing retro-elements 303
References 308
8 The arrangement of genes 317
8.1 Gene numbers and spacing 317
8.2 Genes are often discontinuous 318
8.2.1 lntron types 319
8.2.2 The origins and role of introns 320
8.3 Multigene families 321
8.4 Gene clustering 322
8.4.1 Histone genes 322
8.4.2 Globin genes 324
8.4.3 rRNA genes 324
8.4.4 5S RNA genes 329
8.4.5 tRNA genes 330
8.5 The genes of mitochondrial and chloroplast DNA 331
8.5.1 Protein-encoding genes of mitochondria and
chloroplasts 332
8.5.2 Mitochondrial and chloroplast rRNA genes 333
8.5.3 Mitochondrial and chloroplast tRNA genes 334
References 335
Contents xi
9 RNA biosynthesis 339
9.1 Conventions and terms associated with RNA biosynthesis 339
9.2 Transcription is best understood in prokaryotes 340
9.2.1 E. coli RNA polymerase 340
9.2.2 Initiation of prokaryotic transcription 341
9 .2.3 Elongation of prokaryotic transcripts 346
9.2.4 Termination of prokaryotic transcripts 347
9.3 Eukaryotes have three different nuclear RNA polymerases 350
9.4 The initiation of eukaryotic transcription 352
9.4.1 Initiation by RNA polymerase II 353
9.4.2 Initiation by RNA polymerase III 355
9.4.3 Initiation by RNA polymerase I 360
9.5 Termination of transcription in eukaryotes 363
9.5.1 Termination by RNA polymerase II 363
9.5.2 Termination by RNA polymerase III 365
9.5.3 Termination by RNA polymerase I 365
9.6 Does the nucleoskeleton play a role in transcription? 366
9. 7 The transcription of mitochondrial and chloroplast genes 367
9. 7.1 Mitochondrial transcription 368
9.7.2 Chloroplast transcription 368
9.8 Transcription of DNA viruses 369
9.8.1 Prokaryotic DNA viruses 369
9.8.2 Eukaryotic DNA viruses 369
9.9 The replication of RNA viruses by RNA-dependent RNA
polymerase (replicase) 371
9. 9.1 RNA bacteriophages 371
9.9.2 Eukaryotic RNA viruses 371
References 374
10 Control of transcription 381
10.1 The regulation of prokaryotic transcriptional initiation 381
10.1.1 Induction of the lac operon-a negative control system 381
10.1.2 Repression of the trp operon 385
10.1.3 Catabolite repression-a positive control system 385
10.1.4 Dual control of the araBAD operon 387
10.1.5 Other variations in the control of initiation at bacterial
operons 389
10 .1. 6 The repressor of the bacteriophage lambda 391
10.1. 7 The interaction of prokaryotic repressor and activator
proteins with DNA 392
10.2 The regulation of the termination of transcription in prokaryotes 396
10.2.1 Attenuation 396
10.2.2 Antiterminators of transcription 399
10.3 Modification of prokaryotic RNA polymerase 402