Molecular biology

Cover......Page 1
Title Page......Page 4
Copyright......Page 5
Contents......Page 9
About the Author......Page 7
Preface......Page 16
Acknowledgments......Page 20
Guide to Experimental Techniques in Molecular Biology......Page 22
CHAPTER 1 A Brief History......Page 24
1.1 Transmission Genetics......Page 25
1.2 Molecular Genetics......Page 28
1.3 The Three Domains of Life......Page 32
CHAPTER 2 The Molecular Nature of Genes......Page 35
2.1 The Nature of Genetic Material......Page 36
2.2 DNA Structure......Page 41
2.3 Genes Made of RNA......Page 45
2.4 Physical Chemistry of Nucleic Acids......Page 46
CHAPTER 3 An Introduction to Gene Function......Page 53
3.1 Storing Information......Page 54
3.3 Mutations......Page 68
CHAPTER 4 Molecular Cloning Methods......Page 72
4.1 Gene Cloning......Page 73
4.2 The Polymerase Chain Reaction......Page 85
4.3 Methods of Expressing Cloned Genes......Page 88
CHAPTER 5 Molecular Tools for Studying Genes and Gene Activity......Page 98
5.1 Molecular Separations......Page 99
5.2 Labeled Tracers......Page 105
5.3 Using Nucleic Acid Hybridization......Page 108
5.4 DNA Sequencing and Physical Mapping......Page 112
5.5 Protein Engineering with Cloned Genes: Site-Directed Mutagenesis......Page 120
5.6 Mapping and Quantifying Transcripts......Page 122
5.7 Measuring Transcription Rates in Vivo......Page 127
5.8 Assaying DNA–Protein Interactions......Page 131
5.9 Assaying Protein–Protein Interactions......Page 135
5.10 Finding RNA Sequences That Interact with Other Molecules......Page 137
5.11 Knockouts and Transgenics......Page 138
CHAPTER 6 The Mechanism of Transcription in Bacteria......Page 144
6.1 RNA Polymerase Structure......Page 145
6.2 Promoters......Page 146
6.3 Transcription Initiation......Page 149
6.4 Elongation......Page 167
6.5 Termination of Transcription......Page 179
CHAPTER 7 Operons: Fine Control of Bacterial Transcription......Page 190
7.1 The lac Operon......Page 191
7.2 The ara Operon......Page 205
7.3 The trp Operon......Page 209
7.4 Riboswitches......Page 213
CHAPTER 8 Major Shifts in Bacterial Transcription......Page 219
8.1 Sigma Factor Switching......Page 220
8.2 The RNA Polymerase Encoded in Phage T7......Page 225
8.3 Infection of E. coli by Phage λ\n......Page 226
CHAPTER 9 DNA–Protein Interactions in Bacteria......Page 245
9.1 The λ\n Family of Repressors......Page 246
9.2 The trp Repressor......Page 257
9.3 General Considerations on Protein–DNA Interactions......Page 258
9.4 DNA-Binding Proteins: Action at a Distance......Page 260
CHAPTER 10 Eukaryotic RNA Polymerases and Their Promoters......Page 267
10.1 Multiple Forms of Eukaryotic RNA Polymerase......Page 268
10.2 Promoters......Page 282
10.3 Enhancers and Silencers......Page 290
CHAPTER 11 General Transcription Factors in Eukaryotes......Page 296
11.1 Class II Factors......Page 297
11.2 Class I Factors......Page 322
11.3 Class III Factors......Page 326
CHAPTER 12 Transcription Activators in Eukaryotes......Page 337
12.1 Categories of Activators......Page 338
12.2 Structures of the DNA-Binding Motifs of Activators......Page 339
12.3 Independence of the Domains of Activators......Page 346
12.4 Functions of Activators......Page 347
12.5 Interaction Among Activators......Page 351
12.6 Regulation of Transcription Factors......Page 366
CHAPTER 13 Chromatin Structure and Its Effects on Transcription......Page 378
13.1 Chromatin Structure......Page 379
13.2 Chromatin Structure and Gene Activity......Page 387
CHAPTER 14 RNA Processing I: Splicing......Page 417
14.1 Genes in Pieces......Page 418
14.2 The Mechanism of Splicing of Nuclear mRNA Precursors......Page 422
14.3 Self-Splicing RNAs......Page 450
CHAPTER 15 RNA Processing II: Capping and Polyadenylation......Page 459
15.1 Capping......Page 460
15.2 Polyadenylation......Page 465
15.3 Coordination of mRNA Processing Events......Page 479
CHAPTER 16 Other RNA Processing Events and Post-Transcriptional Control of Gene Expression......Page 494
16.1 Ribosomal RNA Processing......Page 495
16.2 Transfer RNA Processing......Page 498
16.3 Trans-Splicing......Page 500
16.4 RNA Editing......Page 502
16.5 Post-Transcriptional Control of Gene Expression: mRNA Stability......Page 506
16.6 Post-Transcriptional Control of Gene Expression: RNA Interference......Page 511
16.7 Piwi-Interacting RNAs and Transposon Control......Page 524
16.8 Post-Transcriptional Control of Gene Expression: MicroRNAs......Page 525
16.9 Translation Repression, mRNA Degradation, and P-Bodies......Page 533
CHAPTER 17 The Mechanism of Translation I: Initiation......Page 545
17.1 Initiation of Translation in Bacteria......Page 546
17.2 Initiation in Eukaryotes......Page 556
17.3 Control of Initiation......Page 568
CHAPTER 18 The Mechanism of Translation II: Elongation and Termination......Page 583
18.1 The Direction of Polypeptide Synthesis and of mRNA Translation......Page 584
18.2 The Genetic Code......Page 585
18.3 The Elongation Cycle......Page 592
18.4 Termination......Page 607
18.5 Posttranslation......Page 616
CHAPTER 19 Ribosomes and Transfer RNA......Page 624
19.1 Ribosomes......Page 625
19.2 Transfer RNA......Page 646
CHAPTER 20 DNA Replication, Damage, and Repair......Page 659
20.1 General Features of DNA Replication......Page 660
20.2 Enzymology of DNA Replication......Page 669
20.3 DNA Damage and Repair......Page 679
CHAPTER 21 DNA Replication II: Detailed Mechanism......Page 700
21.1 Initiation......Page 701
21.2 Elongation......Page 706
21.3 Termination......Page 717
CHAPTER 22 Homologous Recombination......Page 732
22.1 The RecBCD Pathway for Homologous Recombination......Page 733
22.2 Experimental Support for the RecBCD Pathway......Page 735
22.3 Meiotic Recombination......Page 744
22.4 Gene Conversion......Page 751
CHAPTER 23 Transposition......Page 755
23.1 Bacterial Transposons......Page 756
23.2 Eukaryotic Transposons......Page 760
23.3 Rearrangement of Immunoglobulin Genes......Page 763
23.4 Retrotransposons......Page 768
CHAPTER 24 Introduction to Genomics: DNA Sequencing on a Genomic Scale......Page 782
24.1 Positional Cloning: An Introduction to Genomics......Page 783
24.2 Techniques in Genomic Sequencing......Page 788
24.3 Studying and Comparing Genomic Sequences......Page 797
CHAPTER 25 Genomics II: Functional Genomics, Proteomics, and Bioinformatics......Page 812
25.1 Functional Genomics: Gene Expression on a Genomic Scale......Page 813
25.2 Proteomics......Page 835
25.3 Bioinformatics......Page 843
Glossary......Page 850
Index......Page 879