Verfügbarkeit: Molecular biology

Molecular biology:

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Format:	Buch
Sprache:	English
Veröffentlicht:	New York [u.a.] Taylor & Francis 2005
Ausgabe:	3. ed.
Schriftenreihe:	BIOS instant notes
Schlagworte:	Biologia molecular Biologie moléculaire - Résumés, programmes, etc Molecular Biology > Outlines Molecular biology > Outlines, syllabi, etc Molekularbiologie Molekulargenetik Einführung
Online-Zugang:	Inhaltsverzeichnis
Beschreibung:	XIV, 370 S. Ill., graph. Darst.
ISBN:	0415351677

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Datensatz im Suchindex

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adam_text	Molecular Biology Third Edition RobertFWeaver University of Kansas Mc Graw Hill Higher Education Boston Burr Ridge, IL Dubuque, IA Madison, Wl New York San Francisco St Louis Bangkok Bogota Caracas Kuala Lumpur Lisbon London Madrid Mexico City Milan Montreal New Delhi Santiago Seoul Singapore Sydney Taipei Toronto BRIEFCONTENTS -a -- t% •? • About the Author iv Preface xii Acknowledgments xv Guide to Experimental Techniques in Molecular Biology xvi Introduction 1 A Brief History 1 2 The Molecular Nature of Genes 17 3 Introduction to Gene Function 37 PARTII Methods in Molecular Biology 4 Molecular Cloning Methods 58 5 Molecular Tools for Studying Genes and Gene Activity 90 PARTIII Transcription in Prokaryotes 6 The Mechanism of Transcription in Prokaryotes 132 7 Operons: Fine Control of Prokaryotic Transcription 182 8 Major Shifts in Prokaryotic Transcription 212 9 DNA-Protein Interactions in Prokaryotes 242 PARTIV Transcription in Eukaryotes 10 Eukaryotic RNA Polymerases and Their Promoters 271 11 General Transcription Factors in Eukaryotes 302 12 Transcription Activators in Eukaryotes 342 13 Chromatin Structure and Its Effects on Transcription 385 PARTV Posttranscriptional Events 14 Messenger RNA Processing I: Splicing 424 15 Messenger RNA Processing II: Capping and Polyadenylation 471 16 Other RNA Processing Events 510 PARTVI Translation 17 The Mechanism of Translation I: Initiation 545 18 The Mechanism of Translation II: Elongation and Termination 585 19 Ribosomes and Transfer RNA 630 20 DNA Replication I: Basic Mechanism and Enzymology 665 21 DNA Replication II: Detailed Mechanism 711 22 Homologous Recombination 748 23 Transposition 773 PARTVIII Genomes 24 Genomics and Proteomics 804 Glossary 854 Index 879 About the Author iv Preface xii Acknowledgments xv Guide to Experimental Techniques in Molecular Biology xvi PARTI Introduction CHAPTER1 A Brief History 1 1 1 Transmission Genetics 2 Mendel s Laws of Inheritance 2 The Chromosome Theory of Inheritance 3 Box 1 1 Cell Structure 4 Genetic Recombination and Mapping 5 Box 1 2 Cell Cycle and Mitosis 6 Box 1 3 Meiosis 8 Physical Evidence for Recombination 10 1 2 Molecular Genetics 10 *~— The Discovery of DNA 10 The Relationship between Genes and Proteins 11 Activities of Genes 11 1 3 The Three Domains of Life 15 CHAPTER2 The Molecular Nature of Genes 17 2 1 The Nature of Genetic Material 18 Transformation in Bacteria 18 The Chemical Nature of Polynucleotides 20 2 2 DNA Structure 24 Experimental Background 24 The Double Helix 25 2 3 Genes Made of RNA 28 2 4 Physical Chemistry of Nucleic Acids 28 A Variety of DNA Structures 28 DNAs of Various Sizes and Shapes 32 CHAPTER3 An Introduction to Gene Function 37 3 1 Storing Information 38 Overview of Gene Expression 38 Protein Structure 38 Protein Function 43 Discovery of Messenger RNA 44 Transcription 45 Translation 48 3 2 Replication 53 3 3 Mutations 53 Sickle Cell Disease 54 PARTII Methods of Molecular Biology CHAPTER4 Molecular Cloning Methods 58 4 1 Gene Cloning 59 The Role of Restriction Endonucleases 59 Vectors 62 Identifying a Specific Clone with a Specific Probe 71 4 2 The Polymerase Chain Reaction 72 cDNA Cloning 74 Box 4 1 Jurassic Park: More than a Fantasy? 75 4 3 Methods of Expressing Cloned Genes 78 Expression Vectors 79 Other Eukaryotic Vectors 85 Using the Ti Plasmid to Transfer Genes to Plants 85 CHAPTER5 Molecular Tools for Studying Genes and Gene Activity 90 5 1 Molecular Separations 91 Gel Electrophoresis 91 Two-Dimensional Gel Electrophoresis 94 vi Contents vii Ion-Exchange Chromatography 95 Gel Filtration Chromatography 95 5 2 Labeled Tracers 96 Autoradiography 96 Phosphorimaging 97 Liquid Scintillation Counting 98 Nonradioactive Tracers 98 5 3 Using Nucleic Acid Hybridization 99 Southern Blots: Identifying Specific DNA Fragments 99 DNA Fingerprinting and DNA Typing 101 Forensic Uses of DNA Fingerprinting and DNA Typing 101 DNA Sequencing 105 Restriction Mapping 107 Protein Engineering with Cloned Genes: Site-Directed Mutagenesis 112 5 4 Mapping and Quantifying Transcripts SI Mapping 114 Primer Extension 116 Run-off Transcription and G-Less Cassette Transcription 117 5 5 Measuring Transcription Rates in Vivo Nuclear Run-on Transcription 119 Reporter Gene Transcription 119 Measuring Protein Accumulation in Vivo 122 5 6 Assaying DNA-Protein Interactions 122 Filter Binding 122 Gel Mobility Shift 123 — DNase Footprinting 124 DMS Footprinting and Other Footprinting Methods 124 5 7 Knockouts 126 PART Transcription in Prokaryotes CHAPTER6 The Mechanism of Transcription in Prokaryotes 132 6 1 RNA Polymerase Structure 132 Sigma (a) as a Specificity Factor 133 6 2 Promoters 136 Binding of RNA Polymerase to Promoters 136 Promoter Structure 138 6 3 Transcription Initiation 139 The Function of a 140 Structure and Function of o 147 The Role of the a-Subunit in UP Element Recognition 152 6 4 Elongation 154 Core Polymerase Functions in Elongation 154 Structure of the Elongation Complex 159 6 5 Termination of Transcription 171 Rho-Independent Termination 171 Rho-Dependent Termination 175 CHAPTER7 Operons: Fine Control of Prokaryotic Transcription 182 7 1 The lac Operon 183 Negative Control of the lac Operon 184 Discovery of the Operon 184 Repressor-Operator Interactions 188 The Mechanism of Repression 189 Positive Control of the lac Operon 192 The Mechanism of CAP Action 193 7 2 The ara Operon 198 The ara Operon Repression Loop 198 Evidence for the ara Operon Repression Loop 200 Autoregulation of araC 202 7 3 The trp Operon 202 Tryptophan s Role in Negative Control of the trp Operon 202 Control of the trp Operon by Attenuation 203 Defeating Attenuation 204 CHAPTER8 Major Shifts in Prokaryotic Transcription 212 8 1 Modification of the Host RNA-Polymerase during Phage Infection 213 8 2 The RNA Polymerase Encoded in Phage T7 215 8 3 Control of Transcription During Sporulation 216 8 4 Genes with Multiple Promoters 218 The B subtilis spoVG Gene 218 8 5 The E coli Heat Shock Genes 220 8 6 Infection of E coli by Phage A, 220 Lytic Reproduction of Phage X 221 Establishing Lysogeny 229 Autoregulation of the cl Gene during Lysogeny 231 Determining the Fate of a X Infection: Lysis or Lysogeny 236 Lysogen Induction 238 viii Contents CHAPTER9 DNA-Protein Interactions in Prokaryotes 242 9 1 The A, Family of Repressors 243 Box 9 1 X-Ray Crystallography 244 High-Resolution Analysis of k Repressor-Operator Interactions 249 High-Resolution Analysis of Phage 434 Repressor-Operator Interactions 252 9 2 The trp Repressor 256 The Role of Tryptophan 256 9 3 General Considerations on Protein-DNA Interactions 258 Hydrogen Bonding Capabilities of the Four Different Base Pairs 258 The Role of DNA Shape in Specific Binding to Proteins 259 The Importance of Multimeric DNA-Binding Proteins 260 9 4 DNA-Binding Proteins: Action at a Distance The gal Operon 260 Duplicated X Operators 261 The lac Operon 264 Enhancers 264 PARTIV Transcription in Eukaryotes CHAPTER10 Eukaryotic RNA Polymerases and Their Promoters 271 10 1 Multiple Forms of Eukaryotic RNA Polymerase 272 Separation of the Three Nuclear Polymerases 272 The Roles of the Three RNA Polymerases 273 RNA Polymerase Subunit Structures 274 10 2 Promoters 287 Class II Promoters 287 Class I Promoters 291 Class III Promoters 292 10 3 Enhancers and Silencers 296 Enhancers 296 Silencers 298 CHAPTER11 General Transcription Factors in Eukaryotes 302 11 1 Class II Factors 303 The Class II Preinitiation Complex 303 Structure and Function of TFIID 305 Structure and Function of TFIIB 317 Structure and Function of TFIIF 318 Structure and Function of TFIIH 318 Elongation Factors 323 The Polymerase II Holoenzyme 326 11 2 Class I Factors 327 The Core-Binding Factor 327 The UPE-Binding Factor 328 Structure and Function of SL1 329 11 3 Class HI Factors 331 TFIIIA 332 TFIIIB and C 332 The Role of TBP 336 CHAPTER12 Transcription Activators in Eukaryotes 342 12 1 Categories of Activators 343 DNA-Binding Domains 343 Transcription-Activating Domains 343 12 2 Structures of the DNA-Binding Motifs of Activators 344 Zinc Fingers 344 The GAL4 Protein 346 The Nuclear Receptors 347 Homeodomains 349 The bZIP and bHLH Domains 350 12 3 Independence of the Domains of Activators 351 12 4 Functions of Activators 352 Recruitment of TFIID 353 Recruitment of TFIIB 354 Recruitment of Other General Transcription Factors 357 Recruitment of the Holoenzyme 358 12 5 Interaction among Activators 361 Dimerization 361 Action at a Distance 362 Multiple Enhancers 365 Architectural Transcription Factors 366 Insulators 369 12 6 Regulation of Transcription Factors 372 Coactivators 372 Activator Ubiquitination 375 Activator Sumoylation 377 Activator Acetylation 377 Signal Transduction Pathways 378 Contents ix CHAPTER13CHAPTER15 Chromatin Structure and Its Effects on Transcription 385 13 1 Histones 386 13 2 Nucleosomes 387 The Nucleosome Filament 390 The 30-nm Fiber 391 The Role of Histone HI in Chromatin Folding 394 Higher Order Chromatin Folding 394 13 3 Chromatin Structure and Gene Activity 395 The Effects of Histones on 5S rRNA Gene Transcription 395 The Effects of Histones on Transcription of Class II Genes 398 Nucleosome Positioning 400 Histone Acetylation 405 Histone Deaceytlation 407 Chromatin Remodeling 410 Heterochromatin and Silencing 414 Nucleosomes and Transcription Elongation 419 PARTV Posttranscriptional Events CHAPTER14 Messenger RNA Processing II: Capping and Polyadenylation 470 15 1 Capping 471 Cap Structure 471 Cap Synthesis 472 Functions of Caps 474 15 2 Polyadenylation 477 Poly(A) 477 Functions of Poly(A) 478 Basic Mechanism of Polyadenylation 480 Polyadenylation Signals 482 Cleavage and Polyadenylation of a Pre-mRNA 484 Poly(A) Polymerase 490 Turnover of Poly(A) 491 15 3 Coordination of mRNA Processing Events 493 Effect of Cap on Splicing 493 Effect of Poly(A) on Splicing 494 Binding of the CTD of Rpbl to mRNA Processing Proteins 496 Changes in Association of RNA Processing Proteins with the CTD Correlate with Changes in CTD Phosphorylation 498 Coupling Transcription Termination with mRNA 3 -End Processing 499 Mechanism of Termination 501 Role of Polyadenylation in mRNA Transport 504 CHAPTER16 Messenger RNA Processing I: Splicing 424 14 1 Genes in Pieces 425 Evidence for Split Genes 425 RNA Splicing 426 Splicing Signals 427 14 2 The Mechanism of Splicing of Nuclear mRNA Precursors 428 A Branched Intermediate 428 A Signal at the Branch 431 Spliceosomes 432 Snurps 432 Spliceosome Assembly and Function 444 Role of the RNA Polymerase II CTD 454 14 3 Self-Splicing RNAs 459 Group I Introns 459 Group II Introns 462 14 4 tRNA Splicing 464 Other RNA Processing Events 510 16 1 Ribosomal RNA Processing 511 Eukaryotic rRNA Processing 511 Prokaryotic rRNA Processing 513 16 2 Transfer RNA Processing 514 Cutting Apart Polycistronic Precursors 514 Forming Mature 5 -Ends 514 Forming Mature 3 -Ends 516 16 3 Trans-Splicing 518 The Mechanism of Traws-Splicing 518 Polycistronic Arrangement of Coding Regions in Trypanosomes 520 16 4 RNA Editing 521 Mechanism of Editing 521 Editing by Nucleotide Deamination 524 16 5 Posttranscriptional Control of Gene Expression 526 Casein mRNA Stability 526 Transferrin Receptor mRNA Stability 527 16 6 Posttranscriptional Gene Silencing (RNA Interference) 535 x Contents PARTVI Translation CHAPTER17 The Mechanism of Translation I: Initiation 545 17 1 Initiation of Translation in Prokaryotes 546 tRNA Charging 546 Dissociation of Ribosomes 546 Formation of the 30S Initiation Complex 549 Formation of the 70S Initiation Complex 558 Summary of Initiation in Prokaryotes 559 17 2 Initiation in Eukaryotes 560 The Scanning Model of Initiation 561 Eukaryotic Initiation Factors 565 Overview of Translation Initiation in Eukaryotes 565 17 3 Control of Initiation 572 Prokaryotic Translational Control 572 Eukaryotic Translational Control 573 CHAPTER18 The Mechanism of Translation II: Elongation and Termination 585 18 1 The Direction of Polypeptide Synthesis and of mRNA Translation 586 18 2 The Genetic Code 587 Nonoverlapping Codons 588 No Gaps in the Code 588 The Triplet Code 588 Breaking the Code 590 Unusual Base Pairs between Codon and Anticodon 590 The (Almost) Universal Code 592 18 3 The Elongation Mechanism 594 Overview of Elongation 594 A Three-Site Model of the Ribosome 595 Elongation Step 1: Binding an Aminoacyl-tRNA to the A Site of the Ribosome 598 Elongation Step 2: Peptide Bond Formation 605 Elongation Step 3: Translocation 608 The Structures of EF-Tu and EF-G 611 GTPases and Translation 612 18 4 Termination 613 Termination Codons 613 Stop Codon Suppression 615 Release Factors 616 Dealing with Aberrant Termination 621 18 5 Posttermination 625 CHAPTER19 Ribosomes and Transfer RNA 630 19 1 Ribosomes 631 Gross Ribosomal Structure 631 Fine Structure of the 70S Ribosome 632 Ribosome Composition 636 Ribosome Assembly 637 Fine Structure of the 30S Subunit 638 Fine Structure of the 50S Subunit 644 Polysomes 649 19 2 Transfer RNA 650 The Discovery of tRNA 650 tRNA Structure 651 Recognition of tRNAs by Aminoacyl-tRNA Synthetase: The Second Genetic Code 654 Proofreading and Editing by Aminoacyl-tRNA Synthetases 659 PARTVII DNA Replication, Recombination, and Transposition CHAPTER20 DNA Replication I: Basic Mechanism and Enzymology 665 20 1 General Features of DNA Replication 666 Semiconservative Replication 666 Semidiscontinuous Replication 668 Priming of DNA Synthesis 671 Bidirectional Replication 672 Unidirectional Replication 675 Rolling Circle Replication 675 20 2 Enzymology of DNA Replication 677 Strand Separation 677 Single-Strand DNA-Binding Proteins 678 Topoisomerases 680 Three DNA Polymerases in E coli 685 Fidelity of Replication 690 Multiple Eukaryotic DNA Polymerases 691 20 3 DNA Damage and Repair 692 Damage Caused by Alkylation of Bases 692 Damage Caused by Ultraviolet Radiation 693 Damage Caused by Gamma and X-Rays 694 Directly Undoing DNA Damage 694 Excision Repair in Prokaryotes 695 Excision Repair in Eukaryotes 696 Contents xi Double-Strand Break Repair in Eukaryotes 700 Mismatch Repair 701 Failure of Mismatch Repair in Humans 702 Coping with DNA Damage without Repairing It 702 CHAPTER21 DNA Replication II: Detailed Mechanism 711 21 1 Speed of Replication 712 21 2 Initiation 713 Priming in E coli 713 Priming in Eukaryotes 716 21 3 Elongation 721 The Pol II Holoenzyme and Processivity of Replication 721 21 4 Termination 733 Decatenation: Disentangling Daughter DNAs 733 Termination in Eukaryotes 735 Box 21 1 Telomeres, the Hayflick Limit, and Cancer 739 CHAPTER22 Homologous Recombination 748 22 1 The RecBCD Pathway for Homologous Recombination 749 22 2 Experimental Support for the RecBCD Pathway 752 RecA 752 ~ - RecBCD 756 RuvA and RuvB 757 RuvC 760 22 3 Meiotic Recombination 764 The Mechanism of Meiotic Recombination: Overview 764 • The Double-Stranded DNA Break 764 Creation of Single-Stranded Ends at DSBs 768 22 4 Gene Conversion 768 CHAPTER23 Transposition 773 23 1 Bacterial Transposons 774 Discovery of Bacterial Transposons 774 Insertion Sequences: The Simplest Bacterial Transposons 775 More Complex Transposons 777 Mechanisms of Transposition 777 23 2 Eukaryotic Transposons 779 The First Examples of Transposable Elements: Ds and Ac of Maize 779 P Elements 781 Rearrangement of Immunoglobulin Genes 782 Retrotransposons 787 PARTVIII Genomes CHAPTER24 Genomics and Proteomics 804 24 1 Positional Cloning: An Introduction to Genomics 805 Classical Tools of Positional Cloning 805 Identifying the Gene Mutated in a Human Disease 807 Box 24 1 Problems in Genetic Screening 811 24 2 Sequencing Genomes 812 The Human Genome Project 815 Vectors for Large-Scale Genome Projects 816 The Clone-by-Clone Strategy 817 Shotgun Sequencing 820 Sequencing Standards 821 Early Progress in Sequencing the Human Genome 822 Other Vertebrate Genomes 827 The Minimal Genome 829 24 3 Applications of Genomics 830 Functional Genomics Techniques 830 Other Applications 840 24 4 Proteomics 840 Protein Separations 841 Protein Analysis 841 Protein Interactions 842 Bioinformatics 846 Glossary 854 Index 879
adam_txt	Molecular Biology Third Edition RobertFWeaver University of Kansas Mc Graw Hill Higher Education Boston Burr Ridge, IL Dubuque, IA Madison, Wl' New York San Francisco St Louis Bangkok Bogota Caracas Kuala Lumpur Lisbon London Madrid Mexico City Milan Montreal New Delhi Santiago Seoul Singapore Sydney Taipei Toronto BRIEFCONTENTS -a'-- 't% '•? • About the Author iv Preface xii Acknowledgments xv Guide to Experimental Techniques in Molecular Biology xvi Introduction 1 A Brief History 1 2 The Molecular Nature of Genes 17 3 Introduction to Gene Function 37 PARTII Methods in Molecular Biology 4 Molecular Cloning Methods 58 5 Molecular Tools for Studying Genes and Gene Activity 90 PARTIII Transcription in Prokaryotes 6 The Mechanism of Transcription in Prokaryotes 132 7 Operons: Fine Control of Prokaryotic Transcription 182 8 Major Shifts in Prokaryotic Transcription 212 9 DNA-Protein Interactions in Prokaryotes 242 PARTIV Transcription in Eukaryotes 10 Eukaryotic RNA Polymerases and Their Promoters 271 11 General Transcription Factors in Eukaryotes 302 12 Transcription Activators in Eukaryotes 342 13 Chromatin Structure and Its Effects on Transcription 385 PARTV Posttranscriptional Events 14 Messenger RNA Processing I: Splicing 424 15 Messenger RNA Processing II: Capping and Polyadenylation 471 16 Other RNA Processing Events 510 PARTVI Translation 17 The Mechanism of Translation I: Initiation 545 18 The Mechanism of Translation II: Elongation and Termination 585 19 Ribosomes and Transfer RNA 630 20 DNA Replication I: Basic Mechanism and Enzymology 665 21 DNA Replication II: Detailed Mechanism 711 22 Homologous Recombination 748 23 Transposition 773 PARTVIII Genomes 24 Genomics and Proteomics 804 Glossary 854 Index 879 About the Author iv Preface xii Acknowledgments xv Guide to Experimental Techniques in Molecular Biology xvi PARTI Introduction CHAPTER1 A Brief History 1 1 1 Transmission Genetics 2 Mendel's Laws of Inheritance 2 The Chromosome Theory of Inheritance 3 Box 1 1 Cell Structure 4 Genetic Recombination and Mapping 5 Box 1 2 Cell Cycle and Mitosis 6 Box 1 3 Meiosis 8 Physical Evidence for Recombination 10 1 2 Molecular Genetics 10 *~— The Discovery of DNA 10 The Relationship between Genes and Proteins 11 Activities of Genes 11 1 3 The Three Domains of Life 15 CHAPTER2 The Molecular Nature of Genes 17 2 1 The Nature of Genetic Material 18 Transformation in Bacteria 18 The Chemical Nature of Polynucleotides 20 2 2 DNA Structure 24 Experimental Background 24 The Double Helix 25 2 3 Genes Made of RNA 28 2 4 Physical Chemistry of Nucleic Acids 28 A Variety of DNA Structures 28 DNAs of Various Sizes and Shapes 32 CHAPTER3 An Introduction to Gene Function 37 3 1 Storing Information 38 Overview of Gene Expression 38 Protein Structure 38 Protein Function 43 Discovery of Messenger RNA 44 Transcription 45 Translation 48 3 2 Replication 53 3 3 Mutations 53 Sickle Cell Disease 54 PARTII Methods of Molecular Biology CHAPTER4 Molecular Cloning Methods 58 4 1 Gene Cloning 59 The Role of Restriction Endonucleases 59 Vectors 62 Identifying a Specific Clone with a Specific Probe 71 4 2 The Polymerase Chain Reaction 72 cDNA Cloning 74 Box 4 1 Jurassic Park: More than a Fantasy? 75 4 3 Methods of Expressing Cloned Genes 78 Expression Vectors 79 Other Eukaryotic Vectors 85 Using the Ti Plasmid to Transfer Genes to Plants 85 CHAPTER5 Molecular Tools for Studying Genes and Gene Activity 90 5 1 Molecular Separations 91 Gel Electrophoresis 91 Two-Dimensional Gel Electrophoresis 94 vi Contents vii Ion-Exchange Chromatography 95 Gel Filtration Chromatography 95 5 2 Labeled Tracers 96 Autoradiography 96 Phosphorimaging 97 Liquid Scintillation Counting 98 Nonradioactive Tracers 98 5 3 Using Nucleic Acid Hybridization 99 Southern Blots: Identifying Specific DNA Fragments 99 DNA Fingerprinting and DNA Typing 101 Forensic Uses of DNA Fingerprinting and DNA Typing 101 DNA Sequencing 105 Restriction Mapping 107 Protein Engineering with Cloned Genes: Site-Directed Mutagenesis 112 5 4 Mapping and Quantifying Transcripts SI Mapping 114 Primer Extension 116 Run-off Transcription and G-Less Cassette Transcription 117 5 5 Measuring Transcription Rates in Vivo Nuclear Run-on Transcription 119 Reporter Gene Transcription 119 Measuring Protein Accumulation in Vivo 122 5 6 Assaying DNA-Protein Interactions 122 Filter Binding 122 Gel Mobility Shift 123 — DNase Footprinting 124 DMS Footprinting and Other Footprinting Methods 124 5 7 Knockouts 126 PART Transcription in Prokaryotes CHAPTER6 The Mechanism of Transcription in Prokaryotes 132 6 1 RNA Polymerase Structure 132 Sigma (a) as a Specificity Factor 133 6 2 Promoters 136 Binding of RNA Polymerase to Promoters 136 Promoter Structure 138 6 3 Transcription Initiation 139 The Function of a 140 Structure and Function of o 147 The Role of the a-Subunit in UP Element Recognition 152 6 4 Elongation 154 Core Polymerase Functions in Elongation 154 Structure of the Elongation Complex 159 6 5 Termination of Transcription 171 Rho-Independent Termination 171 Rho-Dependent Termination 175 CHAPTER7 Operons: Fine Control of Prokaryotic Transcription 182 7 1 The lac Operon 183 Negative Control of the lac Operon 184 Discovery of the Operon 184 Repressor-Operator Interactions 188 The Mechanism of Repression 189 Positive Control of the lac Operon 192 The Mechanism of CAP Action 193 7 2 The ara Operon 198 The ara Operon Repression Loop 198 Evidence for the ara Operon Repression Loop 200 Autoregulation of araC 202 7 3 The trp Operon 202 Tryptophan's Role in Negative Control of the trp Operon 202 Control of the trp Operon by Attenuation 203 Defeating Attenuation 204 CHAPTER8 Major Shifts in Prokaryotic Transcription 212 8 1 Modification of the Host RNA-Polymerase during Phage Infection 213 8 2 The RNA Polymerase Encoded in Phage T7 215 8 3 Control of Transcription During Sporulation 216 8 4 Genes with Multiple Promoters 218 The B subtilis spoVG Gene 218 8 5 The E coli Heat Shock Genes 220 8 6 Infection of E coli by Phage A, 220 Lytic Reproduction of Phage X 221 Establishing Lysogeny 229 Autoregulation of the cl Gene during Lysogeny 231 Determining the Fate of a X Infection: Lysis or Lysogeny 236 Lysogen Induction 238 viii Contents CHAPTER9 DNA-Protein Interactions in Prokaryotes 242 9 1 The A, Family of Repressors 243 Box 9 1 X-Ray Crystallography 244 High-Resolution Analysis of k Repressor-Operator Interactions 249 High-Resolution Analysis of Phage 434 Repressor-Operator Interactions 252 9 2 The trp Repressor 256 The Role of Tryptophan 256 9 3 General Considerations on Protein-DNA Interactions 258 Hydrogen Bonding Capabilities of the Four Different Base Pairs 258 The Role of DNA Shape in Specific Binding to Proteins 259 The Importance of Multimeric DNA-Binding Proteins 260 9 4 DNA-Binding Proteins: Action at a Distance The gal Operon 260 Duplicated X Operators 261 The lac Operon 264 Enhancers 264 PARTIV Transcription in Eukaryotes CHAPTER10 Eukaryotic RNA Polymerases and Their Promoters 271 10 1 Multiple Forms of Eukaryotic RNA Polymerase 272 Separation of the Three Nuclear Polymerases 272 The Roles of the Three RNA Polymerases 273 RNA Polymerase Subunit Structures 274 10 2 Promoters 287 Class II Promoters 287 Class I Promoters 291 Class III Promoters 292 10 3 Enhancers and Silencers 296 Enhancers 296 Silencers 298 CHAPTER11 General Transcription Factors in Eukaryotes 302 11 1 Class II Factors 303 The Class II Preinitiation Complex 303 Structure and Function of TFIID 305 Structure and Function of TFIIB 317 Structure and Function of TFIIF 318 Structure and Function of TFIIH 318 Elongation Factors 323 The Polymerase II Holoenzyme 326 11 2 Class I Factors 327 The Core-Binding Factor 327 The UPE-Binding Factor' 328 Structure and Function of SL1 329 11 3 Class HI Factors 331 TFIIIA 332 TFIIIB and C 332 The Role of TBP 336 CHAPTER12 Transcription Activators in Eukaryotes 342 12 1 Categories of Activators 343 DNA-Binding Domains 343 Transcription-Activating Domains 343 12 2 Structures of the DNA-Binding Motifs of Activators 344 Zinc Fingers 344 The GAL4 Protein 346 The Nuclear Receptors 347 Homeodomains 349 The bZIP and bHLH Domains 350 12 3 Independence of the Domains of Activators 351 12 4 Functions of Activators 352 Recruitment of TFIID 353 Recruitment of TFIIB 354 Recruitment of Other General Transcription Factors 357 Recruitment of the Holoenzyme 358 12 5 Interaction among Activators 361 Dimerization 361 Action at a Distance 362 Multiple Enhancers 365 Architectural Transcription Factors 366 Insulators 369 12 6 Regulation of Transcription Factors 372 Coactivators 372 Activator Ubiquitination 375 Activator Sumoylation 377 Activator Acetylation 377 Signal Transduction Pathways 378 Contents ix CHAPTER13CHAPTER15 Chromatin Structure and Its Effects on Transcription 385 13 1 Histones 386 13 2 Nucleosomes 387 The Nucleosome Filament 390 The 30-nm Fiber 391 The Role of Histone HI in Chromatin Folding 394 Higher Order Chromatin Folding 394 13 3 Chromatin Structure and Gene Activity 395 The Effects of Histones on 5S rRNA Gene Transcription 395 The Effects of Histones on Transcription of Class II Genes 398 Nucleosome Positioning 400 Histone Acetylation 405 Histone Deaceytlation 407 Chromatin Remodeling 410 Heterochromatin and Silencing 414 Nucleosomes and Transcription Elongation 419 PARTV Posttranscriptional Events CHAPTER14 Messenger RNA Processing II: Capping and Polyadenylation 470 15 1 Capping 471 Cap Structure 471 Cap Synthesis 472 Functions of Caps 474 15 2 Polyadenylation 477 Poly(A) 477 Functions of Poly(A) 478 Basic Mechanism of Polyadenylation 480 Polyadenylation Signals 482 Cleavage and Polyadenylation of a Pre-mRNA 484 Poly(A) Polymerase 490 Turnover of Poly(A) 491 15 3 Coordination of mRNA Processing Events 493 Effect of Cap on Splicing 493 Effect of Poly(A) on Splicing 494 Binding of the CTD of Rpbl to mRNA Processing Proteins 496 Changes in Association of RNA Processing Proteins with the CTD Correlate with Changes in CTD Phosphorylation 498 Coupling Transcription Termination with mRNA 3'-End Processing 499 Mechanism of Termination 501 Role of Polyadenylation in mRNA Transport 504 CHAPTER16 Messenger RNA Processing I: Splicing 424 14 1 Genes in Pieces 425 Evidence for Split Genes 425 RNA Splicing 426 Splicing Signals 427 14 2 The Mechanism of Splicing of Nuclear mRNA Precursors 428 A Branched Intermediate 428 A Signal at the Branch 431 Spliceosomes 432 Snurps 432 Spliceosome Assembly and Function 444 Role of the RNA Polymerase II CTD 454 14 3 Self-Splicing RNAs 459 Group I Introns 459 Group II Introns 462 14 4 tRNA Splicing 464 Other RNA Processing Events 510 16 1 Ribosomal RNA Processing 511 Eukaryotic rRNA Processing 511 Prokaryotic rRNA Processing 513 16 2 Transfer RNA Processing 514 Cutting Apart Polycistronic Precursors 514 Forming Mature 5'-Ends 514 Forming Mature 3'-Ends 516 16 3 Trans-Splicing 518 The Mechanism of Traws-Splicing 518 Polycistronic Arrangement of Coding Regions in Trypanosomes 520 16 4 RNA Editing 521 Mechanism of Editing 521 Editing by Nucleotide Deamination 524 16 5 Posttranscriptional Control of Gene Expression 526 Casein mRNA Stability 526 Transferrin Receptor mRNA Stability 527 16 6 Posttranscriptional Gene Silencing (RNA Interference) 535 x Contents PARTVI Translation CHAPTER17 The Mechanism of Translation I: Initiation 545 17 1 Initiation of Translation in Prokaryotes 546 tRNA Charging 546 Dissociation of Ribosomes 546 Formation of the 30S Initiation Complex 549 Formation of the 70S Initiation Complex 558 Summary of Initiation in Prokaryotes 559 17 2 Initiation in Eukaryotes 560 The Scanning Model of Initiation 561 Eukaryotic Initiation Factors 565 Overview of Translation Initiation in Eukaryotes 565 17 3 Control of Initiation 572 Prokaryotic Translational Control 572 Eukaryotic Translational Control 573 CHAPTER18 The Mechanism of Translation II: Elongation and Termination 585 18 1 The Direction of Polypeptide Synthesis and of mRNA Translation 586 18 2 The Genetic Code 587 Nonoverlapping Codons 588 No Gaps in the Code 588 The Triplet Code 588 Breaking the Code 590 Unusual Base Pairs between Codon and Anticodon 590 The (Almost) Universal Code 592 18 3 The Elongation Mechanism 594 Overview of Elongation 594 A Three-Site Model of the Ribosome 595 Elongation Step 1: Binding an Aminoacyl-tRNA to the A Site of the Ribosome 598 Elongation Step 2: Peptide Bond Formation 605 Elongation Step 3: Translocation 608 The Structures of EF-Tu and EF-G 611 GTPases and Translation 612 18 4 Termination 613 Termination Codons 613 Stop Codon Suppression 615 Release Factors 616 Dealing with Aberrant Termination 621 18 5 Posttermination 625 CHAPTER19 Ribosomes and Transfer RNA 630 19 1 Ribosomes 631 Gross Ribosomal Structure 631 Fine Structure of the 70S Ribosome 632 Ribosome Composition 636 Ribosome Assembly 637 Fine Structure of the 30S Subunit 638 Fine Structure of the 50S Subunit 644 Polysomes 649 19 2 Transfer RNA 650 The Discovery of tRNA 650 tRNA Structure 651 Recognition of tRNAs by Aminoacyl-tRNA Synthetase: The Second Genetic Code 654 Proofreading and Editing by Aminoacyl-tRNA Synthetases 659 PARTVII DNA Replication, Recombination, and Transposition CHAPTER20 DNA Replication I: Basic Mechanism and Enzymology 665 20 1 General Features of DNA Replication 666 Semiconservative Replication 666 Semidiscontinuous Replication 668 Priming of DNA Synthesis 671 Bidirectional Replication 672 Unidirectional Replication 675 Rolling Circle Replication 675 20 2 Enzymology of DNA Replication 677 Strand Separation 677 Single-Strand DNA-Binding Proteins 678 Topoisomerases 680 Three DNA Polymerases in E coli 685 Fidelity of Replication 690 Multiple Eukaryotic DNA Polymerases 691 20 3 DNA Damage and Repair 692 Damage Caused by Alkylation of Bases 692 Damage Caused by Ultraviolet Radiation 693 Damage Caused by Gamma and X-Rays 694 Directly Undoing DNA Damage 694 Excision Repair in Prokaryotes 695 Excision Repair in Eukaryotes 696 Contents xi Double-Strand Break Repair in Eukaryotes 700 Mismatch Repair 701 Failure of Mismatch Repair in Humans 702 Coping with DNA Damage without Repairing It 702 CHAPTER21 DNA Replication II: Detailed Mechanism 711 21 1 Speed of Replication 712 21 2 Initiation 713 Priming in E coli 713 Priming in Eukaryotes 716 21 3 Elongation 721 The Pol II Holoenzyme and Processivity of Replication 721 21 4 Termination 733 Decatenation: Disentangling Daughter DNAs 733 Termination in Eukaryotes 735 Box 21 1 Telomeres, the Hayflick Limit, and Cancer 739 CHAPTER22 Homologous Recombination 748 22 1 The RecBCD Pathway for Homologous Recombination 749 22 2 Experimental Support for the RecBCD Pathway 752 RecA 752 ~ - RecBCD 756 RuvA and RuvB 757 RuvC 760 22 3 Meiotic Recombination 764 The Mechanism of Meiotic Recombination: Overview 764 • The Double-Stranded DNA Break 764 Creation of Single-Stranded Ends at DSBs 768 22 4 Gene Conversion 768 CHAPTER23 Transposition 773 23 1 Bacterial Transposons 774 Discovery of Bacterial Transposons 774 Insertion Sequences: The Simplest Bacterial Transposons 775 More Complex Transposons 777 Mechanisms of Transposition 777 23 2 Eukaryotic Transposons 779 The First Examples of Transposable Elements: Ds and Ac of Maize 779 P Elements 781 Rearrangement of Immunoglobulin Genes 782 Retrotransposons 787 PARTVIII Genomes CHAPTER24 Genomics and Proteomics 804 24 1 Positional Cloning: An Introduction to Genomics 805 Classical Tools of Positional Cloning 805 Identifying the Gene Mutated in a Human Disease 807 Box 24 1 Problems in Genetic Screening 811 24 2 Sequencing Genomes 812 The Human Genome Project 815 Vectors for Large-Scale Genome Projects 816 The Clone-by-Clone Strategy 817 Shotgun Sequencing 820 Sequencing Standards 821 Early Progress in Sequencing the Human Genome 822 Other Vertebrate Genomes 827 The Minimal Genome 829 24 3 Applications of Genomics 830 Functional Genomics Techniques 830 Other Applications 840 24 4 Proteomics 840 Protein Separations 841 Protein Analysis 841 Protein Interactions 842 Bioinformatics 846 Glossary 854 Index 879
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