Lewin’s GENES XII 12th edition by Jocelyn Krebs, Elliott Goldstein, Stephen Kilpatrick ISBN 1284104494 978-1284104493

PART I Genes and Chromosomes

Chapter 1 Genes Are DNA and Encode RNAs and Polypeptides

1.1 Introduction

1.2 DNA Is the Genetic Material of Bacteria and Viruses

1.3 DNA Is the Genetic Material of Eukaryotic Cells

1.4 Polynucleotide Chains Have Nitrogenous Bases Linked to a Sugar—Phosphate Backbone

1.5 Supercoiling Affects the Structure of DNA

1.6 DNA Is a Double Helix

1.7 DNA Replication Is Semiconservative

1.8 Polymerases Act on Separated DNA Strands at the Replication Fork

1.9 Genetic Information Can Be Provided by DNA or RNA

1.10 Nucleic Acids Hybridize by Base Pairing

1.11 Mutations Change the Sequence of DNA

1.12 Mutations Can Affect Single Base Pairs or Longer Sequences

1.13 The Effects of Mutations Can Be Reversed

1.14 Mutations Are Concentrated at Hotspots

1.15 Many Hotspots Result from Modified Bases

1.16 Some Hereditary Agents Are Extremely Small

1.17 Most Genes Encode Polypeptides

1.18 Mutations in the Same Gene Cannot Complement

1.19 Mutations May Cause Loss of Function or Gain of Function

1.20 A Locus Can Have Many Different Mutant Alleles

1.21 A Locus Can Have More Than One Wild-Type Allele

1.22 Recombination Occurs by Physical Exchange of DNA

1.23 The Genetic Code Is Triplet

1.24 Every Coding Sequence Has Three Possible Reading Frames

1.25 Bacterial Genes Are Colinear with Their Products

1.26 Several Processes Are Required to Express the Product of a Gene

1.27 Proteins Are trans-Acting but Sites on DNA Are cis-Acting

Chapter 2 Methods in Molecular Biology and Genetic Engineering

2.1 Introduction

2.2 Nucleases

2.3 Cloning

2.4 Cloning Vectors Can Be Specialized for Different Purposes

2.5 Nucleic Acid Detection

2.6 DNA Separation Techniques

2.7 DNA Sequencing

2.8 PCR and RT-PCR

2.9 Blotting Methods

2.10 DNA Microarrays

2.11 Chromatin Immunoprecipitation

2.12 Gene Knockouts, Transgenics, and Genome Editing

Chapter 3 The Interrupted Gene

3.1 Introduction

3.2 An Interrupted Gene Has Exons and Introns

3.3 Exon and Intron Base Compositions Differ

3.4 Organization of Interrupted Genes Can Be Conserved

3.5 Exon Sequences Under Negative Selection Are Conserved but Introns Vary

3.6 Exon Sequences Under Positive Selection Vary but Introns Are Conserved

3.7 Genes Show a Wide Distribution of Sizes Due Primarily to Intron Size and Number Variation

3.8 Some DNA Sequences Encode More Than One Polypeptide

3.9 Some Exons Correspond to Protein Functional Domains

3.10 Members of a Gene Family Have a Common Organization

3.11 There Are Many Forms of Information in DNA

Chapter 4 The Content of the Genome

4.1 Introduction

4.2 Genome Mapping Reveals That Individual Genomes Show Extensive Variation

4.3 SNPs Can Be Associated with Genetic Disorders

4.4 Eukaryotic Genomes Contain Nonrepetitive and Repetitive DNA Sequences

4.5 Eukaryotic Protein-Coding Genes Can Be Identified by the Conservation of Exons and of Genome Organization

4.6 Some Eukaryotic Organelles Have DNA

4.7 Organelle Genomes Are Circular DNAs That Encode Organelle Proteins

4.8 The Chloroplast Genome Encodes Many Proteins and RNAs

4.9 Mitochondria and Chloroplasts Evolved by Endosymbiosis

Chapter 5 Genome Sequences and Evolution

5.1 Introduction

5.2 Prokaryotic Gene Numbers Range Over an Order of Magnitude

5.3 Total Gene Number Is Known for Several Eukaryotes

5.4 How Many Different Types of Genes Are There?

5.5 The Human Genome Has Fewer Genes Than Originally Expected

5.6 How Are Genes and Other Sequences Distributed in the Genome?

5.7 The Y Chromosome Has Several Male-Specific Genes

5.8 How Many Genes Are Essential?

5.9 About 10,000 Genes Are Expressed at Widely Differing Levels in a Eukaryotic Cell

5.10 Expressed Gene Number Can Be Measured En Masse

5.11 DNA Sequences Evolve by Mutation and a Sorting Mechanism

5.12 Selection Can Be Detected by Measuring Sequence Variation

5.13 A Constant Rate of Sequence Divergence Is a Molecular Clock

5.14 The Rate of Neutral Substitution Can Be Measured from Divergence of Repeated Sequences

5.15 How Did Interrupted Genes Evolve?

5.16 Why Are Some Genomes So Large?

5.17 Morphological Complexity Evolves by Adding New Gene Functions

5.18 Gene Duplication Contributes to Genome Evolution

5.19 Globin Clusters Arise by Duplication and Divergence

5.20 Pseudogenes Have Lost Their Original Functions

5.21 Genome Duplication Has Played a Role in Plant and Vertebrate Evolution

5.22 What Is the Role of Transposable Elements in Genome Evolution

5.23 There Can Be Biases in Mutation, Gene Conversion, and Codon Usage

Chapter 6 Clusters and Repeats

6.1 Introduction

6.2 Unequal Crossing-Over Rearranges Gene Clusters

6.3 Genes for rRNA Form Tandem Repeats Including an Invariant Transcription Unit

6.4 Crossover Fixation Could Maintain Identical Repeats

6.5 Satellite DNAs Often Lie in Heterochromatin

6.6 Arthropod Satellites Have Very Short Identical Repeats

6.7 Mammalian Satellites Consist of Hierarchical Repeats

6.8 Minisatellites Are Useful for DNA Profiling

Chapter 7 Chromosomes

7.1 Introduction

7.2 Viral Genomes Are Packaged into Their Coats

7.3 The Bacterial Genome Is a Nucleoid with Dynamic Structural Properties

7.4 The Bacterial Genome Is Supercoiled and Has Four Macrodomains

7.5 Eukaryotic DNA Has Loops and Domains Attached to a Scaffold

7.6 Specific Sequences Attach DNA to an Interphase Matrix

7.7 Chromatin Is Divided into Euchromatin and Heterochromatin

7.8 Chromosomes Have Banding Patterns

7.9 Lampbrush Chromosomes Are Extended

7.10 Polytene Chromosomes Form Bands

7.11 Polytene Chromosomes Expand at Sites of Gene Expression

7.12 The Eukaryotic Chromosome Is a Segregation Device

7.13 Regional Centromeres Contain a Centromeric Histone H3 Variant and Repetitive DNA

7.14 Point Centromeres in S. cerevisiae Contain Short, Essential DNA Sequences

7.15 The S. cerevisiae Centromere Binds a Protein Complex

7.16 Telomeres Have Simple Repeating Sequences

7.17 Telomeres Seal the Chromosome Ends and Function in Meiotic Chromosome Pairing

7.18 Telomeres Are Synthesized by a Ribonucleoprotein Enzyme

7.19 Telomeres Are Essential for Survival

Chapter 8 Chromatin

8.1 Introduction

8.2 DNA Is Organized in Arrays of Nucleosomes

8.3 The Nucleosome Is the Subunit of All Chromatin

8.4 Nucleosomes Are Covalently Modified

8.5 Histone Variants Produce Alternative Nucleosomes

8.6 DNA Structure Varies on the Nucleosomal Surface

8.7 The Path of Nucleosomes in the Chromatin Fiber

8.8 Replication of Chromatin Requires Assembly of Nucleosomes

8.9 Do Nucleosomes Lie at Specific Positions?

8.10 Nucleosomes Are Displaced and Reassembled During Transcription

8.11 DNase Sensitivity Detects Changes in Chromatin Structure

8.12 An LCR Can Control a Domain

8.13 Insulators Define Transcriptionally Independent Domains

PART II DNA Replication and Recombination

Chapter 9 Replication Is Connected to the Cell Cycle

9.1 Introduction

9.2 Bacterial Replication Is Connected to the Cell Cycle

9.3 The Shape and Spatial Organization of a Bacterium Are Important During Chromosome Segregation and Cell Division

9.4 Mutations in Division or Segregation Affect Cell Shape

9.5 FtsZ Is Necessary for Septum Formation

9.6 min and noc/slm Genes Regulate the Location of the Septum

9.7 Partition Involves Separation of the Chromosomes

9.8 Chromosomal Segregation Might Require Site-Specific Recombination

9.9 The Eukaryotic Growth Factor Signal Transduction Pathway Promotes Entry to S Phase

9.10 Checkpoint Control for Entry into S Phase: p53, a Guardian of the Checkpoint

9.11 Checkpoint Control for Entry into S Phase: Rb, a Guardian of the Checkpoint

Chapter 10 The Replicon: Initiation of Replication

10.1 Introduction

10.2 An Origin Usually Initiates Bidirectional Replication

10.3 The Bacterial Genome Is (Usually) a Single Circular Replicon

10.4 Methylation of the Bacterial Origin Regulates Initiation

10.5 Initiation: Creating the Replication Forks at the Origin oriC

10.6 Multiple Mechanisms Exist to Prevent Premature Reinitiation of Replication

10.7 Archaeal Chromosomes Can Contain Multiple Replicons

10.8 Each Eukaryotic Chromosome Contains Many Replicons

10.9 Replication Origins Can Be Isolated in Yeast

10.10 Licensing Factor Controls Eukaryotic Rereplication

10.11 Licensing Factor Binds to ORC

Chapter 11 DNA Replication

11.1 Introduction

11.2 DNA Polymerases Are the Enzymes That Make DNA

11.3 DNA Polymerases Have Various Nuclease Activities

11.4 DNA Polymerases Control the Fidelity of Replication

11.5 DNA Polymerases Have a Common Structure

11.6 The Two New DNA Strands Have Different Modes of Synthesis

11.7 Replication Requires a Helicase and a Single-Stranded Binding Protein

11.8 Priming Is Required to Start DNA Synthesis

11.9 Coordinating Synthesis of the Lagging and Leading Strands

11.10 DNA Polymerase Holoenzyme Consists of Subcomplexes

11.11 The Clamp Controls Association of Core Enzyme with DNA

11.12 Okazaki Fragments Are Linked by Ligase

11.13 Separate Eukaryotic DNA Polymerases Undertake Initiation and Elongation

11.14 Lesion Bypass Requires Polymerase Replacement

11.15 Termination of Replication

Chapter 12 Extrachromosomal Replicons

12.1 Introduction

12.2 The Ends of Linear DNA Are a Problem for Replication

12.3 Terminal Proteins Enable Initiation at the Ends of Viral DNAs

12.4 Rolling Circles Produce Multimers of a Replicon

12.5 Rolling Circles Are Used to Replicate Phage Genomes

12.6 The F Plasmid Is Transferred by Conjugation Between Bacteria

12.7 Conjugation Transfers Single-Stranded DNA

12.8 Single-Copy Plasmids Have a Partitioning System

12.9 Plasmid Incompatibility Is Determined by the Replicon

12.10 The ColE1 Compatibility System Is Controlled by an RNA Regulator

12.11 How Do Mitochondria Replicate and Segregate?

12.12 D Loops Maintain Mitochondrial Origins

12.13 The Bacterial Ti Plasmid Causes Crown Gall Disease in Plants

12.14 T-DNA Carries Genes Required for Infection

12.15 Transfer of T-DNA Resembles Bacterial Conjugation

Chapter 13 Homologous and Site-Specific Recombination

13.1 Introduction

13.2 Homologous Recombination Occurs Between Synapsed Chromosomes in Meiosis

13.3 Double-Strand Breaks Initiate Recombination

13.4 Gene Conversion Accounts for Interallelic Recombination

13.5 The Synthesis-Dependent Strand-Annealing Model

13.6 The Single-Strand Annealing Mechanism Functions at Some Double-Strand Breaks

13.7 Break-Induced Replication Can Repair Double-Strand Breaks

13.8 Recombining Meiotic Chromosomes Are Connected by the Synaptonemal Complex

13.9 The Synaptonemal Complex Forms After Double-Strand Breaks

13.10 Pairing and Synaptonemal Complex Formation Are Independent

13.11 The Bacterial RecBCD System Is Stimulated by chi Sequences

13.12 Strand-Transfer Proteins Catalyze Single-Strand Assimilation

13.13 Holliday Junctions Must Be Resolved

13.14 Eukaryotic Genes Involved in Homologous Recombination

1. End Processing/Presynapsis

2. Synapsis

3. DNA Heteroduplex Extension and Branch Migration

4. Resolution

13.15 Specialized Recombination Involves Specific Sites

13.16 Site-Specific Recombination Involves Breakage and Reunion

13.17 Site-Specific Recombination Resembles Topoisomerase Activity

13.18 Lambda Recombination Occurs in an Intasome

13.19 Yeast Can Switch Silent and Active Mating-Type Loci

13.20 Unidirectional Gene Conversion Is Initiated by the Recipient MAT Locus

13.21 Antigenic Variation in Trypanosomes Uses Homologous Recombination

13.22 Recombination Pathways Adapted for Experimental Systems

Chapter 14 Repair Systems

14.1 Introduction

14.2 Repair Systems Correct Damage to DNA

14.3 Excision Repair Systems in E. coli

14.4 Eukaryotic Nucleotide Excision Repair Pathways

14.5 Base Excision Repair Systems Require Glycosylases

14.6 Error-Prone Repair and Translesion Synthesis

14.7 Controlling the Direction of Mismatch Repair

14.8 Recombination-Repair Systems in E. coli

14.9 Recombination Is an Important Mechanism to Recover from Replication Errors

14.10 Recombination-Repair of Double-Strand Breaks in Eukaryotes

14.11 Nonhomologous End Joining Also Repairs Double-Strand Breaks

14.12 DNA Repair in Eukaryotes Occurs in the Context of Chromatin

14.13 RecA Triggers the SOS System

Chapter 15 Transposable Elements and Retroviruses

15.1 Introduction

15.2 Insertion Sequences Are Simple Transposition Modules

15.3 Transposition Occurs by Both Replicative and Nonreplicative Mechanisms

15.4 Transposons Cause Rearrangement of DNA

15.5 Replicative Transposition Proceeds Through a Cointegrate

15.6 Nonreplicative Transposition Proceeds by Breakage and Reunion

15.7 Transposons Form Superfamilies and Families

15.8 The Role of Transposable Elements in Hybrid Dysgenesis

15.9 P Elements Are Activated in the Germline

15.10 The Retrovirus Life Cycle Involves Transposition-Like Events

15.11 Retroviral Genes Code for Polyproteins

15.12 Viral DNA Is Generated by Reverse Transcription

15.13 Viral DNA Integrates into the Chromosome

15.14 Retroviruses May Transduce Cellular Sequences

15.15 Retroelements Fall into Three Classes

15.16 Yeast Ty Elements Resemble Retroviruses

15.17 The Alu Family Has Many Widely Dispersed Members

15.18 LINEs Use an Endonuclease to Generate a Priming End

Chapter 16 Somatic DNA Recombination and Hypermutation in the Immune System

16.1 The Immune System: Innate and Adaptive Immunity

16.2 The Innate Response Utilizes Conserved Recognition Molecules and Signaling Pathways

16.3 Adaptive Immunity

16.4 Clonal Selection Amplifies Lymphocytes That Respond to a Given Antigen

16.5 Ig Genes Are Assembled from Discrete DNA Segments in B Lymphocytes

16.6 L Chains Are Assembled by a Single Recombination Event

16.7 H Chains Are Assembled by Two Sequential Recombination Events

16.8 Recombination Generates Extensive Diversity

16.9 V(D)J DNA Recombination Relies on RSS and Occurs by Deletion or Inversion

16.10 Allelic Exclusion Is Triggered by Productive Rearrangements

16.11 RAG1/RAG2 Catalyze Breakage and Religation of V(D)J Gene Segments

16.12 B Cell Development in the Bone Marrow: From Common Lymphoid Progenitor to Mature B Cell

16.13 Class Switch DNA Recombination

16.14 CSR Involves AID and Elements of the NHEJ Pathway

16.15 Somatic Hypermutation Generates Additional Diversity and Provides the Substrate for Higher-Affinity Submutants

16.16 SHM Is Mediated by AID, Ung, Elements of the Mismatch DNA Repair Machinery, and Translesion DNA Synthesis Polymerases

16.17 Igs Expressed in Avians Are Assembled from Pseudogenes

16.18 Chromatin Architecture Dynamics of the IgH Locus in V(D)J Recombination, CSR, and SHM

16.19 Epigenetics of V(D)J Recombination, CSR, and SHM

16.20 B Cell Differentiation Results in Maturation of the Antibody Response and Generation of Long-lived Plasma Cells and Memory B Cells

16.21 The T Cell Receptor Antigen Is Related to the BCR

16.22 The TCR Functions in Conjunction with the MHC

16.23 The MHC Locus Comprises a Cohort of Genes Involved in Immune Recognition

PART III Transcription and Posttranscriptional Mechanisms

Chapter 17 Prokaryotic Transcription

17.1 Introduction

17.2 Transcription Occurs by Base Pairing in a “Bubble” of Unpaired DNA

17.3 The Transcription Reaction Has Three Stages

17.4 Bacterial RNA Polymerase Consists of Multiple Subunits

17.5 RNA Polymerase Holoenzyme Consists of the Core Enzyme and Sigma Factor

17.6 How Does RNA Polymerase Find Promoter Sequences?

17.7 The Holoenzyme Goes Through Transitions in the Process of Recognizing and Escaping from Promoters

17.8 Sigma Factor Controls Binding to DNA by Recognizing Specific Sequences in Promoters

17.9 Promoter Efficiencies Can Be Increased or Decreased by Mutation

17.10 Multiple Regions in RNA Polymerase Directly Contact Promoter DNA

17.11 RNA Polymerase—Promoter and DNA—Protein Interactions Are the Same for Promoter Recognition and DNA Melting

17.12 Interactions Between Sigma Factor and Core RNA Polymerase Change During Promoter Escape

17.13 A Model for Enzyme Movement Is Suggested by the Crystal Structure

17.14 A Stalled RNA Polymerase Can Restart

17.15 Bacterial RNA Polymerase Terminates at Discrete Sites

17.16 How Does Rho Factor Work?

17.17 Supercoiling Is an Important Feature of Transcription

17.18 Phage T7 RNA Polymerase Is a Useful Model System

17.19 Competition for Sigma Factors Can Regulate Initiation

17.20 Sigma Factors Can Be Organized into Cascades

17.21 Sporulation Is Controlled by Sigma Factors

17.22 Antitermination Can Be a Regulatory Event

Chapter 18 Eukaryotic Transcription

18.1 Introduction

18.2 Eukaryotic RNA Polymerases Consist of Many Subunits

18.3 RNA Polymerase I Has a Bipartite Promoter

18.4 RNA Polymerase III Uses Downstream and Upstream Promoters

18.5 The Start Point for RNA Polymerase II

18.6 TBP Is a Universal Factor

18.7 The Basal Apparatus Assembles at the Promoter

18.8 Initiation Is Followed by Promoter Clearance and Elongation

18.9 Enhancers Contain Bidirectional Elements That Assist Initiation

18.10 Enhancers Work by Increasing the Concentration of Activators Near the Promoter

18.11 Gene Expression Is Associated with Demethylation

18.12 CpG Islands Are Regulatory Targets

Chapter 19 RNA Splicing and Processing

19.1 Introduction

19.2 The 5ʹ End of Eukaryotic mRNA Is Capped

19.3 Nuclear Splice Sites Are Short Sequences

19.4 Splice Sites Are Read in Pairs

19.5 Pre-mRNA Splicing Proceeds Through a Lariat

19.6 snRNAs Are Required for Splicing

19.7 Commitment of Pre-mRNA to the Splicing Pathway

19.8 The Spliceosome Assembly Pathway

19.9 An Alternative Spliceosome Uses Different snRNPs to Process the Minor Class of Introns

19.10 Pre-mRNA Splicing Likely Shares the Mechanism with Group II Autocatalytic Introns

19.11 Splicing Is Temporally and Functionally Coupled with Multiple Steps in Gene Expression

19.12 Alternative Splicing Is a Rule, Rather Than an Exception, in Multicellular Eukaryotes

19.13 Splicing Can Be Regulated by Exonic and Intronic Splicing Enhancers and Silencers

19.14 trans-Splicing Reactions Use Small RNAs

19.15 The 3ʹ Ends of mRNAs Are Generated by Cleavage and Polyadenylation

19.16 3ʹ mRNA End Processing Is Critical for Termination of Transcription

19.17 The 3ʹ End Formation of Histone mRNA Requires U7 snRNA

19.18 tRNA Splicing Involves Cutting and Rejoining in Separate Reactions

19.19 The Unfolded Protein Response Is Related to tRNA Splicing

19.20 Production of rRNA Requires Cleavage Events and Involves Small RNAs

Chapter 20 mRNA Stability and Localization

20.1 Introduction

20.2 Messenger RNAs Are Unstable Molecules

20.3 Eukaryotic mRNAs Exist in the Form of mRNPs from Their Birth to Their Death

20.4 Prokaryotic mRNA Degradation Involves Multiple Enzymes

20.5 Most Eukaryotic mRNA Is Degraded via Two Deadenylation-Dependent Pathways

20.6 Other Degradation Pathways Target Specific mRNAs

20.7 mRNA-Specific Half-Lives Are Controlled by Sequences or Structures Within the mRNA

20.8 Newly Synthesized RNAs Are Checked for Defects via a Nuclear Surveillance System

20.9 Quality Control of mRNA Translation Is Performed by Cytoplasmic Surveillance Systems

20.10 Translationally Silenced mRNAs Are Sequestered in a Variety of RNA Granules

20.11 Some Eukaryotic mRNAs Are Localized to Specific Regions of a Cell

Chapter 21 Catalytic RNA

21.1 Introduction

21.2 Group I Introns Undertake Self-Splicing by Transesterification

21.3 Group I Introns Form a Characteristic Secondary Structure

21.4 Ribozymes Have Various Catalytic Activities

21.5 Some Group I Introns Encode Endonucleases That Sponsor Mobility

21.6 Group II Introns May Encode Multifunction Proteins

21.7 Some Autosplicing Introns Require Maturases

21.8 The Catalytic Activity of RNase P Is Due to RNA

21.9 Viroids Have Catalytic Activity

21.10 RNA Editing Occurs at Individual Bases

21.11 RNA Editing Can Be Directed by Guide RNAs

21.12 Protein Splicing Is Autocatalytic

Chapter 22 Translation

22.1 Introduction

22.2 Translation Occurs by Initiation, Elongation, and Termination

22.3 Special Mechanisms Control the Accuracy of Translation

22.4 Initiation in Bacteria Needs 30S Subunits and Accessory Factors

22.5 Initiation Involves Base Pairing Between mRNA and rRNA

22.6 A Special Initiator tRNA Starts the Polypeptide Chain

22.7 Use of fMet-tRNAf Is Controlled by IF-2 and the Ribosome

22.8 Small Subunits Scan for Initiation Sites on Eukaryotic mRNA

22.9 Eukaryotes Use a Complex of Many Initiation Factors

22.10 Elongation Factor Tu Loads Aminoacyl-tRNA into the A Site

22.11 The Polypeptide Chain Is Transferred to Aminoacyl-tRNA

22.12 Translocation Moves the Ribosome

22.13 Elongation Factors Bind Alternately to the Ribosome

22.14 Three Codons Terminate Translation

22.15 Termination Codons Are Recognized by Protein Factors

22.16 Ribosomal RNA Is Found Throughout Both Ribosomal Subunits

22.17 Ribosomes Have Several Active Centers

22.18 16S rRNA Plays an Active Role in Translation

22.19 23S rRNA Has Peptidyl Transferase Activity

22.20 Ribosomal Structures Change When the Subunits Come Together

22.21 Translation Can Be Regulated

22.22 The Cycle of Bacterial Messenger RNA

Chapter 23 Using the Genetic Code

23.1 Introduction

23.2 Related Codons Represent Chemically Similar Amino Acids

23.3 Codon—Anticodon Recognition Involves Wobbling

23.4 tRNAs Are Processed from Longer Precursors

23.5 tRNA Contains Modified Bases

23.6 Modified Bases Affect Anticodon—Codon Pairing

23.7 The Universal Code Has Experienced Sporadic Alterations

23.8 Novel Amino Acids Can Be Inserted at Certain Stop Codons

23.9 tRNAs Are Charged with Amino Acids by Aminoacyl-tRNA Synthetases

23.10 Aminoacyl-tRNA Synthetases Fall into Two Classes

23.11 Synthetases Use Proofreading to Improve Accuracy

23.12 Suppressor tRNAs Have Mutated Anticodons That Read New Codons

23.13 Each Termination Codon Has Nonsense Suppressors

23.14 Suppressors May Compete with Wild-Type Reading of the Code

23.15 The Ribosome Influences the Accuracy of Translation

23.16 Frameshifting Occurs at Slippery Sequences

23.17 Other Recoding Events: Translational Bypassing and the tmRNA Mechanism to Free Stalled Ribosomes

PART IV Gene Regulation

Chapter 24 The Operon

24.1 Introduction

24.2 Structural Gene Clusters Are Coordinately Controlled

24.3 The lac Operon Is Negative Inducible

24.4 The lac Repressor Is Controlled by a Small-Molecule Inducer

24.5 cis-Acting Constitutive Mutations Identify the Operator

24.6 trans-Acting Mutations Identify the Regulator Gene

24.7 The lac Repressor Is a Tetramer Made of Two Dimers

24.8 lac Repressor Binding to the Operator Is Regulated by an Allosteric Change in Conformation

24.9 The lac Repressor Binds to Three Operators and Interacts with RNA Polymerase

24.10 The Operator Competes with Low-Affinity Sites to Bind Repressor

24.11 The lac Operon Has a Second Layer of Control: Catabolite Repression

24.12 The trp Operon Is a Repressible Operon with Three Transcription Units

24.13 The trp Operon Is Also Controlled by Attenuation

24.14 Attenuation Can Be Controlled by Translation

24.15 Stringent Control by Stable RNA Transcription

24.16 r-Protein Synthesis Is Controlled by Autoregulation

Chapter 25 Phage Strategies

25.1 Introduction

25.2 Lytic Development Is Divided into Two Periods

25.3 Lytic Development Is Controlled by a Cascade

25.4 Two Types of Regulatory Events Control the Lytic Cascade

25.5 The Phage T7 and T4 Genomes Show Functional Clustering

25.6 Lambda Immediate Early and Delayed Early Genes Are Needed for Both Lysogeny and the Lytic Cycle

25.7 The Lytic Cycle Depends on Antitermination by pN

25.8 Lysogeny Is Maintained by the Lambda Repressor Protein

25.9 The Lambda Repressor and Its Operators Define the Immunity Region

25.10 The DNA-Binding Form of the Lambda Repressor Is a Dimer

25.11 The Lambda Repressor Uses a Helix-Turn-Helix Motif to Bind DNA

25.12 Lambda Repressor Dimers Bind Cooperatively to the Operator

25.13 The Lambda Repressor Maintains an Autoregulatory Circuit

25.14 Cooperative Interactions Increase the Sensitivity of Regulation

25.15 The cII and cIII Genes Are Needed to Establish Lysogeny

25.16 A Poor Promoter Requires cII Protein

25.17 Lysogeny Requires Several Events

25.18 The Cro Repressor Is Needed for Lytic Infection

25.19 What Determines the Balance Between Lysogeny and the Lytic Cycle?

Chapter 26 Eukaryotic Transcription Regulation

26.1 Introduction

26.2 How Is a Gene Turned On?

26.3 Mechanism of Action of Activators and Repressors

26.4 Independent Domains Bind DNA and Activate Transcription

26.5 The Two-Hybrid Assay Detects Protein—Protein Interactions

26.6 Activators Interact with the Basal Apparatus

26.7 Many Types of DNA-Binding Domains Have Been Identified

26.8 Chromatin Remodeling Is an Active Process

26.9 Nucleosome Organization or Content Can Be Changed at the Promoter

26.10 Histone Acetylation Is Associated with Transcription Activation

26.11 Methylation of Histones and DNA Is Connected

26.12 Promoter Activation Involves Multiple Changes to Chromatin

26.13 Histone Phosphorylation Affects Chromatin Structure

26.14 Yeast GAL Genes: A Model for Activation and Repression

Chapter 27 Epigenetics I

27.1 Introduction

27.2 Heterochromatin Propagates from a Nucleation Event

27.3 Heterochromatin Depends on Interactions with Histones

27.4 Polycomb and Trithorax Are Antagonistic Repressors and Activators

27.5 CpG Islands Are Subject to Methylation

27.6 Epigenetic Effects Can Be Inherited

27.7 Yeast Prions Show Unusual Inheritance

Chapter 28 Epigenetics II

28.1 Introduction

28.2 X Chromosomes Undergo Global Changes

28.3 Chromosome Condensation Is Caused by Condensins

28.4 DNA Methylation Is Responsible for Imprinting

28.5 Oppositely Imprinted Genes Can Be Controlled by a Single Center

28.6 Prions Cause Diseases in Mammals

Chapter 29 Noncoding RNA

29.1 Introduction

29.2 A Riboswitch Can Alter Its Structure According to Its Environment

29.3 Noncoding RNAs Can Be Used to Regulate Gene Expression

Chapter 30 Regulatory RNA

30.1 Introduction

30.2 Bacteria Contain Regulator RNAs

30.3 MicroRNAs Are Widespread Regulators in Eukaryotes

30.4 How Does RNA Interference Work?

30.5 Heterochromatin Formation Requires MicroRNAs

Glossary

Index