Chapter 30 DNA Replication, Repair, and Recombination

1 DNA Replicaton: An Overview

A. Replication Forks
B. Role of DNA Gyrase
C. Semidiscontinuous Replication
D. RNA Primers
2 Enzymes of Replication
A. DNA Polymerase I
B. DNA Polymerase III
C. Unwinding DNA: Helicases and Single-Strand Binding Protein
D. DNA Ligase
E. Primase
3 Prokaryotic Replication
A. Bacteriophage M13
B. Bacteriophage ϕX174
C. Escherichia coli
D. Fidelity of Replication
4 Eukaryotic Replication
A. The Cell Cycle
B. Eukaryotic Replication Mechanisms
C. Reverse Transcriptase
D. Telomeres and Telomerase
5 Repair of DNA
A. Direct Reversal of Damage
B. Excision Repair
C. Mismatch Repair
D. The SOS Response
E. Double-Strand Break Repair
F. Identification of Carcinogens
6 Recombination and Mobile Genetic Elements
A. Homologous Recombination
B. Transposition and Site-Specific Recombination
7 DNA Methylation and Trinucleotide Repeat Expansions
Chapter 31 Transcription
1 The Role of RNA in Protein Synthesis
A. Enzyme Induction
B. Messenger RNA
2 RNA Polymerase
A. Template Binding
B. Chain Initiation
C. Chain Elongation
D. Chain Termination
E. Eukaryotic RNA Polymerases
3 Control of Transcription in Prokaryotes
A. Protomers
B. Iac Repressor I: Binding
C. Catabolite Repression: An Example of Gene Activation
D. Sequence-Specific Protein−DNA Interactions
E. araBAD Operon: Positive and Negative Control by the Same Protein
F. Iac Repressor II: Structure
G. trp Operon: Attenuation
H. Riboswitches Are Metabolite-Sensing RNAs
I. Regulation of Ribosomal RNA Synthesis: The Stringent Response
4 Post-Transcriptional Processing
A. Messenger RNA Processing
B. Ribosomal RNA Processing
C. Transfer RNA Processing

Chapter 32 Translation
1 The Genetic Code
A. Chemical Mutagenesis
B. Codons Are Triplets
C. Deciphering the Genetic Code
D. The Nature of the Code
2 Transfer RNA and Its Aminoacylation
A. Primary and Secondary Structures of tRNA
B. Tertiary Structure of tRNA
 C. Aminoacyl−tRNA Synthetases
D. Codon−Anticodon Interactions
E. Nonsense Suppression
3 Ribosomes and Polypeptide Synthesis
A. Ribosome Structure
B. Polypeptide Synthesis: An Overview
C. Chain Initiation
D. Chain Elongation
E. Translational Accuracy
F. Chain Termination
G. Protein Synthesis Inhibitors: Antibiotics
4 Control of Eukaryotic Translation
A. Regulation of elF2
B. Regulation of elF4E
C. mRNA Masking and Cytoplasmic Polyadenylation
D. Antisense Oligonucleotides
5 Post-Translational Modification
A. Proteolytic Cleavage
B. Covalet Modification
C. Protein Splicing: Inteins and Exteins
6 Protein Degradation
A. Degradation Specificity
B. Degradation Mechanisms