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Главная Авторы Tina M. Henkin Snyder and Champness Molecular Genetics of Bacteria

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Snyder and Champness Molecular Genetics of Bacteria

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Страница 1Страница 2 Table of Contents List of Illustrations Guide Pages About the Companion Website Snyder & Champness Molecular Genetics of Bacteria Страница 9 Preface Acknowledgments About the Authors Introduction The Biological Universe The Bacteria GRAM-NEGATIVE AND GRAM-POSITIVE BACTERIA The Archaea The Eukaryotes MITOCHONDRIA AND CHLOROPLASTS AND THE ROLE OF ENDOSYMBIOSIS IN EVOLUTION What Is Genetics? Bacterial Genetics Bacteria Are Haploid Short Generation Times Asexual Reproduction Colony Growth on Agar Plates Colony Purification Serial Dilutions Selections Storing Stocks of Bacterial Strains Genetic Exchange Phage Genetics Phages Are Haploid Selections with Phages Crosses with Phages A Brief History of Bacterial Molecular Genetics Inheritance in Bacteria Transformation Conjugation Transduction Recombination within Genes Semiconservative DNA Replication mRNA The Genetic Code The Operon Model Enzymes for Molecular Biology Synthetic Genomics What Is Ahead SUGGESTED READING 1 The Bacterial Chromosome: DNA Structure, Replication, and Segregation DNA Structure The Deoxyribonucleotides The DNA Chain The 5′ and 3′ Ends Base Pairing Antiparallel Construction The Major and Minor Grooves The Mechanism of DNA Replication Deoxyribonucleotide Precursor Synthesis Replication of the Bacterial Chromosome DNA POLYMERASES PRIMASES NUCLEASES DNA LIGASES ACCESSORY PROTEINS Replication of Double-Stranded DNA SEPARATING THE TWO TEMPLATE DNA STRANDS PROCESSING THE TWO TEMPLATE DNA STRANDS COORDINATING REPLICATION OF THE TWO TEMPLATE STRANDS THE GENES FOR REPLICATION PROTEINS Replication Errors Editing RNA Primers and Editing Impediments to DNA Replication Damaged DNA and DNA Polymerase III Mechanisms To Deal with Impediments on Template DNA Strands Physical Blocks to Replication Forks Replication of the Bacterial Chromosome and Cell Division Structure of Bacterial Chromosomes Replication of the Bacterial Chromosome Initiation of Chromosome Replication ORIGIN OF CHROMOSOMAL REPLICATION INITIATION PROTEINS RNA Priming of Initiation Termination of Chromosome Replication BOX 1.1 Structural Features of Bacterial Genomes References Chromosome Segregation RESOLUTION OF DIMER CHROMOSOMES DECATENATION CONDENSATION Condensins Supercoiling KEEPING NEW SISTER CHROMOSOMES SEPARATE INVOLVES COORDINATING MULTIPLE PROCESSES CHROMOSOME PARTITIONING The Par Proteins Macrodomains Coordinating Cell Division and Chromosome Partitioning in E. coli and B. subtilis The Min Proteins Nucleoid Occlusion Coordination of Cell Division with Replication of the Chromosome TIMING OF REPLICATION IN THE CELL CYCLE Timing of Initiation of Replication ROLE OF THE DnaA PROTEIN Inactivation of DnaA by hydrolysis to DnaA-ADP Reactivation of DnaA by nucleotide exchange to DnaA-ATP SeqA-MEDIATED HEMIMETHYLATION AND SEQUESTRATION SeqA activities outside of oriC The Bacterial Nucleoid Supercoiling in the Nucleoid SUPERCOILING OF NATURAL DNAs SUPERCOILING STRESS Topoisomerases TYPE I TOPOISOMERASES TYPE II TOPOISOMERASES BOX 1.2 Antibiotics That Affect Replication and DNA Structure Antibiotics That Block Precursor Synthesis Inhibition of dihydrofolate reductase Inhibition of ribonucleotide reductase Competition with deoxyuridine monophosphate Antibiotics That Block Polymerization of Deoxynucleotides Deoxynucleotide precursor mimics Cross-linking Antibiotics That Affect DNA Structure Acridine dyes Thymidine mimic Antibiotics That Affect Gyrase GyrA inhibition GyrB inhibition The Bacterial Genome Summary QUESTIONS FOR THOUGHT SUGGESTED READING 2 Bacterial Gene Expression: Transcription, Translation, Protein Folding, and Localization Overview The Structure and Function of RNA Types of RNA RNA Precursors RNA Structure PRIMARY STRUCTURE SECONDARY STRUCTURE TERTIARY STRUCTURE RNA Processing and Modification Transcription Structure of Bacterial RNA Polymerase Overview of Transcription PROMOTERS THE STEPS OF TRANSCRIPTION Details of Transcription PROMOTER RECOGNITION ISOMERIZATION INITIATION ELONGATION TERMINATION OF TRANSCRIPTION Factor-Independent Termination BOX 2.1 Antibiotic Inhibitors of Transcription Inhibitors of rNTP Synthesis Inhibitors of Transcription Initiation Inhibitors of RNA Elongation and Termination Inhibitors that Affect the DNA Template Factor-Dependent Termination rRNAs and tRNAs BOX 2.2 Molecular Phylogeny References MODIFICATION OF RNA RNA Degradation RNases MODULATION OF RNase ACTIVITY The Structure and Function of Proteins Protein Structure PRIMARY STRUCTURE SECONDARY STRUCTURE TERTIARY STRUCTURE QUATERNARY STRUCTURE Translation Structure of the Bacterial Ribosome BOX 2.3 Antibiotic Inhibitors of Translation Antibiotics that block translation Inhibitors that Mimic tRNA Inhibitors that Bind to the 23S rRNA Inhibitors of Binding of aa-tRNA to the A Site Inhibitors of Translocation Overview of Translation Details of Protein Synthesis READING FRAMES TRNA AMINOACYLATION TRANSLATION INITIATION REGIONS Initiation Codons Shine-Dalgarno Sequences INITIATOR tRNA STEPS IN INITIATION OF TRANSLATION Translation Initiation from Leaderless mRNAs TRANSLATION INITIATION IN ARCHAEA AND EUKARYOTES TRANSLATION ELONGATION TRANSLATION TERMINATION RELEASE FACTORS REMOVAL OF THE FORMYL GROUP AND THE N-TERMINAL METHIONINE BOX 2.4 Mimicry in Translation References trans-TRANSLATION (tmRNA) The Genetic Code REDUNDANCY BOX 2.5 Exceptions to the Code References WOBBLE TERMINATION CODONS AMBIGUITY CODON USAGE Polycistronic mRNA TRANSLATIONAL COUPLING POLAR EFFECTS ON GENE EXPRESSION Protein Folding and Degradation Protein Chaperones THE DnaK PROTEIN AND OTHER Hsp70 CHAPERONES TRIGGER FACTOR AND OTHER CHAPERONES CHAPERONINS Protein Degradation Protein Localization The Translocase System The Signal Sequence The Targeting Factors THE SecB PATHWAY THE SRP PATHWAY Sec Systems of Archaea and Eukaryotes The Tat Secretion Pathway STRUCTURE OF THE TAT SYSTEM The Tat Signal Sequence Tat Systems in Other Organisms Disulfide Bonds Protein Secretion and Export Protein Secretion Systems in Bacteria with an Outer Membrane TYPE I SECRETION SYSTEMS TYPE II SECRETION SYSTEMS TYPE III SECRETION SYSTEMS TYPE IV SECRETION SYSTEMS TYPE V SECRETION SYSTEMS: AUTOTRANSPORTERS Chaperone-Usher Secretion TYPE VI SECRETION SYSTEMS Protein Secretion in Bacteria That Lack an Outer Membrane INJECTOSOMES Sortases Regulation of Gene Expression Transcriptional Regulation Posttranscriptional Regulation What You Need To Know Open Reading Frames Transcriptional and Translational Fusions Summary QUESTIONS FOR THOUGHT SUGGESTED READING {buyButton}

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