My aim in writing Gene Function has been to present an up-to-date picture ofthe molecular biology of Escherichia coli. I have not attempted a chronological description, believing that a mechanistic account is more useful for such a highly developed field. I have divided the book into four parts. Part I is a general introduction to bacterial systems, their genetic material, structure, composition and growth. It has seemed desirable to include herein a brief preview of the remaining text, to introduce the nomenclature and to help place subsequent chapters in perspective. The expression of…mehr
My aim in writing Gene Function has been to present an up-to-date picture ofthe molecular biology of Escherichia coli. I have not attempted a chronological description, believing that a mechanistic account is more useful for such a highly developed field. I have divided the book into four parts. Part I is a general introduction to bacterial systems, their genetic material, structure, composition and growth. It has seemed desirable to include herein a brief preview of the remaining text, to introduce the nomenclature and to help place subsequent chapters in perspective. The expression of genetic material and its perturbation through mutation is considered in Part II. Part III discusses how the transfer of prokaryotic genetic material can be mediated by plasmids and bacteriophages. It describes the DNA transactions involved (replication, recombination and repair) and ends with a description of the genetic and biochemical techniques employed in the study of gene organisation. Finally, Part IV considers the control of expression of bacterial, plasmid and phage genes. Key reviews are listed at the end of each chapter.
One: Introduction.- 1 The Bacterial Cell.- 1.1 The Nature of the Genetic Material.- 1.1.1 Structural Considerations.- (a) The Composition of Nucleic Acid.- (b) The Double Helix.- (c) Chromosome Structure.- 1.1.2 The Biological Role of Nucleic Acid: A Preview.- (a) Gene Expression.- (b) Replication.- (c) Genetic Recombination.- (d) DNA Repair.- (e) Symmetrical Recognition Sequences.- 1.1.3 Phenotype and Genotype.- 1.2 Cell Composition.- 1.2.1 The Cell Envelope.- 1.2.2 Cellular Appendages.- 1.3 Bacterial Growth.- 1.3.1 An Introduction to Metabolism.- (a) Production of the Chemical Intermediate, ATP.- (b) Biosynthetic Reactions.- (c) Pathway Regulation.- 1.3.2 Growth of Populations.- (a) Growth Requirements.- (b) Culture Characteristics.- (i) Lag Phase; (ii) Exponential Phase; (iii) Stationary Phase.- Two: Gene Expression.- 2 RNA and Protein Production.- 2.1 DNA Transcription.- 2.1.1 The Elements of Transcription.- (a) DNA-Dependent RNA Polymerase.- (b) Transcription Factors.- 2.1.2 The Mechanism of Transcription.- (a) The Transcription Cycle.- (i) Initiation; (ii) Elongation; (iii) Termination.- (b) Control: RNA Synthesis and Decay.- (c) Antibiotic Inhibitors of Transcription.- 2.2 RNA Translation.- 2.2.1 The Elements of Translation.- (a) The Genetic Code.- (b) Transfer RNA.- (c) The Ribosome.- 2.2.2 The Mechanism of Translation.- (a) The Ribosome Cycle.- (i) Initiation; (ii) Elongation; (iii) Termination.- (b) Post-Translational Modification.- (c) Control.- (d) Antibiotic Inhibitors of Translation.- 3 Mutation.- 3.1 Mutation Classification.- 3.1.1 Types of Point Mutation.- (a) Samesense Mutation.- (b) Missense Mutation.- (c) Nonsense Mutation.- (d) Frameshift Mutation.- 3.1.2 Conditional Mutants.- 3.2 Mutagenesis.- 3.2.1 The Molecular Basis of Mutagenesis.- (a) Spontaneous Mutation.- (b) Induced Mutation.- (i) Radiation; (ii) Chemical Mutagens.- (c) Mutational Hotspots.- 3.2.2 The Application of Mutagenesis to Bacterial Systems.- (a) Isolation of Independent Mutants that Carry Single Lesions.- (b) Mutant Selection.- (i) Replica-plating; (ii) Penicillin Enrichment.- 3.3 Suppression.- 3.3.1 Intragenic Suppression.- 3.3.2 Intergenic Suppression.- 3.3.3 Phenotypic Suppression: The Role of the Ribosome in Misreading.- 3.4 Summary: Mutation Identification.- Three: Gene Transfer.- 4 Plasmids.- 4.1 The F Plasmid.- 4.1.1 Vegetative Replication.- 4.1.2 F Transfer.- (a) The Mechanism of Transfer.- (b) Barriers to Transfer.- 4.1.3 F-Mediated Transfer.- (a) F integration: Hfr Formation.- (i) Insertion; (ii) Hfr Transfer; (iii) The One Hundred Minute Map.- (b) F Excision: F-Prime Formation.- 4.2 A Guide to Naturally-Occurring Plasmids.- 4.2.1 R Plasmids.- 4.2.2 Col Plasmids.- 5 Bacteriophages.- 5.1 Bacteriophages and their Life-Cycles.- 5.1.1 Anatomical Considerations.- (a) Phage Morphology.- (b) The Viral Genome.- 5.1.2 Phage Infection.- (a) The Lytic Response.- (b) Morphogenesis.- (c) The Lysogenic Response.- 5.1.3 Phage Methodology.- (a) Titration: The Plaque Assay.- (b) Production of Phage Lines.- 5.2 Bacteriophage-Mediated Gene Transfer.- 5.2.1 Generalised Transduction.- 5.2.2 Specialised Transduction.- 6 Reactions of DNA.- 6.1 DNA Replication.- 6.1.1 The Elements of Replication.- (a) DNA-Dependent DNA Polymerases.- (b) Protein Components of the Replication Fork.- 6.1.2 The Mechanism of Bacterial Replication.- (a) Bidirectional Replication of the E. coli Chromosome.- (i) Initiation; (ii) Elongation; (iii) Termination.- (b) The Role of the Cell Envelope in Replication.- (c) Control of DNA Replication.- (d) Antibiotic Inhibitors of Replication.- 6.1.3 Replication of Small Genetic Elements.- (a) Plasmid Production.- (b) Viral DNA Synthesis.- 6.2 Genetic Recombination.- 6.2.1 General Recombination.- (a) The Elements of General Recombination.- (i) The recA Gene Product; (ii) The Involvement of Other Gene Products in Recombination.- (b) Recombination Pathways.- (i) recA-mediated Pathways; (ii) The To Pathway.- (c) The Mechanism of General
One: Introduction.- 1 The Bacterial Cell.- 1.1 The Nature of the Genetic Material.- 1.1.1 Structural Considerations.- (a) The Composition of Nucleic Acid.- (b) The Double Helix.- (c) Chromosome Structure.- 1.1.2 The Biological Role of Nucleic Acid: A Preview.- (a) Gene Expression.- (b) Replication.- (c) Genetic Recombination.- (d) DNA Repair.- (e) Symmetrical Recognition Sequences.- 1.1.3 Phenotype and Genotype.- 1.2 Cell Composition.- 1.2.1 The Cell Envelope.- 1.2.2 Cellular Appendages.- 1.3 Bacterial Growth.- 1.3.1 An Introduction to Metabolism.- (a) Production of the Chemical Intermediate, ATP.- (b) Biosynthetic Reactions.- (c) Pathway Regulation.- 1.3.2 Growth of Populations.- (a) Growth Requirements.- (b) Culture Characteristics.- (i) Lag Phase; (ii) Exponential Phase; (iii) Stationary Phase.- Two: Gene Expression.- 2 RNA and Protein Production.- 2.1 DNA Transcription.- 2.1.1 The Elements of Transcription.- (a) DNA-Dependent RNA Polymerase.- (b) Transcription Factors.- 2.1.2 The Mechanism of Transcription.- (a) The Transcription Cycle.- (i) Initiation; (ii) Elongation; (iii) Termination.- (b) Control: RNA Synthesis and Decay.- (c) Antibiotic Inhibitors of Transcription.- 2.2 RNA Translation.- 2.2.1 The Elements of Translation.- (a) The Genetic Code.- (b) Transfer RNA.- (c) The Ribosome.- 2.2.2 The Mechanism of Translation.- (a) The Ribosome Cycle.- (i) Initiation; (ii) Elongation; (iii) Termination.- (b) Post-Translational Modification.- (c) Control.- (d) Antibiotic Inhibitors of Translation.- 3 Mutation.- 3.1 Mutation Classification.- 3.1.1 Types of Point Mutation.- (a) Samesense Mutation.- (b) Missense Mutation.- (c) Nonsense Mutation.- (d) Frameshift Mutation.- 3.1.2 Conditional Mutants.- 3.2 Mutagenesis.- 3.2.1 The Molecular Basis of Mutagenesis.- (a) Spontaneous Mutation.- (b) Induced Mutation.- (i) Radiation; (ii) Chemical Mutagens.- (c) Mutational Hotspots.- 3.2.2 The Application of Mutagenesis to Bacterial Systems.- (a) Isolation of Independent Mutants that Carry Single Lesions.- (b) Mutant Selection.- (i) Replica-plating; (ii) Penicillin Enrichment.- 3.3 Suppression.- 3.3.1 Intragenic Suppression.- 3.3.2 Intergenic Suppression.- 3.3.3 Phenotypic Suppression: The Role of the Ribosome in Misreading.- 3.4 Summary: Mutation Identification.- Three: Gene Transfer.- 4 Plasmids.- 4.1 The F Plasmid.- 4.1.1 Vegetative Replication.- 4.1.2 F Transfer.- (a) The Mechanism of Transfer.- (b) Barriers to Transfer.- 4.1.3 F-Mediated Transfer.- (a) F integration: Hfr Formation.- (i) Insertion; (ii) Hfr Transfer; (iii) The One Hundred Minute Map.- (b) F Excision: F-Prime Formation.- 4.2 A Guide to Naturally-Occurring Plasmids.- 4.2.1 R Plasmids.- 4.2.2 Col Plasmids.- 5 Bacteriophages.- 5.1 Bacteriophages and their Life-Cycles.- 5.1.1 Anatomical Considerations.- (a) Phage Morphology.- (b) The Viral Genome.- 5.1.2 Phage Infection.- (a) The Lytic Response.- (b) Morphogenesis.- (c) The Lysogenic Response.- 5.1.3 Phage Methodology.- (a) Titration: The Plaque Assay.- (b) Production of Phage Lines.- 5.2 Bacteriophage-Mediated Gene Transfer.- 5.2.1 Generalised Transduction.- 5.2.2 Specialised Transduction.- 6 Reactions of DNA.- 6.1 DNA Replication.- 6.1.1 The Elements of Replication.- (a) DNA-Dependent DNA Polymerases.- (b) Protein Components of the Replication Fork.- 6.1.2 The Mechanism of Bacterial Replication.- (a) Bidirectional Replication of the E. coli Chromosome.- (i) Initiation; (ii) Elongation; (iii) Termination.- (b) The Role of the Cell Envelope in Replication.- (c) Control of DNA Replication.- (d) Antibiotic Inhibitors of Replication.- 6.1.3 Replication of Small Genetic Elements.- (a) Plasmid Production.- (b) Viral DNA Synthesis.- 6.2 Genetic Recombination.- 6.2.1 General Recombination.- (a) The Elements of General Recombination.- (i) The recA Gene Product; (ii) The Involvement of Other Gene Products in Recombination.- (b) Recombination Pathways.- (i) recA-mediated Pathways; (ii) The To Pathway.- (c) The Mechanism of General
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