Ebook: Gene Function: E. coli and its heritable elements

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 Recombination.- (i) Strand Breakage; (ii) Strand Pairing; (iii) Strand Invasion; (iv) Chiasma Formation; (v) Breakage and Reunion; (vi) Mismatch Repair.- 6.2.2 Non-Homologous Recombination.- (a) Site-Specific Recombination.- (i) Bacteriophages; (ii) Insertion Sequences and Transposons.- (b) Illegitimate Recombination.- 6.2.3 Phylogenetic Implications of Recombination.- 6.3 DNA Repair.- 6.3.1 The Elements of DNA Repair.- (a) Specific Repair Enzymes.- 6.3.2 The Mechanism of DNA Repair.- (a) Pre-Replication Repair.- (i) Excision Repair; (ii) Photoreactivation; (iii) Base Replacement.- (b) Post-Replication Repair.- (i) Daughter-strand Gap Repair; (ii) Error-prone Induced Repair.- 7 Investigation of Gene Structure and Function.- 7.1 Genetic Analysis of Bacteria and their Viruses.- 7.1.1 The Elements of Genetic Analysis.- (a) The cis-trans Complementation Test: The Gene as a Unit of Function.- (b) Recombination: An Indication of Genetic Distance.- 7.1.2 Mapping Bacterial Genes.- (a) Conjugation.- (i) Hfr Mating; (ii) F-Prime Plasmids.- (b) Transduction.- (i) P1 Generalised Transduction; (ii) Specialised Transduction.- (c) Mutagenesis by DNA Insertion Elements.- (i) Bacteriophages as Transposable Genetic Elements; (ii) Insertion Sequences and Transposons.- (d) Pathway Analysis.- 7.1.3 Mapping Phage Genes.- 7.2 Monitoring Gene Function.- 7.2.1 Protein Biosynthesis.- 7.2.2 RNA Production.- 7.3 Physical Analysis of Gene Structure.- 7.3.1 DNA Isolation.- 7.3.2 Heteroduplex Analysis.- 7.3.3 Restriction Technology.- (a) Restriction Cleavage Maps.- (b) DNA Cloning.- Four: Gene Regulation.- 8 Operon Control.- 8.1 Transcriptional Control.- 8.1.1 Control at RNA Chain Initiation.- (a) Promoter Control.- (i) The Elements of Promoter Control; (ii) Promoter Control Circuits.- (b) Cis- and Trans-Acting Regulatory Mutations.- 8.1.2 Control at RNA Chain Termination.- (a) Polarity and its Suppression.- (b) Attenuator Control.- 8.2 Post-Transcriptional Control.- 8.2.1 Control at the Level of the Transcript.- 8.2.2 Translational Control.- 9 Control of Bacterial Gene Expression.- 9.1 Catabolite-Controlled Operons: The Lactose System.- 9.1.1 The lac Operon.- 9.1.2 lac Promoter Control.- (a) Induction and Repression.- (b) Catabolite Control.- 9.2 Attenuator-Controlled Operons: The Tryptophan System.- 9.2.1 The trp Operon.- 9.2.2 trp Control.- (a) trp Promoter Control.- (b) trp Attenuator Control.- 9.3 Multivalent Control of Transcriptional-Translational Operons.- 9.3.1 Organisation of the Genes of the Transcription-Translation Apparatus.- (a) RNA Polymerase Operons.- (b) RNA Operons.- (i) Ribosomal RNA Operons; (ii) Transfer RNA Operons.- (c) Ribosomal Protein Operons.- 9.3.2 Control of Transcriptional-Translational Operons.- (a) Metabolic Control.- (b) Stringent Control.- (c) Co-Transcriptional and Post-Transcriptional Control.- 10 Control of Extrachromosomal Genetic Elements.- 10.1 Regulation of F Plasmid Transactions.- 10.1.1 Organisation of the F Plasmid.- (a) The Transfer Region.- (b) The Replication Region.- (c) The Insertion Region.- 10.1.2 Interaction between F and F-like R Plasmids.- 10.1.3 The ‘Life-Cycle’ of the F Plasmid.- 10.2 Regulation of Phage Lambda Development.- 10.2.1 Organisation of the Intracellular Viral Chromosome.- (a) The Regulatory Region.- (b) The Site-Specific Recombination Region.- (c) Replication Elements.- (d) The Morphogenetic Region.- 10.2.2 Lysogen Formation.- (a) Establishment of Lysogeny: PE-promoted Transcription.- (b) Maintenance of Lysogeny: PM-promoted Transcription.- 10.2.3 Prophage Induction.- (a) Repressor Inactivation.- (b) Immediate-Early Transcription: PL- and PR-promoted Events.- (c) Delayed-Early Transcription: PL and PR-promoted Readthrough Past the Early Terminators tL, tR, and tR2.- (d) Late Transcription: PR’-promoted Readthrough.- 10.2.4 The Lysogenic-Lytic ‘Decision’.