Bacterial Genetics and Genomics

  1. Core Genetic Processes in Bacteria
    1. DNA Replication
      1. Initiation of Replication
        1. Origin of Replication Recognition
          1. DnaA Protein Function
            1. ATP-DnaA vs. ADP-DnaA
              1. Origin Melting Process
              2. Replisome Assembly
                1. Helicase Loading
                  1. Primase Recruitment
                    1. DNA Polymerase Loading
                  2. Replication Fork Progression
                    1. Bidirectional Replication
                      1. Fork Movement Direction
                        1. Replication Rate
                        2. Leading Strand Synthesis
                          1. Continuous Synthesis
                            1. DNA Polymerase III Function
                            2. Lagging Strand Synthesis
                              1. Discontinuous Synthesis
                                1. Okazaki Fragment Formation
                                  1. Primer Removal and Joining
                                2. Key Replication Proteins
                                  1. DNA Polymerases
                                    1. DNA Polymerase III
                                      1. Core Enzyme Structure
                                        1. Proofreading Activity
                                          1. Processivity
                                          2. DNA Polymerase I
                                            1. 5' to 3' Exonuclease Activity
                                              1. Nick Translation
                                                1. Okazaki Fragment Processing
                                              2. Helicase Complex
                                                1. DnaB Helicase Structure
                                                  1. ATP-Dependent Unwinding
                                                    1. Interaction with Primase
                                                    2. Primase Function
                                                      1. RNA Primer Synthesis
                                                        1. Primer Length and Sequence
                                                          1. Primase-Helicase Interaction
                                                          2. Single-Strand Binding Proteins
                                                            1. SSB Protein Structure
                                                              1. DNA Binding Properties
                                                                1. Cooperative Binding
                                                                  1. Replication Fork Stabilization
                                                                  2. Topoisomerases
                                                                    1. DNA Gyrase Structure
                                                                      1. Negative Supercoiling Introduction
                                                                        1. Topoisomerase IV Function
                                                                      2. Replication Termination
                                                                        1. Ter Site Recognition
                                                                          1. Ter Sequence Features
                                                                            1. Tus Protein Binding
                                                                              1. Fork Trap Formation
                                                                              2. Chromosome Decatenation
                                                                                1. Topoisomerase IV Role
                                                                                  1. Sister Chromosome Separation
                                                                              3. Gene Expression
                                                                                1. Transcription
                                                                                  1. RNA Polymerase Structure and Function
                                                                                    1. Core Enzyme Composition
                                                                                      1. Alpha Subunits
                                                                                        1. Beta and Beta-Prime Subunits
                                                                                          1. Omega Subunit
                                                                                          2. Sigma Factors
                                                                                            1. Sigma-70 Family
                                                                                              1. Housekeeping Sigma Factors
                                                                                                1. Alternative Sigma Factors
                                                                                                  1. Promoter Recognition Specificity
                                                                                                  2. Promoter Structure and Recognition
                                                                                                    1. -10 and -35 Elements
                                                                                                      1. Spacer Region Importance
                                                                                                        1. Extended -10 Elements
                                                                                                          1. UP Elements
                                                                                                          2. Transcription Cycle
                                                                                                            1. Initiation Phase
                                                                                                              1. Closed Complex Formation
                                                                                                                1. Open Complex Formation
                                                                                                                  1. Promoter Clearance
                                                                                                                  2. Elongation Phase
                                                                                                                    1. RNA Chain Extension
                                                                                                                      1. Transcription Bubble Movement
                                                                                                                        1. Pausing and Anti-termination
                                                                                                                        2. Termination Phase
                                                                                                                          1. Intrinsic Termination
                                                                                                                            1. Hairpin Loop Formation
                                                                                                                              1. GC-Rich Stems
                                                                                                                                1. Poly-U Tract
                                                                                                                                2. Rho-Dependent Termination
                                                                                                                                  1. Rho Protein Function
                                                                                                                                    1. ATP-Dependent Translocation
                                                                                                                                      1. Rut Sites
                                                                                                                                3. Translation
                                                                                                                                  1. Ribosome Structure and Function
                                                                                                                                    1. 70S Ribosome Assembly
                                                                                                                                      1. 30S Subunit Components
                                                                                                                                        1. 16S rRNA Structure
                                                                                                                                          1. Small Subunit Proteins
                                                                                                                                            1. Decoding Center
                                                                                                                                            2. 50S Subunit Components
                                                                                                                                              1. 23S and 5S rRNA
                                                                                                                                                1. Large Subunit Proteins
                                                                                                                                                  1. Peptidyl Transferase Center
                                                                                                                                                2. Transfer RNA
                                                                                                                                                  1. tRNA Structure
                                                                                                                                                    1. Anticodon-Codon Pairing
                                                                                                                                                      1. Aminoacylation
                                                                                                                                                        1. Modified Bases
                                                                                                                                                        2. Genetic Code Properties
                                                                                                                                                          1. Codon Usage
                                                                                                                                                            1. Degeneracy Patterns
                                                                                                                                                              1. Wobble Base Pairing
                                                                                                                                                                1. Start and Stop Codons
                                                                                                                                                                2. Translation Initiation
                                                                                                                                                                  1. Shine-Dalgarno Sequence
                                                                                                                                                                    1. Ribosome Binding Site
                                                                                                                                                                      1. Initiation Factors
                                                                                                                                                                        1. IF1 Function
                                                                                                                                                                          1. IF2 Function
                                                                                                                                                                            1. IF3 Function
                                                                                                                                                                            2. fMet-tRNA Binding
                                                                                                                                                                            3. Translation Elongation
                                                                                                                                                                              1. Elongation Factors
                                                                                                                                                                                1. EF-Tu Function
                                                                                                                                                                                  1. EF-G Function
                                                                                                                                                                                  2. A, P, and E Sites
                                                                                                                                                                                    1. Peptide Bond Formation
                                                                                                                                                                                      1. Translocation Process
                                                                                                                                                                                      2. Translation Termination
                                                                                                                                                                                        1. Release Factors
                                                                                                                                                                                          1. RF1 Specificity
                                                                                                                                                                                            1. RF2 Specificity
                                                                                                                                                                                              1. RF3 Function
                                                                                                                                                                                              2. Peptide Release
                                                                                                                                                                                                1. Ribosome Recycling
                                                                                                                                                                                              3. Coupled Transcription-Translation
                                                                                                                                                                                                1. Spatial Coupling
                                                                                                                                                                                                  1. Ribosome-RNA Polymerase Interaction
                                                                                                                                                                                                    1. Co-localization in Nucleoid
                                                                                                                                                                                                    2. Temporal Coupling
                                                                                                                                                                                                      1. Translation Initiation During Transcription
                                                                                                                                                                                                        1. Polysome Formation
                                                                                                                                                                                                        2. Regulatory Implications
                                                                                                                                                                                                          1. Attenuation Mechanisms
                                                                                                                                                                                                            1. Translational Control
                                                                                                                                                                                                        3. Regulation of Gene Expression
                                                                                                                                                                                                          1. Transcriptional Control Mechanisms
                                                                                                                                                                                                            1. The Operon Model
                                                                                                                                                                                                              1. Operon Structure
                                                                                                                                                                                                                1. Promoter Elements
                                                                                                                                                                                                                  1. Operator Sequences
                                                                                                                                                                                                                    1. Structural Genes
                                                                                                                                                                                                                      1. Regulatory Genes
                                                                                                                                                                                                                      2. Negative Control Systems
                                                                                                                                                                                                                        1. Repressor Proteins
                                                                                                                                                                                                                          1. Operator Binding
                                                                                                                                                                                                                            1. Allosteric Regulation
                                                                                                                                                                                                                            2. Positive Control Systems
                                                                                                                                                                                                                              1. Activator Proteins
                                                                                                                                                                                                                                1. Activator Binding Sites
                                                                                                                                                                                                                                  1. RNA Polymerase Recruitment
                                                                                                                                                                                                                                2. Classic Operon Examples
                                                                                                                                                                                                                                  1. lac Operon
                                                                                                                                                                                                                                    1. Operon Organization
                                                                                                                                                                                                                                      1. LacI Repressor Function
                                                                                                                                                                                                                                        1. Allolactose Induction
                                                                                                                                                                                                                                          1. CAP-cAMP Activation
                                                                                                                                                                                                                                            1. Glucose Effect
                                                                                                                                                                                                                                            2. trp Operon
                                                                                                                                                                                                                                              1. Operon Structure
                                                                                                                                                                                                                                                1. TrpR Repressor
                                                                                                                                                                                                                                                  1. Tryptophan Corepressor
                                                                                                                                                                                                                                                    1. Attenuation Mechanism
                                                                                                                                                                                                                                                      1. Leader Sequence
                                                                                                                                                                                                                                                        1. Alternative RNA Structures
                                                                                                                                                                                                                                                          1. Translation-Transcription Coupling
                                                                                                                                                                                                                                                      2. Catabolite Repression
                                                                                                                                                                                                                                                        1. cAMP-CRP Complex
                                                                                                                                                                                                                                                          1. Adenylyl Cyclase Regulation
                                                                                                                                                                                                                                                            1. CRP Binding Sites
                                                                                                                                                                                                                                                              1. Glucose Transport Effects
                                                                                                                                                                                                                                                            2. Global Regulatory Networks
                                                                                                                                                                                                                                                              1. Two-Component Signal Transduction
                                                                                                                                                                                                                                                                1. Sensor Kinase Structure
                                                                                                                                                                                                                                                                  1. Response Regulator Structure
                                                                                                                                                                                                                                                                    1. Phosphorylation Cascade
                                                                                                                                                                                                                                                                      1. Environmental Sensing
                                                                                                                                                                                                                                                                      2. Quorum Sensing Systems
                                                                                                                                                                                                                                                                        1. Autoinducer Molecules
                                                                                                                                                                                                                                                                          1. AHL-Based Systems
                                                                                                                                                                                                                                                                            1. AI-2 Systems
                                                                                                                                                                                                                                                                              1. Peptide-Based Systems
                                                                                                                                                                                                                                                                              2. Population Density Sensing
                                                                                                                                                                                                                                                                                1. Regulatory Circuits
                                                                                                                                                                                                                                                                                2. Stringent Response
                                                                                                                                                                                                                                                                                  1. ppGpp Synthesis
                                                                                                                                                                                                                                                                                    1. RelA and SpoT Functions
                                                                                                                                                                                                                                                                                      1. Nutrient Limitation Response
                                                                                                                                                                                                                                                                                        1. Growth Rate Control
                                                                                                                                                                                                                                                                                        2. Stress Response Systems
                                                                                                                                                                                                                                                                                          1. Heat Shock Response
                                                                                                                                                                                                                                                                                            1. Heat Shock Proteins
                                                                                                                                                                                                                                                                                              1. Sigma-32 Regulation
                                                                                                                                                                                                                                                                                                1. Protein Folding
                                                                                                                                                                                                                                                                                                2. Cold Shock Response
                                                                                                                                                                                                                                                                                                  1. Oxidative Stress Response
                                                                                                                                                                                                                                                                                                    1. SOS Response

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                                                                                                                                                                                                                                                                                              1. Foundations of Bacterial Genetics

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                                                                                                                                                                                                                                                                                              3. Mechanisms of Genetic Variation and Adaptation