- The Molecules That Make Up A Cell.
- The Bacterial Cell: A Quick Overview.
- How Do Cells Grow?
- What Is Genetics?
- Summary.
2. The Bacterial Dna Molecule:
- The Structure Of DNA And RNA.
- Deoxyribonucleosides And Deoxyribonucleotides.
- DNA Is Only Polymerized 5’ To 3’.
- Double-Stranded Dna.
- Supercoiling Double-Stranded Dna.
- Replication Of The Escherichia Coli Chromosome.
- Constraints That Influence Dna Replication.
- The Replication Machinery.
- Dna Polymerases.
- Dnag Primase.
- Replication Of Both Strands.
- Theta Mode Replication.
- Minimizing Mistakes In Dna Replication.
- The Dna Replication Machinery As Molecular Tools.
- Summary.
3. Mutations:
- Phenotype And Genotype.
- Classes Of Mutations.
- Point Mutations And Their Consequences.
- Measuring Mutations: Rate And Frequency.
- Spontaneous And Induced Mutations.
- Errors During Dna Replication: Incorporation Errors.
- Errors Due To Tautomerism.
- Spontaneous Alteration By Depurination.
- Spontaneous Alteration By Deamination.
- Alterations By Spontaneous Genetic Rearrangement.
- Alterations Caused By Transposition.
- Induced Mutations.
- Chemicals That Mimic Normal Dna Bases: Base Analogues.
- Chemicals That React With Dna Bases: Base Modifiers.
- Chemicals That Bind Dna Bases: Intercalators.
- Mutagens That Physically Damage The Dna: Ultraviolet Light And Ionizing .
- Radiation.
- Mutator Strains.
- Reverting Mutations.
- Suppression.
- Ames Test.
- How Have We Exploited Bacterial Mutants.
- Summary.
4. Dna Repair:
- Lesions That Constitute Dna Damage
- Reverse, Excise Or Tolerate?
- Mechanisms That Reverse Dna Damage.
- Photoreactivation.
- O6-Methylguanine Or O4-Methylthymine Methyltransferase.
- Mechanisms That Excise Dna Damage.
- Uvrabc Directed Nucleotide Excision Repair.
- Muthls Methyl Directed Mismatch Repair.
- Very Short Patch Repair.
- Glycosylases.
- Uracil-N-Glycosylase Coupled With Ap Excision Repair.
- Deaminated Bases Removed By Dna Glycosylase.
- Alkylated Bases Removed By Dna Glycosylase.
- Mutm/Muty: Oxidative Damage.
- N-Glycosylases Specific For Pyrimidine Dimmers.
- Mechanisms That Tolerate Dna Damage.
- Transdimer Synthesis.
- Post Replication/Recombinational Repair (Prr).
- Introduction To The Sos Regulon.
- Summary.
5. Recombination:
- Homologous Recombination.
- Models For Homologous Recombination.
- The Holliday Or Double-Strand Invasion Model Of Recombination.
- An Alternative To The Holliday Model: The Single Strand Invasion Model Of Meselson And Radding.
- Further Enzymatic Considerations.
- Site-Specific Recombination.
- A Typical Site-Specific Recombinational Event.
- Bacteriophage l:A Model For Site-Specific Recombination.
- Other Examples Of Site-Specific Recombination.
- Illegitimate Recombination.
- Summary.
6. Transposition:
- The Structure Of Transposons.
- The Frequency Of Transposition.
- The Two Types Of Transposition Reactions.
- The Transposition Machinery.
- The Transposition Machinery; Accessory Proteins Encoded By The Transposon.
- The Transposition Machinery: Accessory Proteins Encoded By The Host.
- Non-Replicative Transposition.
- Replicative Transposition.
- Does The Formation Of A Cointegrate Predict The Transposition Mechanism?
- The Fate Of The Donor Site.
- Target Immunity.
- Transposons As Molecular Tools.
- Summary.
- The Structure Of Phage.
- The Life Cycle Of A Bacteriophage.
- Lytic-Lysogenic Options.
- The l Lifecycle.
- l Adsorption.
- l Dna Injection.
- Protecting The l Genome In The Bacterial Cytoplasm.
- What Happens To The l Genome After It Is Stabilized?
- l And The Lytic-Lysogenic Decision.
- The l Lysogenic Pathway.
- The l Lytic Pathway.
- Dna Replication During The l Lytic Pathway.
- Making l Phage.
- Getting Out Of The Cell-The l S And R Proteins.
- Induction Of By The Sos System.
- Superinfection.
- Restriction And Modification Of Dna.
- The Lifecycle Of M13-M13 Adsorption And Injection.
- Protection Of The M13 Genome.
- M13 Dna Replication.
- M13 Phage Production And Release From The Cell.
- The Lifecycle Of P1.
- Adsorption, Injection And Protection Of The Genome.
- P1 Dna Replication And Phage Assembly.
- The Location Of The P1 Prophage In A Lysogen.
- P1 Transducing Particles.
- The Lifecycle Of T4-T4 Adsorption And Injection.
- T4rii Mutations And The Nature Of The Genetic Code.
- Summary.
8. Transduction:
- Generalized Transduction Vs Specialized Transduction.
- P1 As A Model For Generalized Transducing Phage.
- Packaging The Chromosome.
- Moving Pieces Of The Chromosome From One Cell To Another.
- Identifying Transduced Bacteria: Selection Vs Screen.
- Carrying Out A Transduction.
- Uses For Transduciton.
- Two Factor Crosses To Determine Gene Linkage.
- Mapping The Order Of Genes- Three Factor Crosses.
- Uses For Transduction-Strain Construction.
- Uses For Transduction-Localized Mutagenesis.
- Specialized Transducing Phage.
- Making Merodiploids With Specialized Transducing Phage.
- Moving Mutations From Plasmids To Specialized Transducing Phage To The
- Chromosome.
- Summary.
9. Natural Plasmids:
- Origins Of Replication.
- Plasmid Copy Number.
- Setting The Copy Number.
- Plasmid Incompatibility.
- Plasmid Amplification.
- Other Genes That Can Be Carried By Plasmids.
- Plasmids Can Be Circular Or Linear Dna.
- Broad Host Range Plasmids.
- Moving Plasmids From Cell To Cell.
- Summary.
10. Conjugation:
- The F Factor.
- The R Factors.
- The Conjugation Machinery.
- Transfer Of The Dna.
- Surface Exclusion.
- F, Hfr Or F-Prime.
- Formation Of The Hfr.
- Transfer Of Dna From An Hfr To Another Cell.
- Formation Of F-Primes.
- Transfer Of F-Primes From One Cell To Another.
- Genetic Uses Of F-Primes.
- Genetic Uses Of Hfr Strains-Mapping Genes On The E. Coli Chromosome Using Hfr
- Crosses.
- The 50% Rule.
- Using Several Hfr Strains To Cover The Chromosome.
- Mobilization Of Non-Conjugatible Plasmids By R And F.
- Conjugation From Prokaryotes To Eukaryotes.
- Summary.
11. Transformation:
- Natural Competency.
- The Process Of Natural Transformation.
- The Machinery Of Naturally Transformable Cells.
- Artificial Transformation.
- Transformation As A Genetic Tool: Gene Mapping.
- Transformation As A Molecular Tool.
- Summary.
12. Gene Expression And Regulation:
- The Players In The Regulation Game.
- Operons And Regulons.
- Repression Of The Lac Operon.
- Activation Of The Lac Operon By Cyclic Amp And The Cap Protein.
- Regulation Of The Tryptophan Biosynthesis Operon By Attenuation.
- Regulation Of The Heat Shock Regulon By An Alternative Sigma Factor, Mrna Stability And Proteolysis.
- Regulation Of The Sos Regulon By Proteolytic Cleavage Of The Repressor.
- Two Component Regulatory Systems, Signal Transduction And The Cps Regulon.
- Summary.
13. Plasmids, Bacteriophage And Transposons As Tools:
- What Is A Cloning Vector?
- Why Not Use Naturally Occurring Plasmids As Vectors?
- The Importance Of Copy Number.
- An Example Of How A Cloning Vector Works-Pbr322.
- Multiple Cloning Sites.
- Determining Which Plasmids Contain An Insert.
- Expression Vectors.
- Vectors For Purifying The Cloned Gene Product.
- Vectors For Localizing The Gene Product.
- Vectors For Studying Gene Expression.
- Shuttle Vectors.
- Artificial Chromosomes.
- Constructing Phage Vectors.
- Suicide Vectors.
- Phage Display Vectors.
- Combining Phage Vectors And Transposons.
- Summary.
14. DNA Cloning:
- Isolating DNA From Cells - Plasmid DNA Isolation.
- Isolating DNA From Cells - Chromosomal DNA Isolation.
- Cutting DNA Molecules.
- Type I Restriction-Modification Systems.
- Type II Restriction-Modification Systems.
- Type III Restriction-Modification Systems.
- Restriction-Modification As A Molecular Tool.
- Generate Double Stranded Breaks In DNA By Shearing The Dna.
- Joining DNA Molecules.
- Manipulating The Ends Of Molecules.
- Visualizing The Cloning Process.
- Constructing Libraries Of Clones.
- DNA Detection – Southern Blotting.
- DNA Amplification: Polymerase Chain Reaction.
- Adding Novel Dna Sequences To The Ends Of A Pcr Amplified Sequence.
- Site Directed Mutagenesis Using Pcr.
- Cloning And Expressing A Gene.
- Dna Sequencing Using Dideoxy Sequencing.
- Dna Sequence Searches.
- Summary.
15. Bioinformatics And Proteomics:
- Bioinformatics.
- Strategies For Sequencing Genomes.
- Bacterial Genomes.
- Analyzing Genomes.
- The E. Coli K-12 Genome.
- Proteomics.
- Techniques For Examining The Proteome-Sds-Page And 2-Dimensional Sds-Page.
- Techniques For Examining The Proteome-Microarray Technology.
- Summary.
- Glossary.
- Additional References.