DNA Replication, Recombination, and Repair Outline
Notes HERE

DNA Structures

• General (HERE)
• Base pairs (HERE)
• Double helix (HERE)
• B-DNA helix vs. A-DNA helix (HERE)
• Z-DNA helix (HERE)
• ABZ Summary (HERE)

Basic replication strategy (HERE and HERE)

DNA Replication Mechanisms

• DNA Polymerase structure (Klenow fragment) (HERE)
  • Metal ions in catalysis (HERE)
• Primase priming (HERE)
• DNA ligase catalysis (HERE)
• Helicase (Video HERE), SSB, Topoisomerase (HERE)
• DNA Polymerase III holoenzyme (HERE)
• Sliding clamp (HERE)
• Replication fork (HERE)
• Okazaki fragments (HERE) / Leading/lagging considerations (Kevin's figure HERE) - Video HERE
• Leading/lagging strand "trombone" coordination (HERE)
• Video HERE

Topological Considerations

• Topoisomers (relaxed versus supercoiled) (HERE)
• Linking, Twisting, Writhing (HERE / HERE / HERE / HERE / HERE)
• Topoisomerases - enzymes affecting DNA topology
  • Topoisomerase I (HERE)
  • Topoisomerase II (HERE) /Inhibitors (HERE and HERE)

Replication Initiation

• E. coli replication origin (HERE)
• Binding of dnaA (HERE) /
• Pre-priming complext - dnaA, dnaB, dnaC, dnaG, beta Clamp (HERE)
• DNA polymerases (HERE)
• Eukaryotic cell cycle (HERE)
• Telomere formation (HERE / Shortening (Kevin's figure HERE)

DNA Damage

• 8-Oxoguanine-adenine base pair (HERE)
• Adenine deamination (HERE)
• Aflatoxin activation (HERE)
• Thymine dimers (HERE)
• Cross linking agent (HERE)

DNA Repair

• Proofreading (HERE)
• Mismatch repair (HERE)
• Nucleotide excision repair (HERE)
• Uracil repair (HERE)
• Huntington's disease
• Cancer from DNA repair defects
  • HNPCC (Lynch syndrome)
  • p53 damage
  • Agents for treating damage DNA (HERE)
• Ames test (Figure 28.46)

Recombination

• Scheme (HERE)
• Strand Invasion (HERE)
• Holliday junction (HERE)