GMan DNA Repair III

  1. When is NER used?
    Removal of bulky adducts
  2. What governs NER efficiency?
    Helical distortion (by the adduct)
  3. Types of NER
    • Short patch - 12-13nt
    • Long patch - 2kb
  4. Complex used in Short patch NER (prokaryotes)
    UvrABC endonuclease
  5. UvrABC structure
    • Tetramer
    • UvrA dimer
    • UvrB dimer
  6. UvrAB
    • Scans DNA for distortions
    • UvrA bends the helix and dissociates
    • UvrB melts the helix (helicase)
    • UvrA recruits UvrC
  7. UvrBC complex
    • Incises 4-5nt to the 3' side of the lesion
    • Then incises 8nt to the 5' side of the lesion
  8. UvrD
    Helicase, removes the fragment produced by UvrBC
  9. Enzyme(s) responsible for filling in the gap causes by UvrBC (prokaryotes)
    • Pol I
    • DNA Ligase
  10. Robert Painter
    • Discovered eukaryote NER (without knowing it)
    • Noted DNA synthesis not occurring in S-phase (after UV exposure)
    • Unscheduled DNA synthesis
  11. Audioradiographic assay
    • Used by Robert Painter
    • Measured incorporation of [H3]deoxythymidine triphosphate in S-phase
  12. Xeroderma pigmentosum
    • Autosomal recessive
    • Increases susceptibility to skin cancer
  13. Variants of xeroderma pigmentosum
  14. James cleaver
    • Studied patients with Xeroderma pigmentosum
    • Determined that NER was not present in these patients
  15. Dirk Bootsma
    • Discovered genes associated with Xeroderma pigmentosum
    • Fused different XP variant cells
    • Complementation meant cells had different defective genes
    • Non change meant the defective gene was the same in both cells
  16. DNA Damage binding complex proteins (Eukaryotes)
    • XPE (aka DDB2)
    • DBB1
    • XPC
    • RAD23B
  17. First two proteins of the DNA Damage binding protein
    • XPE
    • DBB1
  18. What is TFIIH
    • A transcription factor, melts the DNA
    • Part of the DNA Damage binding protein
  19. What is the role of XPG
    To stabilize the DNA Damage binding protein with the DNA
  20. TFIIH Subunits
    • XPB, 3'-5' helicase
    • XPD, 5'-3' helicase
    • 4 others
  21. How is the helix opened? (eukaryotes)
    TFII opens ~30nt around the lesion (uses ATP)
  22. Proteins that work on the repair bubble (eukaryote)
    ERCC1/XPF (Dimer)
  23. Proteins of the preincision complex
    • XPA
    • XPG
    • TFII H
    • ERCC1/XPF
    • Maybe more..
  24. Incisions made by the preincision complex
    • 22-24nt in the 5' direction (ERCC1/XPF)
    • 5-6nt in the 3' direction (XPG)
  25. Role of XPA and RPA
    Stabilize melted DNA (like SSBs)
  26. Exonuclease
    Remove nucleotides from the end of the polymer
  27. Endonuclease
    Remove nucleotides from the middle of the polymer
  28. Proteins of the NER repairosome with endonuclease activity
    • ERCC1/XPF
    • XPG
  29. Final proteins of eukaryote NER
    • RFC (loader), PCNA, polymerase delta or epsilon
    • DNA ligase I
  30. TCR and GGR
    • Transcription coupled repair (NER) - Similar to GGR, except the polymerase¬†initiates the process
    • Global genome repair (NER)
  31. Proteins not required in TCR NER
    • XPE, DDB1
    • RAD32B, XPC
  32. How does the polymerase detect damage in TCR
    • It pauses on the damaged base
    • Frequent pausing can trigger apoptosis
  33. TCR is NER exclusive (T/F)
    F, TCR is used for BER too
  34. Effect of TCR on rates of CPD repair
    80% CPDs removed from transcribed strands whithin 2hrs, compared with 10% for GGR
  35. TCNER mechanism
    • The RNA pol II stalls
    • CSA and CSB are recruited
    • The pol II is removed and degraded
    • NER proceeds
Card Set
GMan DNA Repair III