BioChem DNA Repair (2)

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mse263
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230355
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BioChem DNA Repair (2)
Updated:
2013-08-24 13:17:09
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Biochemistry
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Exam 1 Content
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  1. What kind of bond is most critical for DNA recognition by proteins?
    Hydrogen bonding
  2. On which part of the DNA helix do proteins typically make contact with DNA bases?
    In the major groove of DNA
  3. Many proteins contain ____ (structural motif) that can fit in the ____ (location) of DNA to play a role in site specific binding.
    α-helices, major groove.
  4. What is the origin recognition complex (ORC) and what is its function?
    The ORC is a group of proteins that binds DNA at origins of replication. It helps initiate DNA replication in eukaryotes.
  5. What is a helicase and what is its function?
    It is an enzyme that unzips double stranded DNA to form two single strands by hydrolyzing the hydrogen bonds between the two DNA strands.
  6. What is the function of human single stranded DNA binding proteins (SSBs)?
    To stabilize single stranded DNA by preventing re-annealing
  7. What is the function of Topoisomerase I?
    Topo I is an enzyme that removes DNA supercoiling by breaking a single DNA strand, allowing the DNA structure to relax. It then covalently re-connects the DNA strands where they were originally cut.
  8. What disease associated with leukemia is caused by a deficiency of a cellular DNA helicase?
    Bloom's Syndrome.
  9. What syndrome associated with pre-mature aging is caused by a defective helicase?
    Werner's syndrome.
  10. In which direction does the DNA polymerase that synthesizes the leading strand of DNA read its template?
    5' to 3' (all DNA and RNA polymerases synthesize oligonucleotides in this direction).
  11. What are Okazaki fragments and in which direction are they synthesized?
    Okazaki fragments are short fragments of DNA that constitute the DNA lagging strand during replication. They are synthesized in the 5’ to 3’ direction.
  12. List three Human DNA polymerases:
    Pol-α, Pol-δ, and Pol-ε.
  13. What is the function of a primase?
    It associates with DNA polymerase α. The resulting complex synthesizes a short RNA strand that serves as a primer for other DNA polymerases.
  14. What is DNA Pol ε and what is its function?
    It is a high fidelity polymerase with 3' - 5' exonuclease proofreading activity. It is required for leading strand synthesis and is PCNA dependent.
  15. What is the function of DNA Pol δ and what other enzyme does it require for proper function?
    It synthesizes the lagging strand during DNA replication with high fidelity due to its exonuclease activity. It requires PCNA to remain attached to the DNA template.
  16. What is the function of Poly α?
    It works with a primase to make the DNA primers required to initiate DNA-synthesis by pol ε and pol δ, which in turn synthesize the leading and lagging strands, respectively.
  17. What is the function of Proliferating Cell Nuclear Antigen (PCNA)?
    PCNA form a clamp around a DNA polymerase and prevents it from dissociating from the template DNA strand.
  18. What is the function of the minichromosome maintenance complex (MCM)?
    It unzips double stranded DNA, resulting in the formation of single strands (MCM is the human DNA helicase complex).
  19. What is the function of replication factor C (RFC)?
    RFC helps to load DNA poly ε and DNA poly δ onto the template DNA.
  20. What is the function of single strand binding proteins (SSBs)?
    SSBs prevent single stranded DNA fragments from re-annealing. Note that human SSBs are often abbreviated RPA.
  21. What is the function of DNA ligases?
    They covalently join (ligate) DNA ends and Okazaki fragments to one another.
  22. What is the function of DNA Polymerase γ?
    It synthesizes mitochondrial DNA.
  23. What is the function of DNA Polymerase β?
    It maintains the integrity of the genome by participating in excision repair. (Do not confuse this with RNA polymerase β, which synthesizes mRNA!)
  24. Acyclovir is used to inhibit the polymerase of what class of viruses?
    Herpes simplex viruses
  25. Which enzyme is inhibited by the drug azidothymine (AZT)?
    HIV reverse transcriptase
  26. List the four stages of the cell cycle:
    • G1 (growth)
    • S (DNA synthesis)
    • G2 (more growth)
    • M (Mitosis, which itself is divided into several stages)
  27. What is p53 and what is its function?
    It is a tumor suppressor protein that is active at the G1/S checkpoint to prevent cells with DNA damage from replicating.
  28. What syndrome is associated with inherited mutant forms of the p53 tumor suppressor gene?
    Li-Fraumeni syndrome
  29. What process does a cell undergo if its genome is so damaged that it cannot be repaired?
    Apoptosis
  30. Name three DNA repair pathways:
    Mismatch repair, Excision repair, Removal of Uracil from DNA
  31. Name the three proteins used in prokaryotic mismatch repair:
    Mut S, Mut H, and Mut L
  32. Name two human proteins that are involved in mismatch repair:
    hMSH and hMLH
  33. What are the functions of Mut S and Mut H in bacteria?
    Mut S recognizes mismatched base pairs while Mut H catalyzes the incision of the section of the strand containing the mismatched base pairs
  34. Name three diseases associated with trinucleotide repeats:
    Fragile-X syndrome, Myotonic Dystrophy, and Huntington's Disease
  35. What are the main steps of excision repair in E.coli?
    Incision, Excision, Resynthesis and Ligation
  36. What complex of proteins is responsible for the repair of pyrimidine dimers in bacteria?
    uvrABC
  37. Which DNA repair mechanism is defective in Xeroderma Pigmentosum?
    The excision repair system. As a result, UV-induced DNA damage cannot be effectively repaired.
  38. Deamination of adenine and cytosine by nitrous acid causes these bases to turn into _____ and ______, respectively:
    Hypoxanthine and uracil
  39. What is the major site of alkylation on DNA bases?
    The N7 of guanine. This results in a loss of the guanine residue.
  40. What are intercalators and what do they cause?
    They are polycyclic rings that have the ability to insert themselves between bases of DNA, causing physical distortion of the DNA, ultimately leading to the addition or loss of base pair(s)
  41. What is the functional difference between DNA Poly δ and DNA ligase with respect to lagging strand synthesis?
    DNA Poly δ removes the RNA primers at every Okazaki fragment and fills in the gaps between the fragments. DNA ligase covalently binds the completed Okazaki fragments to one another.

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