Test3 - 1. a. Describe the activity of bacterial DNA...

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1. a. Describe the activity of bacterial DNA gyrase. What does it do to DNA? Introduces negative supertwists using ATP --> ADP and catenates and decatanates dsDNA circles. b. What is the mechanism of gyrase activity? How does it do what it does? When the first DNA segment (G: “gate”) binds, the gyrase conformation changes with the A' and B' subunits holding it. ATP binding and the binding of a second DNA segment (T: “transported”) induce the conformation to change again, with the tyr side chains attacking the G segment. This allows the T segment to pass through. After T-segment release it can revert to the G-bound form. c. What is the role of gyrase when replication is occurring? Why is this necessary? To maintain a steady level of super coiling in the dsDNA molecule by introducing negative supercoiling. Negative supercoiling is required:, to initiate replication at the origin, in order for replication to proceed d. What other roles does gyrase have? For what processes is its activity required and why? Negative supercoiling is required: to keep the E. Coli chromosome in compact form, and to initiate transcription. e. How is the difference in requirement for an energy source between gyrase and topoisomerase I related to the difference in their activities? Type I relaxes supercoiling, does not need ATP (uses mechanical energy of supercoil). introduces negative supertwists using ATP --> ADP 2. a. The "proofreading" activity of a DNA Polymerase is a (3' to 5' or 5' to 3'?) ________________ (type of activity?). 3' to 5' exonuclease b. Describe the effect of this activity and its purpose. DNA pol “checks” each newly added nucleotide for “correct fit” (base pairing); it catalyzes hydrolysis of the bond just formed if not correct. This is a 3' 5' exonuclease activity. c. Do both DNA Pol I and Pol Ill have this activity? If no, which one has it? Yes d. The third activity of a DNA Pol (in addition to polymerization and the one above) is the ________________. (3' to 5' or 5' to 3'?) (type of activity?) Do both DNA Pol I and Pol Ill have this activity? If no, which one has it? 5' to 3'. No, only DNA Pol I has this activity. 3. a. Why is there a "leading strand" and a "lagging strand" in DNA replication? Why aren't they done the same way? polymerases synthesize in the 5' --> 3' direction, but both parental strands are templates and only one of them opens in the 3' --> 5' direction for synthesis of an antiparallel strand.
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b. Describe in detail, including the effects of all enzymes and other proteins, the synthesis of the lagging strand. Be specific about events in relation to DNA Poll and Poll II. (Do not include a description of the initiation of replication at the origin. Do not discuss the clamp or "clamp loading")) Do this so as to explain how this results in the production of a continuous 2 x 101 residue lagging strand, including an indication of approximately how many times each step would occur. A “special” RNA Pol, “primase”, forms a short RNA oligomer of about 11 residues
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This note was uploaded on 04/22/2011 for the course BIOCHEM 412 taught by Professor Thomas during the Spring '11 term at Tennessee Martin.

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Test3 - 1. a. Describe the activity of bacterial DNA...

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