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Prelim 2 - Spring 2006 ANS

Prelim 2 - Spring 2006 ANS - Prelim 2 regrade requests must...

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Prelim 2 regrade requests must be submitted in writing to Virginia Slator (217 Stimson, M,T,R,F 8-11AM) by Friday 5/5 at 11 AM. 1. a. (6 points) DNA pol I from E. coli has three domains each with a specific enzymatic activity. Name each of the enzymatic activities and briefly describe the function of each of these activities in DNA replication. (Nelson & Cox, pp. 954-956. 962, 972) 5' to 3' polymerizing domain - adds nucleotides to the 3' end of a growing DNA strand 3' to 5' exonuclease activity - "proofreading" - checks most recently added nucleotide (at 3' end) and removes it if it is not properly hydrogen bonded to the template strand 5' to 3' exonuclease activity - removal of RNA primer (at 5' end of okazaki fragments) and also involved in many DNA repair pathways. b. (10 points) In addition to DNA pol I described above, name five other enzymes involved in DNA replication and describe the function of each. (No more than one sentence for each, please.) (Nelson & Cox, pp. 960-2) a. DNA polymerase III - template directed synthesis of DNA from dNTPS b. primase (or RNA polymerase) - template directed synthesis of RNA primer from NTPs c. ligase - formation of a phosphodiester bond between a 3' OH on a DNA chain and a 5' phosphate on another chain d. helicase - unwinds DNA double helix at replication fork e. gyrase - relief of positive supercoils in DNA by introduction of negative supercoils. (telomerase - the enzyme that adds repeated telomeric sequences to the ends of eukaryotic linear chromosomes - also accepted)
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BioBM330 2nd prelim 4/4/06 Name: ___________________________2 2. Beginning in 1956, Arthur Kornberg and his colleagues incubated extracts of E. coli with mixtures of 32-P labeled dATP, dTTP, dGTP, and dCTP. They found that a small amount of new DNA was formed containing the 32-P isotope in its phosphate groups. a. (4 points) Draw the structure of dATP (you may use "A" for the base). (Nelson & Cox, Fig. 8-40, p. 300) - Structure as shown for ATP with -H instead of -OH on the 2' carbon of deoxyribose. b. (1 point) In the structure of dATP (above), circle the phosphorous atom that must be labeled for radioactivity to be incorporated into the newly synthesized DNA. (Nelson & Cox, Fig. 25-5, p. 953) The innermost phosphorous atom should be circled. c. 1) (2 points) Write a balanced chemical equation for the reaction whereby a nucleotide is added to a growing DNA strand (Use words and standard abbreviations, structures not required !). (Nelson & Cox, p. 953) (dNMP) n + dNTP (dNMP) n+1 + PPi 2) (2 points) Write a balanced chemical equation for the reaction that contributes energetically to this nucleotide addition. (Use words and standard abbreviations, structures not required !). (Nelson & Cox, p. 953) pyrophosphate (PPi) + HOH 2 Pi 3) (2 points) Why is this second reaction (part c.2) said to " drive " the nucleotide addition reaction (part c.1)? (Nelson & Cox, p. 953) The reaction in part C1 appears to proceed with only a minimal change in free energy given that one phosphodiester bond is formed at the expense of a somewhat less stable phosphate anhdride. However the formation of products is made irreversible in the cell by the energy released in the subsequent hydrolysis of pyrophosphate.
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