Prelim 2 - Spring 2008 Answers - 1. a. (3 points) DNA pol I...

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1. a. (3 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. (1 point) Specifically, why would DNA replication come to a halt in the absence of topoisomerase II? (Nelson & Cox, pp. 937, 960) Topo II from E. coli (DNA gyrase) introduces negative supercoils in positively supercoiled DNA. In the absence of its activity, the DNA outside the replication would become so highly positively supercoiled that helicase would be unable to separate the strands and replication would halt. c. (4 points) In addition to DNA pol I and topoisomerase II described above, name four other enzymes involved in DNA replication and describe the function of each. (No more than one sentence for each, please.) 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 (telomerase - the enzyme that adds repeated telomeric sequences to the ends of eukaryotic linear chromosomes - also accepted)
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BioBM330 2nd prelim 4/1/08 Answer Key page 2 2. a. (1 point) What are telomeres? (Nelson & Cox, pp. 1025 - 1027) Telomeres are tandem repeats of a short oligonculeotide sequence found at the ends of linear chromosomes. b. (1 point) Are telomeres found in eukaryotic or prokaryotic DNA? Eukaryotic c. (2 points) How are telomeres synthesized? (Nelson & Cox, pp. 1025-1027) Telomerase is a ribonucleoprotein that adds telomeric ends. The RNA component acts as a template for the addition of the telomeric ends. The protein enzyme acts as a reverse transcriptase, that synthesizes a complementary DNA strand on the 3' end of the chromosome. d. (2 points) Why are telomeres important? (Nelson & Cox, p. 1025) The ends of linear chromosomes cannot be replicated by cellular DNA polymerases which require a template and a primer because beyond the end of a linear DNA molecule, no template is available for the pairing of an RNA primer. Telomeres prevent the loss of genetic information by being shortened during replication in place of coding sequences. 3.
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Prelim 2 - Spring 2008 Answers - 1. a. (3 points) DNA pol I...

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