Chem%20142C-08%20midterm1-KEY

Chem%20142C-08%20midterm1-KEY - Name_KEY_Perm Chem...

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Name:____KEY_____________________Perm #__________ Chem 142C/242C April 24, 2008 Midterm #1 Problem Points/Possible 1 / 1 8 2 /12 3 / 1 7 4 / 6 5 / 1 0 6 / 8 7 / 1 5 8 / 2 0 9 / 1 0 10 /34 _______________ TOTAL /150 Bonus Question /15
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1) Briefly (one sentence) describe the biochemical role of the following enzymes in DNA replication in E. coli: (12 pts) DNA helicase DNA helicase unwinds dsDNA during replication Primase Primase synthesizes short RNA primers during lagging strand replication The 3’ to 5’ exonuclease activity of DNA polymerase The 3’ to 5’ exonuclease activity of DNA polymerase “proofreads” newly synthesized DNA, removing mismatched nucleotides DNA ligase DNA ligase seals nicks in the DNA at the boundaries between Okazaki fragments The 5’ to 3’ exonuclease activity of DNA polymerase I The 5’ to 3’ exonuclease activity of DNA polymerase I removes RNA primers Okazaki fragments An Okazaki fragment is a relatively short fragment of DNA(with an RNA primer at the 5' terminus) created on the lagging strand during DNA replication. These fragments are processed by the replication machinery to produce a continous strand of DNA and hence a complete daughter DNA helix. 2) The DNA of virtually every cell is underwound (i.e., negatively supercoiled) relative to B-form DNA. In bacteria, an enzyme called (a) ____________ introduces negative supertwists into DNA using (b) ____________ as a source of energy. This enzyme is classified as a type (c) ____________, which affects the linking number in steps of (d) ___________. The usual substrate for this enzyme within an E. coli cell is the bacterial chromosome. This circular DNA molecule of 4,700,000 base pairs has a linking number of approximately (e) ____________ when it is closed and relaxed. This enzyme would (f) ____________ (decrease/increase/not change) this linking number when acting upon this DNA molecule in the presence of the above energy source. (6 pts) Ans: (a) E. coli topoisomerase II or DNA gyrase; (b) ATP; (c) type II topoisomerase; (d) two; (e) 450,000; (f) decrease
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3) A suitable substrate for DNA polymerase is shown below. Label the primer and template, and indicate which end of each strand must be 3 ' or 5 ' . (17 pnts) To observe DNA synthesis on this substrate in vitro, what additional reaction components must be added? The top strand (the primer) has its 5 ' end to the left; the bottom (template) strand has the opposite polarity. For DNA synthesis with this substrate in vitro, one would have to add DNA polymerase, the four deoxynucleoside triphosphates, Mg 2+ , and a suitable buffer. Compare the transcription of RNA and replication of DNA in terms of the following
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Chem%20142C-08%20midterm1-KEY - Name_KEY_Perm Chem...

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