Midterm Exam II QA - Bio115, Second Midterm Exam (24st of...

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Bio115, Second Midterm Exam (24 st of May, 2007) Q1 (2 points) Fill in the blanks: 1 nanometer equals _____ Angstom. 1 meter equals _____ nanometers. A1 10 Angstrom/ nm, 10 9 nm/m. Q2 (4 points) It has been suggested that glycine-tRNA synthetase does not require an editing mechanism. Explain! A2 Glycine has the smallest side group of all amino acids. It is therefore possible to conceive of an active center that fits glycine, but no other amino acid. Q3 (6 points) Identify the amino acids within the tripeptide glutathione (shown below), which is a naturally occurring reducing agents. Note that one of the amino acids is linked to its neighbor by a peptide bond between the carboxyl group of its side chain rather than its α - carboxyl group. A3 Glutamate, cyteine , and glycine. Q4 (6 points) Dimethylsulfate (DMS) is used to map the extent of melted DNA in the open complex of RNA polymerase bound at a promoter. Describe the experimental approach and explain the underlying chemistry. A4 Single stranded DNA, and only single stranded DNA allows for methylation of the N1 atom of adenine, which functions as a hydrogen bond acceptor in double stranded DNA. Methylation therefore interferes with base pairing after removal of polymerase. The DNA remains single stranded. Single stranded DNA can be digested with the single strand specific nuclease S1. The denatured region can be mapped by partial digest with S1 nuclease and fractionation of the radiolabeled reaction products on a polyacrylamide gel. Q5 (4 points) RNase A catalyzes the hydrolysis of RNA molecules by exploring a chemical instability of RNA. Describe the reaction mechanism employed by RNase A. Which phosphoester bond is hydrolyzed, the 3’ or the 5’ bond? What is the reaction intermediate.
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A5 A histidine side chain serves as an acceptor of the proton from the 2’ hydroxyl group. The resulting nucleophilic oxyanion attacks the viscinal phosphate group replacing the 5’ phosphoester bond of the 3’ nucleotide. A second histidine side chain serves as a proton donor for the oxyanionic leaving group. The intermediate formed is a 2’, 3’ cyclical nucleotide, which is resolved by hydrolysis into either the 2’ or the 3’ nucleotide. Q6 (2 points) Why do cells synthesize RNases? A6 Destruction of gene products is a prerequisite for gene regulation. Q7 (4 points) Propose a mechanism by which 7-methyl GTP inhibits translation in eukaryotes. A7 7-methyl GTP mimics the 5’ cap structure of eukaryotic mRNA and thus competitively inhibits eIF4E. Q8 (4 points) What is the charge of a 5’ cap 1 structure isolated after potassium hydroxide catalyzed hydrolysis of RNA? A8 -5. Q9 (4+2 points) a. What are the enzymatic events that generate the 5’ cap 2 structure. b. It has been proposed that the 5’-terminal nucleotide of a capped mRNA is linked to
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Midterm Exam II QA - Bio115, Second Midterm Exam (24st of...

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