bioc441 - 2008Problemset4

bioc441 - 2008Problemset4 - Biochemistry 441 Ted Young...

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1 Biochemistry 441 Homework set #4 Ted Young Page1/5 1. If a gene normally transcribed by RNA polymerase II is manipulated in the laboratory so that it is transcribed by RNA polI or polIII instead, the pre-mRNA that is produced in the nucleus does not become capped or polyadenylated. What does this suggest about the enzymes responsible for performing these modifications? 2. Why do proteins that recognize specific DNA sequences usually bind in the major groove of DNA? 3. Some proteins profoundly alter the structure of DNA when they bind, bending it far out of its standard B configuration. No ATP is required fro this reaction. How might this be accomplished energetically? 4. The cyclic AMP binding protein, or CAP of bacteria enhances the rate of transcription of a number of genes in E. coli. The binding site for CAP is not located the same distance from the basal promoter, the -10 and -35 region, in all of these genes, but its binding site in most if not all of these genes occurs at approximately multiples of 10 bp from this region. What is significant about the number 10 as it relates to DNA? What is a reasonable explanation for these observations? How could you test your hypothesis? 5. Many genes are regulated in both a negative and a positive manner. The genes mediating lactose metabolism in bacteria are a classical example. What are the two small molecule ligands that control expression of these genes? What does each one do? 6. The ability of cells to survive extremes of temperature, and other rigorous physical conditions, is due to proteins called heat shock proteins, which are induced by the extreme conditions. Some of these proteins help protect other cellular proteins from denaturation. In bacteria one of the heat shock proteins is a new type of sigma factor for RNA polymerase. Outline an experiment that would allow you to determine the sequence
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bioc441 - 2008Problemset4 - Biochemistry 441 Ted Young...

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