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bioc441 - 2008AnsProbSet4 - Biochemistry 441 Ted Young...

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1 Biochemistry 441 Homework set #4-questions and answers 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 modification? Ans: It suggests that polII transcription is physically coupled with capping and poly-adenylation. 2. Why do proteins that recognize specific DNA sequences usually bind in the major groove of DNA? Ans: The major groove is wider and deeper and provides more variety in terms of interaction between amino acid side chains and DNA bases . 3. Some proteins profoundly alter the structure of DNA when they bind, bending it far out of its standard B configuration. Where do you think the energy comes from to distort the DNA? Ans: The energy comes from multiple protein-DNA contacts . 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 related to DNA? What is a reasonable explanation for these observations? How could you test our hypothesis? Ans: The number 10 is significant because this is the helical repeat number of the DNA; this result suggests that the CAP protein must be on one particular “face” or side of the DNA to properly interact with and recruit RNA polymerase. 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? Ans: The small ,molecule lactose, or rather allolactose is an inducer and interacts with the Lac repressor to change its conformation so it no longer can bind DNA; the cyclic AMP binding protein or CAP binds cyclicAMP which is produced when the level of glucose falls. Only with cyclic AMP bound does the CAP protein adopt a DNA conformation . 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. How would you determine the sequence to which RNA polymerase binds when it contains this sigma factor?
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