PS_3_older_key - Bio 115 Problem Set#3 answers 1 How does...

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Bio 115, January 25, 2005 Problem Set #3 answers 1. How does the mechanism of transcription termination by RNA Pol I differ from that used by RNA Pol II? Termination for Pol II is not well understood, but occurs downstream of the site of polyadenylation, which marks the 3' end of the mature transcript. Termination for Pol I is triggered by a protein, TTF1, which binds to a sequence, the Sal I, box that occurs a number of times in the region downstream of the rDNA gene. Note that Pol I transcripts are not polyadenylated. 2. The regulation of transcription by RNA Pol II is complex, requiring the function of many sequence specific transcription factors and the mediator complex. In contrast, the regulation of RNA Pol I is simple, requires only one protein. Give a plausible explanation of the biological reasons underlying this difference. Answer: Pol I only transcribes one gene (although there are many identical copies of that gene) that is not subject to complex regulation. In contrast, Pol II transcribes thousands of different genes that are subject to many different complex regulatory schemes. 3. What protein factor(s) determines which nuclear RNA polymerase is recruited to a particular promoter? The TBP containing factor-TFIID for RNA Pol II and SL-1 for RNA Pol I. 4. What is the mediator complex? A large multisubunit protein complex that binds to the unphosphorylated form of the RNA Pol II CTD and serves as a binding target for transcriptional activator proteins. 5. You discover that the p110 subunit of the yeast mediator complex binds the Gal4 activator. Your colleague has a mutant version of p110 that can no longer bind Gal4. What mutant phenotypes (i.e. observable defects) do you expect this mutation in p110 to cause? Why? The cell should be unable to use galactose as a carbon source, i.e. it should be Gal-. This is because inactivating the protein in mediator that binds Gal 4 is equivalent to inactivating Gal4 (because it has nothing to bind to). In other words, Gal4 will be unable to bind mediator and recruit the RNA Pol II holoenzyme. 6. Why is it advantageous for a sequence specific DNA binding protein to interact with DNA in the major groove? The major groove provides increased access because of its width and it is more chemically diverse, allowing more precise
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PS_3_older_key - Bio 115 Problem Set#3 answers 1 How does...

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