BME50A – W2016 – HW3 Question 1 Your friend discovers a mutant E. coli cell with the following properties: 1) When cells are grown in the presence of glucose and lactose, beta-galactosidase is expressed. 2) When cells are grown in the absence of glucose and in the presence of lactose, beta-galactosidase is expressed. 3) When cells are grown in the presence of glucose and absence of lactose, beta-galactosidase is not expressed. Your friend adds a wild-type copy of the lac operon to these E. coli mutants. She discovers that observations 1), 2), and 3) all still hold. Of the following, which component(s) could be broken in your mutant? (select all that apply) A) lac repressor B) the operator site C) the CRP binding site (also known as the CAP binding site) D) CRP (also known as CAP) E) None of the above What does the mutation(s) do, briefly? If you chose E, why?Question 2 (Taken from the book) 287The activity of the ArgR protein is modulated by arginine. Upon binding arginine, ArgR alters its conformation, dramatically changing its affinity for the DNA sequences in the promoters of the genes for the arginine biosynthetic enzymes. Given that ArgR is a repressor protein, would you expect that ArgR would bind more tightly or less tightly to the DNA sequences when arginine is abundant? If ArgR functioned instead as an activator protein, would you expect the binding of arginine to increase or to decrease its affinity for its regulatory DNA sequences? Explain your answers.QUESTION 8–9When enhancers were initially found to influence transcription many thousands of nucleotide pairs from the promoters they control, two principal models were invoked to explain this action at a distance. In the “DNA looping” model, direct interactions between proteins bound at enhancers and promoters were proposed to stimulate transcription initiation. In the “scanning” or “entry-site” model, RNA polymerase (or another component of the transcription machinery) was proposed to bind at the enhancer and then scan along the DNA until it reached the promoter. These two models were tested using an enhancer on one piece of DNA and a -globin gene and promoter on a separate piece of DNA (Figure Q8–9). The -globin gene was not expressed from the mixture of pieces. However, when the two segments of DNA were joined via a linker (made of a protein that binds to a small molecule called biotin), the -globin gene was expressed. Does this experiment distinguish between the DNA looping model and the scanning model? Explain your answer.QUESTION 8–10Differentiated cells of an organism contain the same genes. (Among the few exceptions to this rule are the cells of the mammalian immune system, in which the formation of specialized cells is based on limited rearrangements of the genome.) Describe an experiment that substantiates the first sentence of this question, and explain why it does.QUESTION 8–11Figure 8–17 shows a simple scheme by which three transcription regulators are used during development to create eight different cell types. How many cell types could you create, using the same rules, with four different transcription regulators? As described in the text, MyoD is a transcription regulator that by itself is sufficient to induce muscle-specific gene expression in fibroblasts. How does this observation fit the scheme in Figure 8–17?QUESTION 8–12Imagine the two situations shown in Figure Q8–12. In cell I, a transient signal induces the synthesis of protein A, which is a transcriptional activator that turns on many genes including its own. In cell II, a transient signal induces the synthesis of protein R, which is a transcriptional repressor that turns off many genes including its own. In which, if either, of these situations will the descendants of the original cell “remember” that the progenitor cell had experienced the transient signal? Explain your reasoning.QUESTION 8–13Discuss the following argument: “If the expression of every gene depends on a set of transcription regulators, then the expression of these regulators must also depend on the expression of other regulators, and their expression must depend on the expression of still other regulators, and so on. Cells would therefore need an infinite number of genes, most of which would code for transcription regulators.” How does the cell get by without having to achieve the impossible?ECB4 eQ8.11/Q8.11enhancerbiotin attached to one end of each DNA moleculeβ-globin geneenhancerβ-globin gene+ avidintranscriptionpromoterFigure Q8–9ECB4 eQ8.14/Q8.14transientsignaltransientsignalOFFgene repressorOFFgene activator(A) CELL I(B) CELL IIARturns on transcriptionof repressor mRNARrepressor protein turns off its owntranscriptionRRRturns on transcriptionof activator mRNAAactivator proteinturns on its owntranscriptionAAAFigure Q8–12Chapter 8 End-of-Chapter QuestionsQuestion 3 (Taken from the book) 286 CHAPTER 8 Control of Gene Expressionamount of mRNA produced50 60 70 80 90 100 110number of nucleotides between enhancer and promoterECB4 EQ8.07/Q8.07Figure Q8–6ECB4 eQ8.09/Q8.09+CNCNCNCNCNCNDNA binding siterepressor dimerrepressor monomerscleavagesiteFigure Q8–7QUESTIONSQUESTION 8–4A virus that grows in bacteria (bacterial viruses are called bacteriophages) can replicate in one of two ways. In the prophage state, the viral DNA is inserted into the bacterial chromosome and is copied along with the bacterial genome each time the cell divides. In the lytic state, the viral DNA is released from the bacterial chromosome and replicates many times in the cell. This viral DNA then produces viral coat proteins that together with the replicated viral DNA form many new virus particles that burst out of the bacterial cell. These two forms of growth are controlled by two transcription regulators, called c1 (“c one”) and Cro, that are encoded by the virus. In the prophage state, cI is expressed; in the lytic state, Cro is expressed. In addition to regulating the expression of other genes, c1 represses the Cro gene, and Cro represses the c1 gene (Figure Q8–4). When bacteria containing a phage in the prophage state are briefly irradiated with UV light, c1 protein is degraded. A. What will happen next?B. Will the change in (A) be reversed when the UV light is switched off?C. Why might this response to UV light have evolved?QUESTION 8–5Which of the following statements are correct? Explain your answers.A.