ps3_sol - Solutions Systems Microbiology 1.084J/20.106J...

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Solutions Systems Microbiology 1.084J/20.106J PROBLEM SET #3 Problem 3.1 a. Describe the stringent response, and at what level and what components of cellular activity it regulates. The stringent response is triggered in response to two modified nucleotides called alarmones guanosine tetraphostpate (ppGpp) and guanosine pentaphosphate (pppGpp). These nucleotides accumulate rapidly during a shift-down from amino acid excess to starvation and are synthesized by an STP-dependent protein, RelA that is associated with the ribosomal 50S subunit. These alarmones have global control effects that inhibit rRNA and tRNA synthesis, and thus adjust the cell’s biosynthesis in response to amino acid limitation. b. Most biosynthetic operons need only be under negative control for effective regulation, while most catabolic operons need to be under both negative and positive control. Why might this be? Biosynthetic operons normally require only negative control for effective regulation because the cell only needs to know when there is “enough” of that biosynthetic product for growth. Catabolic operons, on the other hand, have to be regulated both positively and negatively, since these operons provide the ATP for biosynthesis, and also the carbon intermediates for biosynthesis. c. Why are promoters from E. coli under positive control not close matches to the promoter consensus sequence for E. coli ? If a promoter closely matches the DNA consensus sequence one would expect RNA polymerase to bind to that promoter and induce transcription in the absence of other factors. Therefore, promoters under positive control would be expected to be quite different. d. The attenuation control of some of the pyrimidine biosynthetic pathway genes in E. coli actually involves coupled transcription and translation. Can you propose a mechanism whereby the cell could somehow make use of translation to help it measure the level of pyrimidine nucleotides? If there were a shortage of pyrimidine nucleotides, one would expect transcription to go more slowly. Such a system might include a termination loop that forms unless the ribosome is closely following the RNA polymerase. When polymerase is functioning at maximal rates, it moves out ahead of the ribosome, allowing the termination
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This note was uploaded on 11/11/2011 for the course BIO 20.010j taught by Professor Lindagriffith during the Spring '06 term at MIT.

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ps3_sol - Solutions Systems Microbiology 1.084J/20.106J...

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