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PSwk6 - MCB110, Spring ‘11 Practice problems Week...

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Unformatted text preview: MCB110, Spring ‘11 Practice problems Week 6 1. T/F ____ Sigma is part of the RNA polymerase core enzyme in E. coli ____ The strength of a promoter is determined by its resemblance to the consensus sequence ____ Like DNA polymerase, RNA polymerase also requires a primer and thus cannot start de novo synthesis ____ The template strand in transcription is also the coding strand ____ The sequential hydrolysis of high ­energy phosphate bonds on incoming triphosphate nucleotides drives the equilibrium of the overall reaction toward chain elongation during transcription ____ There is only one version of the sigma that is used by E. coli ____ Termination of transcription in E. coli always utilizes the protein Rho ____ Rho is ATP ­independent ____ The Lac operon is only controlled by negative transcription regulation ____ RNA polymerase has to be just as accurate as DNA polymerase 2. Finding promoter elements that are recognized by an RNA polymerase a. You’ve discovered a new polymerase in a species of Archaea and decide that you want to map where it binds in its own genome. What technique could you use to do this? What kind of information do you need to obtain before you perform this experiment? b. Briefly outline the experiment including the negative control c. What do you need to leave out of your reaction to ensure that you are mapping the polymerase’s promoter binding site and not also the regions of DNA it transcribes? 3. What would the gel pattern look like for Maxam ­Gilbert sequencing of the following nucleotide: 5’ ­CATAGCCGTAAT ­3’? Indicate which end, top or bottom of the gel, would be the 5’ G G+A C+T C 4. What would you expect to be the outcome for the following mutants? Indicate what happens to the polymerase, or its interaction with DNA, and/or transcription output a. mutant sigma subunit incapable of binding the core polymerase b. a mutant sigma subunit that binds the core polymerase more tightly than its wild ­ type version c. mutant alpha subunit d. mutant omega subunit e. mutant beta subunit f. mutant beta’ subunit 5. What are the RNA sequence elements required for Rho ­independent transcription termination? 6. Describe the mechanism by which Rho can terminate transcription. 7. What could be one advantage of coding genes as operons, thus generating polycistronic mRNA? 8. What would one expect to be the outcome for the following mutants? a. LacI that cannot bind Lac operon b. LacI that cannot bind lactose c. Mutant LacI that binds glucose but not lactose d. CAP that cannot bind cAMP e. Adenylate cyclase that is constitutively (i.e. always) inactive 9. What key difference between eukaryotes and prokaryotes makes the regulation of the trp operon possible in bacteria? 10. Describe how the amino acid tryptophan can serve as an allosteric effector? 11. The trp leader sequence affects transcription of the trp operon. Explain the outcome of transcription of the trp operon for both low levels and high levels of tryptophan. 12. What are the possible outcomes from deleting the following sequences from the trp leader sequence? a. Region 1 b. Region 2 c. Region 3 d. Region 4 ...
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