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18 Cards in this Set
- Front
- Back
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Which sigmas can be used to transcribe genes during some stress conditions?
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Sigma S Sigma 32 |
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How does RNAP holoenzyme recognize different gene promoters?
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By binding alternative specialized sigma subunits, which recognize different cis-element sequences and various configurations of the promoter
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Sigma 54 |
1. Some NIF genes have dual promoters, which can be turned on either by sigma 70 or sigma 54. 2. Sigma 54 is very unusual since it can bind promoter in the absence of RNAP core. 3. Sigma 54 is very unusual since it can bind promoter in the absence of RNAP core. 4 Sigma 54 does not have region 1.1. |
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In the transition from abortive cycling to elongation of transcription, which is TRUE?
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Sigma looses affinity for the promoter DNA and RNAP core, and pressure of growing RNA chain dislodges sigma from the RNA exit pore.
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What is the function of heparin in EMSA (gel retardation) and DNase I footprinting assays?
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Heparin is negatively charged; acts as a competitor to knock off any RNAP that is not in a stable open complex formation.
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Which is common for both DNA and RNA polymerases? |
Can slide along DNA
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Listed below are sigma subdomains followed by its function. Which of the following pairings has an incorrect function assigned?
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4.2; melting of the -35 element
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In the GST pull-down experiment, the entire bacterial core and distal promoter was used as a radioactive probe pre-bound with isolated GST-alpha CTD subunit. The outcome was a very sharp decline in the pulled-down radioactivity. What competitor was used to obtain this effect?
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UP element |
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How is the bacterial core promoter recognized by RNAP |
Through contacts of sigma subdomains 2.4/2.3 and 4.2 and cis-acting promoter elements
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What is NOT the activity of the antibiotic rifampicin in fighting tuberculosis?
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Can be easily dislodged by other antibiotics.
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How do sigma factors recognize promoter sequence?
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By sliding, hopping, or transfer between very AT-rich sequences located along DNA helix
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Domain 1.1 |
Domain 1.1 is blocking the region where DNA is located when the promoter is melted. w/Domain 1.1 prevents sigma from binding promoter without first binding the RNAP core. w/Domain 1.1 helps melt the promoter sequence and create an open promoter complex.
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correct pairings |
1. 3.0; contacts upstream sequence in the extended TATA box 2. 2.1/2.2; recognizing conserved region in RNAP core 3. 1.2; contacts discriminator element |
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fun facts |
1. Core binds to random DNA through nonspecific, mostly electrostatic interactions, with a half-life of circa 60 min. 2. Addition of sigma to the core lowers core affinity for random DNA 10,000-fold, and increases core affinity for promoter DNA circa 1,000-fold. 3. The variation in the affinities of holoenzyme for promoter DNA may vary by 1,000,000-fold. |
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correct sigma subdomain pairings |
1. H-T-H 4.2; recognizes -35 element 2. Extended helix 2.3/2.4; recognizes and melts -10 element 3. Hairpin 3.2; keeps contact with the first nucleotide of the nascent RNA until abortive cycling or elongation occurs |
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How can you explain the effect of temperature on the dissociation of RNAP holoenzyme from promoter sequence?
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Transition from closed to open promoter complex happens readily at higher temperatures (DNA melting); open promoter complex is most stable at 37 deg and the least stable at 15 deg.
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Which is the ratio of sigma to core, and how much RNAP is actually elongating?
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1 sigma: 3 core; 25%
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filller
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filler |
