This set of Cytogenetics Problems focuses on “Transcription in Prokaryotes : Sigma Factor”.
1. If you study T4 bacteriophage transcription with holoenzyme which genes will you expect to be transcribed?
a) Immediate early
Explanation: Sigma factor in holoenzyme ensures transcription of immediate early gene first soon after viral infection. This is followed by delayed and late gene transcription. Core Enzyme shows no such specificity.
2. You transcribe a gene and obtain mRNA. To detect which strand is transcribed you replicate each strand in vitro and use the newly synthesized strand for hybridization with mRNA. If mRNA hybridize with the newly replicated strand from 1st strand then the gene transcribed was in ________
a) 1st strand
b) 2nd strand
c) Same copy in both strands
Explanation: mRNA produced from 1st strand and DNA produced by replicating 1st strand should have the same sequence and they will not hybridize. However, if the gene is transcribed from 2nd strand then this result is possible. RNA pol only transcribes one strand at a time so dispersed and both being transcribed are not possible.
3. When sigma subunit dissociates from the RNA polymerase what happens to the DNA binding clamp of the core?
a) It opens again
b) It closes again
c) It enters a semi open stage
d) It is phophorylated and ubiquitination occurs
Explanation: In the absence of the sigma subunit initially the RNA Pol clamp is closed. Sigma makes a window of open clamp conformation when RNA pol loads on the DNA. When sigma dissociates the clamp closes again around the DNA preventing the pol to fall off.
4. In an experiment you wrongly added Rifampicin antibiotic to Rifampicin sensitive bacteria. You try to correct your mistake by adding more core subunits (resistant to Rifampicin) to your mixture. What would you expect to see?
a) Normal transcription to restart
b) Transcription will restart but it will be non-specific as you added core enzyme
c) Impaired transcription with more abortive transcripts
d) No transcription
Explanation: The sigma factor is not affected by Rifampicin and it is dissociable. The sigma already present in mixture will add to the Rifampicin resistant core and restore normal transcription of specific genes. No increased abortive transcription will be seen.
5. Which is the primary sigma factor in Bacillus subtilis?
Explanation: σ43 is the normally active sigma factor for Bacillus subtilis while σ70 is the normally active sigma factor for E. coli. σ32 is expressed under stressed conditions like heat shock when it competes with σ70 for RNA pol core.
6. What is the function of 1st subunit of sigma factor in σ70 and σ43?
a) It helps to bind sigma to DNA
b) It helps to bind sigma to core beta subunit
c) It helps to bind sigma to core alpha subunit
d) It prevents sigma to bind to DNA
Explanation: The 1st region forms a flap like structure that blocks the DNA binding sites. This helps to prevent unbound sigma to bind to DNA. That will only block the DNA binding site and lead to no transcription in absence of RNA pol.
7. Loosening the binding between polymerase and non-specific site is important to confer higher specificity. In Bacillus subtilis what is responsible for this action?
a) Sigma factor
b) Alpha subunit
c) Beta subunit
d) Delta subunit
Explanation: While σ70 in E. coli has an extra 245 amino acid that helps it to loosen the polymerase from non-specific site, σ43 in Bacillus subtilis lacks it. Thus, it needs another subunit of core polymerase- delta subunit to perform this function.
8. We know that region 2.4 of sigma factor binds DNA at -10box. What is the function of 2.1?
a) It is a flexible loop with no known function
b) It binds -35box
c) It binds RNA polymerase
d) It binds region 4.1 to give sigma its specific structure and function
Explanation: Region 2.1 helps to bind the sigma factor to the RNA polymerase. The binding is not absolute as this factor is dissociable. -35box on the other hand is recognized by region 4.2.
9. Which DNA binding domain is seen in region 4.2 of sigma factor?
a) Zinc fingers
b) Helix turn helix
c) Leucine zipper
d) Beta barrel
Explanation: Region 4.2 of sigma subunit has a helix turn helix motif that helps it to bind to the major groove of DNA. The similar motif has been seen in region 3 as well. Zinc fingers and leucine zipper are examples of other DNA binding motif.
10. Which sigma factor is bound to Rse A?
Explanation: Rse A binds σE and prevents it from activating transcription. Under extreme conditions this binding is broken by cleavage of c terminal cytosolic tail of transmambrane Rse A, thus releasing σE for transcribing necessary genes.
11. You artificially increase the level of σ32 in an E. coli culture. What will you expect to see?
a) rpo H transcription permanently inhibited
b) cdc transcription constitutively turned on
c) rpo H temporarily activated
d) cdc 6 permanently turned off
Explanation: σ32 is necessary for transcribing genes like rpo H that helps in surviving heat shock while it doesn’t act on cdc6 that has a role in replication. As σ32 is unstable it temporarily turns on rho H till the concentration ratio of σ32 and σ70 returns to normal.
12. If a bacteria is facing lack of carbon sources in the media, which sigma factor concentration is expected to increase?
a) Sigma E
b) Sigma S
c) Sigma 70
d) Sigma 32
Explanation: Sigma S is synthesized when the cell is under stressed conditions as in stationary phase. It transcribes rpo S gene which helps to overcome carbon starvation in stationary phase. Sigma E works in extreme conditions of shock, while sigma 70 and 43 work in normal conditions.
Sanfoundry Global Education & Learning Series – Cytogenetics.
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