1. For performing EMSA what type of gel should be used?
a) Native
b) Denaturing SDS-PAGE
c) Non-denaturing SDS PAGE
d) Zymography
Explanation: A denaturing SDS PAGE would break the interactions between the factors which is being studied. Thus, a non-denaturing SDS PAGE is used. A native page on the other hand would be less clear while zymography is unrelated.
2. While performing EMSA, in which situation will you see the band highest?
a) You add TFIID, TFIIA and polymerase
b) You add TFIID, TFIIB, TFIIF and polymerase
c) You add TFIID, TFIIA, TFIIF and polymerase
d) You add TFIIA, TFIIB, TFIIF and polymerase
Explanation: TFIID is absolutely necessary for any nucleation to take place at all. The complex formed by this composition is almost functional as TFIIA is not playing that important role. However, TFIIB and TFIID absence hugely effects the formation of pre-IC.
3. Which of these is not true for TFIIH?
a) It is a helicase
b) On initiation the RNA pol starts transcribing leaving TFIIH at pre-IC
c) It has kinase activity
d) It is needed in Double Strand Break (DSB) repair
Explanation: TFIIH is necessary for phosphorylating RNA pol and triggering its initiation. It moves on with the RNA pol after initiation starts. It also acts as a helicase which is put to use during DSB repair.
4. A mediator helps to connect ___________
a) Enhancer to DPE
b) Silencer to Enhancer
c) Enhancer to TAF
d) Insulator to silencer
Explanation: As enhancer elements work from a distance the connecting DNA is often looped and the enhancer connects to the RNA pol bound TAF through a mediator. A silencer may connect to TAF in a similar way.
5. Which factor stimulated phosphorylation of CTD of RNA polymerase II?
a) TFIIA
b) TFIIF
c) TFIIH
d) TFIIE
Explanation: While TFIIH is actually performing the kinase action, TFIIE stimulates TFIIH to phosphorylate the CTD. TFIIA and TFIIF play no role in phosphorylation
6. The absence of which factor will prevent TFIIH and TFIIE recruitment?
a) F
b) D
c) B
d) A
Explanation: RNA polymerase bound TFIIF is necessary for recruiting TFIIH and TFIIE, two important transcription factors that trigger the initiation finally.
7. Which of this is untrue about TBP?
a) It is a part of TFIID
b) It makes a kink in the DNA
c) It is orientation independent
d) It is sequence independent
Explanation: TBP specifically recognizes and binds to TATA consensus sequence which makes it sequence dependent. Its correct orientation is however determined by other factors like TFIIA and TFIIB. It makes an 80 kink in the DNA and is a part of TFIID.
8. While in vitro transcription your RNA pol is stalled at a position due to mistreatment. Which factor could you act to help the RNA pol overcome the stalled stage?
a) TFIID
b) TFIIF
c) TFIIS
d) TFIIH
Explanation: TFIIS is the transcription factor that helps to overcome the transcriptional stalling of RNA polymerases and also to help the polymerase to backtrack.
9. Promoter proximal elements is positioned ________________
a) Outside the core promoter
b) Downstream to start site
c) Within the enhancer
d) Just before the start site
Explanation: The promoter proximal elements are a part of the core promoter. They occur downstream to the promoter start site. Enhancers on the other hand are much farther and outside the core promoter.
10. TATA box in eukaryotes would be present in _________________
a) Housekeeping genes
b) Developmentally regulated genes
c) Cytoskeletal genes like that for actin
d) Highly specialized genes.
Explanation: The highly specialized genes are likely to have a TATA box within their promoter. On the other hand the rest genes have TATAless promoters.