1. While studying the transcripts in vitro you observe that other than the longer transcripts there are some short stretches of RNA oligomer produced as well. You repeat the experiment several times but these oligomers seem to persist. What is the possible explanation?
a) Procedural error
b) They are the un-ligated oligomers of lagging strand
c) Experimental artifact
d) Normal occurrence
Explanation: These short oligomers are abortive transcripts produced by the RNA polymerase before it leaves the promoter. There is no lagging strand in RNA and since the experiment is repeated several times with caution the other justifications are rules out
2. Capping of RNA is necessary as_______
a) It helps us distinguish 5’ from 3’ end
b) It has a rolling action and condenses the transcript as it is produced
c) To protect the transcript from exonuclease
d) To prevent the transcript from sticking to DNA
Explanation: There are several free exonuclease in the nucleus and the 5’ cap protects the mRNA from them. In its absence, valuable information will be lost from the transcript and abnormal proteins would result after translation. RNA normally font stick to DNA and absence of ATPase activity rules out 2nd option.
3. What is the 1st nucleotide of a completely synthesized transcript?
a) A
b) G
c) C
d) T
Explanation: The 5’ cap can be considered as the 1st nucleotide of the complete transcript. And as it is ppGpp the nucleotide is Guanine or G.
4. Processivity of RNA polymerase is ________
a) Very high
b) High
c) Low
d) Very low
Explanation: RNA polymerase is highly processive as when the sigma subunit dissociates the DNA binding arm of RNA polymerase clamps shut around the DNA prevents it from falling off. DNA polymerase I on the other hand has low processivity
5. Which antibiotic inhibits transcription elongation?
a) Rifampicin
b) Streptolydigin
c) Penicillin
d) Tetracyclin
Explanation: Streptolydigin prevents elongation while Rifampicin prevents initiation. Penicillin and Tetracyclin act on the ribosome and not on RNA polymerase although even they ultimately inhibit protein synthesis.
6. You design a reconstructive RNA polymerase where you take the beta and alpha subunit from a rifampicin resistant strain and beta prime and sigma subunit from rifampicin sensitive strain. You check the rate of transcription by this RNA polymerase after the addition of the antibiotic. What will be your observation?
a) No transcription
b) Reduced transcription
c) Normal transcription
d) Improved transcription
Explanation: The beta subunit of the RNA polymerase is mainly sensitive to Rifampicin. Thus the re-constructed RNA pol is overall Rifampicin resistant and transcription rate will be normal.
7. You add labeled Uridine analogue to the mixture of DNA and RNA pol in vitro. What are you trying to determine?
a) Catalytic subunit of RNA pol
b) Processivity of RNA pol
c) Presence of DNA – RNA hybrid
d) Length of DNA already transcribed
Explanation: The Uridine analogue can base pair with the RNA pol enzyme when there is a presence of a complementary strand (here DNA). Thus, its incorporation and cross linking will confirm the presence of RNA-DNA hybrid. We use labeled NTP to detect the other processes mentioned.
8. Which of these is not a part of RNA polymerase elongation machinery?
a) NTP entry channel
b) RNA entry channel
c) DNA entry channel
d) Clamp
Explanation: As the RNA is synthesized there is an RNA exit channel but there is no need of RNA entry channel. Clamp and flap on the other hand help to stabilize the polymerase structure.
9. Melting of DNA would lead to _________________
a) Increase in UV absorption
b) Increase in Fluorescence
c) Decrease in UV absorption
d) Decrease in fluorescence
Explanation: Melting is the separation of the two strands of DNA which causes an increase in the amount of UV rays absorbed by the DNA. This is known as Hyperchromic shift. It has no effect on florescence of DNA.
10. In a stretch of DNA being transcribed, the region forward to the Elongation is __________
a) Positively supercoiled
b) Negatively supercoiled
c) Uncoiled
d) Forms a secondary structure
Explanation: The region forward to the RNA polymerase elongation machinery is positively supercoiled due to the strain. If the gyrase doesn’t release this strain the polymerizing machinery will stall. Such regions can’t be uncoiled or folded.