1. If you consider a transcribing RNA pol II with a transcript as small as 30 bases, which serine residue in its CTD will be phosphorylated?
a) 2
b) 5
c) 7
d) none
Explanation: when RNA transcript is only 30 bases long it is still within the initiation range. Then the 2nd serine residue is phosphorylared only.
2. Which factor phosphorylates the serine residues in RNA pol II CTD?
a) TFIIA
b) TFIIB
c) TFIIH
d) TFIID
Explanation: TFIIH phosphorylates the serine 2 of the heptad repeat that drives the RNA pol into initiation. The other factors mentioned are only part of pre-initiation complex and not of transcribing RNA pol.
3. In what sequence are the serine residues in RNA pol II phosphorylated?
a) 5->2->7
b) 2->5->7
c) 2->7->5
d) 7->2->5
Explanation: The phosphorylation is at the 2nd serine residue with the help of the TFIIH, and then during elongation the phosphorylation is at the 5th serine residue. Between these two there is a short phase of phosphorylation at the 7th serine.
4. In an experiment you add growing concentration of the alpha amanitin. What will be the sequence in which RNA polymerases are affected if at all?
a) Pol I -> pol III , pol II unaffected
b) pol I->pol I ->pol III
c) pol III->pol II -> pol I
d) pol II -> pol III , pol I unaffected
Explanation: RNA polymerase II is inactivated by very small level of alpha amanitin as low as 1 microgram per ml while on the other hand pol III is affected at 10 micrograms per ml concentration. Polymerase I remain unaffected even at very high alpha amanitin concentration.
5. RPA 2 is one of the larger subunits of RNA polymerase in eukaryotes. It is homologous to the prokaryotic _____________
a) Alpha subunit
b) Beta subunit
c) Beta prime subunit
d) Omega subunit
Explanation: RPA 2 is homologous to the beta subunit while RPA 1 is homologous to the beta prime subunit which is the catalytic subunit.
6. How many of eukaryotic RNA polymerase subunits are common for all three polymerases?
a) 3
b) 5
c) 10
d) 7
Explanation: The beta, beta prime, two alpha and one omega subunit homology to eukaryotic RNA polis common in all three RNA polymerases. These are RPA 1-5 respectively. The rest subunits are non-essential or dispensable.
7. All the RNA polymerases share 5 common subunits, which are present in all the three polymerases and are all alike. State whether the statement is true or false.
a) true
b) false
Explanation: Although these 5 subunits are common to all the RNA polymerases yet they share some subtle differences- the CTD of the beta prime subunit of pol II has heptad repeat. Also the alpha subunits in RNA pol II are quite different from that of pol I and III.
8. In a Drosophila polytene chromosome just before molting you add green labelled antibody against unphosphhorylated RNA pol II CTD and red labelled antibody against phosphorylated RNA pol II CTD. These give fluorescence on adding the respective substrates. What will be the colour in gene 74 EF and 75 B?
a) Red
b) Green
c) Yellow
d) Magenta
Explanation: The 74EF and 75B genes are highly transcribed during and before molting. Thus, there would be many RNA pol II with phosphorylated CTD there which will bind the red labelled antibody. Yellow colour is seen when red and green fluorescence mix.
9. Which of this is a cis binding element?
a) TAF
b) TBP
c) TFIIF
d) TFIIH
Explanation: TBP or TATA binding protein is the part of TFIID complex that recognizes and binds the TATA consensus sequence in the promoter (cis element) of eukaryotic genes. The remaining options are also related to eukaryotic transcription but they have protein-protein interactions.
10. You wanted to study the assembly of preinitiation complex in eukaryotes. This is by the means of protein-protein interaction. Which of these methods you can’t absolutely put in use there?
a) Footprinting
b) Crystal structure
c) EMSA
d) Primer extension
Explanation: While primer extension method can be used to locate the 5’ end of the RNA this doesn’t do any help in studying the assembly of pre initiation complex- basically as that’s upstream to even transcription start site. The remaining methods are however very useful.