transcription initiation

Question 1

is synthesis of a polynucelotide favourable or unfavourable?

Answer 1

unfavourable

Question 2

to synthesize RNA what are the steps it must go through?

Answer 2

nucleoside triphosphates must be joined together, the 5’ end of RNA is characterized by the presence of a triphosphate, however in eukaryotic mRNA this is temporary and the phosphates are modified to form a 7-methyl guanine cap

Question 3

in the active site what are the criteria that must be met to synthesize RNA?

Answer 3

A template base must be at the correct place
An incoming NTP must pair with the base
If the NTP is correct the active site must close
Phosphodiester bond formation must be catalyzed. Mg2 ions activate the 3’ OH and stabilize a negative charge on the leaving oxygen
The active site must open to let ppi out to get ready for the next NTP
Translocation of the template ,ust take place so a new template can be positioned there
If there is no primer you need 2 NTPs

Question 4

what does the trigger loop do?

Answer 4

elps position the rNTP and acts as a check that the rNTP should be the correct one. It will only close fully if the base pair forms and stacks correctly.

Question 5

what does the bridge helix help do?

Answer 5

After forming a new bond, the active site has to open. The template and the new RNA must translocate so there is room.

Question 6

what are the possible tautomers?

Answer 6

G:T or G:U and C:A

Question 7

what determines the pattern of abortive products?

Answer 7

promoter-specificity and reaction-dependence

Question 8

what blocks the RNA exit channel and makes and abortive product?

Answer 8

B-reader in TFIIB or
The linker amino acids between 3.2 and 4.1 domains of the sigma subunit

Question 9

once mRNA gets out of the active site in bacteria what happens?

Answer 9

RNA polymerase dislodges from the promoter
The sigma subunit may be discarded completely or stay loosely associated
The 5’ end of bacterial mRNA won’t be modified

Question 10

once mRNA gets out of the active site in eukaryotes what happens?

Answer 10

RNA polymerase disengages from the general transcription factors
CTD of Rpb1 becomes heavily phosphorylated
The 5’ end of eukaryotic mRNA will be modified by addition of the 7-methyl-guanosine cap