Lecture 5- RNA transcription Flashcards
process that leads to nucleotide addition
catalytic phosphoryl transfer- nucleophile action > cascade > covalent bond and proton release
how does RNA polymerase catalyse nucleotide addition
creation of phosphodiester bondsm then excision of incorrect nucleotides by hydrolysis, controlled bt the trigger loop of RNAP
basic structure of the RNAP protein complex
‘claw-like’- has a channel in the middle, up to a ‘wall’ where RNA exit, across from a gap to let nucleotides enter- structure forces DNA open
inter-domain differences in RNAP structure
more subunits on the bottom of euk/arch
common elongation and initiation factors- common ancestor
3 functions of bacterial RNAP subunits
2 for catalysis (beta)
2 for DNA contact
2 as scaffolding
1D hopping
method of finding DNA that involves local binding and unbinding
1D diffusion
local DNA sliding
intersegmental transfer
movement from one DNA site to another, jumping between sites not in direct proximity
3D diffusion
likely to be the major driving force- involves movement across the DNA in 3 dimensions (shocker), but more passive jumping
how do sigma factors work
bind to specific DNA dequences to encourage RNAP binding- when DNA binds, it displaces the N terminus from being bound to the DNA binding domains, and a complex forms
way of regulating sigma factors
antisigma factors- seem to be a general signalling thing, rather than having common ancestry
4 stages of transcription initiation
closed
intermediate
open
scrunching
closed > open stage process
initially no interaction between dsDNA and RNAP
sigma region starts to move out of the channel in the intermediate phase, DNA moves in
open stage- DNA strands separate and dNTPs move in
scrunching
short RNA oligonucleotides start being produced, and once this is over 10nt, the sigma is released and elongation can occur
what does base flipping do
allow access to DNA bases by displacing some specific bases into a sigma factor
