TRANCRIPTION pro+euk and regulation Flashcards
The general transcription factor TFIID recognizes the TATA box in RNA polymerase II promoters. It is
A able to introduce a rather sharp kink in the double helix upon binding to DNA.
B also responsible for the recognition of the BRE element in the promoter.
C responsible for the phosphorylation of the RNA polymerase CTD during transcription initiation.
D the only single-subunit general transcription factor.
E All of the above.
OPTION A
TF||D made up of tatabinding protein and TBP accessory factors so not single-subunit. BRE is recognised by TF||B.
The TATA binding protein is a component of the multi-subunit TFIID. Upon binding to the TATA box, it creates a sharp kink in the double helix that serves as a landmark to attract other transcription factors.
where does transcription take place in euk and pro
pro - in the nucleus alongside translation
euk - in the nucleus alongside the rna processing
describe the structure of prokaryotic RNA pol//subunits
only 1 RNA pol to transcribe all RNA molecules// its a HOLOENZYME
> 2 alpha which form homodimer, 2 beta which are catalytic, sigma and omega subunits which help stabilize
what does the sigma subunit of RNA holoenzyme do?
helps with transcription initiation by melting the DNA to create the transcription bubble revealing the dNTPs. 2 different sigma factors which can bind to different promoters.
The main bacterial sigma factor (σ70) transcribes housekeeping genes, whereas the alternate sigma factor (σ54) transcribes a subset of genes
what does the magnesium cofactor do?
both euk and pro need it to create the phosphodiester bond
> the ions deprotonate the 3’ OH of the previous nucleotide making it more attractive for a new one to join
describe the structure of RNA pol 2//of all RNApol
- bridge helix - melts the DNA helix allowing incorporation of dNTP
- trigger loop which helps stabilize the interaction between DNA and dNTP and helps with the ratchet/loose form of RNA pol which can move forward+back
how do concensus sequences help with prokaryotic transcription?
-10 and -35 concensus sequences help to ORIENT RNA polymerase/holoenzyme correctly onto the core promoter
why are concensus seeuences/promoter elements of both euk and pro largely made up of A=T?
becuase they only have 2 hydrogen bonds joining them together so less stable and easier to melt
how does RNA polymerase move along the DNA?
by scrunching, inchworming or transient excursions (move and pause)
describe how backtracking works in RNA pol?
RNA pol exisits between 2 states either the pre-translocated where the active site is open or the post translated state where the RNA NTPs are added
> there is also paused state which allows quality control if incoorect nucleotide is incorpotared
what is Rho? Decribe how rho dependent prokaryotic termination works
its a hexameric helicase and can terminate transcription in prokaryoticRNApol
- binds to rut sequence on mRNA, use ATPase to change confirmation and move up the mRNA to kick the RNA pol off
- can use tethered tracking model where a loop of a RNA forms and will kick RNA pol off DNA
describe how Rho - independent termination works
RNA pol will transcribe a palindromic / inverted repear sequences
they form hairpin loops with each other and this will signal to RNA pol to dissociate from DNA
ONLY IN PRO
What are cis and trans acting factors?
THESE are dna sequences/ signals and interact with protein/trans acting factors
e.g TATA box promoter element interacting with TF||D
or BRE interacting with TF||B
what would TF ||| A mean?
a basal transcription factor TF-A for RNA pol3
what does TF|| H and K do?
helicase - unwinds and melts the DNA to reveal the ss.DNA template strand
kinase - will phosphorlyate the CTD of RNA pol || allowing recruitment of RNA processing machinery and also transcription termination
