TRANCRIPTION pro+euk and regulation Flashcards

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1
Q

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.

A

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.

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2
Q

where does transcription take place in euk and pro

A

pro - in the nucleus alongside translation

euk - in the nucleus alongside the rna processing

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3
Q

describe the structure of prokaryotic RNA pol//subunits

A

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

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4
Q

what does the sigma subunit of RNA holoenzyme do?

A

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

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5
Q

what does the magnesium cofactor do?

A

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

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6
Q

describe the structure of RNA pol 2//of all RNApol

A
  1. bridge helix - melts the DNA helix allowing incorporation of dNTP
  2. 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
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7
Q

how do concensus sequences help with prokaryotic transcription?

A

-10 and -35 concensus sequences help to ORIENT RNA polymerase/holoenzyme correctly onto the core promoter

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8
Q

why are concensus seeuences/promoter elements of both euk and pro largely made up of A=T?

A

becuase they only have 2 hydrogen bonds joining them together so less stable and easier to melt

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9
Q

how does RNA polymerase move along the DNA?

A

by scrunching, inchworming or transient excursions (move and pause)

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10
Q

describe how backtracking works in RNA pol?

A

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

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11
Q

what is Rho? Decribe how rho dependent prokaryotic termination works

A

its a hexameric helicase and can terminate transcription in prokaryoticRNApol

  1. binds to rut sequence on mRNA, use ATPase to change confirmation and move up the mRNA to kick the RNA pol off
  2. can use tethered tracking model where a loop of a RNA forms and will kick RNA pol off DNA
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12
Q

describe how Rho - independent termination works

A

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

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13
Q

What are cis and trans acting factors?

A

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

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14
Q

what would TF ||| A mean?

A

a basal transcription factor TF-A for RNA pol3

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15
Q

what does TF|| H and K do?

A

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

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16
Q

what are enhancers?

A

they are long-range regulatory elements found upstream of the TRANSCRIPTION START SITE
they can recruit the mediator complex which can activate and finetune transcription and aid the helicase and kinase activity

17
Q

descireb structure of TF

A

bipartate structure so has a DNA binding domain at N terminus and trans-activation domain at C terminus

maybe a dimerisation domain and a ligand binding domain too
> have common motifs

18
Q

what are the different classes of TF structure?

A

helix -turn helix
zinc finger
basic leucine zipper
basic helix turn helix

19
Q

how does histone and dna interact?

A

histone is 147bp protein made up of H1 linker, h2a, H2b H3, H4 OCTASOME

dna will wrap around histone 1.6 times and helps to stabilise and package DNA as histones are postively charged aa and dna phosphates are neg-
> heterochromatin tight
> eukchromatin loose

20
Q

what is the chromatin remodelling complex?

A

MULTIPROTEIN COMPLEX that can modify histones by sliding or detaching// uses protein binding to create nucleosome free zones or even encourage nucelosome formation

or can post-transcriptionally modify histone tails
> basis of epigentics