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Genes and gene expression > methods of transcription > Flashcards

methods of transcription Flashcards

1
Q

genome expression

A

50k genes
only 10k expressed in any given cell
genome identical in all cells
geneome must be differentially expressed

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2
Q

differential gene expression regulation

A

time - devlopment and in response to hormones

space - different tissues express diff genes

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3
Q

importance of differential gene expression ?

A

because gene expression controls metabolism / cell shape / motilitiy / differentiation and proliferation

failure to regulate would cause disease in these processes.

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4
Q

differentiation from a single cell

A

totipotent cell to pluripotent to blood stem cells or other comitted cells

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5
Q

reprogramming

A

comitted cells can be turned into pluripotent cells through reprogramming

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6
Q

regulation of gene expression

A

transcriptional level - turning on/off dna to rna synthesis

post transcriptional - regulation of rna stability / translation

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7
Q

which regulation level is more common ?

A

transcriptional is more common as it is more efficient to express 10k genes than express 50 and stop them from bein translated

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8
Q

genes can be transcribed on different levels

A

abundant
rare
and no transcripts

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9
Q

housekeeping and tissue specific genes ?

A

housekeeping - expressed in all cell types

tissue specific - expressed only in certain tissues.

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10
Q

induicible genes

A

genes that normally dont transcribe anything but can be stimulated to transcribe abundantly

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11
Q

eukaryotic rna polymerases

A

pol 1 pol 3 and pol 2

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12
Q

what does pol 2 do

A

transcribes all protein encoding genes

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13
Q

structure of pol 2

A

crystalised in yeast

dna enters complex through cleft and jaws will grip dna and open / close to allow dna movement dna hits wall which will cause conformational change and allows exit
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14
Q

promoters

A

sequence immideately 5’ to transcription unit
promoters recruit rna polymerase to a dna template
rna polymerase only moves one way

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15
Q

minimal rna pol 2 promoter

A

min bit of dna essential for transcription
2 types
core - containing tata - above start poin
tata-less core promoter - below start point

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16
Q

consensus sequence

A

dna sequences that are found in multiple regions across different organisms,gebnes or regions e.g. TATA box

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17
Q

key points of eukaryotic transcription

A

rna polymerase cannot recognise promotesr and need general transcritiption factors

GTFs + pol2 = basal transcription apparatus

to iniate transcription eukaryotic transcription complexes must gain access to DNA which is packed into nucleosomes

larges pol 2 subunit co ntains C-terminal domain - involved in regulation of transcription,initation,elongation and mRNA processing

18
Q

explain how pol 2 binds to tata box

A

pol2 forms basaltranscritipon appartus with TF2D
TF2D binds to TATA and recruites TF2B which provides binding surface for pol2 and is involved in start site determination
this recruites RNA polymerase 2 which has TF2F which is required for initiation and recruites TF2E and H.
TF2H binds and catalyses ATP - dependent unwinding of start stie DNA and phosphorylation of CTD.

19
Q

CTD - c terminal domain

A

largest subunit of pol2 - 52 repeats
when pol 2 is re4cruited it is hypophosphorylated and becomes hyperphosphorylated on serine 2 and 5 during transcription

Inhibitors of CTD phosphorylation prove its importance

Deletion of CTD in mice and yeast is deadly

phos of CTD required for promoter clearance and for recruitment of rna processing complex

phos by Specific Cyclin-dependent kinases

20
Q

ctd kinase activation

A

tf2h - bibnds to cdk 7 which pho serine 5 more than serine 2
others include c-m,yc and cdk9

21
Q

transcription factors

A

recruit rna polymerase to genes needed to be transcribed
bind specific dna sequence - causing transcription or prevent it

22
Q

regulatory elements

A

needed to regulate recruitment
found upstream tata box

23
Q

how is transcription regulated >

A

by efficiency of recruitment of rna polymerase 2

24
Q

steroid hormone signalling

A

steroid enters cell
goes to receptor protein
receptor - hormone complex enters nucleus
is a trancription factor
binds to specific dna and induces specific genes to hormone

e.g. oestrogen

25
Q

how to interfer with regulatory and general transcription factors

A

drugs - tamoxifen is an antagonist of oestrogen-responsive transcription

26
Q

transcriptional activatyors

A

attract pol 2 to promoter

contain dna binding domain DBD and activation domain AD

dna betwen promoter and enhancer loop out to enable the activation domain to contact promoter associated factors

dna binding and activation domains are distince from one another and can be swapped

27
Q

what determines epcificity for activation

A

dna binding domain by beringing transcriptional activation domain to vicinity of promoter

28
Q

two hybrid screen

A

tells us if two proteins interact
non interacting proteins tagged with dbd and AD
x with dbd and y with ad if they dont interact rna pol 2 is not recruited and no expression

if they interact rna pol 2 is recruited and expression occurs

29
Q

Activation domains

A

likely to mediate non specific p-p interactions
glutamine rich
proline-rich

30
Q

DNA binding domain

A

many common motif that mediate binding of transcription factors to dna like
zinc finger
helix loop helix
coiled coil

31
Q

zinc finger motif

A

cycs2/his2 finger
zing bound between 2 cycteine and 2 histidine
fingers are 23 aa long
usually found in tandem

cys2 cys 2 fingwe

non repetitive in proteins
diff function per finger

32
Q

homeo domain

A

found in develop proteins
60aa long
3 helixes - bind tro major groove of dna

33
Q

how tf become active

A

protein synth
ligan bind
protein phos
addition of second subunit
unmasking- inhibitor unmasked
stimulation of nuclear entry- allowed to enter nucleus
release from membrane

34
Q

enhancers

A

dna sequences non immediately adjacent to where transcription starts
enhance recruitment of rna polymerase to a promoter
reside 5’ or 3’ to transcription unit

very stong binding sites for transcription factors

35
Q

how is thwe dna made accessible

A

DRE binds to TF
regulatory element is accessible
direct recruitment or mediator or other things

36
Q

what is a mediator

a

A

a comples that transduces both negative and positive regulatory information from specific activators or repressors to core transcriptional machinery

37
Q

mediators

A

required to mediate response to activators
does not bind to dna
interacts pol2 via ctd
has a kinasde module includes - cdk8
many forms
most activate transcription some repress
mediator + pol2 + GTFS = holoenzyme

38
Q

Silencers

A

dna sequences that inhibit rna polymerase
can reside 5’ or 3’ of transcription unit

39
Q

transcription repressors

A

competitive DNA bind - binds to same binding site as activator

masking the activation surface - 2 diff binding site for repressor and activator
repressor make contact to activator and stops it recruiting pol2

direct interaction with GTF

binds TF2D preventing it binding activator

40
Q

transcription coactivators

A

two type - closely associated with basal transcription machinery

2 modify chromatin structure - HATS and Chromatin remodelling complexes

Genes and gene expression (8 decks)

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