LEC23: Basal & Regulated Transcription Flashcards Preview

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Flashcards in LEC23: Basal & Regulated Transcription Deck (46):

what are the phases of transcription?

1) pre-initiation complex formation

2) initiation

3) elongation 

4) termination


where/what is the core promoter?

a DNA sequence in immediate vicinity of +1 site 

where RNA Pol II binds, directed by other protein factors 

may contain "consensus" sequence - similar sequence found in promoter regions of many genes


how are upstream ntds designated from txn start site?

negative numbers


where is the TATA box located re: +1 site?

-20 - -30


what are TFIIs?

transcription factors for RNA Pol II

bind DNA, and each other, to direct localization of RNA Pol II for initiation of txn at +1



what is TFIIH kinase?

a ser-thr kinase, one of the transcription factors for RNA pol II

phosphorylates the CTD of RNA Pol II, & this signals to being transcription


what is the CTD?

C-carboxy-terminal domain of one of the RNA Pol II subunits 

has many Ser-Thr residues 

gets phosphorylated by TFIIH kinase - this is the signal to begin transritoin 


what begins txn initiation?

TBP, TATA box binding protein, binding

results in bending of the DNA 


what is the signal to begin txn?

phosphorylation of the Ser-Thr residues of the CTD of one of the RNA Pol II subunits 



what does the TFIID complex consist of?

TBP and many TAFs, TBP-associated factors, and TFIIs (A, B, D, F, H), and mediator


what is the pre-initiation complex?

complete ensemble of protein complexes at txn initiation sit, 

TFIIs, TBP, Mediator, RNA Pol II


what is different between RNA and DNA polymerases?

RNA polymerase can start de novo; DNA polymerase cannot


what needs to happen so that elongation can begin?

PIC formation and binding to the txn initiation site, followed by 

promoter clearance


what is the rate of txn elongation?

50 ntd/second


what happens once RNA Pol II complex leaves promoter region to transcribe downstream sequences?

another RNA Pol II complex can load right behind it, begin txn


what do helicase and topoisomerase do?

helicase: enzyme that unwinds the DNA helix; causes tension in helix; part of TFIIH complex 

topoisomerase: alters topology of DNA dbl helix by cutting 1 strand of the tightly wound DNA dbl helix, relaxing helix, putting it back together again; relieves tension = crucial for elongation


what happens to phosphates on CTD at termination?

when RNA Pol II comes off the DNA template, a CTD phosphatase takes off the phosphates that were added to the CTD 

de-phosphorylate when done w/ txn 

now RNA Pol II transcribes again


what is the core promoter? 

where is it re: +1 site? 

what binds to it?

cis element where txn initiation factors bind 

-40 to +40, in and around +1 site 

TFIIs, mediator bind; but TFIIs may have protein-protein interactions to PIC rather than bind directly to the DNA


what are promoter proximal elements? 

where are they? 

what do they bind?

cis elements that are bound by unregulated txn factors

-40 to -200, close to core promoter

proteins that constituitively enhance the initiation of txn bind here 


what are enhancers? 

where are they? 

what do they bind?

100-500 bp long cis element of DNA where regulated txn factors bind 

can be located anywhere! upstream, downstream, doesn't matter

multiple txn factors bind to an enhancer to enhance the rate of txn initiation


what % of our genome encodes for txn factors?



what are simple vs. complex enhancer sequences?

simple: multiple repeats of the same sequence, are bound by same txn factors 

complex: different DNA boxes w/ different sequences can be bound by different txn factors


what are the elements of a txn factor? 

1) DNA binding domain: binds DNA, recognizes sequence; can be a zinc finger or helix-turn-helix

2) activation domain: talks to another protein to activate txn initiation rate

3) dimerization domain: allows formation of homo- or hetero-dimers (or tetramers) of txn factors


how do txn factors bind?

what are some motif examples?

what does this kind of structure afford txn factors?

as dimers or tetramers

dimers increase txn factor diversity 

leucine zipper, helix-loop-helix, zinc finger


why is the # of txn factor complexes that can bind to enhancers and influence rate of txn >>> total # of txn factor proteins?

b/c they can bind as homodimers, tetramers, heterodimers; gives greater combination possibilities


what can the txn factor activation domain interact w/? 

1) directly w/ constituents of teh PIC to increase the rate of txn

2) w/ co-activators that change the state of local chromatin 


how does it work that enhancers can be very far away from promoter?

DNA loops; not concrete in shape 

can have something v. far away, loops back on itself 

txn factor binding on enhancer & the PIC as formed at promoter then get brought together


if you had a mutation in TFIID, TBP, RNA Pol II, what would likely be result?

incompatible w/ life b/c so crucial to the basal txn of all genes, cannot form life


where do we often see specific txn factors' mutations?


i.e. P53: often mutated in cancer


what enzymes can be recruited to enhancer sequence to modify chromatin?

1) histone modifying enzyme 

2) chromatin remodeling complex


what is histone acetyl transferase (HAT)

a histone modifying enzyme that acetylates histone lysine residues

this changes charge from (+) to neutral; reduces interaction btwn histone & DNA 

this activity assoc w/ loosening of the histone-DNA interaction which we want for enhanced PIC formaiton, txn initiation


what can reverse acetylation of histones?

HDAC, histone deacetylase 

removes acetyl group from histone, restores positive charge to Lysine 

restores chromatin structure

usually has inhibitory effect


what is histone methylase, what does it do?

adds methyl group to epsilon amino; methylation of lysine group 

changes chromatin confroamtion 

can be up or down regulator of gene expression




what does histone demethylase do

removes methyl groups added to chromatin by histone methylase


what does histone kinase do

phosphorylates serine; gives it negative charge 

opposite: histone phosphatase

also changes chromatin structure


what does a chromatin remodeling complex do?

changes how nucleosome looks; doesn't modify histone


what are writers, erasers, readers, re: histone modifications?

writers: enzymes that put on histone marks

erasers: enzymes that take off histones 

readers: recognize, modify histone; bind & do something to chromatin structure


what is the histone code? 

idea that there is some kind of code that's read by the cell about state of histones, to either up/down regulate txn


H3 histone modifications: 

1) what does methylation of K9 do

2) what does methylation of K4+acetylation of K9 do? 

3) what does phosphate on S10 and acetyl on K14 do?

1) heterochromatin formation, gene silencing 

2) gene expression 

3) gene expression


what do chromatin remodeling complexes do?

change histone protein composition of the nucleosome or reposition nucleosomes on the DNA to expose regulatory sequences 

usually involves multiple txn factors in regulation for a single gene 

can: subtitue variant histones; move nucleosomes; move histone cores; reveal DNA that now can be accessed by another protein 


how many kinds of histones are there

mainly think of H2A, H2B, H3, H4, and H1, but know that there are different subtypes of histones of the histone core of chromatin and remodeling complexes can substitute variant histones, change chromatin structure, function


what are epigenetic changes? how are they transmitted?

changes to chromatin that don't change DNA sequence, but change what chromatin looks like

heritable changes via cell division across generations



how can txn factors' activity be regulated?

1) post-translational modification (i.e. MAPK pathway: ERK kinase P-lates a txn factor) 

2) proteolysis: degredation of a txn factor 

3) localization: i.e. NOTCH 

4) ligand binding: txn factors need sthg to bind to it, activate

5) synthesis: need a txn factor's gene to make it!


where/what is a CpG island

high concentration of CG dinucleotide in a small sequence

typially, near promoter sequences


what does DNA methyltransferase do?

what does it do to CpG islands? result?

enzyme that transfers a methyl group to DNA

happens to cytosine of CpG island

causes epigenetic change

recruits MeCP2, methyl CpG binding protein 2: represses txn by recruiting a histone deacetylase


how does Rett Syndrome occur?

knock out of 1 copy of MeCP2 gene 

MeCP2 is on X chromosome 

if have reduced MeCP2 expression, certain genes are expressed at higher level than they should be 


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