Transcription II Flashcards

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1
Q

differences in eurkaryotic transcription

A
  1. ) enhancers and repressors can be really far from the promoter region
  2. ) TATAA box
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2
Q

TATAA box

A

proteins bind to this region and they tell pol II which strand is coding and which strand is template, helps polymerase locate exact transcriptional starting spot, not all genes have TATAA box, located -25 upstream of transcriptional starting point

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3
Q

GC box

A

when no TATAA box (and usually not CCAAT box) the GC box helps bring polymerase to promoter and orient it, not as precise as TATAA box though, upstream of TATAA box around -40bp from stat of transcription, Sp1 binds here

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4
Q

CAP site

A

regulates efficiency in which TATAA box brings in factors to recruit polymerase, downstream of TATAA box

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5
Q

what happens at the TATAA box

A
  1. ) IID binds–protein recognizes TATA sequence and binds by straddling the DNA
  2. ) IIA binds upstream of IID–stabilizes interaction with DNA
  3. ) IIB then binds to IID–function is to interact with IIF (attached to pol II)
  4. ) IIE/H and J arrive
    * *collectively known as the pre-initiation complex**
  5. ) 8-9 nucleotide strand synthesized, IIF falls off and elongation factors bind to complex
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6
Q

IIE/H

A

helicase activity so begins to unwind DNA, IIH also has phosphorylation activity–phosphorylates pol II to ramp up activity

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7
Q

enhancers

A

facilitate formation of the PIC, can change position and orientation of enhancer site and it still retains its function, can’t be too close to the promoter region though

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8
Q

repressors

A

inhibit formation of the PIC

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9
Q

transcription factors

A

elements that bind to DNA that +/- the rate of transcription but CAN’T be part of the PIC, repressors or enhancers, can be tissue specific, can function as dimers, can interact directly with the PIC

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10
Q

glucocorticoid receptor

A

binds GC and regulates the inflammatory response

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11
Q

coactivators/corepressros

A

other elements brought in by transcription factors to regulate transcription

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12
Q

proximal promoter

A

region of the promoter close to the transcription start site, contains TATA and CCAAT boxes

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13
Q

distal promoter

A

more distant upstream promoter

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14
Q

TATA binding protein (TBP)

A

part of IID

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15
Q

cis elements

A

where transcription factors bind

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16
Q

methods of eukaryotic transcriptional repression

A
  1. ) competes with activator for binding site
  2. ) sequesters activator and prevents it from binding to the DNA
  3. ) repressors binds adjacent to DNA and masks the function of the activator
  4. ) chromatin condensation silences the gene, repressors recruits histones to silence the gene
  5. ) bind directly to PIC and locking out transcription
17
Q

methods of eukaryotic transcriptional activation

A
  1. ) phosphorylating activator (ie. AP2)
  2. ) second subunit added (GC receptor)
  3. ) bound to inhibitor, when phosphorylated, inhibitor dissociates (i.e. retinoblastoma (Rb) inhibiting EF2)
  4. ) bound to inhibitor in nuclear, inhibitor must be removed to enter nucleus
  5. ) ligand binding to activator
  6. ) only synthesize TFs when you need them
18
Q

methods of eukaryotic transcriptional activation

A
  1. ) phosphorylating activator (ie. AP2)
  2. ) second subunit added (GC receptor)
  3. ) bound to inhibitor, when phosphorylated, inhibitor dissociates (i.e. retinoblastoma (Rb) inhibiting EF2)
  4. ) bound to inhibitor in nuclear, inhibitor must be removed to enter nucleus
  5. ) ligand binding to activator
  6. ) only synthesize TFs when you need them
19
Q

leucine zippers

A
  1. ) DNA binding region–rich in basic amino acids so it can bind to DNA
  2. ) 6-8 AA connector
  3. ) protein to protein interaction every 7th amino acid is leucine that forms hydrophobic leucine zipper–holds dimerized region together
20
Q

helix loop helix motif

A

contains basic DNA binding region, dimerized protein region interact at carboxy terminal ends with only one pair of leucine residues

21
Q

coactivators and heterochromatin

A

coactivators expose DNA for transcription:
1.) acetylating the Lys residues on H3 to decrease affinity of histones for DNA 2.) moving the now exposed nucleosome out of the way

22
Q

SWI/SNF

A

family of coactivators that moves nucleosomes around in an ATP dependent manner

23
Q

ß-globin gene

A

all varieties of globin controlled by single locus, if point mutation in this region causes genome to remain in condensed form and prevent transcription

24
Q

how are leaky genes completely turned off?

A

genes have “leaky” transcription activity even without TFs, methylation occurs at cytosines on GC islands in the promoter region, proteins recognized methylated cytosines, some of these proteins are deacetylases or proteins that bind to deacetylases

25
Q

acridine dyes and actinomycin D

A

non specific inhibitors of transcription (affect prokaryotes and eukaryotes), have planar structures that intercalate between the G and C bases of DNA, prevents transcription, actinomycin D used as a chemotherapy drug


26
Q

rifampicin

A

affects prokaryotes only by targeting the ß subunit of their polymerase, many antibiotics use this mechanism

27
Q

α-amantin

A

blocks eukaryotic pol II at low doses and pol III at high doses