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Mol Bio - Exam 2 > Transcriptional Control of Gene Expression 2 (L11) > Flashcards

Transcriptional Control of Gene Expression 2 (L11) Flashcards

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1
Q

what are the 4 binding domains?

A
  • homeodomain/ helix-turn-helix
  • Leucine-zipper/ basic-zipper (bZIP) domain
  • basic helix-loop-helix (bHLH) domain
  • zinc-finger domain
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2
Q

mechanism of interaction for homeodomain

A

specific aa’s allow for specific H-bonding w/ nucleotides in the recognition sequence

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3
Q

example of homeodomain binding

A

antennapedia - get a leg instead of a normal antenna

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4
Q

mechanism of interaction for leucine zipper (bZIP)

A
  • C-terminal binds to DNA as a heterodimer of coils held together by Leu hydrophobic stripe
  • N-terminal binds w/ positive residues to DNA phosphate backbone and bases
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5
Q

mechanism of interaction for basic helix-loop-helix (bHLH)

A
  • heterodimer w/ same N and C-terminal arrangement as basic zipper
  • DIFFERENCE: loop in polypeptide chain
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6
Q

example for leucine zipper and mechanism of action

A

CREB - cAMP response element binding

  • activation domain normally a free 3D structure
  • when phosphorylated, facilitates change in structure to a defined a-helix -> allows binding of cofactors (CBP) -> stabilizes binding of basal transcription machinery -> activates transcription
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7
Q

what is CBP?

A

CREB binding protein

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8
Q

mechanism of interaction of C2H2 zinc-finger domain

A

2 Cys + 2 His that interact w/ zinc -> bind to recognition site as a monomer w/ multiple repeats

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9
Q

mechanism of interaction of C4 zinc-finger domain

A

4 Cys that interact w/ zinc -> bind as a dimer, w/ 2 finger repeats in each subunit

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10
Q

which type of zinc-finger domain is often found in nuclear receptors?

A

C4

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11
Q

1st and 2nd largest group of target for drugs?

A

1st: G-protein coupled receptors
2nd: nuclear receptors

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12
Q

describe nuclear receptor

A

transcription factor:

  • has variable activation domain (AD)
  • has DNA-binding domain (DBD)
  • has ligand-binding domain (LBD) -helps bind hormones
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13
Q

where are nuclear receptors found and why?

A

in nucleus or cytoplasm, NOT on plasma membrane
-b/c many hormones are lipid soluble, so they are able to get into the cell to interact with the receptor intracellularly

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14
Q

2 nuclear receptor recognition states

A

homodimer: both subunits same, binds inverted repeats
heterodimer: subunits different, binds direct repeats

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15
Q

mechanism of action for homodimer nuclear receptors

A
  1. hormone binds inactive nuclear receptor in cytoplasm
  2. triggers dimerization of receptor
  3. translocation of dimer into nucleus
  4. binds corresponding response element
  5. activate gene transcription
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16
Q

mechanism of action for heterodimer nuclear receptors

A

heterodimers always in nucleus bound to recognition element of DNA:
-w/o hormone: bound to co-repressor

-w/ hormone binding: change in 3D structure -> co-repressor switched w/ co-activator -> activates gene transcription

17
Q

example of nuclear receptor LBD antagonist

A

estrogen receptor and Tamoxifen:

-Tamoxifen interferes w/ action of co-activator -> no transcription

18
Q

what is Tamoxifen used for and what are side effects?

A

anti-cancer drug for breast cancer

side effects: promotes endometrial cancer - binding of drug in endometrium promotes transcription due to different co-activators in different tissues

19
Q

function of combinatorial binding of nuclear receptors

A

heterodimers can recognize different binding sites in the promoter and control different subsets of genes

  • increases variety of possible regulation
  • can tell a gene to express in multiple different ways
20
Q

what does cooperative binding mean?

A

dimer binds stronger than individual components

21
Q

cooperative binding of enhancers?

A

enhancers can bind many transcription factors -> enhancesome

22
Q

function of TBP

A

TATA binding protein - binds TATA box and binds DNA to allow for binding of TF’s (TFIID, TFIIF, TFIIH) -> facilitates binding of RNA pol II

23
Q

function of TFIID

A

= TAF + TBP

-binding of this is 1st step of transcriptional initiation

24
Q

function of TFIIF

A

brings RNA pol II to basal transcription factor (BTF) binding site

25
Q

function of TFIIH

A

once bound, becomes pre-initiation complex:

  1. has helicase activity - unwinds dsDNA
  2. phosphorylates C-terminal domain of RNA pol II -> transcription continues
26
Q

what are phosphorylated C-terminal regions related to?

A

regions that have active gene transcription

27
Q

what does CBP stabilize?

A

RNA pol II -> activates transcription

28
Q

what is a mediator?

A

protein complex that can act as a molecular bridge b/w TF’s and basal TFs

(TF binds bridge, which binds basal TF’s/RNA pol II on the transcription start site)

29
Q

transcription repression by H3K9 -HP1

A
  1. histone H3K9 methyltransferase methylates decondensed chromatin
  2. HP1 chromodomain binds H3K9Me3 (recognizes Me3)
  3. HP1 oligomerization
  4. chromatin condenses (heterochromatin) -> transcription off
30
Q

transcription repression by H3K27 - polycomb proteins

A
  1. binding of repressors to enhancers
  2. repression domain recruits polycomb repression complex
  3. methylate different Lys’s (H3K27)
  4. PRC1 recognizes MeH3K27 w/ chromodomain, binds
  5. chromatin condensation
31
Q

what is repressor directed histone deacetylation?

A

repressor domain can recruit proteins that have HDAC’s -> make transcription activation harder

32
Q

what is activator directed histone hyperacetylation?

A

activation domains can recruit HATs -> make transcription easier

33
Q

two functions of CBP

A
  1. stabilization

2. open up chromatin

34
Q

what does CBP contain related to transcription regulation?

A
  • HAT: can acetylate histones in surrounding nucleosome -> open up chromatin
  • bromodomain: helps bind to Ac-histone proteins
35
Q

chromatin remodeling complex on nucleosome

A

using ATP hydrolysis, either:

  1. slide nucleosome on DNA to pull out/expose region that has regulatory elements so that TF’s can bind
  2. twist to make regions more accessible
36
Q

ABC mnemonic for bromodomain vs. chromodomain

A

A is closer to B:
Bromodomain bines Acetylated histones
Chromodomain bines methylated histones

Mol Bio - Exam 2 (9 decks)

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