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BIOL 202 > Lecture 26 > Flashcards

Lecture 26 Flashcards

1
Q

describe ON/OFF states of bacterial transcription

A

ground state = ON –> basal activity bc sigma factor can easily find promoter to bind

repressed state = OFF

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2
Q

describe ON/OFF states of eukaryotic transcription

A

ground state = OFF –> DNA is inaccessible

active state = ON –> DNA changes conformation to be accessible

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3
Q

2 types of chromatin structure

A
  1. heterochromatin
  2. euchromatin
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4
Q

what is heterochromatin?

A

tightly packed nucleosomes/CLOSED DNA

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5
Q

where do we find heterochromatin?

A

structural DNA and non-transcribed regions (centromeres, telomeres, repetitive elements)

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6
Q

what is euchromatin?

A

loosely packed nucleosomes/OPEN DNA

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7
Q

where do we find euchromatin

A

transcribed regions

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8
Q

2 general components of transcription initiation

A
  1. cis-acting DNA sequences
  2. trans-acting proteins
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9
Q

3 examples of cis-acting DNA sequences

A
  1. promoter
  2. promoter-proximal elements
  3. enhancers/silencers
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10
Q

4 examples of trans-acting proteins

A
  1. general TF
  2. common TF
  3. cell/tissue-specific TF
  4. transcription co-factors
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11
Q

general TF vs common TF

A

general TF is for most genes, common TF is for some genes

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12
Q

what are transcription co-factors?

A

no DNA-binding domain –> relies on binding of other TFs

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13
Q

where do general TF bind?

A

core promoter upstream of protein-coding genes

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14
Q

what is an enhancer?

A

DNA region with multiple TF binding sites

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15
Q

describe distance and position requirements of prokaryotic transcription

A

prokaryote has operator btwn promoter and gene –> has specific distance and position requirements

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16
Q

describe distance and position requirements of eukaryotic transcription

A

in eukaryotes, TFs can act anywhere in the gene so there are no distance/position requirements –> relies on distance-independent cis-acting DNA sequences

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17
Q

where are distance-independent cis-acting DNA sequences located?

A
  1. can be close or far from TSS
  2. can be upstream/downstream/within a gene (introns)

i.e. ANYWHERE!

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18
Q

2 types of distance-independent cis-acting DNA sequences

A
  1. enhancer
  2. silencer
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19
Q

what is the role of enhancers?

A

promote transcription

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20
Q

what is the role of silencers?

A

prevent transcription

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21
Q

what do TFs influence? how?

A

can influence transcription and chromatin structure directly or indirectly

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22
Q

how are TFs expressed in an organism?

A

cell/tissue/time-specific manner

23
Q

what is an enhanceosome?

A

sum of all proteins interacting DNA to bring far away regions close together and allow RNA pol to bind

24
Q

4 domains of TFs

A
  1. DNA-binding domain
  2. dimerization domain
  3. ligand-binding domain
  4. activation/repression domain
25
Q

difference btwn eukaryotic and prokaryotic TFs

A

prokaryotic TFs don’t have the distinct domains

26
Q

describe the TF DNA-binding domain

A

unique to a TF

27
Q

why do TFs have a dimerization domain?

A

most TFs are dimers

28
Q

why do TFs have a ligand-binding domain?

A

acts as a sensor and determines whether TF can bind DNA

29
Q

why do TFs have an activation/repression domain?

A

mediates interactions with other transcription machinery

30
Q

difference between TFs and transcription co-factors

A

transcription co-factors have similar domains but no DNA-binding domain

31
Q

2 types of transcription co-factors

A
  1. corepressors
  2. coactivators
32
Q

purpose of reporter gene assay

A

link reporter gene (GFP, B-gal) with sequence of DNA to see if it has enhancer activity

33
Q

describe the reporter gene assay results of Pax6 enhancer

A

every cell has the gene but pancreatic and lens cells have TF that binds enhancer to allow gene expression

34
Q

why don’t different cells and tissues just have different genes rather than having cell/tissue-specific expression of 1 gene?

A

more efficient to have 1 coding sequence and just use different enhancers/silencers to change expression pattern

35
Q

how does yeast use galactose?

A

yeast converts galactose to glucose for energy and carbon metabolism

36
Q

how does yeast induce enzyme production for galactose metabolism?

A

enzymes involved are only produced in presence of galactose

37
Q

4 galactose-dependent enzymes

A
  1. Gal1
  2. Gal2
  3. Gal7
  4. Gal10
38
Q

3 regulatory enzymes in yeast gal system

A
  1. Gal3
  2. Gal4
  3. Gal80
39
Q

what does Gal4 do in general?

A

has DNA binding domain that binds UAS enhancers upstream of Gal1/2/7/10 to induce their transcription

40
Q

is the yeast gal system an operon?

A

no, each Gal gene has its own promoter

41
Q

what happens in Gal4- cells? What does this mean about the role of Gal4?

A

gal enzymes uninducible by galactose

Gal4 is required for activation

42
Q

what happens in Gal80- cells? What does this mean about the role of Gal80?

A

gal enzymes constitutive

Gal80 is part of repression

43
Q

what happens in Gal3- cells? what does this mean about the role of Gal3?

A

gal enzymes uninducible by galactose

Gal3 is part of activation

44
Q

describe the activation of Gal4

A
  • Gal4 binds UAS but is inactive bc Gal80 binds its activation domain
  • Galactose and Gal3 bind
  • ATP changes Gal3 structure so it can bind Gal80 and remove it from Gal4
  • Gal4 is active and can drive transcription
45
Q

what is the role of Gal3?

A

Sensor - responds to galactose

Inducer - binds Gal80 to remove it from Gal4

46
Q

how does GAL4 induce transcription?

A

activation domain of Gal4 binds proteins in transcriptional machinery
- recruits RNA pol II
- recruits chromatin modifying proteins

47
Q

diff between TFs binding enhancer vs promoter

A

enhancer binds common TFs, promoter binds general TFs

48
Q

what is TFIID?

A

general TF that binds TATA binding protein

49
Q

what is the role of TATA binding protein?

A

positions TFs at TATA box (TSS) to get RNA pol to correct gene

50
Q

what is the role of insulators?

A

as a complex, binds DNA sequences to organize DNA into TADs

51
Q

why are TADs required?

A

to ensure that enhancer works on specific gene –> enhancer only works on a gene that is in the same TAD

52
Q

example of a chromatin remodelling protein complex

A

Swi/Snf

53
Q

describe the Swi/Snf system

A

uses energy from ATP hydrolysis and moves nucleosomes to expose binding sites, like TATA box at promoter so it can form enhancesome

54
Q

is Swi/Snf an activator or coactivator? why?

A

coactivator –> doesn’t bind DNA but gets recruited by enhancer-bound TFs

BIOL 202 (29 decks)

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