Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

CMB2001 > L1-4: Control of transcription and chromatin > Flashcards

L1-4: Control of transcription and chromatin Flashcards

1
Q

gene expression

A

process by which information in DNA is decoded into protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

promoters

A

cis-acting DNA regulatory element initiating and controlling transcription.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

prokaryotic promoters

A

involves consensus sequences

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

eukaryotic promoters

A

has a regulatory and core region prior to open reading frame

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

core promoter elements

A

TATA box -31–26
initiator -2-+4
CpG islands

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

CpG islands

A

CG sequence high frequency
~100-1000 bp
C res escapes methylation (hypomethylation)
CpG methylation associated with silencing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

regulatory promoter elements

A

UAS and enhancer
URS and silencer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

identification of promoter elements tools

A

sequence comparison
reporter analysis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

sequence comparison to identify promoter elements

A

TATA box identification

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

reporter analysis to identify promoter elements

A

reporter genes encoding easily measurable proteins (e.g. GFP/lacZ/luciferase)
reporters identify when, where, quantity and signal response

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

luciferase

A

enzymes that emit light when they oxidise their substrate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

RNA pol I/ II/ III location

A

pol I> nucleolus
pol II/III > nucleus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

bacterial RNA polymerase structure

A

B / B’ unit
2 alpha sub-units
w sub-unit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

eukaryotic RNA polymerase structure

A

12 sub-units

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

general transcription factors

A

TFII A/B/D/E/F/H
sigma factor role in eukaryotes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Bacterial RNA polymerase requirements

A

sigma factor to recognise promoter DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

general transcription factor characteristics

A

RNA pol specific
multi-component factors
complex on TATA box
recruit RNA pol II to promoter
direct initiation at start-site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

PIC

A

Pre initiation complex

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

RNA polymerase II transcription initiation of prokaryotes

A
  1. helicase of TFIIH at start-site> open complex
  2. promoter clearance with extensive phosphorylation on CTD
  3. TFIIA/D may stay
    TFIIB/E/H released
    TFIIF moves down template w pol II
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

CTD

A

C terminal domain
repeat series at C-terminal of largest B’ homologous sub-unit of RNA pol II

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

TFIID function
structure?

A

TATA box binding
TFIIB recruitment
central RNA pol II txn factor
associated w TBP
trilobular > molecular saddle?

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

TBP

A

TATA binding protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

TFIIA function

A

stabilizes TFIID binding
anti-repression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

TFIIB function

A

recruits RNA pol II-TFIIF
IMPT for site selection start

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

TFIIH function

A

promoter melting and clearance
CTD kinase activity
DNA repair coupling
contains ATPase for promoter melting

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

TFIIH structure

A

9-10 sub-units
core + CAK

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

CAK

A

contains kinase phosphorylating CTD of RNAPII

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

TBP vs TFIID

A

TBP can direct assembly of PIC on TATA promoter but TFIID can direct PIC assembly on TTA-less assembly, supporting activated txn
TFIID require TAFs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

TAF

A

promote interaction of TFIID w basal promoter and interact w activators

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

UAS / enhancer element function

A

increases basal transcription from low and inactive to activated transcription which is high

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

classes of UAS

A

Common
response

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

common UAS

A

close to core promoter/ promoter proximal
bind relatively abundant activators in cell> constitutively active

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

common UAS examples

A

GC box
octamer
CAAT box

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

response UAS

A

bind factors induced by specific stimuli

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

response UAS examples

A

SRE (binds serum response factor/ induced by growth factors)
HSE (binds heat shock factor and induced by heat shock)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

combinatorial control of transcription

A

type and combination of elements dictates when and at what level the gene is transcribed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

UAS location

A

adjacently upstream to TATA box

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

methods of activator basal transcription contact

A

tracking
looping

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

euk activators characteristics

A

modular

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

DNA binding domains

A

homeodomain
helix loop helix
leucine zipper
zinc finger

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

activation domains example

A

acidic patch (clusters of negative residues > asp/glu)
glutamine rich
proline rich

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

activation domain characteristics

A

low sequence conservation/ structural info
unstructured
short segments working additively
interact w other proteins like TAFs

43
Q

activator analysis tools
in vitro

A

DNA footprinting
electrophoretic mobility assays
transcription assays

44
Q

electrophoretic mobility assays/ gel shifts

A

ability of activator to bind to specific sequence
*radiolabelled probe DNA

45
Q

transcription assays

A

activator has functional DNA binding domain and activation domain

46
Q

in vivo activator analysis

A

reporter assays
chromatin immunoprecipitation

47
Q

chromatin immunoprecipitation

A
  1. cross-link bound proteins to DNA
  2. isolate chromatin and shear DNA
  3. precipitate chromatin w protein-specific antibody
  4. reverse cross-link and digest protein
  5. analyse DNA w PCR/ sequencing
48
Q

activator functions

A
  1. promote binding of additional activator
  2. recruitment/ stimulate complex assembly
  3. release stalled RNA polymerase
  4. chromatin modulation
49
Q

mediator structure

A

22 polypeptides
associated w RNA pol II via C-terminal domain / on own
3 domains: head/ middle/ tail

50
Q

mediator function

A

provides bridge between activators and RNA pol II
aids recruitment of RNA pol II and increases PIC function

51
Q

chromatin basic function

A

DNA compaction
histone units

52
Q

2 types of histones

A

core
linker

53
Q

core histone structure

A

N-terminal tail (v basic / Arg and Lys rich)
globular domain (alpha helices and loops)

54
Q

nucleosome

A

core histone repeating unit
~147 bp 2* wrapped around octamer of histone proteins

55
Q

core histone

A

highly conserved
v basic > rich in Lys/ Arg
nucleosome repeating unit

56
Q

histone structure

A

N-terminal tail
globular domain
2* form ‘handshake’ interaction

57
Q

nucleosome octamer

A

central H3-H4 tetramer + 2 flanking H2A-H2B dimers

58
Q

what type of histone is H1

A

linker

59
Q

nucleosome organisation

A

DNA transfer between nucleosomes via a 10nm fibre
linker histones bind to DNA between histones resulting in formation of a thicker fibre

60
Q

evidence that chromatin inhibits transcription

A
  1. in vivo reconstitution experiments
  2. in vivo nucleosome positioning experiments
  3. genetic studies in Saccharomyces cerevisiae
61
Q

in vivo reconstitution studies

A

RNA pol II + txn factors only caused txn w DNA template not chromatin template

62
Q

in vivo nucleosome positioning experiments

A

nucleosomes are disrupted/ lost in txn activation

63
Q

saccharomyces cerevisiae

A

engineered yeast strain

64
Q

genetic studies in saccharomyces cerevisiae

A

plasmid expressing H4 replaces chr H4 genes with a GAL4 regulatable promoter (turns off w glucose and on w galactose)
glucose presence> nucleosome depletion/ inducible gene expression

65
Q

characteristic of chromatin due to its inhibition of txn

A

dynamic

66
Q

3 chromatin structure modulation mechanisms

A
  1. histone variants
  2. PTM
  3. ATP-dependent chromatin remodelling
67
Q

histone w no variants

A

H4

68
Q

histone variants

A

encoded by genes different to conserved major types exp at low levels
confers structural/ functional properties of nucleosome

69
Q

PTM of chromatin effects

A

folding/ structural alteration
control of recruitment of non-histone proteins to chromatin

70
Q

chromatin PTM examples

A

lysine acetylation
acetylation
methylation

71
Q

histone lysine acetylation

A

mediated by HATs (histone acetyl transferases)
reversible by HDACs (histone deacetylases)
v dynamic

72
Q

HATs

A

correlate w high levels of acetylation/ txn
yeast GCN5 homologue (Txn activator) in 1st nuclear HAT
recruitment via activators to specific promoters/ part of txn machinery

73
Q

nuclear HAT 2 large sub-unit complexes

A

GNAT/ MYST

74
Q

acetylation chromatin structure mediation

A
  1. charged N+ terminal binding DNA
  2. bromodomain protein direct recruitment
75
Q

bromodomain proteins

A

recognise specific acetylated Lysine residues/ promote txn

76
Q

where does histone methylation take place

A

lys
Arg

77
Q

histone methylation

A

via histone lysine methyl transferases (HKMTs) and lysine demethylases
HKMTs mono/di/tri methylate w SET domain
not readily reversible

78
Q

does histone methylation affect charge

A

no
therefore minor influence on structure

79
Q

Snf-2 related ATPase

A

found in cells of ATP-dependent chromatin remodellers
helicase/ NTP driven nucleic acid translocase super family 2
snf-2=swi2

80
Q

DNA-dependent processes on nucleosome

A

sliding
unwrapping
eviction
spacing
variant exchange

81
Q

SWI/SNF

A

snf2 is catalytic sub-unit
hydrolyzes 1000 ATP/min (in DNA/nucleosome presence)

82
Q

Snf2

A

DNA helicases
molecular motor tracks and induces torsion
therefore histone-DNA disruption and nucleosome movement

83
Q

bromo-domain

A

recognize acetyl lysines

84
Q

cooperation between ATP-dependent remodellers and histone acetylases (HATs)

A

recruited to same promoters
bromodomains tether to acetylated nucleosomes
PIC recruitment

85
Q

PIC

A

Pre Initiation Complex

86
Q

yeast swi/snf

A

reg expression of 5% yeast genes
reg 25% of genes expressed at end of mitosis

87
Q

human PBAF/cBAF/ncBAF

A

3 complexes w shared sub-units
required for txn factors/ glucocorticoid/ retinoid receptors/ heat shock factor/ MyoD
interacts w Rb/ cyclin E
embryonic lethality in mice deletion
role in tumour suppressor pathways

88
Q

swi/snf relation to Cancer

A

mutations associated w tumour variety
role in txn factor function

89
Q

txn repression chromatin-modifying factors

A

HDACs
ATP-dependent remodellers
histone methylases

90
Q

HDAC vs HATs

A

HDAC co-repressor of hypoacetylated regions
HAT co-activator of hyperacetylated regions

91
Q

4 groups of HDAC

A

1/2/4 > classical, Zn dependent HDACs
3> Sir2 family (NAD required as co-factor)

92
Q

HDAC characteristics

A

multisubunit complexes
promoter recruitment via interaction w site-specific DNA-binding proteins (co-repression)

93
Q

ATP-dependent remodellers in txn repression

A

conserved in plants/ animals
broad expression in normal differentiation/ tumourogenesis
multi-subunit containing HDACs

94
Q

NuRD action

A

closes chromatin to turn off txn of tumour suppression genes

95
Q

2 chromatin types

A

euchromatin (gene-rich/ transcribable)> light
heterochromatin (gene poor/ repetitive regions/txn silencing) dark

96
Q

biochemical features of heterochromatin

A

hypoacetylated
associated w specific histone 3 methylation
associated w silencing factors

97
Q

heterochromatin protein 1

A

chromodomain protein
recognize / bind to methylated Lys
chromodomain specific to Lys9me2/3

98
Q

HP1 binding function

A

compacts nucleosomal arrays
base of recruitment for activities preventing RNA pol II activity

99
Q

heterochromatin assembly

A
  1. HDAC deacetylases Lys9
  2. histone methyl transferase (suvar39) methylates Lys9 on H3 (docking site for HP1)
    3.HP1 recognizes methylated lysine and binds
100
Q

reporter silencing assays to analyse heterochromatin

A

Ade6 gene expression forms white colonies on Adenine-limiting medium in NORMAL
Ade6 moved to heterochromatin and switched off > RED COLONIES (silencing)

101
Q

X chromosome inactivation

A

1/2 X genes inactivated in females to equalize X-linked genes in M/F (Barr body of heterochromatin)

102
Q

Barr body formation

A

controlled by non-coding RNA’s Xist and Tsix
1 Chr inhibits Tsix and upregulates Xist> coats chr and recruits methylase via H3K27 therefore inactive
other becomes active, repressing Xist

103
Q

Xist and Tsix relation

A

antisense transcript
Tsix prevents Xist

104
Q
A

CMB2001 (4 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions