Brainscape's Knowledge GenomeTM

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


See full index

Health and Disease: Genes > Boyes Transcription Factors > Flashcards

Boyes Transcription Factors Flashcards

1
Q

How many DNA contacts do TFs make?

A

10-20 H bonds into Major groove

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

What DNA contacts do TFs make?

A

R-Guanine

D-Adenine

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

What are the 4 types of DNA binding motif?

A

Helix-turn-helix
Zinc finger (2C2C/2C2H)
Leucine Zipper
Helix-loop-helix

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

What is the structure of Plant homeobox TFs?

A

60 residues. 3 helices
1&2 for context,
3 and N-extension (minor) for DNA

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

Which organisms have plant homeobox TFs?

A

mammals, insects, amphibians

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

What does the HTH C terminal helix do?

A

Binds DNA

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

What does the HTH N terminal helix do?

A

Position units 1 turn apart to form dimers

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

What benefit does dimerisation have?

A

Squares the affinity constant

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

What are the 2 types of Zinc Finger?

A

2cys-2cys

2cys-2his

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

How to 2Cys-2His fingers bind?

A

2Cys in beta-sheet
2His in alpha helix
continuous alpha helix
3bp contacts

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

Do TFs have to use all their zinc fingers?

A

No

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

How do 2Cys-2Cys fingers bind?

A

Dimers separated by 1 turn of helix
2 fingers x 2 = 4Zn
N finger binds DNA
C finger controls dimer spacing of palindromic sequence

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

What motif do steroid hormones have?

A

Zinc fingers

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

What is the general structure of transcription factors?

A

Modular with domains for DNA, Ligand and activation

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

What action do Leucine Zippers have?

A

Mostly repressive

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

What is the structure of a Leucine Zipper?

A

dimer of 2 alpha helices with hydophobe every 7 repeats

both helices have DNA binding domain

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

Which TFs have leucine zippers?

A

Myc:Max activates, Mad:Max represses
Fos:Jun represses with 30x affinity of Jun:Jun for API site

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

When do HLH and Leucine zippers become repressive?

A

Heterodimerisation in absence of a DBD

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

Which helix contacts DNA in HLH?

A

Long/C terminal

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is the function of the loop in HLH?

A

Allows packing between N/short helix dimers

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

Which TFs have HLH?

A

MyoD:MyoD activation of B cell myosin
Myc:Max:Mad
E2A:E12/E47

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

How is expression of a gene varied between cells?

A

Homo/hetero/inactivation of TFs

Epigenetics

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

What are 2 types of designer TFs?

A

Zinc fingers hooked to Fok endonuclease

Transcription Activator Like Elements

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

What are the disadvantages of Zinc finger designer TFs?

A

Palindromic sequences required for dimerisation

Non -specific triplet binding of 2Cys-2His

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

How are TALEs produced?

A

Developed from Xanthomas
34residues
12&13 residue pinpoint 16 residue sequence

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

What are the trans domains of Tfs?

A

Activation domains

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

What are the 3 types of activation domains?

A

Acidic, Glu-rich, Pro-rich

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

What are the 6 TF activation domains?

A 
TF11D
TF11B
Mediator for Pol 2 CTD and TF11H
Coactivators: HAT, Basal Machinery
Remodelling complexes
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Which TF11D component do Acididc domains bind?

A

TAF11 31

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

Which TF11D component do Glu domains bind?

A

TAF11 110

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

Which TF11D component do Pro domains bind?

A

TAF11 55

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

What affects do the activation domains have on TF11B/TF11D?

A

Recruitment or modify conformation to recruit other components more effectively.

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

What motif do steroid hormones have?

A

HOMODIMERS of Zinc fingers

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

Which TAF component of TF11D has HAT activity?

A

250

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

Which type of activation domain recruit remodelling complexes?

A

Acidic

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

What are the advantages of TF regulation?

A

Rapid,
Response to signalling
Fine control
Tissue specific

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

What are the 4 main mechanism of TF activation?

A

Ligand binding
Cleavage from precursor
Release of inhibitor
Covalent modification

38
Q

What type of activation do nuclear hormone receptors have?

A

Ligand binding cause dimerisation (steroid hormones are zinc finger homodimers)

39
Q

What are the examples of Ligand binding regulation?

A

Thyriod hormone binds to TF receptor bound to DNA, activating HAT domain
Glucocorticiod hormone binds to TF receptor to release receptor-hormone from HSP 90 to migrate to nucleus to activate HAT

40
Q

What are examples of cleavage from precursor?

A

Notch delta-epsilon intercellular interaction releases N for cleavage and migration to nucleus
Cholesterol synthesis from SREBPp

41
Q

How is HSF1 activated?

A

Released from HSP90, interacts with eEF1A for trimerisation and phosphorylation to bind to HSE

42
Q

What are 3 examples of covalent modification?

A

Phosphorylation,
Acetylation,
Ubiquination

43
Q

How do cytokine stimulate transcription?

A

JAKs phosphorylate STAT TF for dimerisation

44
Q

How do MAPK cascades stimulate transcription?

A

RTKs stimulate MAPK to phosphorylate TFs

45
Q

How have the Early Response genes been studied?

A

Starvation then addition of growth factors
Phosphorylation and interaction of TCF and SRF
Activates SRE in early response genes

46
Q

How are TFs acetylated?

A

By HATs

47
Q

How is ubiquination activated?

A

By other modifications:
Srb10 kinase acts on GCN4 as part of holoenzyme
ScFcdc34 E3 ligase recruited

48
Q

What is the function of ubiquination?

A

Prevents overactivation of the gene- 1 time/de novo firing

TF activation and degradation domains overlap- unstable

49
Q

How is ubiquitination observed?

A

ChIP detects cmyc E3 ligase, 19S proteasome at the promoter

oestrogen receptor S2 promoter and degradation overlap

50
Q

How are tissue specific TFs degraded?

A

eg Acetylated GATA1 is preferentially MAPK phosphorylated, promoting ubiquitin degradation

51
Q

What is the structure of an enhancer?

A

100bp long
positive control elements
forward or reverse orientation
1-1000kb upstream or downstream

52
Q

What is the structure of an insulator?

A

promoter specific/position dependant

hypersensitive site

53
Q

What is the structure of LCRs?

A 
Strong enhancers
Upstream or downstream
Position independant, 
Copy number dependant
Tissue specific
54
Q

What is the function of LCRs?

A

open >100kb chromatin, promoting euchromatin

55
Q

What are the 4 potential mechanisms of enchancers?

A

Looping,
Tracking,
Faciliatated Tracking,
Linking

56
Q

How was looping of enhancers observed?

A

Chromosome conformation capture crosslinks, digestd, religates and PCR of spatially distant but related sequences.
Different globin genes during different stages of development
Kissing chromosomes in naive T cells to produce interleukins or interferons as Th1/Th2 differentiation

57
Q

What are the caveats of looping?

A

Inflexibility of looping,

Effects of insulators would be reduced

58
Q

Which mechanism of enhancers has most evidence?

A

Facilitated tracking

59
Q

What is the evidence for facilitated tracking?

A

Moving non-coding transcripts of B-globin gene

HAT activity from tracking and associated H3K4me3 increasing flexibility

60
Q

What evidence is there for linking?

A

Chip proteins indentified in Drosophilia cut locus

LIM homologues in vertebrates

61
Q

What is the main caveat of the linking theory?

A

Enhancers can lie in introns of other genes

62
Q

What are the 2 main functions of insulators?

A

Barrier to enhancers

Stop spreading of heterochromatin

63
Q

How was barrier function observed?

A

Insertion of enhancer before/after HS4 insulator in B-globin with neomycin reporter
Flanking of IL2R gene maintained expression for 100 days, observed by FACS

64
Q

How is barrier function produced in B-globin?

A

USF1/2 proteins bind HS4 site to recruit HATs

Acetylation blocks H3K9 repression

65
Q

How can enhancer function be observed?

A

Using quantifiable reporters transfected either stabley or transiently

66
Q

What function do CTCF proteins have?

A

Enhancer blocking
Binds cohesin to prevent external enhancers acting on loops (e.g. If2 blocked but H19 expressed)
Adjacent LAD domains tether to nucloephosmin in laminae.

67
Q

What are the 3 models for enhancer blocking?

A

Promoter decor,
Physical blocking of tracking
Organising chromatin into loops to separate external enhancers

68
Q

What is the Transcription factory theory?

A

High concentration of immobile Pol2. DNA loops to the factory

69
Q

What is the unifying/relaxed factory model?

A

Regions of high [TF] and [Pol2] that is mobile. Genes loop to the factory

70
Q

What are the caveats of the Factory model?

A

2-10 polymerases per gene, too small for multiple gene loci, no colocalisation of TFs

71
Q

What are the potential downfalls of the relaxed factories?

A

Trans-splicing and chromosome translocations

72
Q

What is the evidence for factories?

A

Pulses of biotin-CTP show transcripts localised
Antibodies localise Pol2
Genes leave chromosome domains when active

73
Q

Which vectors are suitable for studies of Long range control?

A

BACs and YACs

74
Q

How are BACs generated?

A

Stored in DY380 E.coli cells that have 42’C recombineering by c1857 repressor release from lamda phage.
50bp homologous flanking region

75
Q

How is a transgene inserted into an embryo?

A

Injection into male pronucleus before nuclear fission of embryo.
Insertion is random, copy number varies and head-to-tail

76
Q

Outline expression of transgenic mice?

A 
Isolation of gene from vector. 
Linearisation
Screen by PCR to identify gene fragment
Injection into nucleus
Implant into pseudo-pregnant mother
Analyse genome of offspring by PCR
77
Q

What is the function of knock-out mice?

A

To delete whole genes, regions of genes or regulatory elements

78
Q

How are knockout mice produced?

A

Vector produced with flanks homologous to chromosome. Gene replaced by observable phenotype selection cassette. TK identifies random insertion.
Introduce gene into dominant cells, culture growth and neomycin resistance
Injection into recessive blastocyst 3-5 days old
Inject into 2-5 day pseudopregnant mother
Chimeric offspring can be mated with recessive to get heterozygotes

79
Q

What is the main caveat of knock out mice?

A

15% embryonicaly lethal

80
Q

What are the caveats of knock out mice?

A

15% embryonicaly lethal, some show no effect, some mutate other locations

81
Q

How are conditional knockout produced?

A

Cre recombinase expressed in specific tissues to generate knockout of transgene between 34bp LoxP sites

82
Q

How is Flp Recombinase used?

A

To remove negative selection cassette from within LoxP/Cre

83
Q

What placement of LoxP sites excise a transgene?

A

Cis (outside) in same direction

84
Q

What does LoxP cis, opposite placement do?

A

Invert gene

85
Q

What does trans placement of LoxP do?

A

In between genes for chromosome translocation

86
Q

What do knock-in mice do?

A

Introduce point mutations in a gene or regulatory element

87
Q

What can Cre be used for?

A

To inactivate a gene - deleting a stop codon or gene

Generate inducible changes in DNA

88
Q

What does the HS4 site of chicken B-globin do?

A

Binds USF1,2 to prevent heterochromatin spreading

Binds CTCF to hold cohesin sister chromatids together and looping to prevent enhancers

89
Q

What does the downstream HS1 site do in chicken B-globin?

A

Binds CTCF to tether 100kb regions to laminae.

90
Q

What is the structure of the chicken B-globin locus?

A 
Folate
16kb condensed
5' HS4
LCR
Genes
3' HS1
Olfactory

Health and Disease: Genes (6 decks)

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