Brainscape's Knowledge GenomeTM

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


See full index

Regulation of Gene Expression > Ferrari: Lecture VII > Flashcards

Ferrari: Lecture VII Flashcards

Eukaryotic Gene Control

1
Q

What makes the difference between different cells of the same organism?

A

the regulation of gene expression (how the transcriptome and the proteasome are regulated)

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

Are the decision taken at a molecular level during development and differentiation reversible?

A

not in complex organisms (only in bacteria)

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

What are the regions on the DNA that control gene expression?

A

promoter
regulatory sequences
regulatory proteins & transcription factors
interfering RNA

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

Promoter

A

essential part of the gene responsible for expression by binding the RNA polymerase with the accessory TF (true for polymerase I, II and II in eukaryotes)

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

Regulatory Sequences

A

allow the binding of the regulatory proteins

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

Regulatory Proteins and Transcription Factors

A

role in gene expression and regulation

(RNA can also control gene expression)

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

Interfering RNA

A

regulation of gene expression

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

How are things brought closer to the promoter?

A

looping of DNA (job of enhancers)

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

What are 2 main actors responsible for the looping of DNA?

A

trans-acting proteins
cis-acting elements

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

trans-acting proteins

A

in transcription factors

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

cis-acting elements

A

on the DNA; they are sequences recognized by the TF on DNA

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

How is transcription controlled?

A

binding of trans-acting proteins to the cis-acting regulatory DNA sequences

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

ENCODE Project

A

objective was to identify all the elements on the DNA and do all the annotations on them in a functional way

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

Sequences of Regulatory Proteins (cis-regions) act in genes that are usually involved in:

A

DNA replication
chromatin condensation
chromosome regulation
gene expression

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

What is the most used model of simple eukaryotes?

A

Yeast Saccharomyces Cerevisiae and Saccharomyces Probe

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

WHy are Yeast Saccharomyces Cerevisiae and Saccharomyces Probe the most used simple eukaryotic model?

A

the regulatory regions are very short, they are easy to study, and they are close to the core promoter

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

What was hard about studying complex eukaryotes?

A

the elements (enhancers, insulators, or silencers) were far away and hard to identify, but now we know the distance between promoter and regulatory sequences

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

Enhancers

A

cis-acting elements on the DNA which offer multiple binding sites for TF

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

What is the general size of enhancers?

A

500bp

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

What do enhancers do?

A

relay different regulatory signals that come from activators to the basal machinery of the promoter

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

Enhanceosome

A

soma of the enhancer that defines all the TF that are bound to the same enhancer (needed because there are multiple binding sites for different proteins on the enhancer)

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

What is an example of the enhanceosome?

A

beta-interferon gene

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

In the beta-interferon complex, what is the function of HMG1?

A

bends the DNA and allows for the interaction between proteins and DNA at different distances

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

How many TF are there in humans?

A

more than 3000

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

What are the 3 classes of regulatory proteins?

A

sequence-specific DNA-binding proteins
general transcription factors (GTFs)
chromatin remodeling and modification complex

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

general transcription factors (GTFs)

A

recognize the same sequence in all the genes in the promoters

part of the RNA polymerase II complex

required for promoter recognition and catalysis of RNA synthesis

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

chromatin remodeling and modification complex

A

change chromatin by assisting the transcriptional machinery in order to facilitate access of proteins to DNA

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

RNA polymerase II

A

initiates transcription without TF because it has affinity for the DNA, but without the TF, it cannot bind in a specific way

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

What do transcription factors do for RNA polymerase II?

A

bring specific polymerase to a specific region

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

RNA polymerase II promoter

A

region upstream of the coding region for the +1 (+1 is where transcription starts and the promoter is usually 200bp upstream

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

What defines a core promoter?

A

core promoter is the minimal sequence needed for effective transcription

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

Which sequences identify the presence of a promoter?

A

TATA BOX
BRE
INITIATOR
DCE & DPE

33
Q

TATA BOX

A

fixed position in prokaryotes and eukaryotes (all transcription starts at +1, and all upstream sequences are annotated by - and all downstream are annotated by +)

TATAAT is the TATA binding protein sequence (TBP sequence)

34
Q

BRE

A

sequence rich in G & C

binding site for TF2B, a general transcription factor of RNA polymerase II

it is the TF2B recognition element

35
Q

INITIATOR

A

middle of the sequence and includes the +1 (so it is not upstream like the TATA BOX)

it has a couple of nucleotides upstream and 4 nucleotides downstream the +1

36
Q

DCE & DPE

A

sequences are all bound to TF2D and works with RNA polymerase II

37
Q

Why are the TATA BOX or the other listed sequences needed?

A

they are needed so that the DNA can bend and bind

38
Q

How are RNA polymerases recruited on promoters?

A

by TBP containing complexes

39
Q

role of polymerase I

A

enzyme that transcribes for ribosomal RNA

40
Q

role of polymerase III

A

transcribes all the transfer RNA and 5S ribosomal RNA

41
Q

What TFs is polymerase II associated with?

A

TF2E
TF2F
Tf2H (helicase)

42
Q

Why is TF2H (helicase) needed?

A

needed to open the double stranded DNA to start transcription

43
Q

When are the factors that facilitate transcription released?

A

once they enter the elongation phase

44
Q

What are the major changes in polymerase II when transcription is in the elongation phase?

A

phosphorylation in the C-terminal domain, which is needed to change kinetics from transcription initiation to transcription elongation

45
Q

Polymerase II is also a binding site for other factors required during transcription…what are these factors?

A

splicing factors as they all occur on the C-terminus of the enzyme

46
Q

What 2 things happen cotranscriptionally at the C-terminus of enzymes? Why?

A

phosphorylation to change transcription kinetics

splicing of RNA

makes the process more efficient

47
Q

Cofactors

A

large complexes that mediate interactions between regulatory factors and general transcription factors using activators or repressors

48
Q

Mediator

A

mediates the interaction between transcription factors (activators) and RNA polymerase II

49
Q

Analyze the gene regulation graph of eukaryotes:

A
50
Q

How can regulatory proteins bind DNA?

A

they use transcription factors to identify the pattern of particular chemical groups, such as:
hydrogen bond donors
hydrogen bond acceptors
hydrophobic patches

51
Q

Where does TF recognition occur?

A

ONLY in major grooves as the patterns are marked differently here

52
Q

What kind of features must regulatory proteins have?

A

DNA binding domain
activation domain
flexible domain

53
Q

DNA binding domain

A

responsible for the interaction with the DNA (can be present in the N-ter/C-ter/middle of the protein)

54
Q

activation domain

A

interacts with other proteins

55
Q

flexible domain

A

links together other domains

56
Q

DNA-binding domain has different motifs. Every TF must have one of these motifs:

A

Helix-turn-helix
Homeodomain
Zinc-finger
Winged helix (forkhead)
Leucine-zipper
Helix-loop-helix

57
Q

Helix-turn-helix (simplest motif)

A

characterized by an 𝛼-helix (blue), a small turn (white), and another 𝛼-helix (red)

58
Q

Zinc-finger

A

zinc atom linked to a cysteine or histidine residue

the zinc atom is linked to four amino acids: they can be cysteines or histidines in any combination - e.g., 4xHis, 3xHis and 1xCys, 2xHis and 2xCys…

generally, in TF there is more than 1 zinc-finger domain

59
Q

Leucin-Zipper

A

leucine frequency is high

form homodimers or heterodimers, which can alter the DNA-binding ability of the TF and a way to expand regulation

60
Q

What is heterodimerization an example of?

A

combinatorial control (combination of different proteins control a cellular process, which increases the number of DNA sites that are recognized)

61
Q

What is special about the N-terminal tail of histones?

A

protrude outside the nucleosome and can be modified post-translationally by enzymes that reside in the nucleus

62
Q

Describe the histone modification: acetylation of lysines:

A

removes the charge from the lysine and promotes the formation of euchromatin (less compact chromatin) and allows transcription of nearby genes

deacetylation: repression
hyperacetylation: activation

63
Q

What is the most famous acetyltransferase in eukaryotes?

A

p300/CBP complex

64
Q

What does the p300/CBP complex do?

A

interacts with activators and is responsible for the acetylation of histone 4

65
Q

What does the acetyltransferase, PCAF, do?

A

preferentially acetylates histone 3

66
Q

Acetylation is always related to __________

A

enhanced expression

67
Q

Histone methylation can have different outcomes based on:
_____
_____
_____

A

number of methyl groups
residue
histone that is methylated

68
Q

The region in a genome that is transcriptionally active is in the presence of _____

A

euchromatin

69
Q

The region in a genome that is transcriptionally repressed is in the presence of _____

A

heterochromatin

70
Q

Why do we need factors that remodel nucleosomes?

A

because the position of adjacent nucleosomes varies a lot

71
Q

What are chromatin remodelling complexes?

A

found in eukaryotic cells

use energy of ATP hydrolysis to change the structure of nucleosomes temporarily so that DNA becomes less tightly bound to the histone core

72
Q

What does the remodelling of nucleosomes permit?

A

access to nucleosomal DNA by proteins involved in several processes such as gene expression, DNA replication and repair

73
Q

What is the most famous chromatin remodelling complex? Why?

A

SWI/SNF family

it is a complex of proteins that is very conserved among different species

74
Q

What is conserved in the SWI/SNF family?

A

presence of an ATPase domain, which requires energy to remodel the chromatin

75
Q

During the transcription of RNA, there is the cycling mechanism of nucleosome remodelling. When is this disrupted?

A

ONLY during DNA replication

76
Q

ATP-dependent remodelling complexes….

A

loosen the interaction between DNA and histones to permit the entrance of DNA-binding proteins

77
Q

Once DNA-binding proteins have done their job, another ATP-dependent remodelling complex….

A

restores the normal nucleosome structure

78
Q

Histone-modifying enzymes and chromatin remodelling enzymes…

A

work together to release and recondense stretches of chromatin

79
Q

Where does DNA bending occur?

A

minor groove of double helix

Regulation of Gene Expression (28 decks)

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