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BC 2- > Regulation of gene expression > Flashcards

Regulation of gene expression Flashcards

1
Q

How does tretinoin reduce acne?

A
  • Acne occurs due to increased cell-cycle and increased
    inflammation
  • Tretinoin normalizes cell cycle and reduces expression of nitric-oxide synthase which is pro-inflammatory
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2
Q

Are all genes expressed all the time?

A

No, only the necessary genes are expressed

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3
Q

What does the expression of certain egens depend on?

A

Amount, activity, functional protein depends on regulation at multiple levels

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4
Q

Housekeeping gene vs regulated gene

A

Housekeeping genes - expressed in cells all the time as they are necessary for these cells to survive
Regulated genes are the genes that are expressed only when they are necessary for a cells function at that point of time

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5
Q

What restricts access to promoter?

A

Chromatin structure

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6
Q

Regulatory proteins are usually ___

A

Regulatory proteins are usually multimeric

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7
Q

What does nucleus separates in terms of gene expression in eukaryotes?

A

Transcription (happens in nucleus) and translation (happens in cytoplasm) are separated by
nucleus

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8
Q

Define a gene

A

Gene is a string of DNA sequence that codes for a protein or a functional entity

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9
Q

Where is regulatory sequence found on the gene

A

It is found at 5’ end- left side

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10
Q

The sequences on the right side are called ___ sequences

The sequences on the left side is called _____ sequences

A

The sequences on the right side are called downstream sequences
The sequences on the left side is called upstream sequences

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11
Q

What is a promoter?

A

Promoter is a DNA sequence that regulates/promotes gene expression

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12
Q

What is a transcription factor?

A

Transcription factor is a protein that affects the regulation and transcription initiation of a gene by binding to a regulatory sequence near or within the gene and interacting with RNA polymerase and/or other transcription factors

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13
Q

What can serve as a molecular signal that participates in gene regulation?

A

Hormone
Covalent modification
Allosteric regulator
Interacting protein

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14
Q

Where does RNA polymerase binds to the gene?

A

RNA polymerase binds at promoter sites generally found near points at which RNA synthesis begins on the DNA template

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15
Q

What is a coactivator?

A

Acoactivatoris a type of transcriptional coregulator that binds to an activator (a transcription factor) to increase the rate of transcription of ageneor set of genes

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16
Q

Do coactivators and corepressors bind to promoter region directly?

A

NO

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17
Q

Do regulatory proteins bind to promoter region directly?

A

yes, it is absolutely necessary

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18
Q

What happens after regulatory proteins bind to promoter region?

A

After binding innate enzyme (RNA polymerase) binds and then functions

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19
Q

What is negative regulation Describe 2 ways of negative regulation

A

Negative regulation- bound repressor inhibits transcription . A) Gene is off. Molecular signal causes dissociation of regulatory protein from DNA. Transcription can take place.
The signal could be anything- hormone, covalent modification, a protein
B) Gene is on. Molecular signal causes binding of repressor to DNA. Transcription is inhibited

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20
Q

What is positive regulation Describe 2 ways of positive regulation

A

Positive regulation- bound activator facilitates transcription.
A) Gene is on. Molecular signal causes dissociation of an activator from DNA, inhibiting transcription
B) Gene is off. Molecular signal causes binding of activator to DNA, inducing transcription. is made to dissociate by a signal. . Gene is turned off

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21
Q

Define regulatory sequence

A

Regulatory sequence is a DNA sequence involved in regulating the expression of a gene e.g. a promoter o operator

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22
Q

Promoters in prokaryotes vs eukaryotes

A

Prokaryotes commonly have a string of genes that a regulated by common promoters
In eukaryotes each gene has its own promoter

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23
Q

Define an operator

A

Operators are the binding sites for repressors. They are generally near the promoter

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24
Q

Where are activator binding sites? What are they?

A

Upstream there are activator binding sites- where positive regulators bind

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25
Q

How do regulatory proteins bind to dna?

A

When a regulatory protein has to bind to DNA, its amino acids have to interact with nucleotides of DNA
These interactions are specific and depend on hydrogen bonding
Hydrogen bonds occur between amino acids of a protein and nucleotide base of DNA

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26
Q

What are the most common AA involved in hydrogen bonding of regulatory proteins to DNA?

A

Asn, Gln, Glu, Lys and Arg

Asparagine, Glutamine, Glutamic acid, Lysine, Arginine

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27
Q

What are DNA binding motifs/domains?

A

Regions of proteins that bind to DNA

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28
Q

What are the 3 common typed of DNA binding motifs?

A

Helix-turn-helix
Zn finger domain
Leucine zipper domain

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29
Q

Describe Helix-turn-helix

A

Has about 20 amino acids in two short α-helical segments
One of the two α-helical segments is called the recognition helix, because as it is the one that contains the amino acids
interact with the DNA.

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30
Q

Describe Zn finger domain

A

Many transcription factors in eukaryotic systems have this
In a zinc finger, about 30 amino acid residues form an elongated loop held together at the base by a single Zn2 ion
Weaker binding
Proteins may have >1Zn finger To make up for the weak binding and provide sufficient interaction
Can also act as RNA binding motif Thus participate in regulation of RNA binding

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31
Q

Describe leucine zipper

A

This motif is an amphipathic helix with a series of hydrophobic amino acid residues concentrated on one side forming a straight line along the hydrophobic
surface
Leu occurs at every 7th position
Regulatory proteins with leucine zippers often have a separate DNA-binding domain with a high concentration of basic (Lys or Arg) residues that can PARTIALLY interact with the negatively charged phosphates of the DNA backbone-> Weak interaction

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32
Q

Apart from DNA binding motifs what else do regulatory proteins have? What does this result in?

A

Regulatory proteins have protein-interaction domains, in addition to DNA binding motifs-> allow to interact with other proteins - that’s why they can be multimeric

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33
Q

Promoters are located near the___

A

Promoters are located near thetranscription start sites

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34
Q

Regulatory proteins function by ___ to regulate gene expression

A

Regulatory proteins function by combinations (mix-match) to regulate gene expression

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35
Q

Define nucleosome

A

Nucleosome is DNA coiled around a core of histones

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36
Q

What are the 2 states of a chromatin

A

depending on how tightly nucleosomes are arranged:
Euchromatin is loosely arranged. This one is accessible
Heterochromatin - chromatin is tightly woven; is transcriptionally inactive

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37
Q

What is histone made up of?

A

Of proteins which are present in a dimer- 2 copies of each are present
H1- conditionally
H2A, H2B, H3, H4- always

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38
Q

What is H1? Its function

A

It’s a linker protein, brings several nucleosomes together

No H1= transcriptionally active region

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39
Q

What is chromatin made up of

A

DNA + histones (H1, H2A, H2B, H3, H4)

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40
Q

Transcriptionally active chromatin – deficient in __

A

Transcriptionally active chromatin – deficient in H1

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41
Q

Describe Transcriptionally active chromatin

A

Transcriptionally active chromatin- enriched with histone variants such as H3.3 and H2AZ

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42
Q

What do SWI/SNF enzymes do?

A

SWI/SNF enzymes deplete H1 and replace histone variants

43
Q

Name and describe possible modifications of histones (5)

A 
Methylation (lysine and arginine)
Phosphorylation (serine and threonine)
Acetylation (lysine)
Ubiquitination
Sumoylation (lysine)
44
Q

Which part of histones is modified? Which type of bonding is it?

A

Histone tails

Covalent

45
Q

Modification can only occur when chromatin is ___

A

Modification can only occur when chromatin is open

46
Q

How is histone acetylation regulated?

A

Regulated by enzymes HATs and HDACs

  • (HDAC) is an enzyme that removes the acetyl group from histone proteins on DNA, making the DNA less accessible to transcription factors.
  • HAT -Histone acetyltransferase- adds acetyls
47
Q

What is the role of histone acetylation?

A
  • The acetylation and deacetylation of histones figure prominently in the processes that activate chromatin for transcription
    • Acetylation may also prevent or promote interactions with other proteins involved in transcription or its regulation
48
Q

Name and describe a modification of DNA

A

DNA can be methylated in CpG sequences
Methylation occurs at CpG C is followed by a G. C is methylated.
P is phosphate bond that occurs between the 2 nucleotides
This inhibits access to promoter region
These genes have inaccessible promoter - not expressed

49
Q

What is the next step after TF bind?

A

Assembly of preinitiation complex

50
Q

What are enhancers?

A

Regions of DNA that can be bound by activators to increase the likelihood that transcription of a particular gene will occur

51
Q

What are transcription factors?

A

Transcription factors are proteins which recruit RNA polymerase and control and regulate the transcription of DNA into mRNA.

52
Q

What are the three main portions that make up a promoter?

A

core promoter, proximal promoter, and distal promoter

53
Q

Where is TATA box found?

A

In the core promoter region

54
Q

Where are enhancers found?

A

A bit upstream of gene

55
Q

What are activators?

A

Proteins that bind to enhancers

They decide which genes need to be activated

56
Q

Activators are able to initiate ____ at promoter site

A

Activators are able to initiate histone nucleosome modification at promoter site

57
Q

What are the 2 common regulatory sequences in eukaryotes?

A

TATA box and initiator element/sequence (Inr)

58
Q

TATA box and Inr- which are present in eukaryotes? Prokaryotes

A

TATA is present in eukaryotes and prokaryotes

Initiator sequences are unique to large mammals such as humans

59
Q

Do all genes contain TATA and Inr

A

Not all genes have TATA and Inr. Some have just TATA or Inr, some bo

60
Q

What is the 1st protein that binds to TATA box?

A

TATA binding protein (TBP) -it is a TF that identifies TATA box in promoter region

61
Q

What are basal TF?

A

General TF that are common for all gene expressions

62
Q

What is the second protein that binds after TBP?

A

TF2B- a coactivator

63
Q

What are the coactivator complexes and where do they function?

A

TBP and TFIIB

Coactivator complexes function at or near the promoter’s TATA box.

64
Q

What is preinitiation complex made up of? Where is it formed?

A

pol II along with basal TFs

It is formed at TATA box and Inr site

65
Q

___ stimulates pol II to start transcription

A

TFIIH stimulates pol II to start transcription

66
Q

What are mediators? Why are they needed?

A

Mediators are any proteins that link enhancers to promoter region
Enhancer is usually far away from the gene

67
Q

How do mediators link enhancers to promoter region ?

A

Either structurally or functionally
Structurally - mediators stack up so much, causing a physical contact between enhancer and promoter
Functionally- mediators begin their process at enhancer region and become modified. The protein floats to promoter region from the region where activation was taking place

Mediators bring in the information from enhancer region to promoter region

68
Q

Mediators can be ___ or ____ regulators

A

Mediators can be positive or negative regulators

69
Q

What do positive mediators do?

A

Positive mediators stabilize RNA Pol II and help in formation of pre-initiation transcription complex

70
Q

What do negative mediators do?

A

Negative/repressor mediators inhibit the formation of active pre- initiation complexes.

71
Q

In what ways can mediators inhibit the formation of active pre- initiation complexes.

A

Can inhibit:

  • binding of proteins to UAS (Upstream activating sequence)
  • binding of HMG proteins
  • binding of nearby transcription factors
72
Q

What are HMG proteins?

A

HMG proteins enable bending of DNA to enable far part regions closer

73
Q

What is lncRNA?

A

Long non-coding RNA- lacRNA or lncRNA

Can act as enzymes that enable proteins that are not translated to play role in transcription

74
Q

Give an example of a non-protein repressor

A

lncRNA

75
Q

How do TF recognize DNA sequence?

A

Transcription factors recognize DNA sequence based on their AA sequence

76
Q

How is core promoter defined?

A

Core promoter is defined as anything -40 to +40 nucleotides before and after start site

77
Q

How is the start site denoted?

A

+1

78
Q

_ means either A or T

_ means either G or C

A

W means either A or T

Y means either G or C

79
Q

Nuclear receptors are ___ that are regulated by __

A

Nuclear receptors are TF that are regulated by hormones

80
Q

How can nuclear receptor be further regulated, apart from hormones?

A

Can further be regulated by covalent modification - phosphorylation, methylation

81
Q

All TF that bind to DNA have ___ domains

A

All TF that bind to DNA have DNA binding domains

82
Q

What is a DNA binding domain?

A

This domain will have short AA sequence that will interact with DNA element
protein domain that contains at least one structural motif that recognizes double- or single-stranded DNA

83
Q

Which 3 domains do nuclear receptors have?

A

DNA-binding domain
Hormone binding domain
transcription activation domain

84
Q

Which domains do all TF have

A

DNA-binding domain

transcription activation domain

85
Q

What is the role of

transcription activation domain?

A

This domain helps all the mediators and TF to help in the formation of pre-initiation complex

86
Q

Which type of domain do nuclear receptors have a domain type in the DNA binding domain region ?

A

Zinc finger

87
Q

What are the 2 main types of nuclear receptors?

A

cytoplasmic and nuclear

88
Q

Where are the two types of nuclear receptors found?

A

Type I- cytoplasm

Type 2- nucleus

89
Q

Which type of ligands do type 1 nuclear receptors have?

A

Lipid soluble hormones that can cross the cell membrane and enter the cytoplasm easily by diffusion

90
Q

In which state are type I nuclear receptors found in the cytoplasm? Why?

A

Type I nuclear receptors are found in the cytoplasm in an inactive state
Remain inactive being bound to proteins Hsp70- chaperon proteins

91
Q

What do chaperon proteins do?

A

Chaperon proteins take protein from one place to another or hold protein in inactive state

92
Q

What happens when a ligand binds to type I nuclear receptor?

A

When ligand binds to the receptor- it dimerizes, but has to find an active receptor
Dimerized receptor goes into nucleus and acts as TF - act as activators and interact with other TF; help in the process of pre-initiation complex and regulate target gene

93
Q

How can nuclear receptor be inhibited? What does this result in?

A

can be inhibited by other repressor such as protein repressors or lncRNA
These do not allow nuclear receptors to bind to their elements - no transcriptional activity

94
Q

In which condition are type II nuclear receptors found?

A

Found in nucleus either bound to promoter region already or floating in nucleoplasm
When they are in an inactive state, they are bound to a corepressor

95
Q

What happens when a ligand binds to type II nuclear receptor?

A

Binding of hormone (ligand) will remove the corepressor and brings in the activator allowing transcription to take place

96
Q

Where do nuclear receptors bind to?

A

to hormone response elements

97
Q

What is RNA processing?

A

RNA processing- introns are removed from mRNA

98
Q

Does one gene mean 1 protein?

A

No - alternative splicing

99
Q

__% of genes with multiple exons undergo alternative splicing

A

95% of genes with multiple exons undergo alternative splicing

100
Q

What are the ways of regulation of gene expression at translation?

A
  • Micro-RNAs (miRNAs)

- siRNA

101
Q

Describe micro-RNAs

A

Micro-RNAs (miRNAs) silence genes by binding to mRNAs and cleaving it (via endonuclease Drosha or Dicer) or by blocking i. Bind to mRNA due to sequence complementarity
These are short, non-coding RNAs
They are endogenous

102
Q

Describe siRNAs

A

Short inhibitory RNAs- they are synthesized, not endogenous
siRNA are also called stRNA
Long RNA is synthesized
Because of it’s length it can form hairpin structure- RNA double stranded on itself
OR
Double stranded RNA can be made separately
These double stranded RNA are targeted by dicers which bring them back to single stranded RNAs that are short in sequence
As this sequence can be complementary mRNA- they can bind (nucleotide to nucleotide hydrogen bonding as in DNA)
Once these siRNA/stRNA bind to target mRNA- they can lead to cleavage of mRNA or inhibit translation

103
Q

TFIIh vs TFIIB

A

TFIIH enables pol II to start transcription

TFIIB is a coactivator that binds afte TBP

BC 2- (19 decks)

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