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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
How do regulatory proteins bind to dna?
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
26
What are the most common AA involved in hydrogen bonding of regulatory proteins to DNA?
Asn, Gln, Glu, Lys and Arg | Asparagine, Glutamine, Glutamic acid, Lysine, Arginine
27
What are DNA binding motifs/domains?
Regions of proteins that bind to DNA
28
What are the 3 common typed of DNA binding motifs?
Helix-turn-helix Zn finger domain Leucine zipper domain
29
Describe Helix-turn-helix
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.
30
Describe Zn finger domain
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
31
Describe leucine zipper
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
32
Apart from DNA binding motifs what else do regulatory proteins have? What does this result in?
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
33
Promoters are located near the ___
Promoters are located near the transcription start sites
34
Regulatory proteins function by ___ to regulate gene expression
Regulatory proteins function by combinations (mix-match) to regulate gene expression
35
Define nucleosome
Nucleosome is DNA coiled around a core of histones
36
What are the 2 states of a chromatin
depending on how tightly nucleosomes are arranged: Euchromatin is loosely arranged. This one is accessible Heterochromatin - chromatin is tightly woven; is transcriptionally inactive
37
What is histone made up of?
Of proteins which are present in a dimer- 2 copies of each are present H1- conditionally H2A, H2B, H3, H4- always
38
What is H1? Its function
It's a linker protein, brings several nucleosomes together | No H1= transcriptionally active region
39
What is chromatin made up of
DNA + histones (H1, H2A, H2B, H3, H4)
40
Transcriptionally active chromatin – deficient in __
Transcriptionally active chromatin – deficient in H1
41
Describe Transcriptionally active chromatin
Transcriptionally active chromatin- enriched with histone variants such as H3.3 and H2AZ
42
What do SWI/SNF enzymes do?
SWI/SNF enzymes deplete H1 and replace histone variants
43
Name and describe possible modifications of histones (5)
``` Methylation (lysine and arginine) Phosphorylation (serine and threonine) Acetylation (lysine) Ubiquitination Sumoylation (lysine) ```
44
Which part of histones is modified? Which type of bonding is it?
Histone tails | Covalent
45
Modification can only occur when chromatin is ___
Modification can only occur when chromatin is open
46
How is histone acetylation regulated?
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
What is the role of histone acetylation?
- 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
Name and describe a modification of DNA
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
What is the next step after TF bind?
Assembly of preinitiation complex
50
What are enhancers?
Regions of DNA that can be bound by activators to increase the likelihood that transcription of a particular gene will occur
51
What are transcription factors?
Transcription factors are proteins which recruit RNA polymerase and control and regulate the transcription of DNA into mRNA.
52
What are the three main portions that make up a promoter?
core promoter, proximal promoter, and distal promoter
53
Where is TATA box found?
In the core promoter region
54
Where are enhancers found?
A bit upstream of gene
55
What are activators?
Proteins that bind to enhancers | They decide which genes need to be activated
56
Activators are able to initiate ____ at promoter site
Activators are able to initiate histone nucleosome modification at promoter site
57
What are the 2 common regulatory sequences in eukaryotes?
TATA box and initiator element/sequence (Inr)
58
TATA box and Inr- which are present in eukaryotes? Prokaryotes
TATA is present in eukaryotes and prokaryotes | Initiator sequences are unique to large mammals such as humans
59
Do all genes contain TATA and Inr
Not all genes have TATA and Inr. Some have just TATA or Inr, some bo
60
What is the 1st protein that binds to TATA box?
TATA binding protein (TBP) -it is a TF that identifies TATA box in promoter region
61
What are basal TF?
General TF that are common for all gene expressions
62
What is the second protein that binds after TBP?
TF2B- a coactivator
63
What are the coactivator complexes and where do they function?
TBP and TFIIB | Coactivator complexes function at or near the promoter’s TATA box.
64
What is preinitiation complex made up of? Where is it formed?
pol II along with basal TFs | It is formed at TATA box and Inr site
65
___ stimulates pol II to start transcription
TFIIH stimulates pol II to start transcription
66
What are mediators? Why are they needed?
Mediators are any proteins that link enhancers to promoter region Enhancer is usually far away from the gene
67
How do mediators link enhancers to promoter region ?
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
Mediators can be ___ or ____ regulators
Mediators can be positive or negative regulators
69
What do positive mediators do?
Positive mediators stabilize RNA Pol II and help in formation of pre-initiation transcription complex
70
What do negative mediators do?
Negative/repressor mediators inhibit the formation of active pre- initiation complexes.
71
In what ways can mediators inhibit the formation of active pre- initiation complexes.
Can inhibit: - binding of proteins to UAS (Upstream activating sequence) - binding of HMG proteins - binding of nearby transcription factors
72
What are HMG proteins?
HMG proteins enable bending of DNA to enable far part regions closer
73
What is lncRNA?
Long non-coding RNA- lacRNA or lncRNA | Can act as enzymes that enable proteins that are not translated to play role in transcription
74
Give an example of a non-protein repressor
lncRNA
75
How do TF recognize DNA sequence?
Transcription factors recognize DNA sequence based on their AA sequence
76
How is core promoter defined?
Core promoter is defined as anything -40 to +40 nucleotides before and after start site
77
How is the start site denoted?
+1
78
_ means either A or T | _ means either G or C
W means either A or T | Y means either G or C
79
Nuclear receptors are ___ that are regulated by __
Nuclear receptors are TF that are regulated by hormones
80
How can nuclear receptor be further regulated, apart from hormones?
Can further be regulated by covalent modification - phosphorylation, methylation
81
All TF that bind to DNA have ___ domains
All TF that bind to DNA have DNA binding domains
82
What is a DNA binding domain?
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
Which 3 domains do nuclear receptors have?
DNA-binding domain Hormone binding domain transcription activation domain
84
Which domains do all TF have
DNA-binding domain | transcription activation domain
85
What is the role of | transcription activation domain?
This domain helps all the mediators and TF to help in the formation of pre-initiation complex
86
Which type of domain do nuclear receptors have a domain type in the DNA binding domain region ?
Zinc finger
87
What are the 2 main types of nuclear receptors?
cytoplasmic and nuclear
88
Where are the two types of nuclear receptors found?
Type I- cytoplasm | Type 2- nucleus
89
Which type of ligands do type 1 nuclear receptors have?
Lipid soluble hormones that can cross the cell membrane and enter the cytoplasm easily by diffusion
90
In which state are type I nuclear receptors found in the cytoplasm? Why?
Type I nuclear receptors are found in the cytoplasm in an inactive state Remain inactive being bound to proteins Hsp70- chaperon proteins
91
What do chaperon proteins do?
Chaperon proteins take protein from one place to another or hold protein in inactive state
92
What happens when a ligand binds to type I nuclear receptor?
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
How can nuclear receptor be inhibited? What does this result in?
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
In which condition are type II nuclear receptors found?
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
What happens when a ligand binds to type II nuclear receptor?
Binding of hormone (ligand) will remove the corepressor and brings in the activator allowing transcription to take place
96
Where do nuclear receptors bind to?
to hormone response elements
97
What is RNA processing?
RNA processing- introns are removed from mRNA
98
Does one gene mean 1 protein?
No - alternative splicing
99
__% of genes with multiple exons undergo alternative splicing
95% of genes with multiple exons undergo alternative splicing
100
What are the ways of regulation of gene expression at translation?
- Micro-RNAs (miRNAs) | - siRNA
101
Describe micro-RNAs
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
Describe siRNAs
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
TFIIh vs TFIIB
TFIIH enables pol II to start transcription | TFIIB is a coactivator that binds afte TBP

BC 2- (19 decks)

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