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Regulation of gene expression Flashcards

1
Q

The difference between housekeeping and regulated genes

A

expressed at a more or less constant level in virtually every cell of a species or
organism. -> housekeeping genes

For other gene products, cellular levels rise and fall in response to molecular signals; they are needed for the specific moment-> this is
regulated gene expression.

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2
Q

7 steps in overall gene expression

A
  1. Transcription initiation
  2. Posttranscriptional regulation
  3. RNA stability
  4. Translational regulation
  5. Protein modification
  6. Protein transport
  7. Protein degradation
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3
Q

Access to promoters is restricted by ___ in eukaryotic genes

A

Chromatin structure

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4
Q

What does it mean that positive regulation is most common in eukaryotic gene regulation?

A

Cells are usually turned off and turned on when necessarily

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5
Q

Regulatory proteins , including transcription factors , are usually ___ that is why it can be called ___

A

Multimeric and it can be called transcriptional machinery

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6
Q

in Eukaryotes transcription and translation are physically separated by ____

A

Nucleus

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7
Q

Gene is

A

Any string of DNA sequence that codes for protein

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8
Q

In what order does the gene usually written

A

5’ to 3’ direction
everything on the left is called upstream
On the right downstream

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9
Q

Gene products that increase in concentration under particular molecular
circumstances are referred to as ____

A

inducible

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10
Q

What is a promoter

A

the DNA sequence that promotes gene expression

sites generally
found near points at which RNA synthesis begins on the DNA template.

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11
Q

A consensus sequence is

A

A consensus sequence is an ideal promoter sequence in DNA

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12
Q

What do regulatory proteins do?

A

The ultimate role of regulatory proteins is regulate RNA polymerase
Some of them called transcription factors, activators, repressors- they may not directly bind to the gene, but regulate the expression

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13
Q

Describe negative regulators and the role of regulatory proteins in it

A

The gene is turned off, because its promoter is blocked by a repressor , then the signal binds to the repressor and take it away, so the gene will start to be expressed
OR
Molecular signal causes binding of repressor to DNA, inhbiting transcription.

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14
Q

What molecular signals can influence the binding of RNA polymerase?

A

covalent modification ( methylation, phosphorylation), allosteric modulaters ( change the strucutre of the moleucle)
Hormone ( nuclear receptors)
Interacting protein

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15
Q

Describe positive regulators and the role of regulatory proteins in it

A

With the RNA polymerase that is bound to the promoter region , there is an activator that helps RNA polymerase.
When molecular signal comes, it binds too activator and dissociate with it

OR

Molecular signal causes binding of activator to DNA, inducing transcription

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16
Q

What is lncRNA and its function

A

long, noncoding RNAs
(lncRNAs),

Known functions of lncRNAs include
regulation of nucleosome positioning and chromatin structure, control of DNA methylation and
posttranscriptional histone modifications, transcriptional gene silencing, multiple roles in
transcriptional activation and repression,

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17
Q

Negative regulation of transcription is regulated by ___ and positive regulation is mediated by ___

A
  • Negative->repressor

- Positive->activator

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18
Q

What is operon?

A

The

gene cluster and promoter plus additional sequences that function together in regulation

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19
Q

How do regulatory proteins know how and where bind to DNA

A

To bind specifically to DNA sequences, regulatory proteins must recognize surface features on the
DNA. Most of the chemical groups that differ among the four bases and thus permit discrimination
between base pairs are hydrogen-bond donor and acceptor groups. The interaction between the DNA and AA in the protein

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20
Q

What AA interact most frequently with the DNA?

A

Asn(Asparagine), Gln(glutamine), Glu (glutamic acid), Lys(Lysine), and Arg(Arginine)

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21
Q

Common types of binding motifs

A

1) Helix-turn-helix domain
2) Zinc finger domain
3) Leucine zipper

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22
Q

Describe helix-turn - helix domain

A

many regulatory
proteins with DNA in bacteria, and similar motifs occur in some eukaryotic regulatory proteins

20 AA long in two short α-helical segments

One of the two α-helical
segments is called the recognition helix, because it usually contains many of the amino acids that
interact with DNA in a sequence-specific way.

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23
Q

Describe Zinc finger domain

A

-30 AA long
-Common in transcription factors in eukaryotes
-Loops are cross-linked by Zn
-The interaction of a single zinc
finger with DNA is typically weak, thus protein might have more than 1 zinc finger domain

-Zinc fingers can also function as RNA-binding
motifs, such as in certain proteins that bind eukaryotic mRNAs and act as translational repressors

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24
Q

describe leucine zippers

A

amphipathic α helix with a series of hydrophobic amino
acid residues concentrated on one side ,
-Leucine occurs at every 7th position
-Week interaction through Lysine and Arginine that can
interact with the negatively charged phosphates of the DNA backbone

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25
Regulatory proteins have ____, in a addition to DNA binding motifs
protein-interaction domains
26
What are protein-interaction domains?
This domains interact with other domains and this domains bring different proteins together Different transcription function can come together to regulate different genes
27
Approximately how many transcription factors regulate gene expression
1557 TFs about 25000 genes
28
The difference between euchromatin and heterochromatin
Euchromatin->the histones are not so losely packed, ready for expression
29
Chromatin is ____
Chromatin= DNA+ histones
30
Types of histones and their function
``` H2A H2B H3 H4 They form nucleosone, for one nucleosome two histones of each kind ``` H1-linker histone
31
Trancriptionally active chromatin is rich in ___ and deficient in ___
Rich in Deficient in H1, because chromatin needs to loosen and to open Rich in histone variants such as H3.3 and H2AZ (replacement for H3 and H2). They make the chromatin continue expressing
32
What enzymes deplete H1 and replace histone variants?
SWI SNF They also stimulate binding of TFs
33
Why are histones modified?
To suppress or activate gene expression | Modification takes place at histone tails
34
How are histones modified and what usually occurs to them
Methylation ( methyl groups on lysine or arginine histone residues ) - Phosphorylation (serine and threonine residues) - Acetylation-acetylCoA (lysine) - Ubiquitination and sumoylation(lysine)
35
What enzymes regulate histone acetylation?
Histone acetyletransferase (HAT) and histone deacetylase (HDAC)
36
What modification can be done with DNA and in what sequence
Methylation can be done on cytosine in the sequence | Cytosine (some nucleotide) -Guanine
37
Once the access to histones is given, ____ occurs
The assembly of preinitiation complex
38
The assembly of preinitiation complex starts with
Starts with activator , bonding enhancers
39
Enhancer region lies
Before the promoter region
40
Enhancer is
places in the gene that play a role in expressing some gene or group of genes at a distance from the gene itself
41
After the activators are bound to enhancers
Histone/nucleosome modification at promoter
42
What happens as soon as the promoter region gets accessible?
Mediator bimds to the enhancer/activator site-> only then TATA binding protein (TBP) and Transcription factor IIB (TFIIB) bind to the promoter. They are usually assistant by general transcription factors that are not specific for the gene expressed
43
To what place TBP and TFIIB anchors
To TATA and Inr sequence in the promoter region
44
The composition of preinitiation complex
TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, pol II and Mediator
45
After TFIIB bind to promoter what happens
Basal TF and RNA Pol II bind at transcription start site
46
What stimulates Pol II to transcribe?
TFIIH
47
What is the mediator
any proteins that link the enhancers with the promoter region, either functionally(there can be no physical contact between the , the protein that begins at enhancer will move to the promoter region or structurally(they stack so much , so there is a physical contact) and greatly facilitates formation of the PIC.
48
Some regulatory proteins | that bind to Pol II promoters or that interact with transcription activators can ____
act as repressors, | inhibiting the formation of active PICs or activate and help the transcription
49
What is the important point in Pol II that interact with Mediator and other protein complexes
The carboxylterminal | domain (CTD)
50
What is the function of HMG proteins, what is it
High-mobility group Furthermore, these HMG-box DNA-binding proteins increase the flexibility of the DNA upon binding, allowing the looping
51
What is UAC and its function
upstream activating sequence -where everything begins. | Is not a part of the promoter region
52
lncRNA what is it and what does it do
Long non-coding RNAs (lncRNAs) are nucleotides that do not encode proteins . They help in promoting transcription by acting on UAC that will activate the mediator and Pol II OR they can inhibit the assembly of preinitiation complex They inhibit- the assemble of the protein at the promoter region, or at UAS, or at transcription factors,or HMG protein,
53
What can act as a repressor for the assemble of PIC
lncRNA or some protein repressor
54
How do hormones act on the gene expression
the hormone interacts with steroid-binding nuclear receptor .the hormone receptor complex acts by binding to highly specific DNA sequences called hormone response elements (HREs), thereby altering gene expression. This response elements have a very specific consensus sequence.
55
What does N ,Y,R,+1mean in Consensus sequence
N- any R- any purine,A or G Y-pyrimidines, either cytosine or tyrine +1 where the transcription starts
56
What is the promoter
Everything that is upstream from the the transcription start site ( -1,-2,etc.)
57
Transcription factors are regulated by ____
- Steroids and vitamins | - Covalent modification ( phosphorylation, for example)
58
DNA binding domain represent the sequence at which
All TFs that bind to DNA
59
What is the common sequence for steroid hormone receptor
It is a polypeptide chain to which the hormone binds and then influences the transcription. Transcription activation DNA binding site, that has specific Zinc fingers Hormone binding
60
What is particular about steroid-hormone receptor?
It has a transcription activation site that helps the mediators and other TFs in assembly of PIC
61
Explain type 1 nuclear receptor
Type 1 is found in the cytoplasm, when they remain inactive. Inactive,when bound to Hsp 70( chaperons, they just take the protein from one place to another) As soon as they nuclear receprtor is bound with the ligand(that came through the membrane by diffusion), Hsp 70 it dimirizes, and only the dimirized form can go into the nucleus Once the receptors are in the nucleus, they act as TFs and help in the assembly of PIC-> regulation of targeted genes
62
How do two types of nuclear receptors are differentiated
Where the receptor is present in inactive situation
63
How type 1 nuclear receptors can be suppressed
By lncRNA, it just disallow to bind to their binding elements (HREs)
64
Explain type 2 nuclear receptors
usually found in the nucleus itself either bond to the region already or floating in the cytoplasm In inactive states they are always bound to proteins called corepressors Binding of the hormone to the receptor allows the activation and bringing the activator
65
What is alternative splicing and why it is important
Splicing-most of eukaryote genes have introns,not coding for protein, and exons. This process removes selectively introns or exons Alternative splicing can lead to different sequences by slicing out different exons
66
Primary transcripts are
not processed mRNA, before alternative splicing
67
Alternative splicing can happen only in genes with ___
Introns
68
What are miRNA
Certain types of RNA that can regulate TRANSLATION, they do not code for any protein miRNA silence genes by binding to mRNAs. They prevent translation of the mRNA by cleaving it(destruction) or by blocking translational machinery. It binds to miRNA by complementaruty to mRNA
69
Example of miRNA
siRNA(small interfering RNA)
70
How do we get siRNA
A long RNA is synthesized It bends, forming a double-stranded RNA OR A separate double-stranded RNA is synthesized Then those double stranded RNAs are targeted by Dicers ( enzymes that cleaves double stranded RNA), making them single stranded with shorter sequence As they are complementary to some mRNA sequence, now they can bind and either degrade mRNA or inhibit translation
71
Types of gene regulation
- Transcriptional regulation ( histone regulation, PIC regulation) - mRNA processing regulation - mRNA translation regulation

Biochemistry 2 (17 decks)

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