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Biochemistry 2 > Regulation of gene expression > Flashcards

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
Q

Regulatory proteins have ____, in a addition to DNA binding motifs

A

protein-interaction domains

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26
Q

What are protein-interaction domains?

A

This domains interact with other domains and this domains bring different proteins together

Different transcription function can come together to regulate different genes

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27
Q

Approximately how many transcription factors regulate gene expression

A

1557 TFs about 25000 genes

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28
Q

The difference between euchromatin and heterochromatin

A

Euchromatin->the histones are not so losely packed, ready for expression

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29
Q

Chromatin is ____

A

Chromatin= DNA+ histones

30
Q

Types of histones and their function

A 
H2A 
H2B
H3
H4
They form nucleosone, for one nucleosome two histones of each kind

H1-linker histone

31
Q

Trancriptionally active chromatin is rich in ___ and deficient in ___

A

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
Q

What enzymes deplete H1 and replace histone variants?

A

SWI
SNF
They also stimulate binding of TFs

33
Q

Why are histones modified?

A

To suppress or activate gene expression

Modification takes place at histone tails

34
Q

How are histones modified and what usually occurs to them

A

Methylation ( methyl groups on lysine or arginine histone residues )

  • Phosphorylation (serine and threonine residues)
  • Acetylation-acetylCoA (lysine)
  • Ubiquitination and sumoylation(lysine)
35
Q

What enzymes regulate histone acetylation?

A

Histone acetyletransferase (HAT) and histone deacetylase (HDAC)

36
Q

What modification can be done with DNA and in what sequence

A

Methylation can be done on cytosine in the sequence

Cytosine (some nucleotide) -Guanine

37
Q

Once the access to histones is given, ____ occurs

A

The assembly of preinitiation complex

38
Q

The assembly of preinitiation complex starts with

A

Starts with activator , bonding enhancers

39
Q

Enhancer region lies

A

Before the promoter region

40
Q

Enhancer is

A

places in the gene that play a role in expressing some gene or group of genes at a distance from the gene itself

41
Q

After the activators are bound to enhancers

A

Histone/nucleosome modification at promoter

42
Q

What happens as soon as the promoter region gets accessible?

A

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
Q

To what place TBP and TFIIB anchors

A

To TATA and Inr sequence in the promoter region

44
Q

The composition of preinitiation complex

A

TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, pol II and Mediator

45
Q

After TFIIB bind to promoter what happens

A

Basal TF and RNA Pol II bind at transcription start site

46
Q

What stimulates Pol II to transcribe?

A

TFIIH

47
Q

What is the mediator

A

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
Q

Some regulatory proteins

that bind to Pol II promoters or that interact with transcription activators can ____

A

act as repressors,

inhibiting the formation of active PICs or activate and help the transcription

49
Q

What is the important point in Pol II that interact with Mediator and other protein complexes

A

The carboxylterminal

domain (CTD)

50
Q

What is the function of HMG proteins, what is it

A

High-mobility group

Furthermore, these HMG-box DNA-binding proteins increase the flexibility of the DNA upon binding, allowing the looping

51
Q

What is UAC and its function

A

upstream activating sequence -where everything begins.

Is not a part of the promoter region

52
Q

lncRNA what is it and what does it do

A

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
Q

What can act as a repressor for the assemble of PIC

A

lncRNA or some protein repressor

54
Q

How do hormones act on the gene expression

A

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
Q

What does N ,Y,R,+1mean in Consensus sequence

A

N- any
R- any purine,A or G

Y-pyrimidines, either cytosine or tyrine
+1 where the transcription starts

56
Q

What is the promoter

A

Everything that is upstream from the the transcription start site ( -1,-2,etc.)

57
Q

Transcription factors are regulated by ____

A
  • Steroids and vitamins

- Covalent modification ( phosphorylation, for example)

58
Q

DNA binding domain represent the sequence at which

A

All TFs that bind to DNA

59
Q

What is the common sequence for steroid hormone receptor

A

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
Q

What is particular about steroid-hormone receptor?

A

It has a transcription activation site that helps the mediators and other TFs in assembly of PIC

61
Q

Explain type 1 nuclear receptor

A

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
Q

How do two types of nuclear receptors are differentiated

A

Where the receptor is present in inactive situation

63
Q

How type 1 nuclear receptors can be suppressed

A

By lncRNA, it just disallow to bind to their binding elements (HREs)

64
Q

Explain type 2 nuclear receptors

A

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
Q

What is alternative splicing and why it is important

A

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
Q

Primary transcripts are

A

not processed mRNA, before alternative splicing

67
Q

Alternative splicing can happen only in genes with ___

A

Introns

68
Q

What are miRNA

A

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
Q

Example of miRNA

A

siRNA(small interfering RNA)

70
Q

How do we get siRNA

A

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
Q

Types of gene regulation

A
  • Transcriptional regulation ( histone regulation, PIC regulation)
  • mRNA processing regulation
  • mRNA translation regulation

Biochemistry 2 (17 decks)

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