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Genetics > Regulation of Gene Expression > Flashcards

Regulation of Gene Expression Flashcards

0
Q

What distinguishes higher organisms isn’t a difference of genes, but rather a difference in the …

A

regulation of genes

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1
Q

Because all nucleated cells contain the same DNA, the difference in cell phenotype must be based on _______

A

differential regulation of gene expression

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2
Q

Think of 6 ways eukaryotic gene expression can be controlled.

A

1) DNA structure
2) Frequency
3) Splicing
4) where mRNAs go
5) which mRNAs are translated
6) rate of mRNA degredation
7) control of proteins

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3
Q

Just know that increasing the number of gene copies can increase expression. More copies, more expression.

A

Gene Copy Number

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4
Q

Euchromatin __________

A

Transcriptionally active; loose chromatin

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5
Q

Heterochromatin____________

A

compact chromatin (SILENCING genes), transcriptionally inactive

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6
Q

Acetylation of Histones=

A

euchromatin, active transcription

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7
Q

Deacetylation of histones=

A

Heterochromatin, inactive transcription

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8
Q

Regulatory regions near transcription initiation contain short stretches of DNA called ______ and gene regulatory proteins, _______, that recognize and bind to these stretches for gene regulation

A

DNA- cis-acting

protein- trans-acting

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9
Q

The _____ groove of the DNA helix is accessible for regulatory proteins to bind to for regulation

A

Major

*** proteins can bend DNA and change the structure of DNA for gene regulatioin

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10
Q

Gene regulatory proteins contain specific structural motifs that recognize DNA sequences. Numerous contacts are made to ensure that the interaction between protein and DNA is strong.

A

Cool.

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11
Q

Motif __________ is one of the most simplest and common motifs.

A

Helix-turn-helix

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12
Q

Motif– _________ proteins are a special subclass of helix-turn-helix proteins that are key Regulators of animal development (embryonic)

A

Homeodomain proteins

***** important

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13
Q

Motif- another important group of regulatory proteins is ________ proteins because they have zinc atoms and they look like fingers.

A

Zinc Finger Motif…..pretty obvious

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14
Q

Motif- This dimer grips DNA like a clothespin on a clothesline. It’s called the _______ motif

A

Leucine Zipper

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15
Q

Motif– _______ motifs can create both homodimers and heterodimes

A

Helix-Loop-Helix

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16
Q

Many regulatory proteins can bind as heterodimers. Heterodimerization increases….

A

the variety of DNA sequences recognized

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17
Q

In bacteria, gene switches allow for the expression of genes to be dependent on the available food in the environment. “Gene switches in action”.

A

Awesome.

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18
Q

Explain the E.Coli tryptophan operator. ie. What happens when tryptophan is present in the cells environment?

A
  • the 5 genes needed to produce tryptophan are next to each other and are controlled by one operator
  • when tryptophan is present in environment, expression of 5 genes no longer needed–> production needs to be shut off
  • tryptophan activates tryptophan repressor protein which attaches to the operator, blocking the binding of the promoter
  • NEGATIVE CONTROL
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19
Q

Activator proteins can ….

A

assist in the binding of RNA poly to help promote transcription

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20
Q

Negative regulation:

A

bound repressor protein prevents transcription

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21
Q

Positive regulation:

A

bound activator protein promotes transcription

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22
Q

______can bind regulatory protein to remove it from DNA or bind to allow regulatory protein to bind to DNA– for both repressor protein or activator protein

A

ligands

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23
Q

Go study lac operon

A

Quick quesiton: what if there was a mutation of the enzyme that converts Lactose into Allolactose…?

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24
Q

Regulation in eukaryotes is very complex. Regulatory regions can be very long, and unlike prokaryotes, RNA poly cannot initiate transcription on its own; it must have __________ proteins that assemble at the promoter for transcription to occur

A

basal transcription factor proteins

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25
Q

Regulatory sites that are distant from the promoter are called ______. These sequences loop to join the promoter

A

enhancers

***can also repress

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26
Q

Many gene regulatory proteins consist of two domains: a _____ that recognizes specific DNA and an _____ that accelerates transcription

A

structural motif; activation domain

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27
Q

Transcriptional synergy:

A

multiple activators can have a greater than additive effect on gene transcription

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28
Q

Don’t forget how important opening and closing chromatin is for gene regulation. Histone acetylases and histone deacetlyases…..

A

Acetlyation opens=transcription active

Deacetylation closes= transcription inactive

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29
Q

Competitive DNA binding: gene ____ proteins can compete with gene activator proteins for the same regulatory DNA sequence.

A

Gene Repressor Proteins

30
Q

Masking the activation surface: repressor proteins can….

A

bind the activation site of the activator protein thereby preventing activation of transcription

31
Q

Direct interaction with the general transcription factors: the repressor blocks assembly of the….

A

general transcription factors

32
Q

Recruitment of chromatin remodeling complexes: repressor proteins recruit chromatin remodeling proteins which essentially…

A

closes up the DNA, silencing the promoter

33
Q

Recruitment of histone deacetylases: the repressor attracts histone deacetylases to the ______

A

promoter

34
Q

gene regulatory proteins often assemble into complexes on DNA. An example is the ______; a group of proteins that form together on an enhancer to regulate transcription at a distant site

A

Enhanceosome

35
Q

Insulators are….

A

DNA sequences that prevent regulatory proteins from influencing distant genes (like non related genes)

36
Q

Insulator sequences both prevent the spread of ______ and directionally block the action of _____

A

heterochromatin; enhancers

37
Q

An example of a gene that would be coordinated by a single protein is ________

A

human glucacorticoid receptor protein, which makes things like cortisol

*** Rapid change wanted in gene expression

38
Q

Chromosome-wide alterations in chromatin structure ( and ultimately gene expression) can be _____

A

inherited

39
Q

Epigenetics is defined as ________, ________ changes in the genome (no changes in the sequence) that regulate gene expression, most often resulting in _______. It can be influenced by the environment

A

heritable, reversible; gene silencing

40
Q

_______is a classic example of epigenetics, which is involved in imprinting, development, X-inactivation, and diseases

A

DNA methylation

41
Q

Explain X inactivation

A

Female= 2X chromosome
only one can be active, the other becomes bar-body of heterochromatin–>silenced chromosomes<– which is mediated by noncoding RNA called XIST

42
Q

What are four mechanisms that produce epigenetic form of inheritance:

A

1- positive feedback
2- histone modification (production of heterochromatin)
3- DNA methylation —leads to heterochromatin
4- Protein aggregation state, conformational change to aggregate state

43
Q

The inactivation of the X chromosome in inherited, meaning…

A

the progeny cells of the early embryo will have the same X silenced –> clonal inheritance

44
Q

The “5th most common base” is _______.

When something gets methylated, it is maintained in progeny cells of replication.

A

5-methylcytosine

45
Q

Imprinting is differential expression of gene allele depending on _________

A

parental origin

46
Q

The purpose of imprinting is to control….

A

gene dosage= only one allele is expressed as the other allele is imprinted and silent

47
Q

Imprint is created in the _______ cells

A

parental germ cells

***paternal or maternal

48
Q

The mechanism of gene silencing for imprinting is….which leads to….

A

5-cytosine DNA methylation which leads to chromatin condenstation

49
Q

Read through mouse slides about imprinting….Male sticks with male, female with female?

A

ok.

50
Q

Silencing of tumor suppressor genes is common in cancer. Think about it.

A

Tumor suppressor gene methylated probably….heterochromatin…silenced….gene doesn’t express tumor suppressor protein.

51
Q

Transcription of genes can be increased by extracellular signals that induce signal transduction cascades. Examples:

A

hormones

growth factors

52
Q

Splicing can be regulated by ____, _____, _____ and _______

A

tissue
stage of development
age
disease

53
Q

Abnormal splicing of mRNA can give rise to proteins with oncogenic properities

A

bummer

54
Q

Gene expression can be regulated by nuclear transport. How is that?

A

mRNA is regulated by signal-mediated transport through the nuclear pore grated channel
-only fully processed mRNAS can be transported

55
Q

The ____ protein of HIV transports unspliced HIV mRNA from nucleus to cytoplasm, skipping regulation by nuclear transportation

A

Rev Protein

56
Q

The amount of mRNA in the cell is due to ____ and ____ of mRNA

A

the rates of synthesis and decay

57
Q

To control the amount of mRNA, the _______ can be tightly regulated. Increase ______, decrease mRNA, decrease expression.

A

rate of degradation for both blanks

58
Q

Two ways metabolism is regulated in cells:

A

1- amount of DNA

2- amount of protein translated

59
Q

If there’s a question about antisense mRNAS just pick answer with …..

A

circadian clock

60
Q

_______ and _____ are short RNAs that are used to silence viral gene expression

A

microRNA and short interfering RNA (siRNA)

61
Q

Low iron (Fe) requires that cell to shut off _____

A

Ferritin production

62
Q

Ferritin does what?

A

Ferritin binds and sequesters intracellular iron. Therefore in a low Fe state, ferritin would need to be shut off

63
Q

in state of low Fe, Ferritin is inhibited by..

A

IRE-BP protein that inhibits ferritin translation

64
Q

Transferrin receptors do what?

A

import iron across the plasma membrane of a cell

65
Q

Ferritin and Transferrin are both mediated by the same iron-responsive regulatory protein _____ , that dissociates from mRNA when it binds Fe.

A

Aconitase

***** but both ferritin and transferrin are regulated differently

66
Q

Binding of aconitase to the 5’ end of ferritin receptor mRNA blocks…..
So:
-Fe starvation
-Fe excess

A

blocks translation initiaiton

Fe starvation: not bound by Fe so translation blocked, therefore ferritin can’t sequester Fe
Fe excess: Fe binds aconitase, releasing it from ferritin hair loop, allowing for translation of ferritin gene–Fe going to be sequestered

67
Q

Binding of aconitase to the 3’ end of transferrin receptor mRNA….

  • Fe starvation
  • Fe excess
A

… stabilizes mRNA by preventing endonucleases from cleaving/degrading mRNA

  • Fe starvation: aconitase binds mRNA hairpin, allowing for Transferrin translation–> uptake of Fe into cell
  • Fe excess: aconitase bound by Fe, released from mRNA, leaving hairpin free for degredation –> transferrin receptor gene not translated
68
Q

glycosylation:

A

addition of a carbohydrate to protein

69
Q

phosphorylation:

A

kinases add proteins to make them active/inactive

dephosphorylation: removes p (phosphatases)

70
Q

Lipid modification:

A

addition of lipid to protein

71
Q

Cleavage of protein:

A

unmasks functional group of protein

72
Q

Circadian clock runs on 24 hour clock that….

A

produces Tim and Per proteins that repress own transcription in nucleus on 24 hours cycle. Light degrades Tim

73
Q

you can also degrade and allosterically regulated proteins

A

Last card.

Genetics (6 decks)

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