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2) Biochemistry II > Regulation of Gene Expression > Flashcards

Regulation of Gene Expression Flashcards

1
Q

Are all genes expressed at a given time?

A

No, only a fraction of the genome is active

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2
Q

What are the 7 levels that regulate gene expression?

A

1) Transcription initiation
2) Posttranscriptional processing
3) RNA stability
4) Translational regulation
5) Protein modification
6) Protein transport
7) Protein degradation

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3
Q

Where does RNA stability take place?

A
  • In the cytoplasm

- Once RNA is near the ribosomes, the translation takes place

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4
Q

Where does protein synthesis take place?

A

In the cytoplasm

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5
Q

What are the two classes of genes?

A
  • Housekeeping genes

- Regulated genes

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6
Q

What are housekeeping genes?

A
  • Genes that are expressed by most cells in the body
  • Constitutively expressed
  • HAVE to be regulated
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7
Q

What are regulated genes?

A

Genes that are regulated based on the cell’s environment/the cell’s life

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8
Q

Where does RNA polymerase bind to DNA?

A

At the promoter region

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9
Q

How is DNA represented?

A

From 5’ to 3’

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10
Q

What happens at the transcription start site?

A

Where mRNA synthesis beings (RNA start site)

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11
Q

What is left of the RNA start site?

A
  • Upstream

- Regulatory sequence, promoter sequence, binding elements

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12
Q

What is the function of the upstream sequences?

A

Sequences that regulate/promote gene expression

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13
Q

What do regulatory proteins bind to in order to regulate RNA polymerase operators?

A
  • Transcription factors, coregulators
  • Bind to promoter to regulate RNA polymerase operators
  • Operators: activators, repressors
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14
Q

What are negative transcription regulators?

A
  • Gene is not being expressed

- The promoter sequence is bound by a repressor

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15
Q

How can a negative transcription regulator be regulated?

A
  • Signal comes in an binds to the repressor and takes it away from the promoter region
  • Negative regulator is taken away
  • Gene expression is turned on (induced)
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16
Q

What are positive transcription regulators?

A
  • Gene is transcribed

- Promoter is activated

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17
Q

How can a positive transcription regulator be regulated?

A
  • Signal comes in; brings in a repressor that binds to the promoter; gene is turned off
  • ALSO, an activator can be brought in to an inactive gene, which will turn it on
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18
Q

Why can bacteria synthesize multiple mRNAs based on one promoter region?

A

There are common regulatory sequences (promoters in bacteria) for related genes

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19
Q

What is located downstream and upstream of a promoter in a typical procaryote?

A

Downstream of promoter: repressor

Upstream of promoter: activator

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20
Q

How does a protein bind in gene regulation?

A
  • Specific interaction promoted by HYDROGEN bonds between AA and specific nucleotides
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21
Q

What does thymine and adenine bind to?

A

Glutamine (H-bonds)

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22
Q

What does cytosine and guanine bind to?

A

Arginine (H-bonds)

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23
Q

What does arginine bind to?

A

Cytosine and guanine

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24
Q

What does glutamine bind to?

A

Thymine and adenine

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25
Q

Depending on the sequence of AA, a transcription factor can identify a specific sequence of ___________

A

base pairs

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26
Q

What are the most common AA involved and present in DNA binding sequences of transcription factors?

A

Asparagine, Glutamine, Glutamate, Lysine, Arginine

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27
Q

What are the features of the helix-turn-helix domain?

A

20 AA long with 2 a-segments (2 flaps)

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28
Q

How does the helix-turn-helix act as a recognition helix?

A
  • One a-segment acts

- Reads the sequence and interacts

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29
Q

What are the features of the zinc finger domain?

A
  • 30 AA long

- Loops are coordinated by Zn2+

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30
Q

How do proteins solve weak DNA binding?

A

By having several zinc finger domains between them

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31
Q

Which DNA binding motif can read RNA sequences and act as RNA-binding motif?

A

Zinc finger domain

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32
Q

Which DNA binding motif is found only in Eukaryotes?

A

Homeodomain

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33
Q

How long is the homeodomain?

A

60 AA

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34
Q

What does the homeodomain ressemble in terms of function?

A

Helix-turn-helix

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35
Q

In the leucine zipper, how often does leucine occur?

A

At every 7th position

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36
Q

How does part of the domain of the leucine zipper interact with DNA?

A

Through lysines and arginines

37
Q

Helix-loop-helix contains 1 ____ residue

A

leucine

38
Q

How does helix-loop-helix partially interact with DNA? What does the rest interact with?

A
  • Through lysines and arginines

- The rest interacts with other regulatory proteins that still regulate gene expression

39
Q

Do all transcriptional regulators need to bind to DNA? What could they bind to in order to still regulate gene expression?

A
  • No

- They can bind to helix-loop-helix (which is bound to DNA) and regulate gene expression

40
Q

How many transcription factors that have DNA binding domain do humans have? How many genes do they regulate?

A
  • 1557 transcription factors

- 20 000 genes

41
Q

How do transcription factors work together?

A
  • Multiple transcription factors that in different combinations can regulate different genes
  • Function by combination (mix-match)
42
Q

What do transcription factors also interact with?

A
  • TFs and coregulators
43
Q

What features of gene regulation are different in Eukaryotes?

A
  • Access to promoters is restricted by chromatin structure
  • Positive regulation is the most common
  • Regulatory proteins are multimeric
  • Transcription and translation are separated by the nucleus
44
Q

In Eukaryotes, what is the access to promoters restricted by?

A

By the chromatin structures

45
Q

What is chromatin?

A

DNA + Histones (proteins)

46
Q

What is the main function of histones?

A
  • Involved in tight packaging of a long length of DNA to form chromosomes
  • Involved in gene expression
47
Q

In Eukaryotes, what is the access to promoters regulated by?

A
  • By the structure of chromatin
  • Tight: less access
  • Loose: more access
48
Q

Which type of regulation is most common in Eukaryotes?

A

Positive regulation

49
Q

In Eukaryotes, regulatory proteins are ___________.

A

multimeric (not individual proteins; present in groups)

50
Q

In Eukaryotes, where do transcription and translation take place?

A
  • Separated by the nucleus
  • Transcription: nucleus
  • Translation: cytoplasm
51
Q

How many histones are there? What are they called?

A
  • 5 different histones

- H1, H2A, H2B, H3, H4

52
Q

What is the function of the histones?

A
  • H1 histones do NOT play a huge role in transcriptional regulation
  • The other 4 make a block around which DNA is wound
53
Q

What are the two types of chromatin?

A

Heterochromatin: when chromatin is tightly bound (no access to transcription factors)
Euchromatin: when chromatin is loosely bound (easy access)

54
Q

When a region of chromatin is transcriptionally active, it is deficient in ___.

A

H1

55
Q

When a region of chromatin is transcriptionally active, what variants may form?

A
  • Histone variants
  • H3.3 instead of H3
  • H2AZ instead of H2
  • Occurs when there is gene transcription occurring
56
Q

Which enzymes are important for histone modifications? What is their function?

A
  • SWI/SNF enzymes

- Modification of histones (replacement, removal, bringing in variants)

57
Q

When histones are modified, _____ is modified.

A

Chromatin

58
Q

Histones are covalently/non-covalently modified.

A

Covalently

59
Q

What are the possible modifications of histones that can cause positive or negative effects on gene expression through different combinations?

A

○ Methylation of lysine and arginine
○ Phosphorylation (serine and threonine)
○ Acetylation (lysine)
○ Ubiquitination and sumoylation (lysine)

60
Q

Which enzymes regulate histone acetylation?

A

HATs and HDACs

61
Q

How can DNA be modified by methylation? In which sequences?

A

Methylation of cytosine (nucleotide) in CpG sequences (whenever C is followed by a G)

62
Q

What happens when DNA is methylated?

A

It is associated with transcriptional inhibition (genes are turned off in that region)

63
Q

_______________ help in the assembly of the pre-initiation complex.

A

Regulatory proteins

64
Q

Which far away region can regulate gene expression?

A

UAS: upstream activator sequence

65
Q

What are HMG proteins? What is their function?

A
  • High mobility group

- Bend the DNA to form a loop so that far away sequences come closer to the promoter sequences

66
Q

Which proteins promote the binding of the polymerase complex?

A

UAS and HMG

67
Q

Which complex has to form before a gene is transcribed?

A

Pol II initiation complex

68
Q

What will allow the Pol II initiation complex to form?

A

Binding of various regulator and mediator proteins will allow this to happen

69
Q

What can inhibit the assembly of the pre-initiation complex?

A
  • Repressors

- Upstream inhibition sequence can repress the Pol II initiation complex and turn off gene expression

70
Q

Activators and regulators get associated with _________

A

mediators

71
Q

What do activation domains activate?

A

Mediators

72
Q

What are the three protein interaction domains that display characteristic features?

A
  • “ppp” proline-rich domains
  • “QQQ” glutamine-rich domains
  • ”—” acidic AA (Aspartate and Glutamate)
73
Q

Why can sequences be taken to see which genes are affected by nuclear receptors in bioinformatics?

A

Because specific nuclear receptors recognize specific DNA sequences

74
Q

What does the transcription activation domain interact with?

A
  • Transcription factors

- Proteins of initiation factors

75
Q

What does the hormone binding domain interact with?

A

Binds to hormones

76
Q

What kind of domains can be located in a transcription factor?

A
  • DNA binding protein
  • Transcription activation domain
  • Hormone binding domain
77
Q

Can procaryotes go through alternative splicing?

A
  • No

- Unique to Eukaryotes because genes are not a continuous sequence of DNA that is transcribed

78
Q

What are exons and introns?

A
  • Exons: genes that are present in blocks

- Introns: anything in between exons

79
Q

It is the sequence of ______ that results in the sequence of AA from protein synthesis.

A

exons

80
Q

What is splicing?

A
  • Introns are removed and exons are joined together

- If certain exons are spliced out and others are retined, they can leave completely different proteins

81
Q

What is alternative splicing?

A
  • One gene can be spliced to form different proteins that are synthesized
  • Achieved by a combination of different exons
82
Q

What is the reason behind the fact that humans can produce 200 000 proteins from 20 000 genes?

A

Alternative splicing

83
Q

How do micro-RNAs regulate mRNAs?

A
  • Prevent translation of mRNA by binding to it

- Cleaves it or blocks it

84
Q

What happens when micro-RNAs bind to mRNAs?

A
  • mRNA can be degraded

- mRNA’s translation can be inhibited

85
Q

What are the two classes of micro-RNAs?

A

1) SiRNA

2) stRNA

86
Q

How does SiRNA act?

A

Turns a double-stranded RNA into a single-stranded RNA

87
Q

How do nuclear receptors function?

A

Receptor is in the cytoplasm; gets dimerized; gets taken into the nucleus;
transcription

88
Q

Where can nuclear receptors be located? (2)

A
  • In the cytoplasm

- Directly bound to chromatin

2) Biochemistry II (23 decks)

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