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INTRGEN > MOD 7: Regulation of Gene Expressions in Eukaryotes > Flashcards

MOD 7: Regulation of Gene Expressions in Eukaryotes Flashcards

1
Q

In bacteria, transcription and translation both take place in the __________

A

Cytoplasm

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2
Q

In bacteria, transcripts are readily translated into ___________

A

Proteins

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3
Q

In eukaryotes, this is associated with histones and other proteins to form the chromatin

A

DNA

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4
Q

In eukaryotes, transcription and translation are separated __________ and __________

A

Spatially and temporally

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5
Q

In eukaryotes, transcription occurs in the __________, while translation occurs in the __________

A

Nucleus; cytoplasm

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6
Q

DNA are bound to __________ and form __________.

A

Histones; nucleosomes

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7
Q

Where is the DNA located?

A

Inside the nucleus

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8
Q

This refers to the discrete domain occupied by each chromosome within the interphase nucleus

A

Chromosome territory

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9
Q

Where are transcriptionally active genes located?

A

Edges of chromosome territories

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10
Q

These affect the regulation of genes

A

Histone modifications and chromatin remodeling

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11
Q

What is the basic unit of chromatin?

A

Nucleosome

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12
Q

This is the DNA wrapped around histone proteins

A

Nucleosome

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13
Q

What are the four histone proteins?

A

H2A, H2B, H3, and H4

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14
Q

This refers to how tight DNA are wound around histones, allowing for efficient packaging of DNA.

A

Compaction

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15
Q

Tightness of DNA-histone compaction regulates __________ to genetic information for transcription

A

Access

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16
Q

These refer to the protruding ends of histone proteins

A

Histone tails

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17
Q

This is referred to as the inhibitory conformation that involves the tight association of DNA with histones and other chromatin-binding proteins.

A

Closed chromatin

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18
Q

TRUE OR FALSE: In closed chromatin, access to the DNA by proteins is inhibited

A

TRUE

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19
Q

What are the four histone modifications?

A
  1. Methylation
  2. Acetylation
  3. Ubiquitination
  4. Phosphorylation
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20
Q

TRUE OR FALSE: In DNA methylation, methylation happens on the DNA itself.

A

TRUE

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21
Q

Where does DNA methylation in eukaryotes usually occur?

A

Position 5 of cystosine (5-methylcytosine)

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22
Q

This refers to the area in DNA that is rich in DNA methylations

A

CpG islands

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23
Q

TRUE OR FALSE: DNA methylation activates gene expression.

A

FALSE; DNA methylation represses gene expression sometimes

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24
Q

What do you call the enzyme involved in DNA methylation?

A

DNA methyltransferase

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25
Q

This is referred to as changes in terms of expression of traits; it is heritable and is not related to DNA sequences.

A

Epigenetics

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26
Q

These elements are required for the accurate and regulated transcription of genes transcribed by RNAP II

A

Cis-acting elements

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27
Q

Where are cis-acting DNA elements located?

A

On the same chromosome as the gene that they regulate

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28
Q

These factors can influence the expression of a gene on any chromosome

A

Trans-acting factors

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29
Q

This type of eukaryotic promoter refers to the minimum part of the promoter needed for accurate initiation of transcription

A

Core promoters

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30
Q

This type of eukaryotic promoter has the TATA box

A

Core promoters

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31
Q

This type of eukaryotic promoter is generally located up to 250 nucleotides upstream of the transcription start site and contain binding sites for sequence-specific DNA-binding proteins that modulate the efficiency of transcription

A

Proximal promoters

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32
Q

These promoters affect the regulation of gene factors

A

Core promoters

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33
Q

This type of core promoter has transcription initiation at a single specific start site; One promoter transcribing for one gene

34
Q

This type of core promoter has direct initiation from a number of weak transcription start sites located over a 50- to 100- nucleotide region

35
Q

This type of core promoter may give multiple transcripts for different proteins and variation

36
Q

These are regions in the DNA that can happen either upstream or downstream

A

Enhancers and silencers

37
Q

Where are enhancers and silencers located?

A

Near the promoter, forming association with the promoter

38
Q

This promotes the expression of DNA by recruiting associated transcription factors on promoter region

39
Q

This allows proteins to be formed to repress expression on the gene

40
Q

Eukaryotic transcription initiation is regulated by __________ that bind to __________

A

Transcription factors; cis-acting sites

41
Q

Activator proteins bind to pieces of DNA called __________ that cause their DNA to bend, bringing them near a gene promoter

42
Q

Other ____________ join the activator proteins, forming a protein complex which binds to the gene promter

A

Transcription factor proteins

43
Q

The complex (transcription factor proteins + activator proteins) make it easier for the __________ to attach to the promoter and start transcribing a gene

A

RNA polymerase

44
Q

A/An __________ can stop the enhancers from binding to the promoter, if a protein called __________ binds to it

A

Insulator; CTCF

45
Q

This refers to the addition of a methyl group to the C nucleotides, allowing enhancers to bind to the promoter

A

Methylation

46
Q

These refer to the binding sites along the promoter region

A

Cis-acting elemtns

47
Q

This refers to the core promoter region

48
Q

This gene has a lot of cis-acting regulatory sites and is dependent of presence of transcription factors

A

Metallothionein 2A gene

49
Q

These interact with general transcription factors and affect chromatin structure

A

Activators and repressors

50
Q

The mechanism of transcription activation and repression forms what?

A

The RNA polymerase II transcription initiation complex

51
Q

TRUE OR FALSE: Regulation of alternative splicing determines which RNA splices forms of a gene are transcribed

A

FALSE; translated

52
Q

TRUE OR FALSE: Gene expression is regulated by DNA stability and degradation

A

FALSE; It is regulated by mRNA stability and degradation

53
Q

What happens to mRNAs and gene expression when mRNA stability and decay are modulated?

A

Aberrant mRNAs are eliminated and gene expression is regulated

54
Q

An mRNA is capped at the __________ — __________

A

5’ end — 5’cap

55
Q

The RNA is susceptible to degradation or decay by __________

A

Exoribonucleases

56
Q

This enzyme removes poly-A

A

Deadenylase

57
Q

In what direction does the exosome decay?

A

3’ —> 5’

58
Q

TRUE OR FALSE: The exosome can only act if deadenylase has already removed the poly-A tail

59
Q

What does the decapping enzyme remove?

A

7-methylguanosine (m7G)

60
Q

In what direction does the decapping enzyme decay?

A

5’ —> 3’

61
Q

What protein helps the decapping enzyme?

A

XRN1 protein

62
Q

TRUE OR FALSE: The decapping enzyme can only act if the m7G cap is removed

63
Q

TRUE OR FALSE:

The exosome enzyme can only act if deadenylase has removed the m7G cap, while the decapping enzyme can only act if the poly-A-tail is removed.

A

FALSE;

Exosome = poly-A tail
Decapping = m7G cap

64
Q

What are the two main subtypes of sncRNAs?

A
  1. Small interfering RNAs (siRNAs)
  2. microRNAs (miRNAs)
65
Q

This type of sncRNA originates from long, double-stranded RNA and can be found external to the nucleus

A

Small interfering RNAs (siRNAs)

66
Q

This type of sncRNA is derived from the DNA of the cell

67
Q

This protein processes pri-miRNA and exports to the cytoplasm

68
Q

TRUE OR FALSE: Because siRNAs and miRNAs arise from different sources, their mechanisms of actions are also very different

A

FALSE; Their mechanisms of action are similar

69
Q

What unwinds the siRNAs into single-stranded siRNAs and cleaves mRNAs complementary to the siRNA

A

RNA-induced Silencing Complex (RISC)

70
Q

If the miRNA and mRNA are __________, the mRNA is destroyed.

If there is a __________. translation is inhibited.

A

Perfectly complementary; partial match

71
Q

If the miRNA and mRNA are __________, the mRNA is destroyed.

If there is a __________. translation is inhibited.

A

Perfectly complementary; partial match

72
Q

This is involved in RNA processing

A

Argonaute (AGO)

73
Q

TRUE OR FALSE: IncRNAs do not have start and stop codons, indicating that they do not encode protein

74
Q

Match the letter to the descriptions below:

A. Intergenic
B. Intronic
C. Antisense
D. Bidirectional

  1. Opposite complementary strand
  2. Inside the two exons of the same genes
  3. Shares a promoter region
  4. In between two genes
A

C, B, D, A

75
Q

Noncoding RNAs can mediate sequence-specific degradation or translational inhibition of target mRNAs in a process called __________

A

RNA interference

76
Q

TRUE OR FALSE: Long, noncoding RNA have only a few specific functions in the cell

A

FALSE; They have a variety of functions

77
Q

TRUE OR FALSE: Long, noncoding RNA have only a few specific functions in the cell

A

FALSE; They have a variety of functions

78
Q

Phosphorylation usually induces __________ of protein

A

Conformational changes

79
Q

Enzymes may be turned on or off by __________ where conformational changes alter substrate binding

A

Phosphorylation

80
Q

TRUE OR FALSE: The shorter the length of ubiquitin, the more proteasome recognizes it for degradation

A

FALSE; When ubiquitin gets longer, proteasome recognizes it for degradation

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