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Genetics - BIO 2306 > Ch 17 Control of Gene Expression in Eukaryotes > Flashcards

Ch 17 Control of Gene Expression in Eukaryotes Flashcards

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1
Q

explain the differences between gene expression regulation in prokaryotes and eukaryotes

A

bacterial and archaeal genes organized into operons, and genes are transcribed together into a single mRNA molecule
eukaryotic genes have their own promoters and transcribed separately ; chromatin structure affects gene expression; transcription takes place in nucleus, whereas translation takes place in the cytoplasm

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2
Q

why is modification of chromatin structure important for gene expression?

A

DNA is tightly coiled to create chromatin, which is wrapped tightly around histones. transcription factors and regulatory proteins cannot access the DNA unless modifications to the chromatin are made to make the DNA more accessible

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3
Q

regions around the genes that become highly sensitive to DNase I, and develop upstream of transcription start site

A

DNase I hypersensitive sites

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4
Q

explain the significance of DNase I hypersensitive sites?

A

when genes become transcriptionally active, these sites become sensitive to DNase I, which digests the DNA. the chromatin structure relaxes, allowing regulatory proteins to access the binding sites. they support the fact that chromatin must have a more open configuration for transcription

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5
Q

what are three processes that affect gene regulation by altering chromatin structure?

A
  1. chromatin remodeling
  2. modification of histone proteins
  3. DNA methylation
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6
Q

protein complexes that bind directly to particular DNA sites and reposition nucleosomes to allow TFs and RNA polymerase to bind and initiate transcription
alters chromatin structure without altering the chemical structure of histones directly

A

chromatin-remodeling complexes

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7
Q

describe the two mechanisms by which chromatin-remodeling complexes reposition nucleosomes

A

CR complexes cause nucleosome to slide along DNA
CR complexes cause conformational change to DNA or nucleosomes or both
-both allow segment of DNA to be exposed and more accessible to TFs and RNA polymerase for transcription

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8
Q

what are the two domains of a histone and what do they associate with?

A

globular domain - associates with other histones and the DNA
positively charged tail - interacts with negatively charged phosphate groups on DNA

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9
Q

modifications of histone proteins that encode information affecting how genes are expressed

A

histone code

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10
Q

describe how histone proteins are modified

A

addition/removal of phosphate groups, methyl groups, or acetyl groups to phosphate tails
ubiquitination - ubiquitin added/removed from histones

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11
Q

describe how methylation of histones affect gene expression

A

addition of methyl groups to tails of histones may activate or repress transcription, depending on which histone and amino acid is methylated.

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12
Q

enzymes that add methyl groups to specific amino acids of histones

A

histone methyltransferases

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13
Q

what amino acids are usually methylated in histones?

A

lysine or arginine

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14
Q

enzymes that remove methyl groups from histones

A

histone demethylases

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15
Q

describe how acetylation of histones affect gene expression

A

addition of acetyl groups to histones usually stimulates transcription. acetyl groups destabilize the chromatin structure, allowing transcription to take place

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16
Q

enzymes that add acetyl groups to histone proteins, allowing transcription

A

acetyltransferases

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17
Q

enzymes that remove acetyl groups from histones, thus repressing transcription

A

deacetylases

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18
Q

describe DNA methylation and how it affects gene expression

A

methylation of cytosine bases to yield 5-methylcytosine, which represses transcription

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19
Q

where is DNA methylation most common

A

it is most common on cytosine bases adjacent to guanine nucleotides (CpG)

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20
Q

DNA regions with many CpG sequences

A

CpG Islands

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21
Q

describe the effect of CpG Islands being commonly around transcription start sites

A

when CpG sites are methylated, genes are not transcribed and transcription is repressed
when CpG sites are unmethylated, transcription is initiated

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22
Q

explain the association between DNA methylation and histone acetylation

A

DNA methylation attracts deacetylases, that remove acetyl groups from histones; both play role in repressing transcription
Demethylation allows acetyltransferases to add acetyl groups, thus stimulating transcription

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23
Q

describe the function of transcription factors

A

TFs bind to DNA and regulate transcription
can recruit cofactors that either stimulate or repress transcription

24
Q

other proteins stimulate or repress transcription when recruited by transcription factors

A

cofactors

25
Q

transcription factors that are part of the basal transcription apparatus and bind to the core promoter

A

general transcription factors

26
Q

what is required for initiation of transcription

A

general transcription factors that are part of the basal transcription apparatus

27
Q

transcription factors that bind to regulatory promoter and enhancers

A

transcription activator proteins (TAPs)

28
Q

transcription factors that stimulate transcription

A

activators

29
Q

transcription factors that inhibit transcription

A

repressors

30
Q

proteins that help stimulate or stabilize the basal transcription apparatus at the core promoter

A

coactivator proteins

31
Q

complex of proteins that interact with TFs in regulatory promoter (or enhancer) and RNA polymerase, affecting the rate at which transcription is initiated

A

mediator

32
Q

regulatory elements that affect the transcription of distant genes (usually stimulate transcription)

A

enhancers

33
Q

how can enhancers affect initiation of transcription at a promoter that is far away?

A

binding of transcription factors to enhancer causes the DNA to loop out, bringing the enhancer closer to the promoter

34
Q

what are super-enhancers and what is the purpose of them?

A

enhancers clustered together, which are then occupied by a higher number of transcription factors, and stimulate higher levels of transcription

35
Q

sequences that have an inhibitory effect on transcription of distant genes

A

silencers

36
Q

DNA sequences that block the effects of enhancers, as long as they lie between an enhancer and a promoter

A

insulators

37
Q

explain how genes can coordinately be expressed by responding to the same stimulus

A

these genes share response elements, which can all be activated by the same stimulus and give the same response

38
Q

short stretches of DNA that usually contain the same consensus sequences at varying distances from the genes being regulated

A

response elements

39
Q

what is the purpose of pre-mRNA splicing?

A

it allows pre-mRNA to be spliced in multiple ways, to yield different proteins

40
Q

what is mRNA splicing dependent on?

A

presence of consensus sequences at 5’ splice site, 3’ splice site, and branch point, which determine the locations of introns and exons

41
Q

what are the purpose of exonic/intronic splicing enhancers and splicing silencers

A

they help promote or repress the use of particular splice sites during the process of RNA splicing, resulting in alternative splicing outcomes

42
Q

SF2 protein (SR proteins)

A

serine- and arginine- rich proteins that are involved in splice-site selection

43
Q

explain how SF2 proteins interact with multiple 5’ splice sites

A

usage of two different 5’ splice sites produce mRNA with different lengths, and different proteins
SF2 proteins enhance the use of one of the other splice site

44
Q

purpose of snRNPs (small nuclear ribonucleoproteins)

A

snRNPs participate in pre-mRNA splicing by recognizing the critical sequence elements present in the introns, thereby forming active spliceosomes, and splice the pre-mRNA

45
Q

the amount of available mRNA depends on what two things?

A

the rate of mRNA synthesis and the rate of mRNA degradation

46
Q

what are more stable, eukaryotic mRNAs or bacterial mRNAs

A

eukaryotic mRNAs are more stable, where bacterial mRNAs are degraded quickly

47
Q

cellular RNA is degraded by what enzymes?

A

ribonucleases

48
Q

describe mRNA degradation

A

shortening of 3’ poly(A) tail allows for 5’ cap to be removed, then ribonucleases degrade the mRNA by removing nucleotides from the 5’ end.

49
Q

what are the role of Poly(A)-binding proteins (PABPs)

A

they bind to the poly(A) tail and enhance its stability to the 5’ end and protection

50
Q

how do P bodies help control gene expression through mRNA degradation?

A

A lot of RNA degradation takes place in P bodies, where they temporarily store mRNA molecules
P bodies regulate which RNA molecules are degraded and which are saved for later release

51
Q

describe RNA silencing (RNA interference)

A

miRNAs or siRNAs combine with proteins to form RISC, which pairs with complementary base sequences in specific mRNA molecules, silencing it

52
Q

what are the four mechanisms siRNAs and miRNAs regulate gene expression through?

A
  1. cleavage of mRNA
  2. inhibition of translation
  3. transcriptional silencing
  4. degradation of mRNA
53
Q

describe how cleavage of mRNA regulates gene expression

A

RISCS with siRNA pair with an mRNA molecule and mRNA is cleaved by Slicer enzyme. mRNA is further degraded, preventing its translation into proteins

54
Q

describe how inhibition of translation regulates gene expression

A

miRNAs inhibit translation of complementary mRNAs through stalling the ribosome or prematurely terminating transcription

55
Q

describe how transcriptional silencing regulates gene expression

A

siRNAs combine with proteins to form RITS, which binds to complementary sequence in mRNA, and represses transcription
RITS attracts enzymes that methylate the histone tails. this alters the chromatin structure, in which DNA binds more tightly and restricts protein access

56
Q

describe how slicer-independent degradation of mRNA regulates gene expression

A

miRNAs bind to AU-rich elements and trigger RNA degradation

57
Q

how can eukaryotic proteins be modified after translation (posttranslational modifications)

A

-selective cleavage and trimming of amino acids
-acetylation
-adding phosphate groups, carboxyl groups, methyl groups, carbohydates…

Genetics - BIO 2306 (20 decks)

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