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bi304 > Regulation of Gene Expression > Flashcards

Regulation of Gene Expression Flashcards

1
Q

operons

A

clusters of metabolic genes with related functions

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2
Q

expression of the gene clusters is controlled by…

A

an operator region embedded into the promoter

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3
Q

operons are transcribed as

A

polycistronic mrna molecule

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4
Q

enhancing transcription

A

activatory factors bind to the promoter

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5
Q

inhibiting transcription

A

repressor proteins bind to the operator blocking access to rna polymerase

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6
Q

lac operon

A

regulates lactose metabolism

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7
Q

expression of lac operon genes are controlled by…

A

glucose

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8
Q

what happens when glucose is present

A

repression of lac operon and transcription is off

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9
Q

what happens when glucose is absent

A

cAMP levels rise binds to CAP and binds to lac promoter, expression of lac operon and transcription on

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10
Q

operator

A

negative regulatory site bound to repressor protein
blocks rna polymerase

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11
Q

CAP binding site

A

positive regulatory site bound to CAP (catabolite activator protein)

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12
Q

CAP function

A

binds to rna polymerase enabling transcription

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13
Q

what happens when lactose is present

A

inactivates lac repressor

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14
Q

what happens when lactose is absent

A

lac repressor binds to operator that overlaps with promotee inhibiting rna polymerase transcribing lac operon

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15
Q

tryptophan operon

A

encodes proteins involve tryptophan synthesis

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16
Q

trp operon is regulated by…

A

trp repressor
it is a sensor for the tryptophan levels

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17
Q

low tryptophan levels

A

expression of trp opreron

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18
Q

high tryptophan levels

A

repression of trp operon

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19
Q

rna polymerase I

A

large rRNA

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20
Q

rna polymerase II

A

mrna and mirna

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21
Q

rna polymerase III

A

small rRNA and tRNA

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22
Q

how do rna polymerase (eukaryotes) bind to promoter

A

basal transcription factors

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23
Q

common core promoter elements

A

BRE TATA INR DPE

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24
Q

core promoter function

A

recruits general transcription factors and position rna polymerase II complex at transcription start site

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25
Q

TFIID

A

recognises TATA and regulates DNA-binding to TATA box promoter

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26
Q

TFIIB

A

positions rna polyII at transcription start site

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27
Q

TFIIE

A

recruits and regulates TFIIH

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28
Q

TFIIH

A

unwinds double stranded dna at transcription start point and phosphorylates C-terminal domain of rna poly.II and releases it from promoter

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29
Q

inducible transcription factors

A

recognises specific sequences within wider promoter and enhancer regions of genes

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30
Q

how are inducible transcription factors usually activated

A

from external stimuli i.e. changes in environment

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31
Q

different ways inducible tf are activated in cell

A

protein synthesis
ligand binding
covalent modification (phosphorylation, ubiquitination)
addition of second subunit (dimersation)

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32
Q

nf-kb activation

A

external stimulus activates kinase complex
phosphorylates ikb protein
k-48 linked ubiquination and proteasomal degradation
activates nf-kb and trnaslocates to nucleus

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33
Q

inducible tf binds to..

A

specific short dna sequences in promoter regions of genes

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34
Q

inducible tf contans an activation domain that

A

regulates activation of transcription when bound to dna

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35
Q

inducible tf mediates transactivation wen

A

either ineracting with rna poly.II complex or by recruiting chromatin remodelling enzymes

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36
Q

when inducible tf are activated they….

A

translocate to the nucleus

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37
Q

the edge of each base pair in dna contains..

A

a distinctive pattern of h-bond donors acceptors and methyl groups

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38
Q

hwo tf binds to dna

A

amino acid side chains interact with specific dna bases
dna-binding proteins bind with dna through h-bonding ionic bonding and hydrophobic interactions

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39
Q

dna-binding proteins

A

helix-turn-helix
zinc fingers
leucine zippers

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40
Q

helix-turn-helix

A

they bind forming dimers and bind to major groove of dna

41
Q

zinc fingers

A

bind as dimers and binds to major groove of dna

42
Q

leucine zippers

A

two helices held together by hydrophobic interactions
sit on dna like a clamp

43
Q

b-sheet structural motifs

A

double stranded b-sheet with amino acid side chains reads info on the surface of the major groove of dna

44
Q

chromatin function

A

condenses long dna into more compact structures

45
Q

chromatin

A

complex of dna with histones

46
Q

chromatin condensing

A

less accesible for transcription factors

47
Q

chromatin loosening

A

transcription factors more accesible and enables transcription

48
Q

euchromatin

A

composed of 30nm fibres and looped domains

49
Q

euchromatin are associated with…

A

actively expressed areas of the genome

50
Q

heterochromatin

A

highly condensed compact dna

51
Q

heterochromatin are associated with….

A

non-expressed areas of the genome

52
Q

tyoes of heterochromatin

A

constitutive and faculative

53
Q

constitutive heterochromatin

A

highly concentrated in specific regions (telomeres and centromeres)
has no coding region

54
Q

faculative heterochromatin

A

can covert between heterochromatin and euchromatin

55
Q

drosphila- expression of red eye colour

A

heterochromatin is blocked from entering the euchromatin regions by a barrier made out of dna sequences

56
Q

drosphika - expression of white-speckled eye colour

A

barrier sequenced reomved and heterochromatin spreads to euchromatin region

57
Q

during interphase chromatin is

A

is in its loosely state

58
Q

during prophase

A

chromatin condenses and chromosomes become more visible

59
Q

acetylation and methylation occur on

A

lysine residues

60
Q

phosphorylation occurs on

A

serine residues

61
Q

acetylation of histones is often associated with…

A

gene expressing

62
Q

acetylation function

A

removes the positive charge on the lysine residues decreasing the affinity of the dna-histone complex

63
Q

histone acetylation is carried out by….. and removed by…..

A

histone acetyltransferases
histone deacetylases

64
Q

histone acetylation creates…..

A

binding sites for certain chromatin remodelling enzymes

65
Q

methylation of histones is often associated with….

A

gene silencing

66
Q

histone methylation is carried out by… and removed by….

A

histone methyltransferases
histone demethylases

67
Q

why acetylation and methylation cannot occur at the same time

A

they are both competing reactions and cant be on the same lysine at the same time
methylation - repressing
acetylation - expressing

68
Q

histone code hypothesis

A

the transcription of genetic info encoded in dna is regulated by chemical modifications

69
Q

histone code readers determine either…

A

chemical modification or specificity

70
Q

histone code readers funcrion

A

mediate the downstram consequences of histone modifications or recruit other effector proteins

71
Q

effector proteins

A

enzymes that can alter chromatin structure or nucleosome position in an atp dependent manner

72
Q

bromodomains

A

recognises aceylated lysine

73
Q

chromodomain

A

recognises methylated lysines

74
Q

dna methylation in eukaryotes…

A

regulates gene expression in 5’ position of cytosine

75
Q

cpG islands

A

GC-rich regions
promoter regions of genome

76
Q

cpg methylation

A

results in gene repressing by blocking promoters

77
Q

dna methyltransferases

A

transfers a methyl group from s-adenyl methionine to the 5th carbon of a cytosine residue to form 5mC

78
Q

state of dna in globin gene promoter in embryo

A

unmethylated

79
Q

state of dna in globin gene promoter in embryo

A

unmethylated

80
Q

state of dna in globin gene promoter in fetus

A

activates fetal globin genes -> methylated dna

81
Q

x-inactivation/lyonization

A

since female xx chromosomes carries twice the amount of x-linked genes than males one or two are randomly inactivated early in embryonic development

82
Q

what happens to the inactivated x chromosome

A

it condenses into a compact structure called a barr body and remains inactive throughout the lifetime of the cell

83
Q

x-inactivation is commonly….

A

randomly distributed unevenly

84
Q

epigenetics

A

the study of how cells control gene activity without changing the dna sequence

85
Q

epigenetic changes are…

A

modifications of dna that regulate gene turning on or off

86
Q

epigenetic changes results in….

A

inheritable phenotypes that are not due to a change or alteration to the dna sequence

87
Q

epigenetic mechanisms constrain expression by….

A

adapting regions that either associates with gene silencing or gene activity

88
Q

after dna replication chromatin are

A

reinstated by reader-writet complexes

89
Q

the expression of imprinted genes … between the maternal and paternal allele

A

differs

90
Q

genomic imprinintg

A

ppl inheriting two copies of their genes from mother and father and only one is acitve

91
Q

luciferase reporter assay

A

promoter region of interest clones into plasmid vector that contains luciferase gene
can quantift promoter activity by measuring luciferase activity

92
Q

chromatin immunprecipitation

A

determines tf binding to promoter, rna poly.II binding to promotwrs and presence of histone modifications
cross-link bound prtoeins to dna
use antibody to immunoprecipitate protein of interest
remove and detect bound dna with pcr

93
Q

mrna processing

A

5’ cap added to start and 3’ poly-A-yail added to the end
splicing - introns removed and exon ligated together

94
Q

5’ cap

A

a modified G nucleotide that protects transcript from being broken down

95
Q

poly-A-tail

A

allows mature mrna to be exported from the nucleus and translated into protein by ribosomes in cytoplasm

96
Q

5’ utrs

A

involved in translation

97
Q

3’ utrs

A

responsible for the stability of mrna

98
Q

splicing

A

the removal of introns and ligation of exons by splicesomes
catalysed by snRNPs

bi304 (2 decks)

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