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BIO107 - Cell and Molecular Biology > Transcription > Flashcards

Transcription Flashcards

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1
Q

DNA-dependent synthesis of RNA

A

transcription

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2
Q

template of transcription

A

DNA (anti-coding/antisense strand)

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3
Q

product of transcription

A
  1. messenger RNA (mRNA)
  2. ribosomal RNA (rRNA)
  3. transfer RNA (tRNA)
  4. miRNA, siRNA, and other regulatory RNAs
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4
Q
  • more on regulation
  • degrades mRNA
  • ribonuclease action
  • delay translation
A

microRNA (miRNA)

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5
Q

able to regulate the expression of genes, by a phenomenon known as RNAi (RNA interference)

A

siRNA (small interfering RNA)

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6
Q

DNA sequences that code for RNA

A

coding regions

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7
Q

do not code for an RNA

A

noncoding regions

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8
Q

3 general steps of transcription

A
  1. initiation
  2. elongation
  3. termination
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9
Q

major point of control of gene expression

A

initiation

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10
Q

main enzyme for transcription

A

RNA Polymerase

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11
Q

basic unit of a gene which extends from promoter to terminator

A

transcription unit

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12
Q

immediate product of RNA polymerase before any changes occur to the RNA

A

primary transcript/ pre mRNA/ heterogenous nuclear RNA (hnRNA)

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13
Q

regions close to promoter

A

proximal

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14
Q

regions farther away from promoter

A

distal

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15
Q

base pair of DNA which corresponds to the first RNA nucleotide added by RNA polymerase

A

start point

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16
Q

DNA sequence from startpoint to any nucleotides located towards the direction of transcription

A

downstream sequences (+)

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17
Q

DNA sequence from startpoint to any nucleotide(s) located opposite/away from the direction of transcription

A

upstream sequences (-)

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18
Q

nucleotide sequence which when aligned with each other have certain nucleotides that at certain positions occur at high frequency

A

consensus

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19
Q
  • DNA-directed
  • adds ribonucleotide units to the 3”OH end of the RNA chain
  • no proofreading ability
A

RNA Polymerase

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20
Q

RNA polymerase builds RNA in the __ direction

A

5’ - 3’

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21
Q

core enzyme of RNA polymerase

A

2αββ’

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22
Q

holoenzyme of RNA polymerase

A

(2αββ’)σ

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23
Q

subunit of RNA polymerase

A
  1. 2α
  2. β
  3. β’
  4. σ
  5. ω
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24
Q

aids in promoter recognition

A

2α

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25
Q

gene of 2α

A

rpoA

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26
Q

binds ribonucleotide substrate

A

β

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27
Q

gene of β

A

rpoC

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28
Q

binds DNA template

A

β’

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29
Q

gene of β’

A

rpoB

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30
Q

recognizes and binds tightly to promoter

A

σ

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31
Q

gene of σ

A

rpoD

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32
Q

facilitate assembly

A

ω

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33
Q
  • binds to β subunit of bacterial RNA pol
  • prevents initation of transcription
A

rifampicin

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34
Q

where does rifampicin bidn to

A

β subunit of bacterial RNA pol

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35
Q

what does rifampicin prevent

A

initation of transcription

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36
Q

types of eukaryotic RNA polymerases

A
  1. I
  2. II
  3. III
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37
Q

RNA pol I: location

A

nucleolus

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38
Q

RNA pol I: no. / cell

A

40, 000

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39
Q

RNA pol I: genes transcribed

A

rRNA

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40
Q

RNA pol I: % activity

A

50-70%

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41
Q

RNA pol II: location

A

nucleoplasm

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42
Q

RNA pol II: no. / cell

A

40,000

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43
Q

RNA pol II: genes transcribed

A

hnRNA (precursor of mRNA)

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44
Q

RNA pol II: % activity

A

20-40%

45
Q

RNA pol III: location

A

nucleoplasm

46
Q

RNA pol III: no. / cell

A

10, 000

47
Q

RNA pol III: genes transcribed

A
  • tRNA
  • 5s rRNA (small stable RNAs)
48
Q

RNA pol III: % activity

A

0.1

49
Q

Six sites of activity of RNA polymerase

A
  1. DNA coding strand
  2. DNA template strand
  3. RNA binding
  4. RNA-DNA hybrid
  5. Unwinding point
  6. Rewinding point
50
Q

antisense/ anticoding/ minus (-) strand

A

DNA template strand

51
Q
  • sense/coding/plus (+) strand
  • DNA strand complementary to the template
  • identical in sequence with RNA transcribed (U instead of T)
A

noncoding strand

52
Q

noncoding strand is a DNA strand __ to the template

A

complementary

53
Q
  • specific sequences that are required for initiation
  • promotes gene expression
A

promoter/s

54
Q

several proteins that interact with RNA pol

A

transcription factors (TFs)

55
Q

what is required in the initation of transcription

A
  1. promoter/s
  2. transcription factors
56
Q

promoters are binding site of what?

A

RNA polymerase

57
Q

Prokaryotic Promoters

A
  1. Pribnow box/ -10 sequence
  2. -35 sequence
58
Q

who discovered the Pribnow box

A

David Pribnow

59
Q

consensus sequence of the Pribnow box

A

TATAAT

60
Q

where is the -35 sequence found

A

upstream from Pribnow box

61
Q

consensus sequence of -35 sequence

A

TTGACA

62
Q
  • one for each type of RNA polymerase
  • because there is a specific RNA polymerase for each type of RNA
A

eukaryotic promoters

63
Q

promoter for RNA pol I

A

bipartite (core + UCE)

64
Q

promoter for RNA pol III

A

located within the gene it promotes

65
Q

Eukaryotic promoters: general structure

A
  1. TATA box or Goldberg-Hogness box
  2. CCAAT box
  3. GC box
66
Q

TATA box or Goldberg-Hogness box

A
  • TATAWAW
  • 19-27 bases before startpoint
67
Q

W in TATAWAW

A

Adenine or Thymine

68
Q

CCAAT box

A

~70 bases before startpoint

69
Q

GC box

A

~40 bases before startpoint

70
Q

Roles of Eukaryotic Promoters

A
  1. AT rich region makes initial unwiding easier
  2. orientation of RNA polymerase relative to startpoint
  3. binding of auxillary proteins to facilitate RNA polymerase binding
71
Q

auxillary protiens

A

transcription factors

72
Q

Two types of promoter

A
  1. strong promoter
  2. weak promoter
73
Q
  • same as consensus sequence
  • RNA pol binds strongly
  • initiation - more frequent
  • more transcripts made
A

strong promoter

74
Q
  • deviates significantly from consensus sequence
  • RNA pol binds weakly
  • initiation - less frequent
  • less RNA transcript made
A

weak promoter

75
Q

Two types of promoter mutation

A
  1. down mutation
  2. up mutation
76
Q

causes deviation from consensus sequence

A

down mutation

77
Q

example of down mutation

A

TATAAT -> TAGCAT

78
Q

causes a given sequence to become more/exactly similar to an established consensus sequence

A

up mutation

79
Q

example of up mutation

A

TATGTT (lac operon) -> TATATT

80
Q
  • protein factors
  • essential for transcription initiation of any eukaryotic gene
  • sufficient to direct basal/genneral level of transcription from many core promoters
  • position RNA polymerase at the promoter and send it on its way
A

general transcription factors

81
Q

where are general transcription factors essential for

A

transcription initiation

82
Q

general transcription factors are sufficient to direct what?

A

basal/general level of transcription

83
Q

where do general transcription factors position RNA polymerase

A

promoter

84
Q

where phosphorylation happens

A

alpha CTD

85
Q
  • proteins involved in inclusive interaction and selective activation of particular genes or groups of genes
  • different sets in different cell types -> different patters of gene expression
A

gene-specific transcription factors

86
Q

where are gene-specific transcription factors involved in

A

inclusive and selective activation of particular genes

87
Q

different sets in different cell types -> ?

A

different patters of gene expression

88
Q

example of gene-specific transcription factors

A
  1. steroid hormone receptor
  2. myogenic proteins
89
Q

activtes glucocorticoid response element

A

steroid hormone receptor

90
Q

activates genes for muscle differentiation

A

myogenic proteins

91
Q

what happens to the RNA polymerase during transcription initiation

A
  1. binds promoter
  2. melts DNA
  3. remains stationary
  4. incorporates the 1st ribonucleotide - retails all 3 phosphate groups
92
Q

amount of nucleotides in elongation of transcription

A

50 nucleotides / sec

93
Q

direction of transcription

A

5’-3’ wrt RNA product

94
Q

end which unwinds the DNA

A

leading end

95
Q

end which rejoin the DNA

A

tailing end

96
Q
  • intercalates DNA
  • prevents movement of RNA pol
  • inhibits elongation
A
  1. actinomycin D
  2. acridine
97
Q

what do the actinomycin D and acridine inhibit

A

elongation

98
Q

what does the acridine specifically inhibit

A

topoisomerase II

99
Q

signals RNA pol to stop

A

termination sequence

100
Q

what happens during termination

A
  1. RNA transcript released
  2. RNA polymerase detaches
101
Q

Two types of Termination

A
  1. Rho-independent
  2. Rho-dependent
102
Q
  • simple termination
  • no need for rho factor
  • ends in a stretch of AAAAAAA (DNA), UUUUUUU (RNA)
  • palindrome rich in GC
  • mRNA forms a hairpin
A

rho-independent termination

103
Q

what is formed in rho-independent termination

A

hairpin

104
Q

termination: __ rich in GC

A

palindrome

105
Q
  • requires rho factor
  • palindrome: less GC-rich
  • no UUUUU at end of RNA
A

rho-dependent termination

106
Q

where does the rho bind to transcript

A

rut site (rho utilization site)

107
Q

releases transcript during rho-dependent termination

A

rho helicase

108
Q

what happens after the rho catches up to the RNA polymerase that is paused at terminator

A

rho unwinds DNA-RNA hybrid

BIO107 - Cell and Molecular Biology (18 decks)

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