Transcription Flashcards
(108 cards)
1
Q
DNA-dependent synthesis of RNA
A
transcription
2
Q
template of transcription
A
DNA (anti-coding/antisense strand)
3
Q
product of transcription
A
- messenger RNA (mRNA)
- ribosomal RNA (rRNA)
- transfer RNA (tRNA)
- miRNA, siRNA, and other regulatory RNAs
4
Q
- more on regulation
- degrades mRNA
- ribonuclease action
- delay translation
A
microRNA (miRNA)
5
Q
able to regulate the expression of genes, by a phenomenon known as RNAi (RNA interference)
A
siRNA (small interfering RNA)
6
Q
DNA sequences that code for RNA
A
coding regions
7
Q
do not code for an RNA
A
noncoding regions
8
Q
3 general steps of transcription
A
- initiation
- elongation
- termination
9
Q
major point of control of gene expression
A
initiation
10
Q
main enzyme for transcription
A
RNA Polymerase
11
Q
basic unit of a gene which extends from promoter to terminator
A
transcription unit
12
Q
immediate product of RNA polymerase before any changes occur to the RNA
A
primary transcript/ pre mRNA/ heterogenous nuclear RNA (hnRNA)
13
Q
regions close to promoter
A
proximal
14
Q
regions farther away from promoter
A
distal
15
Q
base pair of DNA which corresponds to the first RNA nucleotide added by RNA polymerase
A
start point
16
Q
DNA sequence from startpoint to any nucleotides located towards the direction of transcription
A
downstream sequences (+)
17
Q
DNA sequence from startpoint to any nucleotide(s) located opposite/away from the direction of transcription
A
upstream sequences (-)
18
Q
nucleotide sequence which when aligned with each other have certain nucleotides that at certain positions occur at high frequency
A
consensus
19
Q
- DNA-directed
- adds ribonucleotide units to the 3”OH end of the RNA chain
- no proofreading ability
A
RNA Polymerase
20
Q
RNA polymerase builds RNA in the __ direction
A
5’ - 3’
21
Q
core enzyme of RNA polymerase
A
2αββ’
22
Q
holoenzyme of RNA polymerase
A
(2αββ’)σ
23
Q
subunit of RNA polymerase
A
- 2α
- β
- β’
- σ
- ω
24
Q
aids in promoter recognition
A
2α
25
gene of 2α
rpoA
26
binds ribonucleotide substrate
β
27
gene of β
rpoC
28
binds DNA template
β'
29
gene of β'
rpoB
30
recognizes and binds tightly to promoter
σ
31
gene of σ
rpoD
32
facilitate assembly
ω
33
- binds to β subunit of bacterial RNA pol
- prevents initation of transcription
rifampicin
34
where does rifampicin bidn to
β subunit of bacterial RNA pol
35
what does rifampicin prevent
initation of transcription
36
types of eukaryotic RNA polymerases
1. I
2. II
3. III
37
RNA pol I: location
nucleolus
38
RNA pol I: no. / cell
40, 000
39
RNA pol I: genes transcribed
rRNA
40
RNA pol I: % activity
50-70%
41
RNA pol II: location
nucleoplasm
42
RNA pol II: no. / cell
40,000
43
RNA pol II: genes transcribed
hnRNA (precursor of mRNA)
44
RNA pol II: % activity
20-40%
45
RNA pol III: location
nucleoplasm
46
RNA pol III: no. / cell
10, 000
47
RNA pol III: genes transcribed
- tRNA
- 5s rRNA (small stable RNAs)
48
RNA pol III: % activity
0.1
49
Six sites of activity of RNA polymerase
1. DNA coding strand
2. DNA template strand
3. RNA binding
4. RNA-DNA hybrid
5. Unwinding point
6. Rewinding point
50
antisense/ anticoding/ minus (-) strand
DNA template strand
51
- sense/coding/plus (+) strand
- DNA strand complementary to the template
- identical in sequence with RNA transcribed (U instead of T)
noncoding strand
52
noncoding strand is a DNA strand __ to the template
complementary
53
- specific sequences that are required for initiation
- promotes gene expression
promoter/s
54
several proteins that interact with RNA pol
transcription factors (TFs)
55
what is required in the initation of transcription
1. promoter/s
2. transcription factors
56
promoters are binding site of what?
RNA polymerase
57
Prokaryotic Promoters
1. Pribnow box/ -10 sequence
2. -35 sequence
58
who discovered the Pribnow box
David Pribnow
59
consensus sequence of the Pribnow box
TATAAT
60
where is the -35 sequence found
upstream from Pribnow box
61
consensus sequence of -35 sequence
TTGACA
62
- one for each type of RNA polymerase
- because there is a specific RNA polymerase for each type of RNA
eukaryotic promoters
63
promoter for RNA pol I
bipartite (core + UCE)
64
promoter for RNA pol III
located within the gene it promotes
65
Eukaryotic promoters: general structure
1. TATA box or Goldberg-Hogness box
2. CCAAT box
3. GC box
66
TATA box or Goldberg-Hogness box
- TATAWAW
- 19-27 bases before startpoint
67
W in TATAWAW
Adenine or Thymine
68
CCAAT box
~70 bases before startpoint
69
GC box
~40 bases before startpoint
70
Roles of Eukaryotic Promoters
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
auxillary protiens
transcription factors
72
Two types of promoter
1. strong promoter
2. weak promoter
73
- same as consensus sequence
- RNA pol binds strongly
- initiation - more frequent
- more transcripts made
strong promoter
74
- deviates significantly from consensus sequence
- RNA pol binds weakly
- initiation - less frequent
- less RNA transcript made
weak promoter
75
Two types of promoter mutation
1. down mutation
2. up mutation
76
causes deviation from consensus sequence
down mutation
77
example of down mutation
TATAAT -> TAGCAT
78
causes a given sequence to become more/exactly similar to an established consensus sequence
up mutation
79
example of up mutation
TATGTT (lac operon) -> TATATT
80
- 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
general transcription factors
81
where are general transcription factors essential for
transcription initiation
82
general transcription factors are sufficient to direct what?
basal/general level of transcription
83
where do general transcription factors position RNA polymerase
promoter
84
where phosphorylation happens
alpha CTD
85
- 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
gene-specific transcription factors
86
where are gene-specific transcription factors involved in
inclusive and selective activation of particular genes
87
different sets in different cell types -> ?
different patters of gene expression
88
example of gene-specific transcription factors
1. steroid hormone receptor
2. myogenic proteins
89
activtes glucocorticoid response element
steroid hormone receptor
90
activates genes for muscle differentiation
myogenic proteins
91
what happens to the RNA polymerase during transcription initiation
1. binds promoter
2. melts DNA
3. remains stationary
4. incorporates the 1st ribonucleotide - retails all 3 phosphate groups
92
amount of nucleotides in elongation of transcription
50 nucleotides / sec
93
direction of transcription
5'-3' wrt RNA product
94
end which unwinds the DNA
leading end
95
end which rejoin the DNA
tailing end
96
- intercalates DNA
- prevents movement of RNA pol
- inhibits elongation
1. actinomycin D
2. acridine
97
what do the actinomycin D and acridine inhibit
elongation
98
what does the acridine specifically inhibit
topoisomerase II
99
signals RNA pol to stop
termination sequence
100
what happens during termination
1. RNA transcript released
2. RNA polymerase detaches
101
Two types of Termination
1. Rho-independent
2. Rho-dependent
102
- simple termination
- no need for rho factor
- ends in a stretch of AAAAAAA (DNA), UUUUUUU (RNA)
- palindrome rich in GC
- mRNA forms a hairpin
rho-independent termination
103
what is formed in rho-independent termination
hairpin
104
termination: __ rich in GC
palindrome
105
- requires rho factor
- palindrome: less GC-rich
- no UUUUU at end of RNA
rho-dependent termination
106
where does the rho bind to transcript
rut site (rho utilization site)
107
releases transcript during rho-dependent termination
rho helicase
108
what happens after the rho catches up to the RNA polymerase that is paused at terminator
rho unwinds DNA-RNA hybrid
