lec 2: transcription Flashcards
1
Q
give the central dogma
A
dna makes rna, which makes proteins
2
Q
the synthesis of RNA molecules using DNA strands as the templates so that the genetic information can be transferred from DNA to RNA
A
transcription
3
Q
dna to rna
A
transcription
4
Q
rna to protein
A
translation
5
Q
can catalyze, consists of sugar
A
RNA
6
Q
code for proteins
A
mRNA
7
Q
form the basic structure of ribosome
A
rRNA
8
Q
catalyze protein synthesis
A
rRNA
9
Q
central to protein synthesis
A
tRNA
10
Q
adaptors between mRNA and AA
A
tRNA
11
Q
serves as template for telomerase enzyme
A
telomerase RNA
12
Q
extends the ends of chromosome
A
telomerase RNA
13
Q
functions in a variety of nuclear processes
A
snRNA
14
Q
splicing of pre-mRNA
A
snRNA
15
Q
process and chemically modify rRNA
A
snoRNA
16
Q
not all of which appear to have a function
A
lncRNA
17
Q
serve as scaffolds and regulate cell processes
A
lncRNA
18
Q
for x-chromosome inactivation
A
lncRNA
19
Q
regulates gene expression by blocking translation of specific mRNA, causing their degradation
A
miRNA
20
Q
turns off gene expression by directing the degradation of selective mRNA and establish repressive chromatin structure
A
siRNA
21
Q
bind to piwi proteins
A
piRNA
22
Q
protects germ line from transposable elements
A
piRNA
23
Q
DNA regions that can be transcribed into RNA, except regulatory factors
A
structural genes
24
Q
groups of genes that are transcribed together as a unit, shares one promoter
A
operon
25
is the strand from which the RNA is actually transcribed
always 3' to 5'
template strand
noncoding strand
antisense strand
26
Is the strand whose base sequence specifies the amino acid sequence of the encoded protein
always 5' to 3'
coding strand
nontemplate strand
sense strand
27
the enzyme responsible for the RNA synthesis
rna polymerase
28
in E. coli, rna pol consists of 5 different subunits, give them
α
β
β'
σ
ω
29
without sigma factor
core RNA polymerase
apoenzyme
30
consists of protein part and non-protein part, with sigma factor
rna polymerase holoenzyme
31
determine the DNA to be transcribed
α subunit
32
catalyze polymerization
β subunit
33
binds and opens DNA template
β' subunit
34
recognizes the promoter for synthesis initiation
σ subunit
35
non-essential smalles subunit that facilitates the assembly of RNA pol
ω subunit
36
drug for tuberculosis, can bind specifically to the β subunit of RNA-pol and inhibit the RNA synthesis
rifampicin
37
each transcriptable region is called
operon
38
one operon includes several ______ and _______
structural genes
upstream regulatory sequences
39
these sites are regulatory sequences
activator protein binding site
repressor protein binding site
40
regulates transcription
regulator gene
41
is the dna sequence that rna pol can bind
promoter
42
a region of DNA where transcription of a gene is initiated
promoter
43
give the bacterial promoters
-10 element (TATAAT) pribnox region
-35 element (TTGACA)
44
transcription start site
+1
45
transcription of prokaryotes
initiation
elongation
termination
46
RNA-pol recognizes the promoter and starts the transcription
initiation phase
47
the RNA strand is continuously growing
elongation phase
48
the RNA-pol stops synthesis, and the nascent RNA is separated from the DNA template
termination phase
49
the first nucleotide on RNA transcript is always ______
purine triphosphate
50
________ is more often than ATP
GTP
51
free nucleotides triphosphates are added sequentially to the _____ of the nascent RNA strand
3’ OH
52
beginning of rna synthesis
initiation
53
release of sigma factor and growing of rna strand
elongation
54
release of rna pol and completed rna chain
termination
55
sigma factor rebinds
termination
56
where the nascent RNA is released from its complex with RNA pol and template
termination
57
two types of termination in bacterial transcription
intrinsic
rho-dependent
58
depends on rho factor, no formation of hairpin structure
rho-dependent termination
59
is a protein that binds to nascent RNA and tracks along the RNA to interact with RNA polymerase and release it from the elongation complex
rho factor
60
rho is a ______ and _______, that terminates transcription at certain specific genomic sites called a ______
hexameric
ATP-dependent RNA translocase
rut (rho-utilization)
61
termination is determined by specific sequences (termination sites)
rho-independent termination
62
termination sites in rho-independent termination consist of three features:
inverted repeats
rich in G:C
series of 7 U residues (poly-uracil)
63
form a stem-loop structure (hairpin) in RNA transcript
G:C repeats
64
presence of this followed by U-rich region downstream will cause the termination of transcription
RNA hairpin
65
causes the RNA pol to pause
RNA stem-loop
66
while RNA pol pauses, this sequence is not able to hold the RNA-DNA hybrid together
U-rich sequence
67
uses transcription factors
eukaryotic transcription
68
give the three RNA pol in eukaryotic cell
RNA pol I
RNA pol II
RNA pol III
69
genes transcribed of this RNA pol: 5.8S, 18S, 28S rRNA
RNA pol I
70
genes transcribed of this RNA pol: all protein-coding genes, snoRNA, miRNA, siRNA, lncRNA, most snRNA
RNA pol II
71
genes transcribed of this RNA pol: tRNA, rRNA, snRNA, small RNA
RNA pol III
72
the rRNAs were named according to their ___ values, which refer to their rate of ____ in an ________
S
sedimentation
ultracentrifuge
73
the larger the S value, the ____ the rRNA
larger
74
RNA pol I
product:
sensitivity to amanitin:
45S rRNA
no
75
RNA pol II
product:
sensitivity to amanitin:
hnRNA
high
76
RNA pol III
product:
sensitivity to amanitin:
5S rRNA
tRNA
snRNA
moderate
77
a specific inhibitor of RNA polymerase from fungi
amanitin
78
are the specific sequences on the DNA template that regulate the transcription of one or more genes
they are non-coding
cis-acting element
79
eukaryotic promoters include?
-25 TATA (hogness) box (TATAAA)
CAAT box
-75 GC box
80
cis-acting elements in eukaryotes
enhancer
GC
CAAT
TATA
81
recognizes TATA box and other DNA sequences near the transcription start point
TFII D
82
recognizes BRE element in promoters
TFII B
83
accurately positions RNA pol at the start site of transcription
TFII B
84
not required in all promoters
TFII A
85
stabilizes binding of TFIID
TFII A
86
stabilizes RNA pol interaction with TFIIB
TFII F
87
helps attract TFIIE and TFIIH
TFII F
88
attracts and regulates TFIIH
TFII E
89
unwinds DNA at the transcription start point
TFII H
90
phosphorylates Ser5 of the RNA pol C-terminal domain (CTD)
TFII H
91
releases RNA pol from the promoter
TFII H
92
TFIID is composed of ____ and ___ additional subunit called _____
TBP (tata binding protein)
11
TAFs (TBP-associated factors)
93
binds TATA
TBP of TFII D
94
they bind TFII D
TFII A and TFII B
95
binds TFII B
TFII F-RNA-pol complex
96
open the dsDNA
TFII F
TFII E
helicase and ATPase
97
completion of pre-initiation complex (PIC)
TFII H
98
_____ is of protein kinase activity to phosphorylate CTD of RNA-po.
TFII H
99
gene regulatory proteins that help RNA pol, the general factors, and the mediator all to assemble at the promoter
activators
100
binding site for activator protein
enhancer
101
activators are gene regulatory proteins that help ____________ all to assemble at the promoter
RNA pol
general factors
mediator
102
allows the activator proteins to communicate properly with the Pol II and with the general transcription factors
mediator
103
elongation in eukaryotes is similar to that of prokaryotes, give the elongation factors that stabilizes RNA pol.
Spt4
Spt5
Elf1
104
transcription and translation in eukaryotes do not take place simultaneously since they are separated by _______
nuclear membrane
105
enzymes that rapidly remove superhelical tension in DNA
DNA topoisomerase
106
a specialized topoisomerase in bacteria that uses the energy of ATP hydrolysis to pump supercoils continuously into the DNA, thereby maintaining the DNA under constant tension
DNA gyrase
107
the termination sequence in eukaryotes is _____ followed by _____
AATAAA
GT repeats
108
termination in eukaryotic transcription may be ____
rho-dependent/independent
109
primary transcripts of mRNA are called as ________
heteronuclear RNA (hnRNA)
110
modification of hnRNA includes:
capping at the 5' end
tailing at the 3' end
mRNA splicing
111
the capping process occurs in ____
nuclei
112
the cap structure of mRNA will be recognized by the _______ required for translation.
cap-binding protein
113
the capping occurs ______ the splicing
before
114
give the steps in 5' capping
1) one of the three phosphates at 5' end is removed
2) GTP with its phosphate is added at 5' end
3) methylation at position 7 of base of GTP and to 2' position of sugar in second and third nucleotide
4) base of initial nucleotide may also be methylated
115
give the significance of poly-A tailing at 3' end
increased mRNA stability
increased translational efficiency
116
splicing of the last intron
poly-A tailing at 3' end
117
a gene consisting of introns and exons
split gene
118
are the coding sequences that appear on split genes and primary transcripts, and will be expressed to matured mRNA
exons
119
120
the large assembly of small nuclear RNA(snRNAs) and protein molecules that performs pre-mRNA splicing in the cell
spliceosome
120
are the non-coding sequences that are transcripted into primary mRNAs, and will be cleaved out in the later splicing process
introns
121
signals for spliceosome to occur
ubiquitin
122
excised intron has this shape
lariat shape
123
changes (insertion, deletion, base substitution) to specific nucleotide sequences within an RNA molecule after it has been generated
RNA editing
124
give the significance of RNA editing
multiple functions of gene
localization and stability of RNA
has been linked to human diseases
125
rna editing has been first discovered in these cells
HeLA cells
126
they can grow indefinitely and are commonly used in cancer cells bc they are immortal
cell lines
127
an enzyme that edits RNA and DNA
APOBEC1
128
is the catalytic subunit of the apolipoprotein B mRNA editing enzyme complex
APOBEC1
129
an enzyme that edits RNA by converting adenosine (A) to inosine (I)
ADAR2
130
deaminates a specific cytidine (C) to uridine (U) in apolipoprotein B (apoB) mRNA transcripts
APOBEC1
131
mRNA transcribed immediately translated without any modification
prokaryotes
132
mRNA undergoes several post-transcriptional modifications like 5 methyl capping, poly A tail, splicing in the nucleoplasm
eukaryotes
