finals - transcription Flashcards
(140 cards)
1
Q
(T/F) the 3’OH at end of growing DNA chain is a nucleophile and attacks phosphorus next to sugar in nucleotide
A
true
2
Q
(T/F) RNA transcription and subsequent translation into protein is done by the cell at any particular time
A
false
is tighty tied to the cell’s needs. only produced when needed
3
Q
____ the process by which a region of DNA is copied to RNA
A
transcription
4
Q
which of the ff does not apply to RNA?
a. consists of four nucleotide subunits joined by phosphodiester bonds
b. contains pentose sugar ribose instead of deoxyribose
c. Uracil basepairs with thymine through hydrogen bonding
d. RNA is typically single stranded
A
C
U = A
replaces thymine
5
Q
(T/F) Uracil differs from thymine by the absence of a CH3 on carbon 5
A
true
6
Q
(T/F) RNA and DNA contains -OH group attached to the 2’ carbon of ribose
A
false
DNA = H on 2C RNA = -OH on 2C
7
Q
(T/F) Occasionally uracil will also basepair with guanine
A
true
8
Q
(T/F) Single stranded structure of RNA allows it to fold into a variety of shapes dictated by the RNA sequence which is different with the tertiary structure of proteins
A
false
first part true. folding is analogous to 3’ structure of proteins
9
Q
(T/F) RNA shape due to folding is stabilized by both conventional basepairing between complementary
nucleotides and nonconventional basepair interactions
A
true
10
Q
(T/F) RNA transcripts are complementary to both strands of DNA
A
false
only to one strand
11
Q
____ the strand of DNA that is complementary to RNA
A
template or antisense strand
12
Q
______ the strand of DNA that has the same sequence as the RNA except that T replaces U
A
sense / coding / non template strand
13
Q
____ each of the transcribed segment of DNA
A
transcription unit
14
Q
____ usually consist of a single gene and encode a
single RNA or single protein or may encode a group of related protiens
A
Eukaryotic transcription units
15
Q
(T/F) bacterial transcription unit is polycistronic, therefore one RNA thus encodes several distinct proteins
A
true
16
Q
_____ term for when an entire set of adjacent genes is transcribed as a unit
A
polycistronic
17
Q
(T/F) Eukaryotic transcription units may encode a group of related proteins if the initial RNA transcript is spliced
in multiple ways that can produce different proteins
A
true
18
Q
(T/F) In bacteria, a transcription unit often consists of different sets of genes
A
false
unit = set of adjacent genes typically found in operons
19
Q
(T/F) majority of a cell’s genes transcribed into tRNA that encodes amino acids for protein translation
A
false
this is mRNA
20
Q
____ the RNA type that form core of ribosomes and catalyze protein synthesis and is the most abundant type
A
Ribosomal RNA (rRNA)
21
Q
____ the RNA type that serves as adaptors between amino acids and mRNA during protein synthesis
A
Transfer RNA (tRNA)
22
Q
____ the RNA type that results from direct splicing of premRNA to mRNA
A
Small nuclear RNA (snRNA)
23
Q
____ the RNA type that function in the processing and chemical modification of rRNA
A
Small nucleolar RNA (snoRNA)
24
Q
_____ are ds RNAs about 19-25 nucleotides long that are related and regulate gene expression through the mechanism of RNA interference (RNAi)
A
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs)
25
(T/F) miRNAs and siRNAs Inhibit gene expression at posttranscriptional level
true
26
____ the RNA type that typically exhibit imperfect complementarity with the 3’ end of a target mRNA and inhibit its translation
miRNAs
27
____ the RNA type that typically form perfect complementary duplexes with a target mRNA and lead to its degradation through specific enzyme pathways
siRNAs
28
(T/F) RNAs together with proteins, comprises most of the cell's dry mass
false
RNA comprises a few percent of a cell’s dry weight and 3-5% of total RNA
29
_____ process by which siRNA inhibits gene expression in a targeted sequence specific
manner
RNA Interference (RNAi)
30
____ are derived from longer dsRNA precursors and first discovered in C. elegans but has since been found as a gene regulatory mechanism in other organisms including mammals
siRNAs
31
____ the endonuclease that cuts dsRNA into short pieces to form siRNA
dicer
32
(T/F) in the basic RNAi mechanism, the sense strand is loaded into the RISC and binds to target mRNA by basepairing
false
this is done with ANTISENSE strand
33
_____ RISC; degrades mRNA
RNA-induced silencing complex
34
(T/F) Experimental introduction of siRNA into cells induces expression of specific genes
false
it INHIBITS expression of sp genes
35
which of the ff is not part of regulation of gene expression done by RNAi?
a. Elimination of transcripts from mobile elements (transposons) and repetitive DNA
b. Dicer and RISC play central role in destruction of tRNAs
c. Block of protein synthesis by micro RNAs generated within the cell
d. Suppresses transcription and keeps chromatin condensed
B
destruction of invading viral RNA
36
which of the ff is not used to experimentally introduce siRNAs into cells to turn off specific gene products?
a. transfection
b. plasmid
c. viruses
d. direct injection
none of the above :)
37
______ when the X chromosome is transcriptionally inactivated during embryonic development and shows as this structure in the interphase cells
Barr body
38
____ the area in the X chromosome where random inactivation begins
Xinactivation center (XIC)
39
____ is encoded by XIC coats and inactivates one X chromosome apparently by helping to form transcriptionally inactive heterochromatin
XIST RNA
40
(T/F) the XIST RNA is translated into protein before it can perform its function
false
not translated
41
which of the ff does not apply to RNA polymerases?
a. Catalyze formation of phosphodiester bonds between nucleotides
b. unwinds DNA helix just ahead of its active site
c. polymerization is driven by hydrolysis of phosphate bonds
d. adds dNTPs to the growing RNA chain using exposed DNA template
D
adds ribonucleoside triphosphates (ATP, UTP, GTP, and CTP)
42
(T/F) RNA polymerase displaces RNA from DNA/RNA hybrid to allow DNA helix to rewind behind the polymerase
true
43
(T/F) RNA polymerase forms a transient short region of DNA/RNA hybrid
true
44
which of the ff does not apply to RNA synthesis?
a. RNA molecules are synthesized one at a time
b. RNA is released from the DNA strand as it is synthesized
c. Synthesis of new RNA molecules can start at one end of a gene as synthesis is completed at the other end
d. none of the above
A
many RNA molecules can be synthesized from the same gene simultaneously
45
(T/F) RNA pol like DNA pol, requires a primer to initiate RNA synthesis
false
does not require it
46
(T/F) RNA pol makes one mistake per 10^4 nucleotides copied versus one mistake per 10^7 nucleotides copied by DNA pol
true
47
(T/F) RNA pol, like DNA pol, catalyzes linkage of ribonucleotides
false
deoxyribonucleotides for
DNA pol
48
(T/F) Since RNA does not permanently store genetic information in cells like DNA, an error in RNA sequence has less potential to cause severe damage to cell
true
49
(T/F) RNA pol synthesizes RNA chain in the 3’ to 5’ direction
false
5'-3' same direction as DNA pol synthesizes DNA
50
(T/F) RNA can also proofread its activity. it can back up, excise incorrect base and replace with correct one
true
51
____ a detachable subunit of the multisubunit complex bacterial RNA pol that is responsible for recognizing the site on the DNA where transcription should begin
sigma factor
52
____ The actual site of transcription initiation is indicated along a gene by a specific sequence of nucleotides
promoter
53
(T/F) The σ factor recognizes exposed portions of the bases in the promoter sequence and attaches the RNA pol tightly to the site to begin transcription
true
54
____ core polymerase plus σ factor
RNA pol holoenzyme
55
(T/F) step 1 in the transcriptional cycle in bacteria is the formation of RNA primers along the promoter
false
RNA pol holoenzyme forms and locates a promoter
56
(T/F) step 2 in the transcriptional cycle in bacteria is the unwinding of DNA by RNA pol at transcription initiation site
true
57
(T/F) step 3 in the transcriptional cycle in bacteria is the starting of transcription
true
58
(T/F) step 4-5 in the transcriptional cycle in bacteria is the elongation phase of transcription
true
59
(T/F) step 6-7 in the transcriptional cycle in bacteria: Pol encounters a termination signal (terminator) and releases
just the RNA
false
releases both DNA and RNA
60
(T/F) in step 3 of the transcriptional cycle in bacteria, Once nascent RNA chain is 10 nucleotides long, σ factor loosens from pol and dissociates from it
true
61
(T/F) in step 3 of the transcriptional cycle in bacteria pol undergoes conformational changes which involves tightening of a pair of moveable “jaws” around the RNA and the placement of the growing DNA in the exit channel
false
"jaws" around DNA, RNA exits channel
62
T/F) in step 3 of the transcriptional cycle in bacteria, (after encountering terminator) Pol cannot reassociate with another σ factor and promoter.
false
can reassociate with a σ factor and begin to look for another promoter to
start the process again
63
(T/F) promoters lie downstream from the start of transcription
false
lie upstream
64
(T/F) promoters are found at the 3’ end of the coding strand and 5’ end of the template strands of DNA
false
5' of coding strand, 3' end of DNA
65
_____ an idealized sequence in which each position represents the base most often found across a comparison of many sequences
consensus sequences
66
(T/F) the DNA base that encodes the first base in the RNA transcript (transcription start site) is designated -1 and the upstream promoter sequences are given positive numbers from the transcription start site
false
start of RNA = +1
promoter = -1
67
(T/F) the promoter regions are GC rich
false
A-T rich
68
(T/F) Promoter strength is one way a cell regulates the number of proteins (or structural /catalytic RNAs) it produces
true
69
(T/F) promoters that bind RNA pol strongly tend to be strong promoters but generate less transcripts
false
strong promoter = generate more transcripts
70
(T/F) strong promoters bind RNA polymerase more strongly and weak promoters bind polymerase weakly
true
71
(T/F) promoter consensus sequences differ when read from the 5’ or 3’ directions
true
aka are ASYMMETRIC
72
which of the ff is false about promoters?
a. are asymmetric
b. RNA pol can only bind to promoter sequences in one orientation
c. an RNA pol can synthesize RNA only in the 3’ to 5’ direction
d. can only transcribe one of the strands of DNA depending on the orientation of the promoter
C
can synthesize 5'-3'
73
(T/F) only one strand is transcribed in bacterial DNA
false
74
(T/F) Direction of transcription is determined by location of the promoter in front of the gene
true
75
which of the ff is not true about the elongation process of transcription?
a. induces supercoiling
b. Topoisomerases remove supercoils that form ahead of the bubble
c. Topoisomerases remove supercoils that form behind the bubble
d. supercoils hinder the movement of helicases
D
hinders RNA pol
76
which of the ff is false regarding the transcription termination signals in bacteria?
a. they occur at various distances upstream from the coding region
b. consists of two inverted repeats
c. repeats are separated by few bases d a stretch of A’s that are transcribed to a string of U’s
d. Inverted repeats are sequences that are complementary to each other
A
they occur DOWNSTREAM
77
(T/F) Inverted repeats are sequences that are complementary to each other such that the transcript will form a hairpin loop structure
true
78
______ functions as a wedge to open the movable flap on RNA pol and release transcript from exit tunnel of enzyme
formation of hairpin loop
79
(T/F) The stretch of 3’ terminal U residues also facilitates the release of the transcript because these residues are strongly hydrogen bonded to the A residues of the
template
false
weakly H-bonded = makes it easier for the flap to release the transcript from the template DNA
80
which of the ff is not involved in the termination of transcription in bacteria?
a. hairpin loop
b. Rho protein
c. 5' U residues
d. termination sequences
C
3' end U residues!
81
____ termination sequences that terminate the transcription of genes in bacteria
intrinsic termination
82
which of the ff does not apply to rho protein?
a. is ATP dependent
b. Rho binds to RNA and travels towards and associates w/ the RNA pol
c. rho to pol binding facilitates the dissociation of the pol
and RNA from the DNA
d. rho binds to rRNA
D
binds to naked RNA only, ribosomes blocks the movement of rho along the transcript
83
(T/F) bacteria, transcription and translation are often coupled
true
84
(T/F) Ribosomes frequently bind to RNA that is being transcribed and start synthesizing protein
true
85
(T/F) Mutations that affect the binding of ribosomes to mRNA have been shown to inhibit rho-dependent
termination of transcription
false
induces rho-dependent
termination
86
(T/F) polycistronic mRNAs are rho-dependent so the absence of ribosomes prevents premature termination of a polycistronic mRNA
false
first part true
presence of ribosomes PREVENT termination
87
____ the major σ factor in E. coli
σ^70
88
(T/F) the bacterial cell contains one common signal factor for transcription
false
different sigma factors are produced to regulate transcription
89
(T/F) bacteria express minor σ factors that each recognize different promoter sequences
true
90
which of the ff σ factors in E.coli recognize promoters for genes for stationary phase and stress response?
a. σ^28
b. σ^32
c. σ^54
d. σ^70
A
91
which of the ff σ factors in E.coli recognize promoters for genes induced by heat shock?
a. σ^28
b. σ^32
c. σ^54
d. σ^70
B
92
which of the ff σ factors in E.coli recognize promoters for genes involved in nitrogen metabolism?
a. σ^28
b. σ^32
c. σ^54
d. σ^70
C
93
which of the ff σ factors in E.coli recognize promoters for genes involved in motility and chemotaxis?
a. σ^28
b. σ^32
c. σ^54
d. σ^70
A
94
which of the ff σ factors in E.coli recognize most promoters?
a. σ^28
b. σ^32
c. σ^54
d. σ^70
D
95
(T/F) multiple σ factors allows one large set of genes to be turned off and another set to be activated by simply switching the type of σ factor produced
true
96
(T/F) having multiple σ factors is efficient since this allows regulation of genes one by one
false
Efficient because multiple genes are regulated at once instead of one by one
97
which of the ff is not a disadvantage of using σ
factors?
a. bacterial virus SPO1 uses the bacterial RNA pol to transcribe its early genes immediately after the viral DNA enters the cell
b. SPO1 virus product gp28 increases bacterial σ factor binding to its pol
c. SPO1 early gene product, gp28, is a σ-like factor
d. Bacterial viruses also use multiple σ factors to take over the bacterial host RNA polymerase
B
it displaces the bacterial σ factor from its pol
98
_____ are the σ-like factors encoded by bacterial virus SPO1 "middle" genes
gp33 and gp34
99
which of the ff does not apply to bacterial virus SPO1?
a. The bacterial pol with gp28 turns on the transcription of the SPO1 “middle” genes
b. gp33 and gp34 directly transcribes the viral “late” genes
c. Late genes encode proteins that are necessary to package the virus DNA into
a virus coat
d. Late genes encode proteins that are necessary to lyse the cell
B
direct the host pol to transcribe the viral “late” genes
100
(T/F) the SPO1 virus directs the efficient synthesis of its gene products as they are required to produce new viral particles
true
101
which of the ff does not apply to enhancers?
a. can be found at great distances from the promoter
b. May be rotated (alter the orientation) or moved to different locations along
the DNA
c. are usually located upstream of a gene it acts upon
d. are usually longer distances in eukaryotes; up to thousands of base pairs away)
C
May be located upstream or downstream
102
```
______ are a special class of DNA sequences to which transcription factors (or gene activators) bind . they are DNA regions that “enhanced” or increased the rate
of transcription of particular genes
```
Enhancers
103
_____when region of DNA between the promoter and enhancer loops out to allow proteins bound to the enhancer to interact with proteins bound to the promoter (RNA pol and other transcription factors )
Looping mechanism
104
(T/F) Enhancers only increase the rate of transcription of particular genes
false
some are now known to decrease transcription rates of certain genes when they bind transcription factors
105
_____ DNA elements that decrease transcription rates of certain genes when they bind transcription factors
silencers
106
(T/F) the looping mechanism of enhancers facilitate the formation of a transcription complex and does not require energy
false
first part true
requires energy from the hydrolysis of ATP
107
(T/F) looping is common in both bacteria and eukaryotes
false
common only in eukaryotes
108
____ the transcription factor that bacterial enhancers bind to upstream from a promoter
Fis
109
(T/F) bacterias and eukaryotes both exhibit differential gene expression
true
110
____ the process that increases cellular efficiency and reduces expenditure of energy producing gene products that cells do not need
differential gene expression
111
(T/F) prokaryotic differential gene expression is largely determined by environment (availability of energy sources,
etc.)
true
112
_____ a mode of gene expression where gene products are produced at a constant rate at all times/ always requires
Constitutive expression
| e.g., enzymes for glycolytic pathways
113
____ a mode of gene expression where gene expression varies in response to particular conditions
Inducible expression
| e.g., enzymes in bacteria that break down available sugars for energy
114
_____ a group of contiguous genes along a bacterial chromosome that are under the control of a common promoter and encode proteins that function in a common
metabolic pathway
operon
115
(T/F) E. coli are able to utilize different sugars in their growth medium by coordinately altering the expression of operons
true
116
______ Operon model proposed by François Jacob and Jacques Monod in 1961 which regulates the catabolism of lactose in bacteria
lac operon
117
which of the ff is not found in the lac operon?
a. lacZ
b. promoter for structural genes
c. inducer
d. lacA
C
presence depends on environmental conditions
118
which of these structural genes in the lac operon encodes for lactose permease?
a. lacZ
b. lacY
c. lacA
d. lacl
B
119
which of these structural genes in the lac operon encodes for β-galactosidase?
a. lacZ
b. lacY
c. lacA
d. lacl
A
120
which of these structural genes in the lac operon encodes for transacetylase?
a. lacZ
b. lacY
c. lacA
d. lacl
C
121
which of the ff enzymes (may) inactivate antibiotics that enter the cell through the permease?
a. βgalactosidase
b. Lactose permease
c. Transacetylase
C
122
____ the enzyme that is also called a lactose/proton symport that transports lactose into the cell
Lactose permease
123
____ the enzyme that hydrolyzes the disaccharide lactose by breaking down the glycosidic link between galactose and glucose
β-galactosidase
124
(T/F) coli can survive in the presence of lactose as its only carbon source and relies on β-galactosidase to catalyze the breakdown of lactose
true
125
(T/F) the synthesis of β-galactosidase occurs at substantial levels in the presence of lactose and glucose
false
ONLY when lactose is the only one present
126
(T/F) lactose is the inducer of the lac operon
false
127
______ Actual inducer of the lac operon is a metabolite of lactose
allolactose
128
(T/F) allolactose is synthesized from lactose by transglycosylation reaction
true
129
(T/F) β- galactosidase must first be produced by the bacteria before synthesis of allolactose from lactose can occur
FALSE!
Synthesis of allolactose from lactose is catalyzed by the few (less than 10) β-galactosidase
molecules that are present in the bacterium before induction occurs
130
(T/F) the levels of allolactose increases as lactose levels decrease
false
proportional relationship!
131
(T/F) The lac operon thus provides an efficient mechanism to produce gene products only when necessary
true
132
_____ the regulatory gene that is the critical regulator of the lac operon which encodes the repressor protein
lacl
133
_____ inhibits the expression of the structural genes in an operon by binding to a region of the operon called the operator
repressor protein
134
_____ the regulation type that occurs when structural genes are transcribed unless they are turned off by the repressor
negative regulation
135
(T/F) in negative regulation, the presence of an inducer results in the binding of the repressor protein to the operator
false
presence of inducer removes the inhibition (repressor)
136
____ the region in the operon where repressor proteins bind to
operator
137
_____ a promoter in the lac operon that regulates the transcription of the structural genes
Plac
138
(T/F) Binding of the repressor to the operator interferes with binding of the RNA polymerase Plac
true
139
(T/F) allolactose induces the operon by binding to Plac which initiates transcription followed by translation of the structural genes
false
allolactose binds to repressor and inactivates it
140
which of the ff does not apply to the inducing process in the lac operon (with inducer)?
a. inducer binds to the repressor and inactivates it
b. In absence of repressor bound to operator, RNA pol binds to Plac
c. lacI (the regulatory gene) is close to the structural genes in the lac operon
d. regulatory gene in many other operons is far removed from the
structural genes
none of the above :)
