finals - transcription Flashcards
(T/F) the 3’OH at end of growing DNA chain is a nucleophile and attacks phosphorus next to sugar in nucleotide
true
(T/F) RNA transcription and subsequent translation into protein is done by the cell at any particular time
false
is tighty tied to the cell’s needs. only produced when needed
____ the process by which a region of DNA is copied to RNA
transcription
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
C
U = A
replaces thymine
(T/F) Uracil differs from thymine by the absence of a CH3 on carbon 5
true
(T/F) RNA and DNA contains -OH group attached to the 2’ carbon of ribose
false
DNA = H on 2C RNA = -OH on 2C
(T/F) Occasionally uracil will also basepair with guanine
true
(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
false
first part true. folding is analogous to 3’ structure of proteins
(T/F) RNA shape due to folding is stabilized by both conventional basepairing between complementary
nucleotides and nonconventional basepair interactions
true
(T/F) RNA transcripts are complementary to both strands of DNA
false
only to one strand
____ the strand of DNA that is complementary to RNA
template or antisense strand
______ the strand of DNA that has the same sequence as the RNA except that T replaces U
sense / coding / non template strand
____ each of the transcribed segment of DNA
transcription unit
____ usually consist of a single gene and encode a
single RNA or single protein or may encode a group of related protiens
Eukaryotic transcription units
(T/F) bacterial transcription unit is polycistronic, therefore one RNA thus encodes several distinct proteins
true
_____ term for when an entire set of adjacent genes is transcribed as a unit
polycistronic
(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
true
(T/F) In bacteria, a transcription unit often consists of different sets of genes
false
unit = set of adjacent genes typically found in operons
(T/F) majority of a cell’s genes transcribed into tRNA that encodes amino acids for protein translation
false
this is mRNA
____ the RNA type that form core of ribosomes and catalyze protein synthesis and is the most abundant type
Ribosomal RNA (rRNA)
____ the RNA type that serves as adaptors between amino acids and mRNA during protein synthesis
Transfer RNA (tRNA)
____ the RNA type that results from direct splicing of premRNA to mRNA
Small nuclear RNA (snRNA)
____ the RNA type that function in the processing and chemical modification of rRNA
Small nucleolar RNA (snoRNA)
_____ are ds RNAs about 19-25 nucleotides long that are related and regulate gene expression through the mechanism of RNA interference (RNAi)
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs)
(T/F) miRNAs and siRNAs Inhibit gene expression at posttranscriptional level
true
____ the RNA type that typically exhibit imperfect complementarity with the 3’ end of a target mRNA and inhibit its translation
miRNAs
____ the RNA type that typically form perfect complementary duplexes with a target mRNA and lead to its degradation through specific enzyme pathways
siRNAs
(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
_____ process by which siRNA inhibits gene expression in a targeted sequence specific
manner
RNA Interference (RNAi)
____ 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
____ the endonuclease that cuts dsRNA into short pieces to form siRNA
dicer
(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
_____ RISC; degrades mRNA
RNA-induced silencing complex
(T/F) Experimental introduction of siRNA into cells induces expression of specific genes
false
it INHIBITS expression of sp genes
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
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 :)
______ when the X chromosome is transcriptionally inactivated during embryonic development and shows as this structure in the interphase cells
Barr body
____ the area in the X chromosome where random inactivation begins
Xinactivation center (XIC)
____ is encoded by XIC coats and inactivates one X chromosome apparently by helping to form transcriptionally inactive heterochromatin
XIST RNA
(T/F) the XIST RNA is translated into protein before it can perform its function
false
not translated
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)
(T/F) RNA polymerase displaces RNA from DNA/RNA hybrid to allow DNA helix to rewind behind the polymerase
true
(T/F) RNA polymerase forms a transient short region of DNA/RNA hybrid
true
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
(T/F) RNA pol like DNA pol, requires a primer to initiate RNA synthesis
false
does not require it
(T/F) RNA pol makes one mistake per 10^4 nucleotides copied versus one mistake per 10^7 nucleotides copied by DNA pol
true
(T/F) RNA pol, like DNA pol, catalyzes linkage of ribonucleotides
false
deoxyribonucleotides for
DNA pol
(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
(T/F) RNA pol synthesizes RNA chain in the 3’ to 5’ direction
false
5’-3’ same direction as DNA pol synthesizes DNA
(T/F) RNA can also proofread its activity. it can back up, excise incorrect base and replace with correct one
true
____ 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
____ The actual site of transcription initiation is indicated along a gene by a specific sequence of nucleotides
promoter
(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
____ core polymerase plus σ factor
RNA pol holoenzyme
(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
(T/F) step 2 in the transcriptional cycle in bacteria is the unwinding of DNA by RNA pol at transcription initiation site
true
(T/F) step 3 in the transcriptional cycle in bacteria is the starting of transcription
true
(T/F) step 4-5 in the transcriptional cycle in bacteria is the elongation phase of transcription
true
(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
(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
(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
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
(T/F) promoters lie downstream from the start of transcription
false
lie upstream
(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
_____ an idealized sequence in which each position represents the base most often found across a comparison of many sequences
consensus sequences
(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
(T/F) the promoter regions are GC rich
false
A-T rich
(T/F) Promoter strength is one way a cell regulates the number of proteins (or structural /catalytic RNAs) it produces
true
(T/F) promoters that bind RNA pol strongly tend to be strong promoters but generate less transcripts
false
strong promoter = generate more transcripts
(T/F) strong promoters bind RNA polymerase more strongly and weak promoters bind polymerase weakly
true
(T/F) promoter consensus sequences differ when read from the 5’ or 3’ directions
true
aka are ASYMMETRIC
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’
(T/F) only one strand is transcribed in bacterial DNA
false
(T/F) Direction of transcription is determined by location of the promoter in front of the gene
true
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
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
(T/F) Inverted repeats are sequences that are complementary to each other such that the transcript will form a hairpin loop structure
true
______ functions as a wedge to open the movable flap on RNA pol and release transcript from exit tunnel of enzyme
formation of hairpin loop
(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
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!
____ termination sequences that terminate the transcription of genes in bacteria
intrinsic termination
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
(T/F) bacteria, transcription and translation are often coupled
true
(T/F) Ribosomes frequently bind to RNA that is being transcribed and start synthesizing protein
true
(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
(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
____ the major σ factor in E. coli
σ^70
(T/F) the bacterial cell contains one common signal factor for transcription
false
different sigma factors are produced to regulate transcription
(T/F) bacteria express minor σ factors that each recognize different promoter sequences
true
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
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
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
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
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
(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
(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
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
_____ are the σ-like factors encoded by bacterial virus SPO1 “middle” genes
gp33 and gp34
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
(T/F) the SPO1 virus directs the efficient synthesis of its gene products as they are required to produce new viral particles
true
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
\_\_\_\_\_\_ 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
_____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
(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
_____ DNA elements that decrease transcription rates of certain genes when they bind transcription factors
silencers
(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
(T/F) looping is common in both bacteria and eukaryotes
false
common only in eukaryotes
____ the transcription factor that bacterial enhancers bind to upstream from a promoter
Fis
(T/F) bacterias and eukaryotes both exhibit differential gene expression
true
____ the process that increases cellular efficiency and reduces expenditure of energy producing gene products that cells do not need
differential gene expression
(T/F) prokaryotic differential gene expression is largely determined by environment (availability of energy sources,
etc.)
true
_____ 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
____ 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
_____ 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
(T/F) E. coli are able to utilize different sugars in their growth medium by coordinately altering the expression of operons
true
______ Operon model proposed by François Jacob and Jacques Monod in 1961 which regulates the catabolism of lactose in bacteria
lac operon
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
which of these structural genes in the lac operon encodes for lactose permease?
a. lacZ
b. lacY
c. lacA
d. lacl
B
which of these structural genes in the lac operon encodes for β-galactosidase?
a. lacZ
b. lacY
c. lacA
d. lacl
A
which of these structural genes in the lac operon encodes for transacetylase?
a. lacZ
b. lacY
c. lacA
d. lacl
C
which of the ff enzymes (may) inactivate antibiotics that enter the cell through the permease?
a. βgalactosidase
b. Lactose permease
c. Transacetylase
C
____ the enzyme that is also called a lactose/proton symport that transports lactose into the cell
Lactose permease
____ the enzyme that hydrolyzes the disaccharide lactose by breaking down the glycosidic link between galactose and glucose
β-galactosidase
(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
(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
(T/F) lactose is the inducer of the lac operon
false
______ Actual inducer of the lac operon is a metabolite of lactose
allolactose
(T/F) allolactose is synthesized from lactose by transglycosylation reaction
true
(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
(T/F) the levels of allolactose increases as lactose levels decrease
false
proportional relationship!
(T/F) The lac operon thus provides an efficient mechanism to produce gene products only when necessary
true
_____ the regulatory gene that is the critical regulator of the lac operon which encodes the repressor protein
lacl
_____ inhibits the expression of the structural genes in an operon by binding to a region of the operon called the operator
repressor protein
_____ the regulation type that occurs when structural genes are transcribed unless they are turned off by the repressor
negative regulation
(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)
____ the region in the operon where repressor proteins bind to
operator
_____ a promoter in the lac operon that regulates the transcription of the structural genes
Plac
(T/F) Binding of the repressor to the operator interferes with binding of the RNA polymerase Plac
true
(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
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 :)
