PCB exam 3 – Flashcards
Unlock all answers in this set
Unlock answersquestion
In the uvr excision repair system of E. coli, long patch repair replaces _______ nucleotides, and a short patch repair replaces ______ nucleotides?
answer
1500-9000; 12
question
In the uvr excision repair system in E. coli, which enzyme unwinds damaged DNA?
answer
UvrD
question
What is the enzyme in bacteria that directly photoreactivates pyrimidine dimers?
answer
Photolyase phr
question
Which statement is TRUE in regard to eukaryotic transcription-linked nucleotide excision repair NER?
answer
The large subunit of RNA polymerase is degraded; TFIIH remains and recruits XP proteins to repair DNA damage.
question
In the uvr excision repair system in E. coli, which enzyme routinely synthesizes DNA to replace the excised strand?
answer
DNA polymerase I
question
In the uvr excision repair system in E. coli, which enzyme recruits uvrC?
answer
UvrB
question
Which type of DNA damage does NOT result in stopped replication or stopped transcription?
answer
Mismatch; deamination
question
What step is NOT part of excision repair?
answer
Dam methylation
question
In eukaryotic BER, long patch repair replaces _______ nucleotides, and a short patch repair replaces ______ nucleotides?
answer
2-10; 1
question
In base excision repair, the uracil glycosylase enzyme corrects DNA damage by biased replacement of ________ to ______?
answer
U-G; C-G
question
Which of the following is NOT the activity of Mfd protein?
answer
It degrades RNA polymerase
question
What protein is uniquely linked to transcription and DNA repair in eukaryotes?
answer
TFIIH helicases XPB and XPD
question
What protein is uniquely linked to transcription and DNA repair in E. coli?
answer
Mfd
question
Which statement is FALSE in regard to eukaryotic base excision repair BER?
answer
In BER, polymerase delta and epsilon replaces long stretch of nucleotides, which is 1500-9000 bases.
*correct answer is replace 2-10 bases aka long patch repair
question
In the uvr excision repair system in E. coli, which steps DO NOT require hydrolysis of ATP?
answer
UvrA recognition of damaged nucleotide
question
What statement is FALSE?
answer
The uvr-/recA- double mutants can tolerate up to 50 thymine dimers.
*They can only tolerate 2
question
What statement is FALSE?
Msh2/Msh3 complex binds DNA loops resulting from replication slippage.
Msh2/Msh6 complex binds single base mismatches, while other proteins do the repairing.
Roles of MutS and MutL are completely different between bacterial and MSH eukaryotic proteins.
MSH repair system in yeast is homologous to the E. coli MutS/L system.
answer
Roles of MutS and MutL are completely different between bacterial and MSH eukaryotic proteins.
question
When two bases are mismatched, how does the cell know which base to repair?
answer
Dam methylation system marks the GATC sequence in the original strand and unmethylated daughter strand is repaired.
question
Which step is NOT a part of the SOS repair?
answer
RecA cuts LexA thus inhibiting the inhibitors activity
question
What activity is encoded by MutY and what does it do?
answer
Adenosine glycosylase; creates apurinic site
question
In dam methylation mismatch repair, which protein acts as the nuclease and nicks the unmethylated strand?
answer
MutH
question
Which induction conditions do NOT trigger the SOS response?
answer
Mismatch mutations
question
Which statement is FALSE in regard to recombination repair of the replication errors?
answer
A replication fork may stall when it encounters a mismatch.
question
Mutations in genes that encode __________ represent the Mutator phenotype.
answer
proteins that participate in recombination and chiasmata formation w/
proteins that direct transcription w/
proteins responsible of ligating DNA w
repair system proteins, or fidelity of replication proteins
question
Which gene is NOT an example of a Mutator gene?
answer
FEN1 endonuclease
question
Retrieval or recombination-repair systems in E. coli do NOT use these proteins (______) to perform these (_______) functions?
answer
RecBC and RecF; help associate RecA with single stranded DNA w/
RecBC and RecA; restart stalled replication forks w/
RecA and SSB; bind to double stranded DNA f
question
In yeast mismatch repair system, which proteins ______recognize mismatches, and which are specificity factors_______?
answer
Msh2; Msh3 and Msh6
question
Which of the following best describes the SOS repair system?
answer
By-pass or tolerance system that allows DNA replication across damage areas at the cost of fidelity.
question
In dam methylation mismatch repair, which protein recognizes the mismatch?
answer
MutS
question
Which function is NOT an activity of RecA?
answer
Act as a nuclease, which directly cleaves LexA repressor
question
In dam methylation mismatch repair, what is the signal that causes MutH to join the Mut complex and to nick the unmethylated strand?
answer
Recognition of the GATC site by MutS
question
Which step is NOT a part of the SOS repair?
answer
Inducible promoter of uvrB repair gene is repressed by LexA under normal conditions w/
All targets of RecA are cleaved at the dipeptide Ala-Gly w/
Constitutive promoter of uvrB is repressed by LexA under normal conditions
question
Default repair systems show bias in error correction. Which statement is FALSE?
MutS/L removes T from GT and CT mismatch pairs, and this depends on GATC methylation.
MutM removes oxidated dGTP that is paired with C, but is not able to hydrolyze it as a free nucleotide .
MutS/L removes T from GT and CT mismatch pairs, and is not dependent on GATC methylation.
MutY removes A from CA and GA mismatches, and does not use MutS/L system.
answer
MutS/L removes T from GT and CT mismatch pairs, and this depends on GATC methylation.
question
What step is NOT a part of the SOS repair?
answer
After damage, RecA is continuously activated and, therefore, SOS response is irreversible.
question
In dam methylation mismatch repair, which protein translocates to the GATC site and is able to bind to two sites simultaneously, thus making a DNA loop?
answer
MutS
question
Which SOS repair proteins are motivated by RecA to self-cleave, which protein activates them?
answer
LexA and UmuD2C
question
Which of the following statements are TRUE regarding "€œPolarity" in terms of bacterial gene expression?
answer
It is when termination in a coding region located near the 5-end of a polycistronic mRNA causes the loss of both transcriptional and translational expression of all genes that follow it
question
In the diagram below, which configuration would result in NO expression of coding region D at the translational level, but there would still be mRNA present?
answer
four w/
one w/
two w/
three
question
In the diagram below showing bacterial RNA polymerase, what is indicated by the circle and arrow? (golden orange)
answer
newly transcribed RNA
question
What is the energy source that provides movement to Rho?
answer
ATP hydrolysis
question
What is the source of energy that allows an intrinsic terminator to function?
answer
ATP provided during transcription w/
thermal energy due to the temperature
question
In the diagram below showing bacterial RNA polymerase, what is indicated by the circle and arrow? (red)
answer
coding strand w/
template strand
question
Polarity: what condition must occur in order for a spontaneous STOP mutation to activate a Rho terminator embedded within a coding region?
answer
The STOP mutation must occur in the coding region immediately upstream of the coding region that contains the rho terminator. w/
The STOP mutation must be located upstream of the rut site within the same coding region that contains the rho terminator.
question
In the diagram below showing bacterial RNA polymerase, what is indicated by the circle and arrow? (yellow)
answer
template strand w/
coding strand
question
What is the role of the hairpin in an intrinsic terminator?
answer
The hairpin produces DNA scrunching of the non-template strand resulting in a misalignment of the RNA:DNA hybrid portion of the transcription bubble. w/
It alters the conformation of the active site of RNA polymerase causing the synthesis reaction to run backwards. w/
It causes the polymerase to stall, which requires either processing of the 3-end or termination to occur.
It causes the RNA polymerase to pause so that the stretch of U:As are positioned in the RNA:DNA region of the transcription bubble.
question
True/False: Normal polycistronic RNA's can be terminated by either intrinsic or factor-dependent terminators located downstream of the last coding region (in the 3'-untranslated region; 3'-UTR).
answer
True
question
Termination: The diagram below shows a GC-rich hairpin sequence of DNA followed by a stretch of A's. Why is this NOT an intrinsic terminator?
answer
The As are on the coding strand.
question
In the diagram below, which configuration would result in NO expression of RNA encoding regions C and D?
answer
one
question
What is required for a Rho-dependent terminator? (Note: inverted repeats in DNA form hairpins if transcribed into RNA.)
answer
an inverted repeat downstream of a very C-rich stretch of DNA
question
Sigma reduces affinity of RNAP core for non-promoter sequences _______fold and increases affinity for specific promoter DNA _______fold?
answer
10,000; 1,000
question
Which subunit of bacterial RNAP is required for promoter specificity?
answer
sigma
question
What is abortive cycling?
answer
When RNAP transcribes 2-9 nt, then restarts again and does not leave the promoter
question
What is DNA scrunching?
answer
Occurs during transcription and abortive cycling; 6-9 nts of DNA template are pulled into the RNAP active site where the template is bunched up
question
What two enzymes help RNAP to eliminate supercoiling generated by the mechanism of transcription?
answer
Gyrase; topoisomerase
question
What is the rate of transcription and the rate of translation?
answer
40-50 nt/second; 15 amino acids/sec
question
What is the function of RNAP Bridge?
answer
Dynamically changes its conformation with each cycle of new nucleotide addition; keeps in contact with the growing RNA strand as enzyme moves forward
question
What percentage of RNAP (RNA polymerase) is present in a storage form (core) and how much is actually in elongation mode?
answer
50%; 25%
question
Which statement is FALSE?
answer
T7 RNAP recognizes 1000 phage promotersf
question
Which statement is FALSE?
answer
T7 RNAP activity is stringently regulated
question
What is the function of the RNAP Rudder/Lid domain?
answer
Limits the length of RNA/DNA hybrid; separates nascent RNA chain from DNA template as it exits through the exit pore
question
How many Mg2+ ions are present in the RNAP active site during transcription?
answer
2
question
What statement is FALSE in regard to how RNA polymerase (RNAP) interacts with promoter DNA vs. non-promoter DNA?
answer
Binding of sigma causes RNAP core to bind much tighter to non-promoter sequence
question
Which mechanism is NOT how RNA polymerase finds a promoter?
answer
Sliding on a single stranded noncoding DNA molecule
question
What is a promoter?
answer
Control region for gene expression
question
What statement is FALSE in regard to how RNA polymerase (RNAP) interacts with promoter DNA vs. non-promoter DNA?
answer
By increasing the stability of non-promoter complexes sigma allows RNAP core to slide along DNA much faster, and find promoter sequence easier
question
Which statement is FALSE?
answer
The ternary complex is the least stable promoter complex
question
What is the function of RNAP Clamp/Jaws?
answer
Clamp is initially out of position; after DNA has melted, it gets repositioned to keep DNA in the active site tighter
question
What is the function of RNAP Wall?
answer
Causes DNA bend; bending of DNA helps melt the strands and flip bases in the template strand to be accessible
question
RNAP changes conformation during the transcription cycle. Given below are stages of transcription and the amount of promoter DNA that is protected from DNase digestion: Which one is NOT correct?
answer
Elongation complex (more than 15-20 nt transcript): -75/+20
question
What are three roles of alpha subunit?
answer
Enzyme assembly, promoter recognition, interactions with transcription activators
question
How many different types of subunits are there in bacterial RNAP holoenzyme and what are their names?
answer
6; alpha, beta, beta prime, omega, and sigma
question
What is the most important stage of transcription for regulation?
answer
Initiation
question
Which subunits form the catalytic center of RNAP?
answer
Alpha and sigma w/
Beta and beta prime
question
What is the size of the transcription bubble and RNA/DNA hybrid in it?
answer
12-14 nt; 8-9 nt
question
Which statement is FALSE?
answer
As bent DNA template is in the RNAP active site, it presses on the sigma 3.2 domain, thus releasing it from the holoenzyme.
question
Fill in the blank: Transcription occurs by _____________ in a _______?
answer
Base pairing; bubble of unpaired DNA
question
Which statement is FALSE?
Domain 1.1 is blocking the region where DNA is located when the promoter is melted.
Domain 1.1 prevents sigma from binding promoter without first binding the RNAP core.
Domain 1.1 helps melt the promoter sequence and create an open promoter complex.
If domain 1.1 is deleted, sigma will bind promoter sequence.
answer
Domain 1.1 is blocking the region where DNA is located when the promoter is melted. w/
Domain 1.1 prevents sigma from binding promoter without first binding the RNAP core. w/
Domain 1.1 helps melt the promoter sequence and create an open promoter complex.
question
Which is common for both DNA and RNA polymerases?
answer
Can slide along DNA
question
How is the bacterial core promoter recognized by RNAP?
answer
Through contacts of sigma subdomains 2.4/2.3 and 4.2 and cis-acting promoter elements
question
Which protein(s) helps RNAP to recover from a stall caused by the temporary shortage of nucleotides, and how?
answer
GreA and GreB; reposition Mg2+ ions in the active site, which makes RNAP cleave trailing end off nascent RNA to align it correctly in the catalytic site.
question
How can you explain the effect of temperature on the dissociation of RNAP holoenzyme from promoter sequence?
answer
Transition from closed to open promoter complex happens readily at higher temperatures (DNA melting); open promoter complex is most stable at 37 deg and the least stable at 15 deg.
question
Which statement is FALSE?
The strongest bacterial promoter is that for Lac repressor and it reinitiates 1 time per second.
Core binds to random DNA through nonspecific, mostly electrostatic interactions, with a half-life of circa 60 min.
The variation in the affinities of holoenzyme for promoter DNA may vary by 1,000,000-fold.
Addition of sigma to the core lowers core affinity for random DNA 10,000-fold, and increases core affinity for promoter DNA circa 1,000-fold.
answer
The strongest bacterial promoter is that for Lac repressor and it reinitiates 1 time per second.
question
Sigma 54 has a safety check that prevents it from continuously expressing the glutamine synthase gene. What is the basis for this control?
answer
Sigma 54 is unable to melt the promoter without added ATP and a helper protein NtrC bound to the enhancer element at least 70 bp away.
question
Which is the ratio of sigma to core, and how much RNAP is actually elongating?
answer
1 sigma: 3 core; 25%
question
Which is NOT the function of sigma 3.2?
answer
Pulls DNA template into active center (scrunching)
question
What is the function of unlabeled competitor DNA in various footprint assays?
answer
Substitutes for labeled probe originally bound to the protein of interest (outcompeting it) and allows for analysis of kinetics (off-constants) and/or specificity/strength of binding.
question
Which sigmas can be used to transcribe genes during some stress conditions?
answer
Sigma S, sigma 32
question
Listed below are sigma subdomains followed by its function. Which of the following pairings has an incorrect function assigned?
answer
H-T-H 1.1; blocks the exit pore of RNA
question
What is NOT the activity of the antibiotic rifampicin in fighting tuberculosis?
answer
Can be easily dislodged by other antibiotics.
question
What technique can be used to evaluate protein: DNA contacts on the single-stranded DNA?
answer
DNase I footprinting w/
Filter binding assay w/
GST pool down assays w/
DMS footprinting
question
What statement is FALSE?
Some NIF genes have dual promoters, which can be turned on either by sigma 70 or sigma 54.
Sigma 54 does not have region 1.1.
Sigma 54 activates the constitutive promoter of nitrogen starvation gene glnA.
Sigma 54 is very unusual since it can bind promoter in the absence of RNAP core.
answer
Sigma 54 activates the constitutive promoter of nitrogen starvation gene glnA
question
In the transition from abortive cycling to elongation of transcription, which is TRUE?
answer
Sigma looses affinity for the promoter DNA and RNAP core, and pressure of growing RNA chain dislodges sigma from the RNA exit pore.
question
Listed below are sigma subdomains followed by its function. Which of the following pairings has an incorrect function assigned?
answer
4.2; melting of the -35 element
question
How does RNAP holoenzyme recognize different gene promoters?
answer
By binding alternative specialized sigma subunits, which recognize different cis-element sequences and various configurations of the promoter
question
Listed below are sigma subdomains followed by its function. Which of the following pairings has an incorrect function assigned?
answer
2.3; contacts alpha CTD
question
How do sigma factors recognize promoter sequence?
answer
By sliding, hopping, or transfer between very AT-rich sequences located along DNA helix w/
By recognition of specific DNA cis-elements at position -10 and the equivalent of -35, as well as promoter configuration (distance between cis-elements)
question
What is the function of heparin in EMSA (gel retardation) and DNase I footprinting assays?
answer
Heparin is negatively charged; acts as a competitor to knock off any RNAP that is not in a stable open complex formation.
question
In the GST pull-down experiment, the entire bacterial core and distal promoter was used as a radioactive probe pre-bound with isolated GST-alpha CTD subunit. The outcome was a very sharp decline in the pulled-down radioactivity. What competitor was used to obtain this effect?
answer
UP element
