In the uvr excision repair system of E. coli, long patch repair replaces _______ nucleotides, and a short patch repair replaces ______ nucleotides? |
1500-9000; 12 |
In the uvr excision repair system in E. coli, which enzyme unwinds damaged DNA? |
UvrD |
What is the enzyme in bacteria that directly photoreactivates pyrimidine dimers? |
Photolyase phr |
Which statement is TRUE in regard to eukaryotic transcription-linked nucleotide excision repair NER? |
The large subunit of RNA polymerase is degraded; TFIIH remains and recruits XP proteins to repair DNA damage. |
In the uvr excision repair system in E. coli, which enzyme routinely synthesizes DNA to replace the excised strand? |
DNA polymerase I |
In the uvr excision repair system in E. coli, which enzyme recruits uvrC? |
UvrB |
Which type of DNA damage does NOT result in stopped replication or stopped transcription? |
Mismatch; deamination |
What step is NOT part of excision repair? |
Dam methylation |
In eukaryotic BER, long patch repair replaces _______ nucleotides, and a short patch repair replaces ______ nucleotides? |
2-10; 1 |
In base excision repair, the uracil glycosylase enzyme corrects DNA damage by biased replacement of ________ to ______? |
U-G; C-G |
Which of the following is NOT the activity of Mfd protein? |
It degrades RNA polymerase |
What protein is uniquely linked to transcription and DNA repair in eukaryotes? |
TFIIH helicases XPB and XPD |
What protein is uniquely linked to transcription and DNA repair in E. coli? |
Mfd |
Which statement is FALSE in regard to eukaryotic base excision repair BER? |
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 |
In the uvr excision repair system in E. coli, which steps DO NOT require hydrolysis of ATP? |
UvrA recognition of damaged nucleotide |
What statement is FALSE? |
The uvr-/recA- double mutants can tolerate up to 50 thymine dimers. *They can only tolerate 2 |
What statement is FALSE? |
Roles of MutS and MutL are completely different between bacterial and MSH eukaryotic proteins. |
When two bases are mismatched, how does the cell know which base to repair? |
Dam methylation system marks the GATC sequence in the original strand and unmethylated daughter strand is repaired. |
Which step is NOT a part of the SOS repair? |
RecA cuts LexA thus inhibiting the inhibitors activity |
What activity is encoded by MutY and what does it do? |
Adenosine glycosylase; creates apurinic site |
In dam methylation mismatch repair, which protein acts as the nuclease and nicks the unmethylated strand? |
MutH |
Which induction conditions do NOT trigger the SOS response? |
Mismatch mutations |
Which statement is FALSE in regard to recombination repair of the replication errors? |
A replication fork may stall when it encounters a mismatch. |
Mutations in genes that encode __________ represent the Mutator phenotype. |
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 |
Which gene is NOT an example of a Mutator gene? |
FEN1 endonuclease |
Retrieval or recombination-repair systems in E. coli do NOT use these proteins (______) to perform these (_______) functions? |
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 |
In yeast mismatch repair system, which proteins ______recognize mismatches, and which are specificity factors_______? |
Msh2; Msh3 and Msh6 |
Which of the following best describes the SOS repair system? |
By-pass or tolerance system that allows DNA replication across damage areas at the cost of fidelity. |
In dam methylation mismatch repair, which protein recognizes the mismatch? |
MutS |
Which function is NOT an activity of RecA? |
Act as a nuclease, which directly cleaves LexA repressor |
In dam methylation mismatch repair, what is the signal that causes MutH to join the Mut complex and to nick the unmethylated strand? |
Recognition of the GATC site by MutS |
Which step is NOT a part of the SOS repair? |
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 |
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. |
What step is NOT a part of the SOS repair? |
After damage, RecA is continuously activated and, therefore, SOS response is irreversible. |
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? |
MutS |
Which SOS repair proteins are motivated by RecA to self-cleave, which protein activates them? |
LexA and UmuD2C |
Which of the following statements are TRUE regarding "€œPolarity" in terms of bacterial gene expression? |
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 |
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? |
four w/ one w/ two w/ three |
In the diagram below showing bacterial RNA polymerase, what is indicated by the circle and arrow? (golden orange) |
newly transcribed RNA |
What is the energy source that provides movement to Rho? |
ATP hydrolysis |
What is the source of energy that allows an intrinsic terminator to function? |
ATP provided during transcription w/ thermal energy due to the temperature |
In the diagram below showing bacterial RNA polymerase, what is indicated by the circle and arrow? (red) |
coding strand w/ template strand |
Polarity: what condition must occur in order for a spontaneous STOP mutation to activate a Rho terminator embedded within a coding region? |
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. |
In the diagram below showing bacterial RNA polymerase, what is indicated by the circle and arrow? (yellow) |
template strand w/ coding strand |
What is the role of the hairpin in an intrinsic terminator? |
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. |
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). |
True |
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? |
The As are on the coding strand. |
In the diagram below, which configuration would result in NO expression of RNA encoding regions C and D? |
one |
What is required for a Rho-dependent terminator? (Note: inverted repeats in DNA form hairpins if transcribed into RNA.) |
an inverted repeat downstream of a very C-rich stretch of DNA |
Sigma reduces affinity of RNAP core for non-promoter sequences _______fold and increases affinity for specific promoter DNA _______fold? |
10,000; 1,000 |
Which subunit of bacterial RNAP is required for promoter specificity? |
sigma |
What is abortive cycling? |
When RNAP transcribes 2-9 nt, then restarts again and does not leave the promoter |
What is DNA scrunching? |
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 |
What two enzymes help RNAP to eliminate supercoiling generated by the mechanism of transcription? |
Gyrase; topoisomerase |
What is the rate of transcription and the rate of translation? |
40-50 nt/second; 15 amino acids/sec |
What is the function of RNAP Bridge? |
Dynamically changes its conformation with each cycle of new nucleotide addition; keeps in contact with the growing RNA strand as enzyme moves forward |
What percentage of RNAP (RNA polymerase) is present in a storage form (core) and how much is actually in elongation mode? |
50%; 25% |
Which statement is FALSE? |
T7 RNAP recognizes 1000 phage promotersf |
Which statement is FALSE? |
T7 RNAP activity is stringently regulated |
What is the function of the RNAP Rudder/Lid domain? |
Limits the length of RNA/DNA hybrid; separates nascent RNA chain from DNA template as it exits through the exit pore |
How many Mg2+ ions are present in the RNAP active site during transcription? |
2 |
What statement is FALSE in regard to how RNA polymerase (RNAP) interacts with promoter DNA vs. non-promoter DNA? |
Binding of sigma causes RNAP core to bind much tighter to non-promoter sequence |
Which mechanism is NOT how RNA polymerase finds a promoter? |
Sliding on a single stranded noncoding DNA molecule |
What is a promoter? |
Control region for gene expression |
What statement is FALSE in regard to how RNA polymerase (RNAP) interacts with promoter DNA vs. non-promoter DNA? |
By increasing the stability of non-promoter complexes sigma allows RNAP core to slide along DNA much faster, and find promoter sequence easier |
Which statement is FALSE? |
The ternary complex is the least stable promoter complex |
What is the function of RNAP Clamp/Jaws? |
Clamp is initially out of position; after DNA has melted, it gets repositioned to keep DNA in the active site tighter |
What is the function of RNAP Wall? |
Causes DNA bend; bending of DNA helps melt the strands and flip bases in the template strand to be accessible |
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? |
Elongation complex (more than 15-20 nt transcript): -75/+20 |
What are three roles of alpha subunit? |
Enzyme assembly, promoter recognition, interactions with transcription activators |
How many different types of subunits are there in bacterial RNAP holoenzyme and what are their names? |
6; alpha, beta, beta prime, omega, and sigma |
What is the most important stage of transcription for regulation? |
Initiation |
Which subunits form the catalytic center of RNAP? |
Alpha and sigma w/ Beta and beta prime |
What is the size of the transcription bubble and RNA/DNA hybrid in it? |
12-14 nt; 8-9 nt |
Which statement is FALSE? |
As bent DNA template is in the RNAP active site, it presses on the sigma 3.2 domain, thus releasing it from the holoenzyme. |
Fill in the blank: Transcription occurs by _____________ in a _______? |
Base pairing; bubble of unpaired DNA |
Which statement is FALSE? |
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. |
Which is common for both DNA and RNA polymerases? |
Can slide along DNA |
How is the bacterial core promoter recognized by RNAP? |
Through contacts of sigma subdomains 2.4/2.3 and 4.2 and cis-acting promoter elements |
Which protein(s) helps RNAP to recover from a stall caused by the temporary shortage of nucleotides, and how? |
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. |
How can you explain the effect of temperature on the dissociation of RNAP holoenzyme from promoter sequence? |
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. |
Which statement is FALSE? |
The strongest bacterial promoter is that for Lac repressor and it reinitiates 1 time per second. |
Sigma 54 has a safety check that prevents it from continuously expressing the glutamine synthase gene. What is the basis for this control? |
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. |
Which is the ratio of sigma to core, and how much RNAP is actually elongating? |
1 sigma: 3 core; 25% |
Which is NOT the function of sigma 3.2? |
Pulls DNA template into active center (scrunching) |
What is the function of unlabeled competitor DNA in various footprint assays? |
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. |
Which sigmas can be used to transcribe genes during some stress conditions? |
Sigma S, sigma 32 |
Listed below are sigma subdomains followed by its function. Which of the following pairings has an incorrect function assigned? |
H-T-H 1.1; blocks the exit pore of RNA |
What is NOT the activity of the antibiotic rifampicin in fighting tuberculosis? |
Can be easily dislodged by other antibiotics. |
What technique can be used to evaluate protein: DNA contacts on the single-stranded DNA? |
DNase I footprinting w/ Filter binding assay w/ GST pool down assays w/ DMS footprinting |
What statement is FALSE? |
Sigma 54 activates the constitutive promoter of nitrogen starvation gene glnA |
In the transition from abortive cycling to elongation of transcription, which is TRUE? |
Sigma looses affinity for the promoter DNA and RNAP core, and pressure of growing RNA chain dislodges sigma from the RNA exit pore. |
Listed below are sigma subdomains followed by its function. Which of the following pairings has an incorrect function assigned? |
4.2; melting of the -35 element |
How does RNAP holoenzyme recognize different gene promoters? |
By binding alternative specialized sigma subunits, which recognize different cis-element sequences and various configurations of the promoter |
Listed below are sigma subdomains followed by its function. Which of the following pairings has an incorrect function assigned? |
2.3; contacts alpha CTD |
How do sigma factors recognize promoter sequence? |
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) |
What is the function of heparin in EMSA (gel retardation) and DNase I footprinting assays? |
Heparin is negatively charged; acts as a competitor to knock off any RNAP that is not in a stable open complex formation. |
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? |
UP element |
PCB exam 3
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