Which type of DNA damage does NOT result in stopped replication or stopped transcription? |
Mismatch; deamination |
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. |
In the uvr excision repair system in E. coli, which steps DO NOT require hydrolysis of ATP? |
UvrA recognition of damaged nucleotide |
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 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 recruits uvrC? |
UvrB |
What protein is uniquely linked to transcription and DNA repair in E. coli? |
... |
In eukaryotic BER, long patch repair replaces _______ nucleotides, and a short patch repair replaces ______ nucleotides? |
2-10; 1 |
What step is NOT part of excision repair? |
Dam methylation |
In base excision repair, the uracil glycosylase enzyme corrects DNA damage by biased replacement of ________ to ______? |
U-G; C-G |
In the uvr excision repair system in E. coli, which enzyme unwinds damaged DNA? |
UvrD |
What activity is encoded by MutY and what does it do? |
Adenosine glycosylase; creates apurinic site |
Which gene is NOT an example of a Mutator gene? |
FEN1 endonuclease |
What statement is FALSE? |
The uvr-/recA- double mutants can tolerate up to 50 thymine dimers. |
Which statement is FALSE in regard to recombination repair of the replication errors? |
A replication fork may stall when it encounters a mismatch. |
What statement is FALSE? |
Roles of MutS and MutL are completely different between bacterial and MSH eukaryotic proteins. |
Mutations in genes that encode __________ represent the Mutator phenotype. |
repair system proteins, or fidelity of replication proteins |
In dam methylation mismatch repair, what is the signal that causes MutH to nick the unmethylated strand? |
Contact with MutL |
Which step is NOT a part of the SOS repair? |
RecA cuts LexA thus inhibiting the inhibitors activity |
In yeast mismatch repair system, which proteins ______recognize mismatches, and which are specificity factors_______? |
Msh2; Msh3 and Msh6 |
In dam methylation mismatch repair, which protein recognizes the mismatch? |
MutS |
Which step is NOT a part of the SOS repair? |
Constitutive promoter of uvrB is repressed by LexA under normal conditions |
Which SOS repair proteins are motivated by RecA to self-cleave, which protein activates them? |
LexA and UmuD2C |
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. |
Which function is NOT an activity of RecA? |
Act as a nuclease, which directly cleaves LexA repressor |
In dam methylation mismatch repair, which protein acts as the nuclease and nicks the unmethylated strand? |
MutH |
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. |
Retrieval or recombination-repair systems in E. coli do NOT use these proteins (______) to perform these (_______) functions? |
RecA and SSB; bind to double stranded DNA |
Mismatch repair: Which arrow designates MutS? |
arrow 4 |
Which statement is FALSE? ---T7 RNAP activity is stringently regulated ---Flexible domain of T7 RNAP is part of a single protein and it binds to a major grove recognizing T7 phage promoter ---T7 RNAP synthesizes RNA at a rate of 200 nt/sec ---T7 RNAP is a minimal enzyme, which recognizes only one promoter |
T7 RNAP activity is stringently regulated |
What percentage of RNAP (RNA polymerase) is present in a storage form (core) and how much is actually in elongation mode? |
50%; 25% |
Fill in the blank: Transcription occurs by _____________ in a _______? |
Base pairing; bubble of unpaired DNA |
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 |
Which mechanism is NOT how RNA polymerase finds a promoter? |
Sliding on a single stranded noncoding DNA molecule |
Sigma reduces affinity of RNAP core for non-promoter sequences _______fold and increases affinity for specific promoter DNA _______fold? |
10,000; 1,000 |
What is the most important stage of transcription for regulation? |
Initiation |
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 |
Which subunit of bacterial RNAP is required for promoter specificity? |
Sigma |
What is the rate of transcription and the rate of translation? |
40-50 nt/second; 15 amino acids/sec |
What is abortive cycling? |
When RNAP transcribes 2-9 nt, then restarts again and does not leave the promoter |
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 two enzymes help RNAP to eliminate supercoiling generated by the mechanism of transcription? |
Gyrase; topoisomerase |
Which statement is FALSE? ---The ternary complex is the least stable promoter complex ---The ternary complex is formed after the first phosphodiester bond is formed ---Formation of the open promoter complex is irreversible and involves the melting of DNA by sigma ---Formation of the closed promoter complex is reversible |
The ternary complex is the least stable promoter complex |
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 |
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 |
What are three roles of alpha subunit? |
Enzyme assembly, promoter recognition, interactions with transcription activators |
Which statement is FALSE? ---T7 RNAP uses a specificity loop to recognize the promoter ---T7 RNAP has a DNA binding region and the active site ---T7 RNAP recognizes 1000 phage promoters ---T7 RNAP is a single peptide |
T7 RNAP recognizes 1000 phage promoters |
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 |
Which statement is FALSE? ---As DNA enters the channel in the RNAP active site, it begins to bend 90 degrees and melt as the strands open up close to start of transcription. ---As bent DNA template is in the RNAP active site, it presses on the sigma 3.2 domain, thus releasing it from the holoenzyme. ---In the free holoenzyme of bacterial RNAP, the N-terminal domain of sigma-70 blocks DNA channel by mimicking interaction with DNA. ---When the open promoter complex is formed, sigma 1.1 is displaced from DNA channel and replaced by DNA. |
As bent DNA template is in the RNAP active site, it presses on the sigma 3.2 domain, thus releasing it from the holoenzyme. |
Which statement is FALSE? ---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. ---Domain 1.1 is blocking the region where DNA is located when the promoter is melted. |
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 is the ratio of sigma to core, and how much RNAP is actually elongating? |
1 sigma: 3 core; 25% |
Which sigmas can be used to transcribe genes during some stress conditions? |
Sigma S, sigma 32 |
How do sigma factors recognize promoter sequence? |
By recognition of specific DNA cis-elements at position -10 and the equivalent of -35, as well as promoter configuration (distance between cis-elements) |
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. |
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 |
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. |
What statement is FALSE? ---Sigma 54 is very unusual since it can bind promoter in the absence of RNAP core. ---Sigma 54 activates the constitutive promoter of nitrogen starvation gene glnA. ---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. |
Which statement is FALSE? Core binds to random DNA through nonspecific, mostly electrostatic interactions, with a half-life of approximately 60 min. The strongest bacterial promoter is that for the Lac repressor, and it reinitiates 1 time per second. Addition of sigma to the core lowers core affinity for random DNA 10,000-fold, and increases core affinity for promoter DNA approximately 1,000-fold. The variation in the affinities o |
The strongest bacterial promoter is that for the Lac repressor, and it reinitiates 1 time per second. |
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. |
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 |
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. |
Listed below are sigma subdomains followed by its function. Which of the following pairings has an incorrect function assigned? |
2.3; contacts alpha CTD |
Which is NOT the function of sigma domain 3.2? |
Pulls DNA template into active center (scrunching) |
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. |
In Class II CAP-dependent promoters, it is possible to have CAP located at both the -41.5 and -61 positions. |
False |
In the diagram below of the lac operon, what is the sugar composition of the media? |
no glucose and no lactose |
Anti-activation can sometimes occur by an ADP-ribosylation-dependent mechanism. What is the mechanism regarding promoters regulated by catabolite repression? |
The CTD of the alpha subunit of RNA polymerase is modified by the addition of ADP-ribose moieties which block its' interaction with CAP. |
Which of the following is FALSE regarding CAP? |
Most CAP-dependent promoters have a good match to the -35 site consensus. |
At which class(es) of CAP-dependent promoters is CAP always in contact with both the CTD and NTD of the alpha subunit of RNA polymerase? |
Class II |
In which of the following E. coli promoters does CAP binding facilitate the formation of the Open Promoter Complex? |
Galactose (Gal P) |
Which of the following statements regarding CAP is TRUE? |
CAP requires cyclic AMP to bind DNA as a dimer. |
In Class III CAP-dependent promoters, it is possible to have CAP located at both the -41.5 and -61 positions. |
True |
In the Cytr promoter (purine metabolism), the Cytr regulatory protein binds in between the two CAP dimers. This is an example of what type of regulation? (best answer) |
Anti-activation |
In E. coli, approximately _______ promoters are activated by CAP. |
100 |