PCB4522: Genetics Exam 3

Which is the ratio of sigma to core, and how much RNAP is actually elongating? 3 sigma: 1 core; 25 % 1 sigma: 3 core; 25% 1 sigma: 3 core; 75% 1 sigma: 1 core; 50 %

1 sigma: 3 core; 25%

Sigma reduces affinity of RNAP core for non-promoter sequences _______fold and increases affinity for specific promoter DNA _______fold? 15,000; 800 10,000; 1,000 1,000; 10,000 5,000; 500

10,000; 1,000

What is the size of the transcription bubble and RNA/DNA hybrid in it? 12-14 nt; 8-9 nt 10-12 nt; 5-6 nt 8-9 nt; 6-7 nt 16-18 nt; 10-12 nt

12-14 nt; 8-9 nt

In the uvr excision repair system of E. coli, long patch repair replaces _______ nucleotides, and a short patch repair replaces ______ nucleotides? 2-10; 1 1500-9000; 12 700-900; 24 500-700; 5

1500-9000; 12

How many Mg2+ ions are present in the RNAP active site during transcription? 2 0 1 5

2

Mismatch repair: Which arrow designates MutH? 1 (yellow on T) 2 (purple on mCTAG and GATC) 3 (Blue blob) 4 (yellow on G)

2 (purple on mCTAG and GATC)

In eukaryotic BER, long patch repair replaces _______ nucleotides, and a short patch repair replaces ______ nucleotides? 700-900; 24 2-10; 1 500-700; 5 1500-9000; 12

2-10; 1

Listed below are sigma subdomains followed by its function. Which of the following pairings has an incorrect function assigned? 3.0; contacts upstream sequence in the extended TATA box 2.3; contacts alpha CTD 1.2; contacts discriminator element 2.1/2.2; recognizing conserved region in RNAP core

2.3; contacts alpha CTD

Mismatch repair: Which arrow designates UvrD? MutSLH mismatch repair-Exam fig.png 1 (yellow on T) 2 (purple on mCTAG and GATC) 3 (Blue blob) 4 (yellow on G)

3 (Blue blob)

Mismatch repair: Which arrow designates MutS? ( 1 (yellow on T) 2 (purple on mCTAG and GATC) 3 (Blue blob) 4 (yellow on G)

4 (yellow on G)

What is the rate of transcription and the rate of translation? 40-50 nt/second; 15 amino acids/sec 800 nt/sec; 45 amino acids/sec 40-50 nt/sec; 45 amino acids/sec 50-60 nt/sec; 5 amino acids/sec

40-50 nt/second; 15 amino acids/sec

What is the energy source that provides movement to Rho? It is derived from breaking the phosphodiester bonds during transcription. ATP hydrolysis temperature of the cell sunlight

ATP hydrolysis

Which function is NOT an activity of RecA? Act as a nuclease, which directly cleaves LexA repressor Single strand-exchange of recombination-repair Normal recombination Induces latent protease activity in its target proteins

Act as a nuclease, which directly cleaves LexA repressor

What activity is encoded by MutY and what does it do? DNA polymerase I; repairs DNA Dam methylase; methylates GATC site Reverse transcriptase; synthesizes complementary DNA strand using RNA as a template Adenosine glycosylase; creates apurinic site

Adenosine glycosylase; creates apurinic site

What step is NOT a part of the SOS repair? After damage, RecA is continuously activated and, therefore, SOS response is irreversible. RecA gene is induced approximately 50-fold, which results in protein induction of 1200 x50=60,000 molecules/cell upon UV. LexA repressor protein normally keeps levels of LexA, RecA, and excision repair enzymes low. LexA gene itself is de-repressed when LexA is self-cleaved.

After damage, RecA is continuously activated and, therefore, SOS response is irreversible.

Fill in the blank: Transcription occurs by _____________ in a _______? Base pairing; bubble of unpaired DNA Reading DNA coding sequence; terminal loop Splicing; spliceosome DNA replication; DNA loop

Base pairing; bubble of unpaired DNA

Which subunits form the catalytic center of RNAP? Alpha and sigma Alpha and beta Beta prime and omega Beta and beta prime

Beta and beta prime

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 Affinity of RNAP core for loose binding sites is too high to allow it to distinguish promoter sequence from non-promoter sequence Binding of sigma subunit reduces affinity of RNAP core for non-promoter sequence and increases affinity for promoter sequence Core RNAP is stored bound to nonspecific DNA sites before sigma subunit binds to core

Binding of sigma causes RNAP core to bind much tighter to non-promoter sequence

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 By the removal of the sigma 1.1 subdomain from its active site, thus making specific space for DNA binding available By using hairpin structure of the sigma 3.2 subdomain, which touches the first nucleotide in the active site By changing the conformation of it active site/DNA binding site

By binding alternative specialized sigma subunits, which recognize different cis-element sequences and various configurations of the promoter

What is NOT the activity of the antibiotic rifampicin in fighting tuberculosis? Binds close to the active site and blocks the formation of RNA beyond 2-3 nts. Prevents exit of growing RNA chain from RNAP itself. Can be easily dislodged by other antibiotics. It is in contact with nascent RNA past nucleotides 1-3.

Can be easily dislodged by other antibiotics.

Which is common for both DNA and RNA polymerases? Can melt the DNA duplex Can recognize promoter sequences Can slide along DNA Can scrunch DNA

Can slide along 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 Blocks exit of the nascent RNA transcript Protects first nucleotides as they form first phosphodiester bond Helps stabilize double stranded DNA structure

Causes DNA bend; bending of DNA helps melt the strands and flip bases in the template strand to be accessible

Which step is NOT a part of the SOS repair? All targets of RecA are cleaved at the dipeptide Ala-Gly Constitutive promoter of uvrB is repressed by LexA under normal conditions Inducible promoter of uvrB repair gene is repressed by LexA under normal conditions RecA activates LexA to self-cleave and this inhibits repressor activity of LexA

Constitutive promoter of uvrB is repressed by LexA under normal conditions

In dam methylation mismatch repair, what is the signal that causes MutH to nick the unmethylated strand? UvrD helicase DNA unwinding DNA excision by exonuclease VII or I Recognition of the mismatched bases by MutL Contact with MutL

Contact with MutL

What is a promoter? Gene template Control region for gene expression Signal to terminate transcription 3 untranslated region

Control region for gene expression

What is a promoter? Signal to terminate transcription Gene template 3 untranslated region Control region for gene expression

Control region for gene expression

What technique can be used to evaluate protein: DNA contacts on the single-stranded DNA? DMS footprinting DNase I footprinting Filter binding assay GST pool down assays

DMS footprinting

In the uvr excision repair system in E. coli, which enzyme routinely synthesizes DNA to replace the excised strand? DNA polymerase I DNA polymerase III RNA polymerase II DNA polymerase V

DNA polymerase I

What step is NOT part of excision repair? Dam methylation Incision by endonuclease Excision by exonuclease Damage recognition

Dam methylation

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. UvrA and B system recognizes the mismatch and knows which base to cut out. Cell is not able to distinguish new and old DNA strands, hence it does not repair a mismatch. RecBC recognizes mismatch in the daughter strand and corrects it by replacing DNA fragment using the Okazaki fragment.

Dam methylation system marks the GATC sequence in the original strand and unmethylated daughter strand is repaired.

Which statement is FALSE? 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. Domain 1.1 prevents sigma from binding promoter without first binding the RNAP core. If domain 1.1 is deleted, sigma will bind promoter sequence.

Domain 1.1 helps melt the promoter sequence and create an open promoter complex.

Which gene is NOT an example of a Mutator gene? FEN1 endonuclease MutH, S, L DnaQ-Polymerase III epsilon subunit uvrD

FEN1 endonuclease

Which protein(s) helps RNAP to recover from a stall caused by the temporary shortage of nucleotides, and how? NtrC; using ATP it provides the energy to continue elongation. GreA and NtrC; by pushing nascent RNA out of the exit pore, thus helping to convert scrunched RNA/DNA hybrid. RNAP core active site; by scrunching more DNA template into the catalytic site. 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.

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 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. 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. It alters the conformation of the active site of RNA polymerase causing the synthesis reaction to run backwards. 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.

Which SOS repair proteins are motivated by RecA to self-cleave, which protein activates them? LexA and UmuD2C RecA and uvrD LexA and DNA polymerase I UvrA, uvrB, and uvrC

LexA and UmuD2C

What protein is uniquely linked to transcription and DNA repair in E. coli? Mfd Dam methylase DNA polymerase I Reverse transcriptase

Mfd

What is the enzyme in bacteria that directly photoreactivates pyrimidine dimers? MutS, L AP1 endonuclease FEN1 endonuclease Photolyase phr

Photolyase phr

Which is NOT the function of sigma 3.2? Blocks exit channel for the RNA Positions the first nucleotide in nascent RNA Facilitates promoter clearance by RNAP (displacement by the nascent RNA) Pulls DNA template into active center (scrunching)

Pulls DNA template into active center (scrunching)

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 RecBC and RecA; restart stalled replication forks RecF, RecO and RecR; to repair gaps due to T-T dimers left in after replication in daughter strand RecA and SSB; bind to double stranded DNA

RecA and SSB; bind to double stranded DNA

Which statement is FALSE? 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 uses a specificity loop to recognize the promoter

T7 RNAP recognizes 1000 phage promoters

What protein is uniquely linked to transcription and DNA repair in eukaryotes? XPC recognition protein TFIIH helicases XPB and XPD XPG XPF/ERCC1

TFIIH helicases XPB and XPD

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 template strand. The As should come before the hairpin, not after. The hairpin region has too many mismatched base pairs. The As are on the coding strand.

The As are on the coding strand.

Which statement is FALSE? 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. The strongest bacterial promoter is that for Lac repressor and it reinitiates 1 time per second.

The strongest bacterial promoter is that for Lac repressor and it reinitiates 1 time per second.

Which statement is FALSE? The ternary complex is the least stable promoter complex 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 formed after the first phosphodiester bond is formed

The ternary complex is the least stable promoter complex

What statement is FALSE? Replication in uvr-/recA- double mutant results in production of DNA fragments as long as distance between individual T-T dimers. In uvr (excision repair) mutants, additional RecA mutation eliminates all remaining repair capabilities. The uvr-/recA- double mutants can tolerate up to 50 thymine dimers. In retrieval repair, uvr (excision repair) and rec (recombination) pathways are interconnected.

The uvr-/recA- double mutants can tolerate up to 50 thymine dimers.

How is the bacterial core promoter recognized by RNAP? Discriminator element binds subdomain 3.2 and this helps melt the promoter Upstream promoter element recruits 2 copies of omega subunit Through contacts of sigma subdomains 2.4/2.3 and 4.2 and cis-acting promoter elements Strong contacts between sigma and alpha CTDs contribute to promoter recognition

Through contacts of sigma subdomains 2.4/2.3 and 4.2 and cis-acting promoter elements

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 False

True

In the uvr excision repair system in E. coli, which steps DO NOT require hydrolysis of ATP? UvrA release from damaged DNA UvrA recognition of damaged nucleotide UvrD helicase DNA unwinding UvrBC nicking on either side of damaged nucleotide

UvrA recognition of damaged nucleotide

In the uvr excision repair system in E. coli, which enzyme recruits uvrC? DNA pol I UvrD UvrA UvrB

UvrB

In the uvr excision repair system in E. coli, which enzyme unwinds damaged DNA? UvrC UvrD UvrB UvrA

UvrD

What is abortive cycling? When RNAP pools template strand into its active site When RNA polymerase hops on and off the DNA molecule searching for promoter sequence When RNAP transcribes 2-9 nt, then restarts again and does not leave the promoter When free RNAP core looses sigma subunit and clears the promoter

When RNAP transcribes 2-9 nt, then restarts again and does not leave the promoter

What is required for a Rho-dependent terminator? an inverted repeat downstream of a very C-rich stretch of mRNA an RNA hairpin upstream of a rut site an inverted repeat rich in Cs downstream of a rut site an inverted repeat in mRNA downstream of a site rich in Gs. an inverted repeat upstream of a stretch of Us on the mRNA

an inverted repeat downstream of a very C-rich stretch of mRNA

In the diagram below showing bacterial RNA polymerase, what is indicated by the circle and arrow? (yellow blob) coding strand newly transcribed RNA template strand non-coding strand

coding strand

In the diagram below showing bacterial RNA polymerase, what is indicated by the circle and arrow? (orange blob) coding strand template strand non-coding strand newly transcribed RNA

newly transcribed RNA

In the diagram below, which configuration would result in NO expression of RNA encoding regions C and D? four (stop codon between rut and hairpin) one (stop codon before rut and hairpin) three (no stop codon) two (stop codon before rut and hairpin)

one (stop codon before rut and hairpin)

Mutations in genes that encode __________ represent the Mutator phenotype. proteins responsible of ligating DNA proteins that direct transcription proteins that participate in recombination and chiasmata formation repair system proteins, or fidelity of replication proteins

repair system proteins, or fidelity of replication proteins

In the diagram below showing bacterial RNA polymerase, what is indicated by the circle and arrow? (red blob) template strand rudder domain newly transcribed RNA coding strand

template strand

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 1.1; blocking DNA binding site within RNAP holoenzyme until finding a real promoter 2.3; aromatic amino acids contribute to promoter melting of the -10 element 2.4; base-specific interactions with the -10 element

4.2; melting of the -35 element

What percentage of RNAP (RNA polymerase) is present in a storage form (core) and how much is actually in elongation mode? 40%; 60% 50%; 50% 25%; 75% 50%; 25%

50%; 25%

How many different types of subunits are there in bacterial RNAP holoenzyme and what are their names? 3; alpha, beta, sigma 4; alpha, beta, beta prime, omega 7; alpha, beta, beta prime, omega, sigma, and delta 6; alpha, beta, beta prime, omega, and sigma

6; alpha, beta, beta prime, omega, and sigma

Which statement is FALSE in regard to recombination repair of the replication errors? A stalled fork may reverse by pairing between the two daughter strands. A replication fork may stall when it encounters a mismatch. A stalled replication fork may restart after repairing the damage and use helicase to move the fork forward. The structure of the stalled fork is the same as Holliday junction and may be converted to a duplex and ds breaks by resolvases.

A replication fork may stall when it encounters a mismatch.

Which statement is FALSE? In the free holoenzyme of bacterial RNAP, the N-terminal domain of sigma-70 blocks DNA channel by mimicking interaction with 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. 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. 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.

What statement is FALSE in regard to how RNA polymerase (RNAP) interacts with promoter DNA vs. non-promoter DNA? When sigma is released from the RNAP, the core and RNA transcript are bound extremely tight onto DNA until termination When sigma is released from the RNAP, the core and RNA transcript form a ternary complex with DNA By increasing the stability of non-promoter complexes sigma allows RNAP core to slide along DNA much faster, and find promoter sequence easier By reducing the stability of non-promoter complexes sigma allows RNAP core to find promoter sequence much faster

By increasing the stability of non-promoter complexes sigma allows RNAP core to slide along DNA much faster, and find promoter sequence easier

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) By sliding, hopping, or transfer between very AT-rich sequences located along DNA helix By recognizing RNA polymerase core bound to the promoter elements and recruiting sigma factor By counting 10 and 35 nucleotides upstream from the start of transcription on one side of the helix

By recognition of specific DNA cis-elements at position -10 and the equivalent of -35, as well as promoter configuration (distance between cis-elements)

Which of the following best describes the SOS repair system? It is a system in eukaryotes, which uses photoreactivation to directly repair thymine dimers. Repair system based on the variation of the nonhomologous end joining mechanism. Repair system that recognizes, which strand is the parental strand, and which is daughter, and fixes mutations in the new strand. By-pass or tolerance system that allows DNA replication across damage areas at the cost of fidelity.

By-pass or tolerance system that allows DNA replication across damage areas at the cost of fidelity.

What is the function of RNAP Clamp/Jaws? Blocks exit of the nascent RNA transcript and separates it from DNA template Clamp is initially out of position; after DNA has melted, it gets repositioned to keep DNA in the active site tighter Changes its conformation with each cycle of new nucleotide addition and keeps in contact with the growing RNA strand Causes DNA bend; bending of DNA helps melt the strands and flip bases in the template strand to be accessible

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 Bridge? Protects first nucleotides as they form first phosphodiester bond Blocks exit of the nascent RNA transcript Causes DNA bend; bending of DNA helps melt the strands and flip bases in the template strand to be accessible Dynamically changes its conformation with each cycle of new nucleotide addition; keeps in contact with the growing RNA strand as enzyme moves forward

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? Reverse transcriptase; topoisomerase Helicase; DNA polymerase I Gyrase; topoisomerase DNA polymerase I; gyrase

Gyrase; topoisomerase

Listed below are sigma subdomains followed by its function. Which of the following pairings has an incorrect function assigned? Hairpin 3.2; keeps contact with the first nucleotide of the nascent RNA until abortive cycling or elongation occurs Extended helix 2.3/2.4; recognizes and melts -10 element H-T-H 4.2; recognizes -35 element H-T-H 1.1; blocks the exit pore of RNA

H-T-H 1.1; blocks the exit pore of RNA

What is the function of heparin in EMSA (gel retardation) and DNase I footprinting assays? Heparin stabilizes binding of RNAP to the double stranded DNA. Heparin acts like sigma 3.2 subdomain and blocks the RNA exit pore within enzyme active site. Heparin is negatively charged; acts as a competitor to knock off any RNAP that is not in a stable open complex formation. Heparin changes the conformation of enzymes/proteins involved in these DNA:protein binding techniques.

Heparin is negatively charged; acts as a competitor to knock off any RNAP that is not in a stable open complex formation.

Which statement is FALSE in regard to eukaryotic base excision repair BER? Base removal triggers the removal and replacement of a stretch of polynucleotide, using either long patch or short path repair. BER starts by directly removing a damaged base from DNA. In BER, polymerase delta and epsilon replaces long stretch of nucleotides, which is 1500-9000 bases. The nature of base removal in BER determines which polymerase is recruited to the DNA by AP1 protein, either delta epsilon or beta.

In BER, polymerase delta and epsilon replaces long stretch of nucleotides, which is 1500-9000 bases.

What is the most important stage of transcription for regulation? Initiation Intron splicing from pre-mRNA Elongation Termination

Initiation

Which of the following is NOT the activity of Mfd protein? It degrades RNA polymerase It displaces RNA polymerase. It recruits the uvrAB proteins and directs repair to the damaged template strand. It binds to stalled RNA polymerase.

It degrades RNA polymerase

Which of the following statements are TRUE regarding "Polarity" in terms of bacterial gene expression? Polarity occurs when all coding regions of a polycistronic transcript are experiencing heavy ribosome traffic. It occurs when a rho-dependent terminator is located in the coding region of the last gene in a polycistronic mRNA. All of the coding regions have the same orientation to form a polycistronic mRNA. 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.

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.

What is the function of the RNAP Rudder/Lid domain? Changes its conformation with each cycle of new nucleotide addition and keeps in contact with the growing RNA strand Limits the length of RNA/DNA hybrid; separates nascent RNA chain from DNA template as it exits through the exit pore Clamp is initially out of position; after DNA has melted, it gets repositioned to keep DNA in the active site tighter Causes DNA bend; bending of DNA helps melt the strands and flip bases in the template strand to be accessible

Limits the length of RNA/DNA hybrid; separates nascent RNA chain from DNA template as it exits through the exit pore

Which induction conditions do NOT trigger the SOS response? Crosslinking and alkylating chemical agents UV irradiation Mismatch mutations Thymine shortage

Mismatch mutations

Which type of DNA damage does NOT result in stopped replication or stopped transcription? Thymine dimers Base alkylation; DNA nicking Depurination Mismatch; deamination

Mismatch; deamination

In yeast mismatch repair system, which proteins ______recognize mismatches, and which are specificity factors_______? Msh3; Msh5 and Msh4 Msh5; Msh3 and Msh4 Msh2; Msh3 and Msh6 Msh6; Msh2 and Msh5

Msh2; Msh3 and Msh6

In dam methylation mismatch repair, which protein acts as the nuclease and nicks the unmethylated strand? MutL MutS MutY MutH

MutH

In dam methylation mismatch repair, which protein recognizes the mismatch? MutH MutS MutL DNA polymerase III

MutS

Default repair systems show bias in error correction. Which statement is FALSE? 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. 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 this depends on GATC methylation.

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 Occurs during transcription, when sigma 1.1 mimics DNA in the DNA channel, and the actual DNA molecule tries to enter the channel Occurs during transcription when double stranded DNA sinks into the channel and hits the RNAP active site wall Occurs during transcription when length of the nascent transcript is limited by RNAP rudder to 6-9 nts

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 step is NOT a part of the SOS repair? Repair uvrB gene is regulated by dual promoter, one constitutive and one inducible UV exposure activates RecA LexA repressor binds to the SOS boxes in repair genes promoters and represses their activity under normal conditions RecA cuts LexA thus inhibiting the inhibitors activity

RecA cuts LexA thus inhibiting the inhibitors activity

What statement is FALSE? 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. 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.

Which subunit of bacterial RNAP is required for promoter specificity? Sigma Alpha Beta Omega

Sigma

What statement is FALSE? Sigma 54 does not have region 1.1. 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 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.

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. GreA and GreB proteins are necessary to activate sigma 54. DNA looping and ATP hydrolysis inhibit sigma 54 from activating NIF genes under control conditions. Negative factor NtrC inhibits transcription regulated by sigma 54 under control conditions.

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 sigmas can be used to transcribe genes during some stress conditions? Sigma S, sigma 32 Sigma fecl, sigma E Sigma A, sigma E Sigma 70, sigma F

Sigma S, sigma 32

In the transition from abortive cycling to elongation of transcription, which is TRUE? Sigma 1.1 subdomain pretends to be a promoter and confuses RNAP, which looses its mind, does not know what to do, and aborts transcription. The wall separates RNA transcript from DNA template, thus facilitating abortive cycling . DNA scrunching contributes to a stronger binding between RNAP core and sigma 3.2 subdomains. Sigma looses affinity for the promoter DNA and RNAP core, and pressure of growing RNA chain dislodges sigma from the RNA exit pore.

Sigma looses affinity for the promoter DNA and RNAP core, and pressure of growing RNA chain dislodges sigma from the RNA exit pore.

Which mechanism is NOT how RNA polymerase finds a promoter? Sliding along double stranded DNA molecule back and forth Transferring off and onto the same DNA molecule in a close vicinity Transferring between distant DNA segments located on the same molecule Sliding on a single stranded noncoding DNA molecule

Sliding on a single stranded noncoding DNA molecule

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. Protects first nucleotides as they form first phosphodiester bond in DNA footprinting assays. Stops double stranded DNA from melting, thus making protein binding to DNA more feasible. Helps stabilize double stranded DNA structure and makes protein:DNA binding stronger.

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 statement is FALSE? T7 RNAP activity is stringently regulated T7 RNAP synthesizes RNA at a rate of 200 nt/sec Flexible domain of T7 RNAP is part of a single protein and it binds to a major grove recognizing T7 phage promoter T7 RNAP is a minimal enzyme, which recognizes only one promoter

T7 RNAP activity is stringently regulated

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 be located between the rut site and the hairpin within the same coding region that contains the rho terminator. The STOP mutation must occur in the coding region immediately upstream of the coding region that contains the rho terminator. The STOP mutation must be located after the hairpin of the rho terminator. The STOP mutation must be located upstream of the rut site within the same coding region that contains the rho terminator.

The STOP mutation must be located upstream of the rut site within the same coding region that contains the rho terminator.

Which statement is TRUE in regard to eukaryotic transcription-linked nucleotide excision repair NER? Yeast Rad4 recognizes damaged DNA and this process involves flipping out thymine dimers. In eukaryotic nucleotide excision repair DNA polymerase V synthesized DNA after damage is removed. Global genome repair pathway does not share any common steps with transcription-linked nucleotide excision repair. The large subunit of RNA polymerase is degraded; TFIIH remains and recruits XP proteins to repair DNA damage.

The large subunit of RNA polymerase is degraded; TFIIH remains and recruits XP proteins to repair DNA damage.

How can you explain the effect of temperature on the dissociation of RNAP holoenzyme from promoter sequence? Open promoter complex does not occur at 37 deg (no DNA melting), therefore, the half-life of the closed complex is the longest at higher temperatures. Open promoter complex is not formed at 15 deg; closed promoter complex is the most stable overall and lasts up to hundreds of hours as shown by the bottom curve. Both, closed and open promoter complexes co-exist at 37 deg and this contributes to their long half life. 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.

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.

In base excision repair, the uracil glycosylase enzyme corrects DNA damage by biased replacement of ________ to ______? Methyl-G; unmethylated G U-G; C-G T-T dimer; A-A Depurinated nucleotide; insertion of nucleotide

U-G; C-G

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? Core promoter sequence UP element Discriminator Upstream activating sequence I, II and III

UP element

What is the source of energy that allows an intrinsic terminator to function? thermal energy due to the temperature kinetic energy of the moving RNA polymerase ATP provided during transcription NADP provided by metabolism

thermal energy due to the temperature

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 (stop codon between rut and hairpin) one (stop codon before rut and hairpin) three (no stop codon) two (stop codon before rut and hairpin)

three (no stop codon)