Exam 3 PCB

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

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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

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