PCB exam 3

Your page rank:

Total word count: 2686
Pages: 10

Calculate the Price

- -
275 words
Looking for Expert Opinion?
Let us have a look at your work and suggest how to improve it!
Get a Consultant

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?
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.

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.
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.

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.
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. 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.
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.

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?
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.

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

Share This
Flashcard

More flashcards like this

NCLEX 10000 Integumentary Disorders

When assessing a client with partial-thickness burns over 60% of the body, which finding should the nurse report immediately? a) ...

Read more

NCLEX 300-NEURO

A client with amyotrophic lateral sclerosis (ALS) tells the nurse, "Sometimes I feel so frustrated. I can’t do anything without ...

Read more

NASM Flashcards

Which of the following is the process of getting oxygen from the environment to the tissues of the body? Diffusion ...

Read more

Unfinished tasks keep piling up?

Let us complete them for you. Quickly and professionally.

Check Price

Successful message
sending