genetics retake

Which arrow designates muth

Arrow 2 ( purple)

In long match repair by the uvrabc system, which dna polymerase fills in the excised strand

Dna pol I

Which of the following proteins has adenosine glycosylase activity?

MutY

Mutslh: which protein recruits (makes contact with) muts, muth, and UvrD

Mutl

Which of the following is a helicase

Rho

Which of the following enzymes contains only a single subunit?

T7 phage rna polymerase

In the diagram which of the following statements is true? ( tryptophan levels are low)

Transcription will not terminate at the attenuator site

In eukaryotic NER, which protein is part of the recognition complex in the global repair pathway

XPC (rad 4 yeast)

How many bases are involved in the rna

dna hybrids at the active site of bacterial rna polymerase?- 8-9nt

Which domain of sigma factor is the most conserved and makes contact with the core rna polymerase

2

Which arrow designates UvrD

3- blue things next to purple

Consider the DNA sequence below. Which of the following best characterized this sequence?

A hairpin that could be used downstream of a rut site to create a rho dependent terminator

The _ domain of rna polymerase maintains contact with both the nascent transcript and the template during the translocation step of the enzyme as it moves one nucleotide forward

Bridge

Identify the structure labeled 1 in the figure below (green on right)

CTD of alpha subunit

Of the following below, the _ is considered the only reversible rna polymerase promoter complex

Closed promoter complex

One of the default repair pathways in bacteria automatically removes a T from a G:T mismatch. Why is the T removed instead of the G?

Deamination of 5' methylcytosine to thymine occurs spontaneously at relative high frequencies

What is in common between the mechanisms of factor dependent and factor independent termination of transcription

Disruption of an rna dna hybrid

Which of the following domains or proteins does not recognize the minor groove of dna

Helix present in sigma domains 2.3-2.4

Which of the following is not a property of a rut site

High percentage of G's in the transcript (rna)

In E. coli, which protein serves as a link between transcription and dna repair by displacing a stalled rna polymerase and recruiting the uvrab excision repair proteins

Mfd

Which system in yeast is involved in mismatch (and slippage) repair and is homologous to the muts/l system in ecoli

Msh2/msh3

Which of the bacterial sigma factors is similar to eukaryotic basal factors in that it binds to the promoter before the rna polymerase core binds

Sigma 54

Which sigmas can be used to transcribe genes during some stress conditions (ex high temperatures and the starvation that occurs during stationary phase growth)?

Sigma S, sigma 32

Identify region labeled 1 (red tail with negative charge around) downstream dna

Sigma domain 1.1

Sigma: identify the domain labeled "2" in the figure below (small red spot with 2 negative ions)

Sigma domain 3.2

What would be the predicted outcome from an acquisition of a stop codon by mutation at the location shown in the figure below

Terminator would not be terminated even when tryptophan was abundant

Operon regulation: which if the following is true

The AraC protein can either repress or activate transcription

Identify the domain labeled 1 in the figure below (top of lac repressor)

The dna binding domain that binds the major groove of the operator

Identify the domain labeled "2" in the figure below (lac repressor monomer)

The dna binding domain that binds the minor groove of the operator

Identify the domain labeled 4 in the figure below (tail)

The domain that bind the two dimers together to make the tetramer

Which of the following statements is true

The lac repressor mrna lacks a 5' UTR (and a SD) and is, therefore, poorly translated

Identify the protein below involved in the global eukaryotic NER

XPC (rad4)

Which of the following proteins is a helix add subunit of tfiih and is involved in NER

XPD

Which of the following proteins removes 8

ooo-guanine from a base pairing with cytosine in duplex dna- MutM

Which of the following proteins hydrolyses 8

oxo-dGTP to prevents its incorporation into DNA- MutT

In order for sigma 70 to burn to promoter DNA in the absence of core, the _ domain must be removed

1.1

When bound to the promoter of the lac operon, the lac repressor

Forms a dna loop which blocks open complex formation

Which of the following would not stop dna replication or transcription

G:T mismatch

When cyclic amp binds to cap, the protein shows a large _ in affinity for the cap site in the promoter

Increase

In the diagram below of the ara operon what is the sugar composition of the media

No glucose no arabinose

In the diagram below of the ara operon, what is the sugar composition of the media

No glucose, but arabinose is present

Which of the following statements is false?

Retrieval, or recombination repair systems are characterized by a be very high fidelity of dna synthesis

How does rho actually cause transcription to terminate

Rho acts as a helicase to disrupt the rna:dna duplex (maybe by pulling the rna out of the polymerase)

Which of the following is true

Rna polymerase is bound to the lac promoter even when the lac repressor is present

Identify the gold colored object denoted by the white circle and blue arrow in the diagram of bacterial rna polymerase below

Rna transcript

The ___ domain of bacterial rna polymerase limits the length of the rna:dna duplex

Rudder

Which of the following is false?

Sigma 54 dependent promoters require cyclic AMP and CAP to melt the DNA

Which stop codon would result in no transcription of gene d

1

Which protein has the same

10 and -35 recognition sequences as sigma 70, but is not able to interact with the cats of the alpha subunit- Sigma S

Sigma: which domain melts the dna of the promoter within and a little downstream of the

10 element

Which domain of sigma melts the promoter at the

10 element- 2.3

Which domain of sigma factor contains 2 aromatic amino acids in a long helix that is used to melt (open) the dna strands near the

10 site- 2.3

In eukaryotes: during excision repair which enzyme fills in the gap (2

10nt) in what is called the "long patch pathway"- Dna pol delta/epilson

The _ domain of sigma 70 initially makes contact with the first 1

3 nucleotides at the 5' end of the transcript and block its exit from the enzyme - 3.2

Domain _ of sigma 70 makes contact with the first nucleotide of the transcript and domain _ initially lies in the dna binding groove of polymerase

3.2:1.1

Which of the following promoters has a good match to the

35 consensus sequence - Trp operon

Sigma: which sigma domain folds back and blocks domain sigma 4w from reading

35 site in the promoter when sigma is not attached to the core- 1.1

The _ domain of sigma 70 binds to the

35 site using A helix turn helix domain- 4.2

Lac repressor tetramer: identify the domain denoted by the blue arrow and the circle

4 bundle leucine zipper

Listed below are sigma subdomains followed by its function. Which of the following pairs has an incorrect function assigned

4.2- melting of -35 element

In wild type e coli, what is the upper limit on the number of thymidine dimers that can be tolerated per cell

50

Which of the following statements are true regarding the promoter shown below (cap

72)?- This is a class I CAP- dependent promoter

At any given time, approximately how much of the bacterial core rna polymerase is not in tight association with sigma

75%

In eukaryotes: when a glycolyses removes a base (with no lyase step) what protein binds the site and acts as an ending lease to introduce a nick?

Ape1

Mismatch repair: which of the arrows designated the protein that recruits UvrD in the mut system (middle orange)

Arrow 1

Which arrow designates the protein that determines which strand will be replaced

Arrow 2 (purple thing)

Which arrow designates muts

Arrow 4 ( bottom orange)

In the diagram below of a topological representation of bacterial rna polymerase which panel shows holoenzymes (sigma present)

B- claw open

At which of the following promoters does CAP contribute to the formation of the open promoter complex

Gal P

In what stage of transcription does RNA polymerase respectively make a small abortive transcript with sigma still bound to the promoter

Initiation

What is the biological rationale for the LexA gene ot be fe repressed during periods of heavy mutagen damage when activated RecA is trying to destroy it

It allows for the rapid buildup of LexA to shut error prone repair die as soon as mutagen is removed

Which of the following proteins is involved in non homologous end joining (NHEJ) in eukaryotes?

Ku70/ku80 and Artemis

In the sos error prone repair system, which protein is the major regulator of the system and acts to repress transcription of repair genes until it is targeted by activated reca

LexA

2.3

LexA acts to repress error prone repair pathways in E. coli. During the sis response, activated RecA triggers the destruction of lexa.

Bacterial mismatch: Which protein has affinity for the beta clamp of dna pol III

MutL

Bacterial mismatch repair: which protein forms a dimers and scans the dsdna searching for a mismatch

MutS

Which protein is part of a bacterial mismatch repair system that determines which strand to excise based on the methylation state of the dam site

Muth

A high number of errors resulting form dna slippage during replication was shown to occur in a mutagenized strain of E. coli. In which of the following genes are there likely to be mutations

Muts/l

Which of the following proteins removes A from an 8 o o g base pair in duplex dna

Muty

In the diagram below of the lac operon, what is the sugar composition of the media

No glucose, but lactose is present

The _ protein assists sigma 54 to melt the promoter when atp is present

Ntrc

Which of the following enzymes is able to conduct DIRECT repair of mutagen damage

Photolyase

In the diagram below showing positive regulation of transcription, identity the circled protein

Positive acting transcription factor that can be activated by binding a small signal molecule

Which is not the function of sigma domain 3.2

Pulls dna template into active center (scrunching)

Which of the following does not use a base flipping mechanism

RecA

What is meant by activated recA protein

RecA changes it's confirmation so that it can bind LexA and cause LexA to undergo self cleavage

Which of the following proteins is not a part of the bacterial core RNA polymerase

Sigma 70

Uvr excision repair: which of the following steps does not require atp?

The recruitment of UvrA to join uvrB in a heterodimer

At the trp operon, transcription will terminate when_

The ribosome prevents hairpin region 2 from forming a hairpin with region 3

Which statement is false

The strongest bacterial promoter is that for the Lac repressor, and it reinvigorated 1 time per second

How is the bacterial core promoter recognized by RNAP

Through contacts of sigma subdomains 2.4/2.3 (with -10 promoter region) and 4.2 (with -35 promoter region) and cis acting promoter elements

Trp attenuation: what would be the predicted outcome from the acquisition of a mutation of the location shown in the figure below? (Base pairs in the red box have been mutated from the original sequence at this location)

Transcription would not be terminated, even when tryptophan was abundant

Trp attenuation: what would be the predicted outcome from an acquisition of a stop codon by mutation at the location shown below

Transcription would not be terminated, even when trytophan was abundant

The _ protein must bind _ in order for it to bind its operator site with high affinity

Trp r aporepressor, tryptophan

Which of the following proteins or complexes is processed to form DNA polymerase V when the cell is under heavy mutagen attack

UmuD'x2/UmuC

Which bacterial enzyme or protein listed below functions in base excision repair to correct the mutation resulting from the deaminayion of cytosine

Uracil glycosylase

Bacterial mismatch repair system: which protein is "borrowed" from the uvrabc repair system to unwind the mismatched region on the new strand

UvrD

Which of the following is a component of the UV repair pathway and also participates in the dam methylation mismatch repair

UvrD

The _ domain of rna polymerase helps bend dna, which contribute to formation of the open promoter

Wall

A mutation in which of the following genes would result in extreme UV sensitivity of E. coli (hint: component in the system that removes t

t dimers)- UvrA