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Genetic Exam 2

Terms in this set (51)

Conditional mutations in which of the following would be classified as "slow-stop"?

SeqA
DnaA and DnaG
DnaE
SSB
DnaA and DnaG
Which two auxiliary proteins are required by eukaryotic DNA polymerases delta and epsilon in replication of lagging and leading strands?

ORC and RP-A ssDNA binding protein
Rep helicase and DnaA
Ligase1 and Dam methylase
RF-C clamp loader and PCNA clamp
RF-C clamp loader and PCNA clamp
In eukaryotic DNA replication, which enzyme primes both DNA strands?

Alpha primase
Gamma replicase
DNA polymerase beta
Delta replicase
Alpha primase
Proofreading activity of bacterial DNA polymerase I resides in the __________, and for DNA polymerase III, it's in the __________ subunit?

N-terminal domain and epsilon
C-terminal domain and tau
Central domain and alpha
N-terminal domain and beta
N-terminal domain and epsilon
Which proteins have helicase activity and power replisome movement at replication forks?

DnaB, Mcm2-7 and Rep protein
DnaG, Cdc6 and DnaE
DnaA, Cdt1 and DnaB
SeqA, HU and protein A
DnaB, Mcm2-7 and Rep protein
Initiation at oriC requires the sequential assembly of a large protein complex. Which proteins are necessary for the creation of the replication forks at oriC?

SeqA, VirB, VirG
Rep, protein A, DnaE
DnaC, HU, NF1
DnaB, gyrase, SSB, HU
DnaB, gyrase, SSB, HU
Tension in the bacterial supercoiled genome is relaxed by _____ ?

Terminal protein
Primase
Topoisomerase
Replicase
Topoisomerase
Which protein that uniquely binds oriC is functionally analogous to the eukaryotic licensing factor?

DnaG
DnaB
DnaE
DnaA
DnaA
Which is NOT part of the process of initiation of replication at oriC?

Helicase DnaB unwinds DNA at the replication fork by moving along the template for the leading strand in a 3' to 5' direction.
Helicase DnaB unwinds DNA at the replication fork by moving along the template for the lagging strand in a 5' to 3' direction.
DnaG primase synthesizes RNA primer.
SSB protein binds single stranded DNA.
Helicase DnaB unwinds DNA at the replication fork by moving along the template for the leading strand in a 3' to 5' direction.
DNA polymerase I Klenow fragment is NOT used for _________.

Digesting away protruding 3-overhangs
DNA sequencing
Nick translation
filling-in DNA at recessed 3-ends
Nick translation
Which activity of DNA polymerase I provides proofreading during DNA replication?

3 to 5 exonuclease activity
Endonuclease activity
5 to 3 exonuclease
5 to 3 DNA synthesis activity
3 to 5 exonuclease activity
Which statement is FALSE?

The typical eukaryotic nucleus has five replicases
A single bacterial DNA polymerase undertakes semiconservative replication.
DNA synthesis occurs always from 5 to 3 (This refers to synthesis of the new strand, not movement on the template.)
Bacteria usually have only one replicase comprised of multiple subunits.
The typical eukaryotic nucleus has five replicases
The quick-stop conditional mutants are defective in ______?

DnaB and DnaG
Primase DnaG
DnaA and DnaB
DNA polymerase C (DNA pol III, replicase) and precursors
DNA polymerase C (DNA pol III, replicase) and precursors
Which three proteins recognize various origins of replication?

SeqA, Rep, DnaB
Mcm2-7, Orc1, CDK1
Cdc6, Cdt1, VirE
DnaA, protein A, ORC
DnaA, protein A, ORC
Which both E. coli polymerases are used in translesion replication (SOS repair of damaged DNA, e.g. repair of thymidine dimers)?

DNA polymerase IV and V
DNA polymerase V and III
DNA polymerase IV and I
DNA polymerase II and III
DNA polymerase IV and V
Which answer is FALSE?

DnaB propels the PhiX174 phage leading strand synthesis replication fork.
Six monomers of DnaC bind each hexamer of DnaB.
DnaB is a hexameric protein that hydrolyzes ATP.
DnaA binds to short repeated sequences at oriC.
DnaB propels the PhiX174 phage leading strand synthesis replication fork.
Bacterial DNA polymerase I does NOT have ________ activity?

Endonuclease activity
3 to 5 exonuclease activity
5 to 3 DNA synthesis activity
5 to 3 exonuclease activity
Endonuclease activity
The DNA polymerase I Klenow fragment is missing _____________activity.

3 to 5 exonuclease
5 to 3 exonuclease
5 to 3 DNA synthesis
Endonuclease
5 to 3 exonuclease
Which is NOT the function of eukaryotic alpha DNA polymerase?

Makes RNA primer
Tethers primase to catalytic subunit A
Elongates DNA
Extends RNA primer by making short DNA (iDNA)
Elongates DNA
Which helices of DNA polymerase rotate 60 degrees to recruit the incoming dNTP?

Helices of the exonuclease domain
H helices of the thumb domain
R helices of the palm domain
O helixes of the finger domains
O helixes of the finger domains
Which is FALSE?

DNA polymerases have a common structure of palm, fingers, thumb, exonuclease and N-terminal domains.
The palm is the most conserved domain in the DNA polymerase family.
DNA binds in the cleft between thumb and fingers.
The thumb domain is the most conserved in DNA.
The thumb domain is the most conserved in DNA.
How does DnaA prevent reinitiation at the oriC until the next cell cycle?

DnaA binds single-stranded DNA, and this inactivates it.
DnaA binds to membrane phospholipids, and this inactivates its ATPase activity.
DnaA binds ATP, and this inactivates it.
DnaA hydrolizes ATP, and this inactivates it.
DnaA hydrolizes ATP, and this inactivates it.
Proofreading activity of DNA polymerase improves fidelity of replication by a factor of _____ fold?

Does not improve it at all.
10-100
1000-5000
100-500
100-500
In eukaryotic replication, DNA polymerase _______ elongates lagging strand, and DNA polymerase _________ elongates leading strand?

Delta and epsilon
Gamma and beta
Delta and beta
Alpha and epsilon
Delta and epsilon
Out of _____ eukaryotic DNA polymerases, only ______ replicate(s) almost all nuclear DNA.

15 and 5
15 and 3
7 and 3
10 and 1
15 and 3
Which statement is FALSE?

DnaG associates transiently with primosome.
A hexamer of DnaB propels the replication fork.
DnaB loads DnaC onto the replication fork.
DnaB activates DnaG.
DnaB loads DnaC onto the replication fork.
DNA synthesis can NOT be initiated by the _________.

DNA primer at the 3-OH
RNA primer with a 3-OH
Terminal protein providing the first dCTP nucleotide
DNA primer at the 5-OH
DNA primer at the 5-OH
Which is FALSE?

Primase DnaG is displaced by contact with gamma-delta clamp loader after new RNA primer is synthesized. *****

Primase DnaG is activated by DnaB helicase.

Clamp loader loads the beta clamp onto the priming site, but needs ATP to ADP hydrolysis to complete the action. *****

Polymerase III breaks contact with the beta clamp immediately after the RNA primer is synthesized from the lagging strand.
...
Which proteins are ALL components of the PhiX174 primosome?

PriA, PriB, PriC, dnaT, DnaB, DnaE
DnaA, DnaB, PriC, dnaT, DnaE, PriA
DnaG, DnaE, dnaT, DnaA, PriC, SSB
PriA, PriB, PriC, dnaT, DnaB, DnaG
PriA, PriB, PriC, dnaT, DnaB, DnaG
Which is FALSE?

DNA polymerase III elongates RNA primer into Okazaki fragment after it displaced clamp loader from the new beta clamp
DNA polymerase III prepares for the next round of initiation by the recruitment of the primase DnaG to the beta clamp.
DNA polymerase III releases contact with the beta clamp after it collides with the previous Okazaki fragment
Clamp loader binds another beta clamp to prepare for the next round of initiation.
DNA polymerase III prepares for the next round of initiation by the recruitment of the primase DnaG to the beta clamp.
DNA polymerase _____ removes ________and replaces it with _______in an action that resembles_________.

I, RNA primer, DNA, nick translation
III, RNA primer, DNA, nick translation
III, RNA primer, DNA, ligation
I, DNA primer, RNA, proofreading
I, RNA primer, DNA, nick translation
Which is NOT the function of the replisome?

It elongates lagging strand during synthesis.
It stalls at lesions during DNA synthesis.
It initiates synthesis of a DNA strand.
It elongates leading strand during synthesis.
It initiates synthesis of a DNA strand.
Which is TRUE?

DNA polymerase I removes Okazaki fragments and then ligase fills in.
Each Okazaki fragment is synthesized from 3 to 5'.
Each Okazaki fragment stops at a specific termination site.
DNA ligase connects the 3-OH end of one Okazaki fragment to the 5 phosphate beginning of the next fragment.
DNA ligase connects the 3-OH end of one Okazaki fragment to the 5 phosphate beginning of the next fragment.
Processivity in replication refers to_____?

How well DNA polymerase stays associated with DNA template during replication
How well clamp loader bumps off primase after priming DNA synthesis
How quickly DNA polymerase proofreads during replication
How quickly DNA polymerase terminates replication
How well DNA polymerase stays associated with DNA template during replication
Which statement is FALSE?

A clamp loader places two beta subunits onto a DNA:RNA hybrid.
One catalytic core of DNA polymerase III is associated with each template strand.
Two DNA polymerase monomeric units associate to form a dimer through interactions of the gamma-delta complex.
Two beta subunits form a circular clamp around nucleic acid.
Two DNA polymerase monomeric units associate to form a dimer through interactions of the gamma-delta complex.
Which two proteins do NOT have analogous functions in prokaryotes and eukaryotes?

DnaB and Mcm2-7
SSB and RPA
DNA polymerase I and FEN1 nuclease
DNA polymerase III core and DNA polymerase beta
DNA polymerase III core and DNA polymerase beta
Which two proteins do NOT have similar functions in prokaryotes and eukaryotes?

Beta subunit and PCNA
DNA polymerase III and DNA polymerase alpha
Gamma-delta and RF-C
DnaG and DNA polymerase alpha
DNA polymerase III and DNA polymerase alpha
Which is NOT a characteristic feature of DnaG?

DnaG is a special RNA polymerase used only in DNA replication.
DnaG synthesizes a short DNA primer.
DnaG primes both PhiX174 and E. coli DNA synthesis.
DnaG recognizes a GTA sequence and primes at this site.
DnaG synthesizes a short DNA primer.
Which is FALSE?

The E. coli replicase DNA polymerase III is a 900 kDa complex with dimeric structure.
The catalytic core of DNA polymerase III consists of alpha, epsilon, and theta subunits.
The DNA polymerase III dimerization subunit is tau.
DNA polymerase is tethered to DNA template strands through the proteins of the gamma-delta complex.
DNA polymerase is tethered to DNA template strands through the proteins of the gamma-delta complex.
What is the function of the primosome?

It elongates lagging strand during synthesis.
It initiates synthesis of a DNA strand.
It terminates DNA synthesis.
It elongates leading strand during synthesis.
It initiates synthesis of a DNA strand.
What does NOT contribute directly to increased DNA polymerase III processivity?

Tau subunits dimerization of two monomeric units of DNA polymerase III
Beta subunits tethering DNA Polymerase III cores to the template strands
Recruitment of DNA polymerase by beta subunits clamped on DNA-RNA hybrids at the replication fork
Displacement of gamma-delta clamp loader by DnaG
Displacement of gamma-delta clamp loader by DnaG
The E. coli DNA polymerase III monomeric unit consists of these proteins_______?

Theta, tau, beta, gamma, delta
Alpha, epsilon, delta, tau, gamma
Gamma, delta, theta, chi, psi
Alpha, epsilon, theta, tau, beta
Alpha, epsilon, theta, tau, beta
Which is FALSE?

Initiation of PhiX174 replication requires the primosome complex to displace SSB from the origin.
The primosome does not exist as free complex; it assembles at the replication fork ****
In the E. coli chromosome, the components of the PhiX174 primosome are used to reinitiate at lesions.
The replisome is needed to prime replication at lesions.
...
DnaB helicase cannot open dsDNA. Which protein opens dsDNA at the oriC? (melts the two strands apart)

DnaG-ATP
DnaE-NAD
Replicase-GTP
DnaA-ATP
DnaA-ATP
Which is FALSE?

In eukaryotes there is no DNA polymerase that has 5 to 3 nick translation activity
In eukaryotes, DNA polymerase I activity removes the flap(=primer-overhang) created by synthesis of the next Okazaki fragment.
Prokaryotic ligase and eukaryotic ligase 1 seal gaps between Okazaki fragments in DNA replication
The FEN1 exo/endonuclease (MF1) cuts the flap=primer-overhang created by synthesis of the next Okazaki fragment
In eukaryotes, DNA polymerase I activity removes the flap(=primer-overhang) created by synthesis of the next Okazaki fragment.
Which proteins are present at the eukaryotic replication fork?

DNA polymerase III, DNA polymerase I, DnaB helicase, DnaB primase
DNA polymerase alpha, DNA polymerase delta, DNA polymerase III, Mcm2-7 helicase, beta clamp
DNA polymerase alpha primase, DNA polymerase delta, DNA polymerase epsilon, Mcm2-7 helicase, PCNA
DNA polymerase gamma, DNA polymerase delta, DNA polymerase I, Mcm2-7 helicase, PCNA
DNA polymerase alpha primase, DNA polymerase delta, DNA polymerase epsilon, Mcm2-7 helicase, PCNA
Which statement is FALSE?

DnaB activates DnaG.
DnaB loads DnaC onto the replication fork.
DnaG associates transiently with primosome. ******
A hexamer of DnaB propels the replication fork.
DnaB loads DnaC onto the replication fork.
Which proteins are necessary to maintain the separated strands during PhiX174 replication of the leading strand?

DnaB, SSB
Cdt1, VirE
Orc1, CDK1
SeqA, Rep
DnaB, SSB
Which is NOT the function of the replisome?

It stalls at lesions during DNA synthesis.
It initiates synthesis of a DNA strand.
It elongates leading strand during synthesis.
It elongates lagging strand during synthesis.
It initiates synthesis of a DNA strand.
In synaptonemal complex strand exchange between chromosomes occurs at this average _______distance?

400-800
2-120
120-800
120-400 nm
120-400 nm
What is the "purpose" of recombination? (Or, what benefits to the organism are gained through the process of recombination?)

stimulates cell division
provides a way to initiate DNA synthesis
provides genetic diversity and repair DNA breaks
provides means to terminate replication
provides genetic diversity and repair DNA breaks
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