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MICR 4154 Final - Module 5 - Chapter 11

Terms in this set (51)

Which of the following is a DNA lesion?
A 5-methylcytosine is deaminated to a thymine
Which type of base excision repair involves the removal of an altered base by an N-glycosylase followed by cleavage of the DNA backbone by an AP endonuclease?
long patch repair
long patch repair
An N-glycosylase removes the deaminated base
An AP endonuclease cuts the DNA backbone on the 5ʹ side of the missing base
short-patch repair
An AP lyase simultaneously removes the damaged base and cuts the DNA backbone on the 3ʹ side of the damaged base
An AP endonuclease cuts the DNA backbone on the 5ʹ side of the missing base
DNA polymerase I fills in the missing base
What determines whether MutM AP lyase or MutY N-glycosylase repairs an instance of 8-oxoG?
MutM repairs 8-oxoG if DNA replication hasn't occured yet; MutY repairs 8-oxoG if DNA replication has already occured
Which of the following is not a part of the adaptive response?
Ogt degrades alkyl groups found on the phosphate backbone of the DNA.
adaptive response
Ada transfers alkyl groups from alkylated bases to itself.
- AidB inactivates alkylating agents in the cytoplasm.
- AlkB oxidizes methyl groups and releases them as formaldehyde.
Why doesn't photoreactivation work in the dark?
Because photolyase gets its energy from light photons.
How do base analogs cause mutations?
The base analog pairs correctly during the first round of replication and incorrectly during the second round of replication.
- The base analog pairs correctly during the first round of replication and incorrectly during the second round of replication.
What would happen if the methyl-directed mismatch repair machinery encountered a mismatch on DNA that is fully methylated?
It wouldn't be able to do anything because it wouldn't know which strand to nick.
What do we call a mutation that makes the cell more likely to undergo more mutations?
hypermutator
Which nucleotide excision repair (NER) proteins scan the DNA looking for damage?
UvrA2, UvrB
What is the role of Mfd in transcription-coupled repair?
It pushes RNA polymerase out of the way
- It recruits the nucleotide excision repair machinery.
How does the cell resume replication after the formation of a regressed replication fork?
RecBCD degrades the regressed portion until it reaches the replication fork and replication is restarted by the Pri proteins
- RuvABC resolves the Holliday junction and replication is restarted by recombinatio
Which of the following are used by the cell to repair interstrand crosslinks?
Nucleotide excision repair.
Recombination.
The SOS response is activated
by extensive DNA damage
Which of the following are trans-lesion polymerases?
DNA polymerase II
DNA polymerase IV
DNA polymerase V
The T4 endonuclease V can be used to study
DNA damage due to UV irradiation
Three different pykF mutations arise in a population of E. coli. While each mutation confers an advantage, none of them can outcompete each other and eventually all three are lost from the population. This is an example of
clonal interference
fixation
...
cross-feeding
...
selective sweep
...
clonal interference
...
E. coli strain O has a mutation in rpsL that makes it grow 91% as fast as the wild type. E. coli strain P has a mutation in rpoB that makes it grow 89% as fast as the wild type. E. coli strain Q has both mutations and it grows 25% as fast as the wild type. What type of epistasis is this?
Negative epistasis
negative epistasis
...
reciprocal sign epistasis
...
positive epistasis
...
In the long-term evolution experiment, a member of the Ara-3 population experienced a duplication of the citT gene, placing it under the control of a promoter that is active during aerobic growth. This allowed that strain to utilize citrate under aerobic conditions. Which process in adaptation does this represent?
actualization
potentiation
a genetic background that is favorable to a new function is developed.
elimination
?
actualization
a new function appears
refinement
...
Which Mut protein hydrolyzes cytoplasmic 8-oxodGTP to 8-oxodGMP?
MutM
What transcriptional program is triggered by extensive alkylation of the DNA?
the adaptive response
Which Mut protein recognizes hemimethylated GATC?
MutH
How does nucleotide excision repair (NER) differ from base excision repair (BER)?
NER is a single general repair pathway that recognizes many different types of DNA lesions; BER is a collection of many repair pathways that each recognize one or a few specific types of DNA lesions.
When the replication fork encounters a thymine dimer during leading strand synthesis,
the replication fork regresses so that the halted strand can be extended past the dimer.
What causes LexA to autocleave?
single stranded DNA coated with RecA
You mutagenize a his− strain of E. coli and patch the mutagenized population on plates containing histidine. Then you replica plate those patches onto a plate containing histidine and the mutagen 4NQO. Finally you replica plate those patches onto minimal medium plates lacking histidine. Which of the following patches is from a mutagenic repair mutant?
patch D
Strain A has a mutation that converts flavin mononucleotide (FMN) into a poison. Most of its offspring die because they are weakened by the poison and can't compete with other bacteria in the environment. Strain B has a mutation that pumps FMN out of the cell. Most of its offspring die because they struggle to make enough NADH and can't compete with other bacteria in the environment. Strain C has both mutations, so it converts FMN into a poison and then pumps the poison out of the cell. Most of its offspring thrive because the poison kills off other bacteria in the environment. What type of epistasis is this?
reciprocal sign epistasis
Potentiation is when
a genetic background that is favorable to a new function is developed.
MutY removes the adenine paired with 8-oxoG, which is followed by
long-patch repair
MutY
removes the adenine paired with 8-oxoG
Which nucleotide excision repair (NER) protein cleaves the DNA backbone ~4 nucleotides to the 3ʹ of the damage?
UvrB
RecA regulates DNA polymerase V in all of the following ways, except?
It blocks UmuC from binding to σ factors
how does RecA regulate DNA pol V?
It acts as a coprotease for the LexA repressor.
- It combines with UmuD' and UmuC to form the mutasome.
- It acts as a coprotease for UmuD.
A mutation arises in a population of E. coli that allows that strain to utilize the acetate that is produced by glucose fermentation by the rest of the population. This is an example of
cross-feeding
Short-patch repair involves
the removal of an altered base by an AP lyase, cleavage of the DNA backbone on the 3ʹ of the damaged base, and finally cleavage of the DNA backbone on the 5ʹ side of the damaged base by an AP endonuclease.
How do frameshift mutagens cause mutations?
The frameshift mutagen intercalates into the new DNA strand during replication, causing DNA polymerase to skip (delete) a nucleotide.

The frameshift mutagen intercalates into the old DNA strand during replication, causing DNA polymerase to add (insert) a nucleotide.
You mutagenize a lac− strain of E. coli and plate the mutagenized population on an X-gal plate. Which of the following colonies is a hypermutator?
plate with lots of spots
Which type of base excision repair involves Vsr endonuclease breaking the DNA backbone next to a deaminated cytosine followed by replacement with the correct nucleotide by DNA polymerase I?
very short patch repair
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