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MICR 4154 Final - Module 5 - Chapter 11
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The primary purpose of recombination is to participate in
DNA replication
Which proteins bind single-stranded DNA when restarting a stalled replication fork?
PriB and PriC
How would recombination be affected if recD were inactivated by a mutation?
RecBC would immediately start degrading 5ʹ→3ʹ and loading RecA onto the ssDNA.
Why might χ sites be involved in immunity against phages?
Phages are unlikely to have χ sites by chance, so RecBCD will degrade them entirely.
How are the RecBCD and RecF recombination pathways similar?
How are the RecBCD and RecF recombination pathways similar?
Which protein coats single-stranded DNA and helps it find homologous sequence in double-stranded DNA?
RecA
RecA protein
plays an important role in recombination involving single-strand displacement
RecB
3'-5' helicase, forms 3' strand extensions
RecC
...
RecD
...
Which of the Ruv proteins causes the Holliday junction to migrate?
RuvB
RecG
branched helicase that causes a stalled replication fork to regress
helps form Holliday junctions and promotes branch migration
Why is non-homologous end-joining (NHEJ) sometimes mutagenic?
Sometimes ends are joined that weren't originally together, which results in an inversion.
- Sometimes the ends are partially degraded before they are joined, which results in a deletion.
Which of the following is not part of the recombination of a linear DNA fragment into a genome?
The genome is coated with RecA.
You order a single-stranded DNA oligonucleotide for a λ Red Recombineering experiment. You transform that oligonucleotide into a λ Red strain that doesn't have a functional exo gene. What will be the result of your experiment?
The single-stranded DNA will recombine into the E. coli chromosome.
Sinorhizobium meliloti has two genes, ropA1 and ropA2, that encode similar outer membrane proteins. Sometimes a Holliday junction forms bewteen ropA1 on one daughter DNA and ropA2 on the other daughter DNA during replication. The Holliday junction then migrates, forming mismatches. The mismatches on one of the strands (but not the other) are sometimes repaired by the MDMR system before the next round of replication. What is the outcome of all this?
gene conversion
gene conversion
Mismatches created by the migration of a Holliday junction during recombination can be repaired by MDMR
The target site of group II introns is recognized by
part of the intron RNA
What is the purpose of the group II intron in the Targetron system?
It retrohomes to a target sequence and disrupts it
What organism was used by Gibson et al. to assemble 1-Kb fragments of DNA into 10-Kb fragments?
yeast
Which of the following is not a way that Gibson et al. confirmed that they had replaced the Mycoplasma capricolum with a synthetic Mycoplasma mycoides genome?
mass spectrometry
Which protein binds loads the DnaB/C complex onto the lagging strand of a stalled replication fork?
DnaT
RecBC has all of the following activities except?
synapse formation activity
RecBC activities
- unwinds the DNA and loops out the strand with an exposed 3ʹ end
- 3ʹ→5ʹ exonuclease activity
- 5ʹ→3ʹ exonuclease activity
- RecA loading activity
RecD
- promotes RecBC 3ʹ→5ʹ exonuclease activity, which chops the looped-out strand
- prevents RecBC from loading RecA onto the strand with an exposed 5ʹ end
Choose all that apply. RuvC dimers resolve a Holliday junction when
the Holliday junction is in one of the stacked forms.
- the RuvC dimers encounter the sequence 5ʹ-WTTS-3ʹ.
RecG is responsible for
forming regressed replication forks.
What is the name of the commercial product that allows you to disrupt a gene using a modified group II intron?
Targetron
Which of the following is not a difference that Gibson et al. deliberately introduced into the synthetic Mycoplasma mycoides genome?
An E. coli transposon
Which protein binds a stalled replication fork and begins unwinding the strand with an exposed 5′ end?
PriA
Which recombination protein recognizes χ sites?
RecD
How would recombination be affected if all of the χ sites were removed from the E. coli genome?
RecBC would degrade 3ʹ→5ʹ non-stop and eventually degrade all of the DNA.
What is the outcome on inheritance of recombination between a linear DNA fragment and a genome?
One daughter cell ends up with the original genomic sequence; the other daughter cell ends up with the linear DNA fragment incorporated into its genome.
Gibson et al. created 1078 fragments of Mycoplasma mycoides DNA that were 1,080 base pairs long with 80-bp overlaps. What was the purpose of the overlaps?
So that when they put the fragments into yeast they would be assembled by homologous recombination.
You use PCR to amplify a gene for a λ Red Recombineering experiment. You transform that PCR into a λ Red strain that doesn't have a functional gam gene. What will be the result of your experiment?
The double-stranded DNA will be degraded by RecBCD.
What type of intron has a 15-bp recognition site?
Retrohoming group II introns
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