exam 3 Flashcards
It is movement of the Holliday junction up and down the DNA by breaking and reforming the hydrogen bonds between the bases
a) Sinapse
b) Branch migration
c) Isomerisation
B
_____________ force the ssDNA into the helical conformation
a) RecA
b) SSB
c) RecBCD
d) RecQ
e) a and b
A
what are class 2 transposons
move directly from one place to another within the genome using cut and paste rather than copy and paste using transposase
The transposase cut and paste the transposon
a) True
b) False
true
In the single strand invasion model of genetic recombination one strand of the DNA molecules is cut and invade the other double strand DNA molecule until it finds its complementary sequence
a) True
False
True
____________________ recombinant molecules are generated when each molecule contains a region of heteroduplex DNA that spans the region of branch migration (configuration II)
a) holliday double strand invasion model
b) holliday single strand invasion model
c) Double break repair model
A
The transposons are also name as
a) jumping genes
b) mobile genetic elements
c) junk DNA
d) a and b
e) a, b and c
E
Transposon with inactive transposase continue to jump through the genome
a) True
b) False
true
A common way of delivering transposons is to use ______________ that cannot replicate in the recipient cells. pGP704 is an AmpR plasmid that is unable to replicate unless the Pi protein (encoded by the pir gene) is provided in the recipient cell.
a) Plasmid
b) Phage
Suicide Vector
Suicide Vector
______________ is required for recombination (prepare the single strand end of DNA to invade the other double-strand DNA – first step in recombination), degradation of foreign linear DNA and in restart the replication when the replication fork stalls at single or double-strand-breaks in the template DNA.
a) RecA
b) SSB
c) RecBCD
d) RecQ
C
Which proteins are involved in mismatch repair?
a) MutS
b) MutH
c) MutL
d) all of the above
D
RecBCD is required for
a) Recombination
b) Degradation of foreign linear DNA
c) Restart replication
d) a, b and c
D
In the Out-site end Transposition, each IS element can transpose independently as long as the transposase acts on both of its ends
a) True
False
true
________________ is the cut and ligation of DNA strand in the Holliday junction
a) Synapse
b) Branch migration
c) Isomerisation
d) Resolution
D
In both transposition mechanism the cut 5’ ends of the target DNA are join to the free 3’ end of the transposon and the target DNA 3’ end is used as a primer for replication until the free 5’ end is reached
A) true
B) false
true
Mention the properties of the transposable elements
a) Movement is not totally random, not capable of self-replication, Transposition mediated by site-specific recombination and Transposition can be accompanied by duplication
b) Movement is not totally random, not capable of self-replication, Transposition mediated by site-specific recombination
c) Movement is not totally random, it is capable of self-replication, Transposition mediated by site-specific recombination and Transposition can be accompanied by duplication
B
DnaK binds to sigma-32 and makes sigma-32 more susceptible to protease degradation.
a) True
False
true
Pathway used to prepare single stranded DNA for D-loop formation in E. coli
a) RecBCD pathway
b) RecF pathway
c) RecE pathway
B
In base excision repair, the lesion is removed by \_\_\_\_\_\_\_\_\_\_ a) DNA glycosylase b) Excisionase c) Transposase d) DNA polymerase Integrase
A
The enzyme of Escherichia coli is a nuclease that initiates the repair of double-stranded DNA breaks by homologous recombination.
a) RNA polymerase
b) DNA polymerase
c) DNA ligase
d) RecBCD
e) DNA glycolase
D
The definitive experiment proving non replicative transposition in vivo for transposon Tn10 was done by Bender and Kleckner
a) True
False
True
______________ is formed when two DNA molecules are joined through the formation of the D-loop
a) Synapse
b) Branch migration
c) Isomerisation
d) Resolution
synapse
Resolvase promotes recombination
a) True
False
true
Typically, the transposition frequency is decrease when a transposon enters a naive host or immediately after DNA replication
a) True
False
False,
Increase
\_\_\_\_\_\_\_\_\_\_\_\_\_\_ is formed when two DNA molecules are joined through the formation of the D-loop a) Synapse b) Branch migration c) Isomerisation Resolution
A
The major pathway of recombination in E.coli is
a) RecBCD pathway
b) RecF pathway
c) RecE pathway
A
The rearrangement between the strands after the formation of the Holliday junction called
a) Synapse
b) Branch migration
c) Isomerisation
d) Resolution
C
______________ is required for recombination (prepare the single strand end of DNA to invade the other double-strand DNA – first step in recombination), degradation of foreign linear DNA and in restart the replication when the replication fork stalls at single or double-strand-breaks in the template DNA.
a) RecA
b) SSB
c) RecBCD
d) RecQ
e) RecE
C
In the experiment of Bender and Kleckner on Tn10transposition, why were only 16% of the colonies sectored and not 50%?
They were stable and could be blue or white if amplification was lost
Sigma-32 is transcriptional regulated
a) True
b) False
False
post transcriptional
It has ATP and DNA binding activities and weak ATPase activity
a) RecA
b) SSB
c) RecBCD
d) RecF
e) a and b
D
In the holliday double strand invasion model if the same strands are cleaved a second time then non-recombinant DNA molecule are generated, but they each contain a region of heteroduplex DNA that spans the region of branch migration
a) True
False
True
Retrotransposons copy themselves to RNA (transcription), but instead of being translated the RNA is copied into DNA by a reverse transcriptase
a) True
b) False
true
In the Isomerization hydrogen bonds are broken and therefore energy is used.
a)True
False
False
no bond broken, no energy is used either
It is movement of the Holliday junction up and down the DNA by breaking and reforming the hydrogen bonds between the bases
a) Synapse
b) Branch migration
c) Isomerisation
B
CAP is responsible for the global regulation of carbon utilization.
a) True
False
True
Cut-and-Paste or conservative or non-replicative mechanism, the transposon is removed from one place and inserted into another
a) True
False
true
_______________ bind to ssDNA and form nucleoprotein filaments
a) RecA
b) SSB
c) RecBCD
d) RecF
e) a and b
A
__________________ pass over the site only on the other strand making the orientation of the sequence important
a) RecA
b) SSB
c) RecBCD
d) RecF
C
In nucleotide excision repair, an endonuclease makes nicks on either side of the lesion, which is then removed to leave a gap. This gap is filled by \_\_\_\_\_\_\_\_\_\_ to makes the final phosphodiester bond. I.DNA polymerase II.DNA ligase III. DNA glycolase a)I only b)II only c)III only d)I and II e)I, II, and III
B
Transposition is regulated by Dam methylation
a) True
False
true
umu C, umu D gene family and Rec A proteins are involve in
a) BER
b) NER
c) SOS repair
d) Recombination repair
C
Sigma-32 binds to the RBS of its own mRNA and blocks access of the ribosome
a) True
False
True
Dimer repair mechanism include
a) Excision repair
b) Photoreactivation
c) Recombinant repair
d) all of these
D
Cointegrates are obligate intermediaries in copy and paste transposition
a) True
False
false
__________________ copy themselves to RNA (transcription), but instead of being translated the RNA is copied into DNA by a reverse transcriptase (often coded by the transposon itself) and inserted back into the genome
a) Class I transposon b) Class II transposon c) Retrotansposons d) a and c e) b and c
D
Consequences of the inside end transposition
a) Creation of a new composite transposon
b) Deletion and inversion to a nearby target on the same DNA
c) a and b
d) None of the options
A and B
The distinction between an insertion sequence and a composite transposon is that the insertion sequence only contains genes for the mobility of the sequence
a) True
b) False
True
In hemimetilated DNA the binding of RNA pol to the dam gene promoter decrease and the transposition increase
a)True
False
False, efficently
During the transposition of the insertion elements the repeat in the target DNA is not duplicated
a) True
False
False
The chi sequence is only recognizing in one strand of DNA
a) True
b) False
true
chi site inhibit RecD subunit and stimulate 5’to 3’ activity
True
False
true
Recombination Pathway used to prepare single stranded DNA for D-loop formation in E. coli and initiate recombination at single-stranded gaps in DNA.
a) RecBCD pathway
b) RecF pathway
c) RecE pathway
B
The Inside end transposition occur in
a) Composite transposon
b) Non-composite transposon
c) IS elements
A) composite transposon
Transposons can contribute to genetic diversity by causing mutations
a) True
b) False
True
Insertion sequence elements only encode gene products required for transposase synthesis and regulation
a) True
False
true
In the cut and paste mechanism the transposase makes a double-stranded beak at the ends of the transposon
a) True
False
true
_______________________is the recombination of DNA sequences having nearly the same nucleotide sequence and involving Rec A proteins.
a) homologous recombination
b) heterologous recombination
c) transfer of genetic information
d) Transposition
A
The target DNA has a short direct repeat that bracket the transposon
a) True
False
true
Different species of bacteria have different sequences for chi site
a) True
False
True
In the Holliday double strand invasion model if the same strands are cleaved a second time then non-recombinant DNA molecule are generated, but they each contain a region of heteroduplex DNA that spans the region of branch migration
a) True
b) False
true
One amino acid change in the transposase can convert a non-replicative transposon into a replicative transposon
a) True
False
True
proved by May and Craig studies
Replicative mechanism,PART of the transposon replicates during transposition resulting in two copies of the transposon
a) True
b) False
false, the entire transposon replicates
In heat shock, the Hsp bind to denatured proteins and either help to refold them into their active conformations or, if the protein is extensively denatured, chaperones target these proteins for destruction.
a) True
b) False
True
Recombinational repair is often due to
a) Incorporation of many incorrect nucleotide by DNA polymerase
b) Many cytidine dimer and associated large gaps in a strand
c) many thymidine dimer formation and associated large gaps in a strand
d) all of these
C
Hemimethylation is a signal that DNA has just replicated
a) True
b) False
True
chi site stop RecD 3’ to 5’ nuclease activity and stimulate 5’to 3’ nuclease activity, leaving a single stranded 3’ end
a) True
b) False
True
It is movement of the Holliday junction up and down the DNA by breaking and reforming the hydrogen bonds between the bases
a) Resolution
b) Isomerization
C)Branch migration
C
Recombination depends of the holliday junction configuration when they are resolved, If both junctions with the same configuration-either one or II, then it is not crossover and no recombination happen
a) holliday double strand invasion model
b) holliday single strand invasion model
c) Double break repair model
C
RecA is required both RecBCD and RecF pathway
a) True
False
True
Composite transposon only is composed by two IS sequences
a) True
False
false, also have a gene sandwiched inbetween
In both recombination models, Holliday Double-strand Invasion and Double Break Repair the formation of two Holidays junction is carried out
a) True
False
False
