exam 3 Flashcards by Sebastian Saldivar

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

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_____________ force the ssDNA into the helical conformation

a) RecA
b) SSB
c) RecBCD
d) RecQ
e) a and b

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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

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The transposase cut and paste the transposon

a) True
b) False

true

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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

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____________________ 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

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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

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Transposon with inactive transposase continue to jump through the genome

a) True
b) False

true

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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

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______________ 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

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Which proteins are involved in mismatch repair?

a) MutS
b) MutH
c) MutL
d) all of the above

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RecBCD is required for

a) Recombination
b) Degradation of foreign linear DNA
c) Restart replication
d) a, b and c

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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

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________________ is the cut and ligation of DNA strand in the Holliday junction

a) Synapse
b) Branch migration
c) Isomerisation
d) Resolution

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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

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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

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DnaK binds to sigma-32 and makes sigma-32 more susceptible to protease degradation.
a) True
False

true

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Pathway used to prepare single stranded DNA for D-loop formation in E. coli

a) RecBCD pathway
b) RecF pathway
c) RecE pathway

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In base excision repair, the lesion is removed by \_\_\_\_\_\_\_\_\_\_
a)	DNA glycosylase
b)	Excisionase
c)	Transposase
d)	DNA polymerase
Integrase

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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

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The definitive experiment proving non replicative transposition in vivo for transposon Tn10 was done by Bender and Kleckner
a) True
False

True

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______________ 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

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Resolvase promotes recombination
a) True
False

true

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Typically, the transposition frequency is decrease when a transposon enters a naive host or immediately after DNA replication
a) True
False

False,

Increase

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``` ______________ is formed when two DNA molecules are joined through the formation of the D-loop a) Synapse b) Branch migration c) Isomerisation Resolution ```

The major pathway of recombination in E. coli is a) RecBCD pathway b) RecF pathway c) RecE pathway

The rearrangement between the strands after the formation of the Holliday junction called a) Synapse b) Branch migration c) Isomerisation d) Resolution

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

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

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

__________________ pass over the site only on the other strand making the orientation of the sequence important a) RecA b) SSB c) RecBCD d) RecF

``` 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 ```

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

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

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

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

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

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

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

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

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

exam 3 Flashcards

(72 cards)