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molecular genetics > Transposition 1 > Flashcards

Transposition 1 Flashcards

1
Q

what can transposition events cause?

A
  • may cause deletions or inversions or lead to movement of host sequences to new locations
  • can mix up the genome or move host sequences to new locations
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2
Q

transposons

A
  • genetic elements in the genome that are mobile
  • A major cause of variation in almost all genomes is caused by transposable elements and their presence can have a major impact on the overall size of the genome
  • Transposons are DNA elements that “hop” or transpose to different places within the genome
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3
Q

what part of the genome is comprised of transposons in maize and corn?

A
  • roughly half
  • Usually nonfunctional, transposons is no longer active
  • Effort is suppressing transposons
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4
Q

what are the two major classes of transposons?

A

retroelements and DNA-type elements

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5
Q

what are retroelements?

A
  • make DNA copies of their RNA transcripts
  • Encode a unique enzyme required for their transposition (reverse transcriptase)
  • primarily in eukaryotes
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6
Q

what are the types of retroelements?

A

LTR retrotransposons, Retroviruses, and nonLTR-retroposons

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7
Q

what are DNA-type elements?

A
  • Directly propagate as DNA by jumping to new sites within the host genome.
  • Encode transposase enzyme
  • Sometimes will carry a second gene to dissolve a cointegrate between circular genomes that are a result of replicative transposition - resolvase
  • If they only make copies of themselves it is only transposase
  • common in both eukaryotes and prokaryotes
  • do not affect anything other than DNA
  • nonhomologous recombination
  • only transport their own sequence - no other DNA
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8
Q

LTR retrotransposons

A
  • have long terminal repeats
  • no infectious particle
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9
Q

retroviruses

A
  • closely related to LTR but produce a coat protein to form an infectious particle
  • also has LTRs
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10
Q

non-LTR retrotransposons

A
  • have a different mode of replication than LTR retrotransposons
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11
Q

what are the ways transposition can occur?

A
  • generate a new copy at a random site
  • or the transposon may transpose directly and leave a hole in the donor DNA
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12
Q

what affect can transposition have?

A
  • Transpositions to a new site can have a major impact on genome structure
  • Unequal crossover events between related transposons can cause rearrangements in the order of genes
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13
Q

transposition

A

the movement of a transposon

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14
Q

transposase

A
  • enzyme that cits and ligates DNA
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15
Q

where were transposons first identified?

A

in bacterial operons-spontaneous silencing

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16
Q

what is the simplest transposon?

A

IS elements

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17
Q

what are the two types of transposition?

A

replicative and nonreplicative

18
Q

what is the name of sequences that flank the transposase gene in a simple transposon?

A

ITR

19
Q

what is the rate of transposition?

A

10^-4
- rate of a particular gene picking up a transposon is about equal to rate of a gene undergoing spontaneous mutation

20
Q

what is the rate of spontaneous mutation?

A
  • 10^-5 to 10^-7 per generation
21
Q

what is the rate of reversion?

A

10^-6 to 10^-10 per generation
- reversion is 10^3 times less frequent than insertion

22
Q

what are ITRs?

A
  • inverted terminal repeats
  • define the ends of transposon, closelt related rather than identical
  • the recognition of these ends is critical in transposition and point mutations abort it
  • transposase is encoded by sequences within the transposon and between the ITRs
23
Q

what is the process of insertion elements?

A
  • staggered nicks are made at the target site
  • transposon joined to single-stranded ends
  • gaps at target site are filled in and sealed through direct repeats
24
Q

staggered ends

A
  • As a consequence of jumping, transposase lands on the target and cuts its own 3’ end and ligase to the target site and cutting the target and separating it.
  • Does not make a staggered end cut as an offset between the two ends. The amount of bases is the geometry of the transposase
  • varies between 4-13
25
Q

direct repeats

A

DNA repair on both sides to restore DNA after the staggered ends have been created; repair reaction

26
Q

length constant

A

the amount of bases of direct repeat generated in the target
- how far the cut is staggered

27
Q

what are composite transposons?

A
  • contain chromosomal DNA flanked by two IS elements of the same type
  • the IS elements onlt carry enzymes needed for transposition
  • central region may carry drug resistance
  • flanking IS elements can be in either orientation
28
Q

What constitutes arms of a composite transposon?

A

Composite transposons contain chromosomal DNA flanked by two IS elements of the same type

29
Q

are both arms of a composite transposon functional?

A

Composition transposons usually only one arm has a functional transposase
Only two of the IRs need to be cut for transposition

30
Q

direct repeat of IS elements

A
  • Direct repeats of the IS element recombine to excise material
  • Two identical IS elements oriented in direct repeats (or inverted) when recombination occurs, they gene needs to be twisted around for recombination to occur
  • This cuts out one of the transposons and everything in between
  • Directly excise all the materials in between
31
Q

inverted repeat recombination

A
  • inverts material
  • When the IS elements are lined up, the sequences are flipped, and homologous recombination occurs, you invert the sequences between the two IS elements
  • Inverted repeats result in inversion of the transposon (or any material between direct repeats)
32
Q

what can the loss of a transposon result in?

A

the restoration of gene function at the site of insertion

33
Q

precise excision

A

requires removal of one copy of the transposon and one of the direct repeats at the target site
- rare event that probably involves recombination between the two copies of the target site direct repeats

34
Q

Replicative transposition

A
  • proceeds through a cointegrate structure
  • Fusion of two original molecules; requires host replication machinery
  • proceeds through a strand crossover complex
  • requires site-specific recombination in order for the transposon to be on both copies of DNA
  • Replicative transposition involves attack of the 3’ end of the donor molecule to the target. It cuts and joins to the target at both ends of the transposon (donor)
  • A replication fork forms at one of the ends and extends the 3’ end of the target for leading and lagging strand synthesis
  • the resolution requires the transposon-encoded enzyme resolvase acting at the res site
35
Q

what are the two models for nonreplicative transposition?

A

cut and paste model (cleavage and ligation) and break and reunion model

36
Q

nonreplicative transposition - cut and paste model

A
  • Transposon is excised free of the donor and the 3’ ends attack the recipient DNA
  • Ligate it to the target cut site - 3’ end of transposon is ligated to 5’ end of the target
  • Repair of the gaps formed at both ends in order to connect donor and target DNA for transfer of transposons
  • Since already cut, there is a repair operation to generate the direct repeat
  • Cut both strands as with replicative only one strand is cut until the resolvase step
  • transposon is then transferred to target DNA
37
Q

break and reunion model

A
  • Tn5 shows a different type of double strand cutting mechanism involving hairpin formation
  • Tn5 is cleaved from flanking DNA
  • Tn5 and Tn10 transposases act as dimers
  • each subunit has an active site that creates ds cut at the end of the transposon and then creates a staggered cut at the target site
  • the geometry of the dimer determines the length of the offset in cuts
38
Q

what are the two outcomes of composite transposition?

A
  • Two IS10 modules can mobilize any region of DNA that lies between them
  • Transposon integrates into circular DNA
  • Transposon can move again back into host chromosome and there are two possible outcomes
  • If the inside cut direct repeat, the plasmid genes will move
  • The unit that moves is what contains the intact terminal repeats
  • New transposon configuration created by mobilization of - IS10 module in alternative orientation
  • If cut on the outside of the direct repeat, the IS elements and gene will move
39
Q

Which ends of the donor attack the target DNA and covalently join the target?

A

3’ end of the donor attack the 5’ end of the target DNA

40
Q

In the Strand Crossover Complex, which ends serve as primer for DNA synthesis?

A

3’ end of the target serves as a primer for DNA synthesis

molecular genetics (28 decks)

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