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Lecture 5 Flashcards

0
Q

strands of the helices are cleaved by endonuclease (RuvC)

A

resolution

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1
Q

Holliday junctions

A

only present transiently

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2
Q

What are the two outcomes of resolution?

A

crossing over-complete crossing over of genetic material (rare(

and gene converstion- small portion of genetic material change (90%)

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3
Q

When does meiotic recombination occur?

A

With paired maternal and paternal homologous chromsomes
repari usually occurs btw newly duplicated and identical helicases
-begins with a double strand breaks
yeast Spo11
Mre11 identifies the DNA damage
strand invations and doubl HOlliday junction follow
resolusion

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4
Q

What happens when crossing over and gene converstion occur in the same chromosome?

A

homologous recombination… multiple opportunities for genetic reassortment

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5
Q

What are regions of heteroduplex DNA?

A

A result of recombination….region where the strand from the mternal homolog is base paired with a strand from the paternal homolog

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6
Q

divergence from the expected distribution of alleles during meiosis
both strands are cut in the same way causing minimal exchange

A

gene conversion

  • this occures bc DNA synthesis during homologous recombinnation
  • repair of mismatch
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7
Q

transposons, mobile genetic elements

A

very specialized DNA segments that move from one postion in the genome to another
each w unique sets of genes
encodes enzyme that catalyzes movement of transposons

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8
Q

Why can transposons benefit the cell?

A

antibiotic resistence genes…
can produce genetic variation
no sequence homology requried

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9
Q

enzyme encoded by the transposone intself

acts on specific DNA sequence on each end of the transposon

A

tranposase

  • removes element
  • forms central intermediate
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10
Q

DNA only transposons

A

stay DNA the entire time.
use transposase
moves as DNA, either by cut and paste or replicative pathways
contain: gene encoding transposase
sequences recongized by the enzyme necessary for movement
lgly responseible for antibiotic resistance
P element

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11
Q

Retroviral like retrotransposons

A

directly repeated long tnermal repeats (LTRs) at each end
revers transcriptase and integrase
moves via an RNA intermediate prodcued by a promoter in the LTR

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12
Q

Nonrtroviral retrotransposons

A

Poly A at 3’ end of RNA transcript; 5’ end is often truncated
reverse transcriptase and endonuclease
moves via an RNA intermediate that is often produced from a enighboring promoter

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13
Q

Cut and past transpostion of DNA only Transposons

A

sequences on each end of the element bind transposase
two transposase molecules come together forming a loop juxtaposing two ends of element= transposome
cuts at base of loop; removes element and forms central intermediate

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14
Q

DNA only Transposons

A

Central intermediate catalyzes direct attach on random site of targe DNA

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15
Q

What does the staggered braek in DNA only transposons create?

A

breaks 2 phosphodiester bonds, creating new

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16
Q

Retroviruses

A

they inject their RNA into the genome

consist of a SS RNA genome packed into protein capsid with a virus-endcoded reverse transcriptase enzyme

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17
Q

synthesizes a DNA copy form RNA

A

reverse transcriptase enzyme

18
Q

creates 3’ OH ends on the DNA that attacks the host dNA for retroviruses

A

intergrase

19
Q

Retroviruse stages

A

RNA

20
Q

Retrovirus-like transposones

A

lack a coat, cannot leave resident cell

also uses integrase

21
Q

life cycle of bacterophage lambda

A

….

22
Q

means to generate DNA molecules of novel sequences

A

homologous recombination
-happens during meiosis
forms Holliday junctions- DNA intermediate containgin four DNA strands

23
Q

crossing over and gene conversion can occur

A

in the same chromosome

-multiple opportunities for genetic reassortment

24
Q

Regulation of HR

A

prevent inappropriate cross over

  • if recombination occurs btw repeated sequences could scramble the genome
  • mismatch repair pathway can interrupt HR btw poorly matched sequences preventing recombination events. Could help reserve speciation by blocking recombination btw closely related species
25
Q

enzyme encoded by the transposomn itself
acts on specific DNA sequence on each end of the transposon
allows insertion into a traget DNA site

A

transposase

26
Q

With DNA only transposons staggered breaks produce gaps that are repaired by DNA polymerase and sealed by ligase.

A

results in duplication of the target DNA’s insertion site

27
Q

double stranded break repair, if chromosome has just been replicated and there is an identical copy

A

transposon will be restored

28
Q

homologous recombination using homologus chromosome

A

transposon will not be restored

29
Q

nonhomologous end joining

A

will produce a mutation at the break site

30
Q

How is retroviruses unlike transposons?

A

they encode proteins that package their genetic info into virus particles that can infect other cells
-HIV

31
Q

consist of a SS RNA genome packed into protein capsid with a virus encoded reverse transcriptase (RT) enzyme
-RT synthesizes a DNA copy from RNA

A

retrovirus

32
Q

How does retroviruses respond during infection process?

A

viral RNA enters cell and is converted to a double stranded DNA molecule by RT activity

33
Q

In retroviruses, what creates 3’OH ends on the DNA that attacks the host DNA

A

integrase

34
Q

WHat are new viral RNAs synthesized by?

A

host’s RNA polymerase

35
Q

Transposition by retrovirus or retroviral-like transposon

A
  • integrase cuts one strand at each end of viral sequence
  • each exposed 3’ OH ends attacks a phosphodiester bond of target DNA
  • this inserts viral DNA into target, leaving gaps to be filled/ligated
  • leaves short repeats on each side of integrated DNA segment
36
Q

nonretroviaral transposons

A
  • comprise a lg portion of our genome
  • repeated sequences are mutated and truncated nonretroviral transposons
  • few retain abillity to move
  • L1 element (LINE)
37
Q

What does a nonretroviral transposon require to move?

A

endonuclease
reverse transcriptase
-do not encode the enzyme
-use enzymes from other transposons

38
Q

How do you transposition by a nonretroviral retrotransposon?

A
  • endonuclease and reverse transcriptase bind to L1 RNA
  • Endonuclease nicks the target DNA at insertion point
  • releases 3OH to serve as primer in revers transcription step
  • single-stranded DNA copy of L1 directly linked to target DNA
  • insertion of double-stranded DNA cope of L1 at target site
39
Q

Conservitive site specific recombination

A

mediates rearrangments of other tpes of mobile DNA elements

  • break and join two DNA doulbe helices on each molecule
  • depending on positions and relative orientations of recombination sites can get : DNA integration, DNA excision, or inversion
40
Q

How is conservative site specific recomination different from transposition?

A
  • need speicail sites on each DNA that serve as recognition sites for recominase
  • only transposon sequence is requrired for transposition
  • form transient high energy covalent bonds and use this energy to complete DNA rearrangment
  • no covalent protein/DNA intermediate in transposition
  • gaps must be filled by DNA polymerase and ligase
41
Q

Conservative site, if sites are in same orientation,

A

DNA sequence can be integrated or excised

42
Q

conservative site, if sites are invverted in orientation,

A

DNA sequneces is inverted instead of excised

43
Q

Site- specific recombination can be used to turn genes on and off

A

great tool for knocking out gene function in specific tissues in mice

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