Lecture 5

Question 0

strands of the helices are cleaved by endonuclease (RuvC)

Answer 0

resolution

Question 1

Holliday junctions

Answer 1

only present transiently

Question 2

What are the two outcomes of resolution?

Answer 2

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

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

Question 3

When does meiotic recombination occur?

Answer 3

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

Question 4

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

Answer 4

homologous recombination… multiple opportunities for genetic reassortment

Question 5

What are regions of heteroduplex DNA?

Answer 5

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

Question 6

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

Answer 6

gene conversion

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

Question 7

transposons, mobile genetic elements

Answer 7

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

Question 8

Why can transposons benefit the cell?

Answer 8

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

Question 9

enzyme encoded by the transposone intself

acts on specific DNA sequence on each end of the transposon

Answer 9

tranposase

• removes element
• forms central intermediate

Question 10

DNA only transposons

Answer 10

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

Question 11

Retroviral like retrotransposons

Answer 11

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

Question 12

Nonrtroviral retrotransposons

Answer 12

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

Question 13

Cut and past transpostion of DNA only Transposons

Answer 13

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

Question 14

DNA only Transposons

Answer 14

Central intermediate catalyzes direct attach on random site of targe DNA

Question 15

What does the staggered braek in DNA only transposons create?

Answer 15

breaks 2 phosphodiester bonds, creating new

Question 16

Retroviruses

Answer 16

they inject their RNA into the genome

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

Question 17

synthesizes a DNA copy form RNA

Answer 17

reverse transcriptase enzyme

Question 18

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

Answer 18

intergrase

Question 19

Retroviruse stages

Answer 19

RNA

Question 20

Retrovirus-like transposones

Answer 20

lack a coat, cannot leave resident cell

also uses integrase

Question 21

life cycle of bacterophage lambda

Answer 21

….

Question 22

means to generate DNA molecules of novel sequences

Answer 22

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

Question 23

crossing over and gene conversion can occur

Answer 23

in the same chromosome

-multiple opportunities for genetic reassortment

Question 24

Regulation of HR

Answer 24

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

Question 25

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

Answer 25

transposase

Question 26

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

Answer 26

results in duplication of the target DNA's insertion site

Question 27

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

Answer 27

transposon will be restored

Question 28

homologous recombination using homologus chromosome

Answer 28

transposon will not be restored

Question 29

nonhomologous end joining

Answer 29

will produce a mutation at the break site

Question 30

How is retroviruses unlike transposons?

Answer 30

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

Question 31

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

Answer 31

retrovirus

Question 32

How does retroviruses respond during infection process?

Answer 32

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

Question 33

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

Answer 33

integrase

Question 34

WHat are new viral RNAs synthesized by?

Answer 34

host's RNA polymerase

Question 35

Transposition by retrovirus or retroviral-like transposon

Answer 35

- 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

Question 36

nonretroviaral transposons

Answer 36

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

Question 37

What does a nonretroviral transposon require to move?

Answer 37

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

Question 38

How do you transposition by a nonretroviral retrotransposon?

Answer 38

- 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

Question 39

Conservitive site specific recombination

Answer 39

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

Question 40

How is conservative site specific recomination different from transposition?

Answer 40

- 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

Question 41

Conservative site, if sites are in same orientation,

Answer 41

DNA sequence can be integrated or excised

Question 42

conservative site, if sites are invverted in orientation,

Answer 42

DNA sequneces is inverted instead of excised

Question 43

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

Answer 43

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