DNA Replication, Repair and Recombination 3 (Lec 5)

Question 1

What is a holiday junction?

Answer 1

DNA intermediate containing four DNA strands from two different helices; structures are present only transeintly

Question 2

What resolves a holiday junction?

Answer 2

strands of the helices are cleaved by endonuclease (RuvC)

Question 3

What are the two outcomes of Holiday junction resolution?

Answer 3

crossing over, gene conversion

Question 4

Meiotic recombination occurs between what types of chromosomes?

Answer 4

paired maternal and paternal

Question 5

Meiotic recombination begins with what? What happens after that?

Answer 5

begins with a double strand break; then strand invasion and double holiday junction formation follow, resolution

Question 6

True or False?

in homologous recombination, crossing over and gene conversion can occur in the same chromosome

Answer 6

true, allows for multiple opportunities for genetic reassortment

Question 7

Divergence from the expected distribution of alleles during meiosis is due to what?

Answer 7

gene conversion

Question 8

How does gene conversion occur?

Answer 8

DNA synthesis during homologous recombination, repair of mismatches in regions of heteroduplex DNA

Question 9

HR must be regulated because recombination between repeated sequences could do what?

Answer 9

scramble the genome

Question 10

Which repair pathway can interrupt HR and stop recombination events?

Answer 10

mismatch repair

Question 11

Describe transposons

Answer 11

specialized segments of DNA that move from one position in the genome to another

Question 12

What benefits can transposons offer?

Answer 12

antibiotic resistance in bacteria, produce genetic variation, no sequence homology required meaning they can insert anywhere

Question 13

What two techniques do DNA only transposons utilize?

Answer 13

cut and past transposition or replicative transposition

Question 14

How does cut and paste transposition work?

Answer 14

sequences on each end of element bind transposase, two transposase molecules come together forming a loop juxtaposing two ends of element, transposase introduces cuts at base of loop - removes element and forms central intermediate, central intermediate catalyzes direct attack on random site of target DNA, hole in the donor chromosome is repaired

Question 15

Retroviruses, unlike tranposons, encode proteins that package their genetic info into virus particles that can do what?

Answer 15

infect other cells

Question 16

Retroviruses use what type of enzyme to infect cell?

Answer 16

reverse transcriptase

Question 17

What does integrate do in retroviruses?

Answer 17

creates 3’-OH on the DNA that attacks the host DNA

Question 18

In regards to retroviruses, what synthesizes the new viral RNA?

Answer 18

host’s RNA polymerase

Question 19

How do retrovirus-like transposons work?

Answer 19

entire transposon is transcribed by host, reverse transcriptase makes a double-stranded DNA copy of RNA molecule via hybrid DNA/RNA intermediate, double-stranded DNA integrates into site on chromosome using integral, encoded by element

Question 20

Describe nonretroviral transposons

Answer 20

comprise a large portion of our genome, most are immobile but few retain ability to move, require endonuclease and reverse transcriptase to move

Question 21

How do nonretroviral transposons work?

Answer 21

endonuclease and reverse transcriptase bind to L1 RNA, endonuclease nicks the target DNA at insertion point, release 3’-OH to serve as primer in reverse transcription step, single-stranded DNA copy of L1 directly linked to target DNA, insertion of double-stranded DNA copy of L1 at target site

Question 22

What does conservative site specific recombination mediate?

Answer 22

mediates rearrangements of other types of mobile DNA elements

Question 23

How does conservative site specific recombination work?

Answer 23

break and join two DNA helices on each molecule

Question 24

How does conservative site recombination differ from transposition?

Answer 24

needs special sites on each DNA that serve as recognition sites for recombinase, forms transient high energy covalent bonds and use this energy to complete DNA rearrangement

Question 25

What does the outcome of conservative site specific recombination depend on?

Answer 25

orientation of DNA sites

A. if sites are in same orientation, DNA sequence can be excised

B. if sites are inverted in orientation, DNA sequence is inverted instead of excised

Question 26

Can site-specific recombination be used to turn genes on and off?

Answer 26

yes