10 - recombination

Question 1

What are the 4 different types of recombination?

Answer 1

• homologous
• site-specific
• illegitimate
• transposition

Question 2

What is transposition recombination?

Answer 2

when one transposon jumps from one location to the other or makes a copy and the copy jumps

Question 3

what can recombination lead to?

Answer 3

• deletions
• insertions
• sequence duplication
• small changes - single base pair substitution

Question 4

when does illegitimate recombination happen?

Answer 4

no homology

Question 5

how does HIV use recombination?

Answer 5

• made from 2 RNA molecules
• recognised receptor on outside of cell and enters the cell and releases RNA
• RNA is reverse transcribed into double stranded DNA
• DNA enters nucleus via illegitimate recombination
  -DNA is transcribed, more RNA is made
• new viruses made

Question 6

what is the process of HIV DNA entering the genome?

Answer 6

• viral ends resected to make 3’ overhang 2bp long
• host DNA strand cleaved 5pb apart
• viral strands ligates to cleaved ends by intergrase
• gaps are repaired by host enzymes
• can happen anywhere in the genome

Question 7

what is an example onsite specific recombination?

Answer 7

phage lambda integrating into E. coli chromosome via site-specific recombination

Question 8

What is the lytic cycle?

Answer 8

when a phage hijacks the cell to make more phages, cell the dies

Question 9

What is the lysogenic cycle?

Answer 9

• when DNA is integrated into the host genome

Question 10

What is a prophage?

Answer 10

bacterial cell that has a viral DNA in its genome

Question 11

What is the process of the lytic cycle?

Answer 11

• phage attaches to host cell and injects DNA
• phage DNA circularises
• new phage DNA and proteins are made and viruses assembled
• cell lyses, releasing viruses

Question 12

What is the process of the lysogenic cycle?

Answer 12

• phage attaches to host cell and injects DNA
• phage DNA circularises
• phage DNA integrates within bacterial chromosome
• cell is now a prophage
• bacteria reproduce
• sometimes bacterial will excise from chromosome and enter the lytic cycle

Question 13

what is the details of site specific recombination?

Answer 13

• recombining molecules share a little homology
• ## either side of this is inverted repeats - recombination binding sites

Question 14

Why is homologous recombination important?

Answer 14

genome stability
- repair of broken forks and DSBs
- accurate chromosome segregation in meiosis

genetic diversity
- meiotic and mitotic recombination of different alleles
- HGT in bacteria

Question 15

Explain the process of homologous recombination

Answer 15

• DSB
• DSB resection- helicase and 5’-3’ exonuclease make 3’ overhangs
• strand invasion - 3’ overhang finds homologous chromosome and invades it via base pairing
• repair synthesis - DNA polymerase extends broken strand
• double holiday junction - repair is finished but connected by holiday junctions
• HJ resolution - can either have no cross over were 2 strands still contain original DNA or 2 stranded cross over

Question 16

What is the role of RAD51 in DSB repair?

Answer 16

• Rad51 polymerises into a filament on single stranded DNA by BRCA2
• it finds the homology then invades the strand
• it is then removed so extension can happen

Question 17

What is the role of BRCA2 on DSB repair?

Answer 17

ads the Rad51 onto ssDNA filaments

Question 18

Explain single holiday junction resolution

Answer 18

• one cross over happens

Question 19

What is Spo11?

Answer 19

• endonuclease expressed in meiosis only
• will break both strands in sister sister chromatids both never both sister chromatids

Question 20

what does it mean if the recombination frequency (RF) is high?

Answer 20

the genes are far away on the chromosome

Question 21

what does it mean if the recombination frequency (RF) is low?

Answer 21

the genes are close on the chromosome

Question 22

What does it mean if the Rf is < 50%?

Answer 22

genes are linked

Question 23

What does it mean if Rf = 50%?

Answer 23

genes are not linked

Question 24

How are linkage maps built?

Answer 24

• highest Rf = furthest away
• smaller Rf = closer together

Question 25

Draw out different resolutions of single holiday junctions

Answer 25

look at notes

Question 26

Draw out different resolutions of double holiday junctions

Answer 26

look at notes

Question 27

Give 7 things that hold up replication and may cause it to pause

Answer 27

- R-loops (highly transcribed genes) - G-quartet (4 G bases) - tRNA genes - inactive ori - heterochromatin - telomeres and centromeres - transcription

Question 28

Why is replication pausing an issue?

Answer 28

- replication forks are unstable structures

Question 29

What are stalled replication forks?

Answer 29

forks which cannot get through a replication barrier

Question 30

Explain the process of replication fork repair draw it out too

Answer 30

- 3' overhang created - this ss DNA then looks for homology - invades replicating strand - extension - HJ resolves then cuts the join - replication fork continues

Question 31

give 3 ways a broken replication fork can be made

Answer 31

- ssDNA breaking - nick not being fixed - stalled fork becoming a regressed fork and the HJ resolves breaking it

Question 32

explain the similarities between human Rad51 and E.coli RecA

Answer 32

- highly conserved

Question 33

Why have cells evolved homologous replication?

Answer 33

- repair broken replication forks - eukaryotes evolved later which needed them for genetic diversity, which is why this wasnt evolved first

Question 34

What does the fertility plasmid in bacteria code for?

Answer 34

- proteins that make the pillus

Question 35

Why is recombination not possible in bacteria?

Answer 35

- there would need to be an even number of cross overs - or else there would be 3 chromosomes generated (instead of original 4) - would then generate 2 DSBs - need a mechanism to check number of cross overs - has not happened

Question 36

Why have large animals evolved down regulation of telomerase?

Answer 36

- anti cancer mechanism - if cells divide uncontrollable will run out of telomeres and die - only stem cells have telomerase - no telomerase can lead to cancer also as genome instability - they have a longer life and more cells