Ch. 13 Homologous & Site-Specific Recombination (Exam 2)

Question 1

What is recombination?

Answer 1

The shuffling of the gene

Question 2

What is the greatest result of recombination?

Answer 2

Genetic diversity

Question 3

Define homologous recombination.

Answer 3

Genetic recombination in which nucleotide sequences are exchanged between 2 very similar or identical DNA molecules

Question 4

Homologous recombination was first recognized as being responsible for the process of…

Answer 4

Crossing over (in eukaryotes)

Question 5

What type of recombination do prokaryotes have?

Answer 5

Site-specific recombination

Question 6

What is site-specific recombination responsible for?

Answer 6

Integration of phage genomes into bacterial chromosomes

Question 7

What is the difference between homologous (generalized) recombination and site-specific (specialized) recombination?

Answer 7

Homologous recombination occurs at any point/site between 2 homologous sequences, but site-specific recombination does not require homologous sequences and occurs at a specific site

Question 8

If integrase enzymes catalyze the integration of a sequence in site-specific recombination, what does the reversal of this reaction do?

Answer 8

Excises the sequence

Question 9

Remember this mnemonic for the 5 stages of meiotic prophase.

Answer 9

Linsday Zaps Patients During Dialysis

Question 10

With the mnemonic in mind, list the 5 stages of meiotic prophase.

Answer 10

1) Leptotene
2) Zygotene
3) Pachytene
4) Diplotene
5) Diakinesis

Question 11

What happens during leptotene?

Answer 11

Chromosomes become visible and attach to the nuclear envelope

Question 12

What happens during zygotene?

Answer 12

Chromosomes pair in limited regions

Question 13

What happens during pachytene?

Answer 13

Total synapsis along the length of the chromosomes

Question 14

What happens during diplotene?

Answer 14

Chromosomes separate but are held together by chiasmata i.e. pinched together at certain points

Question 15

What happens during diakinesis?

Answer 15

Chromosomes condense & detach from nuclear envelope, and 4 chromatids become visible

Question 16

What are sister chromatids?

Answer 16

Two identical chromatids connected by a common kinetochore

Question 17

What is a chromatid?

Answer 17

Thread-like strands of the chromosome containing DNA duplexes

Question 18

What is a bivalent?

Answer 18

Pair of homologous chromosomes

Question 19

What is synapsis?

Answer 19

Chromosome pairing

Question 20

What is the synaptonemal complex?

Answer 20

Protein structure resulting from the synapsis of homologous chromosomes

Question 21

What are chiasmata?

Answer 21

Points at which chromosomes remain synapsed for the purpose of crossing over

Question 22

How do double-strand breaks (DSBs) develop in mitotic cells?

Answer 22

DNA damage

Question 23

How do DSBs factor into meiosis I?

Answer 23

They trigger homologous recombination

Question 24

When referring to DSBs, what is 5’ end resection?

Answer 24

The degradation of one strand on either side of the break creating a single-stranded 3’ end

Question 25

What 2 enzymes are responsible for 5' end resection?

Answer 25

Exonucleases and DNA helicase

Question 26

Seeing that 5' end resection results in a new single-stranded 3' end, what does this new 3' end do?

Answer 26

The 3' overhang created by the free 3' end invades a homologous region from the donor DNA duplex

Question 27

What are the 2 purposes for the 3' overhang in a DSB?

Answer 27

1) Serve as substrate for proteins needed to invade the donor strand 2) Serve as primer for DNA repair synthesis

Question 28

What is a recombinant joint?

Answer 28

Point at which an individual DNA strand crosses from one duplex to another i.e. the 3' overhang invading the donor duplex

Question 29

What structure forms after the 3' overhang displaces one strand of the donor duplex?

Answer 29

Displacement loop

Question 30

What is a double Holliday junction (dHJ)?

Answer 30

The result of the 3' overhang crossing over 2 homologous sites on the donor strand

Question 31

What is resolution?

Answer 31

Separation of the dHJ into 2 duplex molecules

Question 32

What determines the outcome of the DSB?

Answer 32

The position that the resolution nicks are cut

Question 33

What is the outcome of DSB repair when the donor duplex is nicked during resolution?

Answer 33

Crossover

Question 34

What is the outcome of DSB repair when the recipient duplex (i.e. the duplex broken at the very beginning) is nicked during resolution?

Answer 34

No crossover

Question 35

Generally describe the synthesis-dependent strand-annealing (SDSA) model.

Answer 35

It is the most relevant model for depicting mitotic homologous recombination from DSBs

Question 36

What are the 2 major results of synthesis-dependent strand-annealing (SDSA)?

Answer 36

No Holliday Junction forms, and the product is always noncrossover

Question 37

What is the mechanism behind no Holliday Junction forming from the SDSA?

Answer 37

The invasive strand does not form the second hook to make the dHJ and instead reanneals to the other end of the DSB

Question 38

What enzyme allows the DNA to reanneal after any DSB?

Answer 38

DNA ligase

Question 39

What is break-induced replication (BIR)?

Answer 39

Repair mechanism brought on DSBs

Question 40

What are fragile sites?

Answer 40

Sites very susceptible to DSBs

Question 41

How does BIR initiate repair from DSBs?

Answer 41

Using the homologous sequence from a repeat on a nonhomologous chromosome

Question 42

The result of the BIR repair is { } translocation

Answer 42

Nonreciprocal

Question 43

What happens after the nonreciprocal translocation?

Answer 43

The repeat sequence from the nonhomologous chromosome ends up becoming part of the chromosome originally broken from the DSB

Question 44

What bacterial protein complex can initiate homologous reproduction?

Answer 44

RecBCD

Question 45

What 2 enzyme activities does RecBCD consist of?

Answer 45

Nuclease & helicase

Question 46

What is a chi sequence?

Answer 46

Eight nucleotide consensus sequence that RecBCD binds to

Question 47

What do chi sequences provide for RecBCD?

Answer 47

Hotspots for recombination

Question 48

What is the function of the chi site (HINT: 2 parts)?

Answer 48

Trigger loss of RecD subunit and nuclease activity

Question 49

How does the chi site affect the RecBCD nuclease?

Answer 49

It loses RecD subunit and subsequently loses nuclease activity, which only retaining helicase activity

Question 50

What is happening to DNA as RecBCD is approaching a chi sequence?

Answer 50

The nuclease activity is degrading the DNA

Question 51

What are the subunits of the RuvABC complex?

Answer 51

1) RuvA 2) RuvB 3) RuvC

Question 52

What is the function of the RuvA subunit?

Answer 52

Bind to all 4 DNA strands to form tetramer

Question 53

What is the function of the RuvB subunit?

Answer 53

Helicase & ATPase activity (branch migration)

Question 54

What is the function of the RuvC subunit?

Answer 54

Cleaves junctions to form recombination intermediates

Question 55

How is phage lambda useful?

Answer 55

It is a good model for site-specific recombination

Question 56

Define lytic.

Answer 56

Cycle of phage reproduction after infecting a bacterium resulting in death of the bacterium

Question 57

Define lysogenic.

Answer 57

Pathway in which phage is integrated, but bacterium divides as normal and phage goes dormant

Question 58

Define prophage.

Answer 58

Condition in lysogenic state when phage DNA becomes integral part of bacterial chromosome

Question 59

Define excision.

Answer 59

Transition from lysogenic to lytic cycle, resulting int he release of prophage DNA from bacterial chromosome

Question 60

What is the enzyme that catalyzes site-specific recombination?

Answer 60

Recombinase

Question 61

What is the name for the group of enzymes involved in phage integration?

Answer 61

Integrase family

Question 62

What are attachment (att) sites?

Answer 62

Specific loci on bacterial and phage DNA where integration and excision occur by recombination

Question 63

What is the name of the attachment site on the bacterial chromosome?

Answer 63

attB

Question 64

What is the name of the attachment site on the phage?

Answer 64

attP

Question 65

While integration requires recognition between attB & attP, excision requires recognition between these two attachment sites...

Answer 65

attL and attR

Question 66

What 2 things does the Cre/lox system allow for?

Answer 66

Targeted mitotic recombination and gene knockout construction

Question 67

What is the general mechanism behind the Cre/lox system, starting from Cre protein production to how it affects the lox sites?

Answer 67

Presence of Cre protein results in Cre expression, which cleaves lox sites that are then rejoined behind a single lox site

Question 68

What happens to the material between the lox sites prior to rejoining?

Answer 68

Any material between the lox sites is excised

Question 69

Why can the Cre/lox system be considered another form of alternative splicing?

Answer 69

Exons between the sites can be excised