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Molecular Biology > Ch. 13 Homologous & Site-Specific Recombination (Exam 2) > Flashcards

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

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1
Q

What is recombination?

A

The shuffling of the gene

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2
Q

What is the greatest result of recombination?

A

Genetic diversity

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3
Q

Define homologous recombination.

A

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

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4
Q

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

A

Crossing over (in eukaryotes)

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5
Q

What type of recombination do prokaryotes have?

A

Site-specific recombination

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6
Q

What is site-specific recombination responsible for?

A

Integration of phage genomes into bacterial chromosomes

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7
Q

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

A

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

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8
Q

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

A

Excises the sequence

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9
Q

Remember this mnemonic for the 5 stages of meiotic prophase.

A

Linsday Zaps Patients During Dialysis

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10
Q

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

A

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

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11
Q

What happens during leptotene?

A

Chromosomes become visible and attach to the nuclear envelope

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12
Q

What happens during zygotene?

A

Chromosomes pair in limited regions

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13
Q

What happens during pachytene?

A

Total synapsis along the length of the chromosomes

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14
Q

What happens during diplotene?

A

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

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15
Q

What happens during diakinesis?

A

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

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16
Q

What are sister chromatids?

A

Two identical chromatids connected by a common kinetochore

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17
Q

What is a chromatid?

A

Thread-like strands of the chromosome containing DNA duplexes

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18
Q

What is a bivalent?

A

Pair of homologous chromosomes

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19
Q

What is synapsis?

A

Chromosome pairing

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20
Q

What is the synaptonemal complex?

A

Protein structure resulting from the synapsis of homologous chromosomes

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21
Q

What are chiasmata?

A

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

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22
Q

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

A

DNA damage

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23
Q

How do DSBs factor into meiosis I?

A

They trigger homologous recombination

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24
Q

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

A

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

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25
Q

What 2 enzymes are responsible for 5’ end resection?

A

Exonucleases and DNA helicase

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26
Q

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

A

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

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27
Q

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

A

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

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28
Q

What is a recombinant joint?

A

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

29
Q

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

A

Displacement loop

30
Q

What is a double Holliday junction (dHJ)?

A

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

31
Q

What is resolution?

A

Separation of the dHJ into 2 duplex molecules

32
Q

What determines the outcome of the DSB?

A

The position that the resolution nicks are cut

33
Q

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

A

Crossover

34
Q

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

A

No crossover

35
Q

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

A

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

36
Q

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

A

No Holliday Junction forms, and the product is always noncrossover

37
Q

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

A

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

38
Q

What enzyme allows the DNA to reanneal after any DSB?

A

DNA ligase

39
Q

What is break-induced replication (BIR)?

A

Repair mechanism brought on DSBs

40
Q

What are fragile sites?

A

Sites very susceptible to DSBs

41
Q

How does BIR initiate repair from DSBs?

A

Using the homologous sequence from a repeat on a nonhomologous chromosome

42
Q

The result of the BIR repair is { } translocation

A

Nonreciprocal

43
Q

What happens after the nonreciprocal translocation?

A

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

44
Q

What bacterial protein complex can initiate homologous reproduction?

A

RecBCD

45
Q

What 2 enzyme activities does RecBCD consist of?

A

Nuclease & helicase

46
Q

What is a chi sequence?

A

Eight nucleotide consensus sequence that RecBCD binds to

47
Q

What do chi sequences provide for RecBCD?

A

Hotspots for recombination

48
Q

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

A

Trigger loss of RecD subunit and nuclease activity

49
Q

How does the chi site affect the RecBCD nuclease?

A

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

50
Q

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

A

The nuclease activity is degrading the DNA

51
Q

What are the subunits of the RuvABC complex?

A

1) RuvA
2) RuvB
3) RuvC

52
Q

What is the function of the RuvA subunit?

A

Bind to all 4 DNA strands to form tetramer

53
Q

What is the function of the RuvB subunit?

A

Helicase & ATPase activity (branch migration)

54
Q

What is the function of the RuvC subunit?

A

Cleaves junctions to form recombination intermediates

55
Q

How is phage lambda useful?

A

It is a good model for site-specific recombination

56
Q

Define lytic.

A

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

57
Q

Define lysogenic.

A

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

58
Q

Define prophage.

A

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

59
Q

Define excision.

A

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

60
Q

What is the enzyme that catalyzes site-specific recombination?

A

Recombinase

61
Q

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

A

Integrase family

62
Q

What are attachment (att) sites?

A

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

63
Q

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

A

attB

64
Q

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

A

attP

65
Q

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

A

attL and attR

66
Q

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

A

Targeted mitotic recombination and gene knockout construction

67
Q

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

A

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

68
Q

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

A

Any material between the lox sites is excised

69
Q

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

A

Exons between the sites can be excised

Molecular Biology (21 decks)

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