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COB Molecular > Lec 5. HR and Transposition > Flashcards

Lec 5. HR and Transposition Flashcards

1
Q

What are uses for HR?

A

Damage repair,Meiosis/Crossing over, and for rescuing stalled replication forks.

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2
Q

What are some implications for HR?

A

Heterozygosity, Linked genes and genomic integrity

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3
Q

What are the types of Transposons?

A

DNA only, Retroviral, Nonretroviral

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4
Q

Which is a more seamless way to resolve double stranded breaks? HR or NHEJ?

A

HR

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5
Q

Using HR causes crossing over in Meiosis resulting in

A

increase offspring diversity and helps link sister chromatids together.

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6
Q

What is one important characteristic about HR?

A

Maintains genome stablility

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7
Q

What does sister chromatids mean pertaining to templates?

A

A perfect template exists during replication. Occurs in late S phase or early G2.

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8
Q

What does a diploid genome mean?

A

Perfect or near perfect template always exists but may not be nearby

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9
Q

Pertaining to a diploid genomes near perfect template, why may it not be nearby?

A

Duplicate genes/elements dont have to be on the homologous chromosome.

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10
Q

What is the first step for HR to work?

A

Single-strand ends must be produced. Nuclease digests 5’ ends of broken strands.

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11
Q

What is the 2nd step for HR to work?

A

RAD51 helps the single strand invade a DNA duplex with an identical sequence (d-loop). This invasion mimics the RNA primer in DNA replication.

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12
Q

What is the 3rd step for HR to work?

A

DNA polymerse extends the invaded strand

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13
Q

During the 3rd step for HR, which pols are likely to be used to extend the invaded strand?

A

Pol δ (delta), Pol ζ (Zeta), and Pol η (eta)

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14
Q

During the 3rd step for HR, which pols are not likely to be used to extend the invaded strand?

A

Pol β, Pol ι (lota), Pol μ (mu). TDT

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15
Q

What is the 4th and final step for HR to work?

A

Disentanglement and ligation

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16
Q

How can you tell when a cell commits to HR versus NHEJ?

A

the creation of single stranded DNA overhangs.

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17
Q

During HR using sister chromatid as a template results in

A

Sealmess repair. Good copy.

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18
Q

During HR using a homolog as a template results in

A

Loss of heterozygosity.

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19
Q

What are the consequences of a loss of heterozygosity?

A

Exposes recessive traits and its a characteristic of cancer progression

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20
Q

During HR when does Crossing over occur?

A

During Meiosis I

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21
Q

During HR where does Crossing over tend to occur near?

A

Methylated CpG islands. H3K4me3 marked histones.

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22
Q

What is the first step for crossing over in HR?

A

Spo11 cleaves the DNA

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23
Q

What is Spo11?

A

Part of a Type 2 topo complex.

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24
Q

How many Spo11 copies are there and where are they located?

A

2 copies one for each strand

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25
Q

What is the 2nd step for crossing over in HR?

A

MRN nuclease complex processes and tethers the newly broken ends

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26
Q

What does the MRN nuclease complex contain?

A

Mre11, Nbs1/Nibrin,RAD50,WDCP

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27
Q

True or False? Mre11 nuclease has only endonuclease functions

A

False. Has endonuclease & exonucleasue functions

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28
Q

Is Mre11 sufficient?

A

No but it is necessary. Needs other proteins

29
Q

What is the 3rd step for crossing over in HR?

A

RPA protects overhangs and RAD51 replaces RPA and assists in D-loop formation/ strand invasion

30
Q

What is the 4th and final step for crossing over in HR?

A

Progression from D-loop structure proceeds as with repair

31
Q

What are the two options during HR?

A

Extend one strand NO crossover, Extend both strands crossover.

32
Q

What is a holliday junction?

A

a four-way DNA junction

33
Q

What are some implications for crossing over?

A

Aids in proper chromosome sorting, increases genetic diversity

34
Q

How does crossing over increase genetic diversity?

A

By uncoupling linked genes.

35
Q

What crossing over implication reduces aneuploidy risk?

A

Proper chromosome sorting

36
Q

What is one implication for stalled replication forks?

A

Maintains genome stability and integrity.

37
Q

When is the CMG helicase unable to bind and what happens?

A

CMG helicase is unable to bind after G1, broken forks must restart by HR

38
Q

What are the 3 steps for Fork-repair by BIR in S-phase?

A
  1. End resection RAD51 loading 2. D-loop formation. 3. BIR (break induced replication) by migrating D loop.
39
Q

What are the 3 steps for DSB repair by BIR in G2-phase?

A

1.End-resection RAD51 loading. 2. D-loop formation. 3. BIR by migrating D-loop

40
Q

What are the 4 steps for fork-repair in G2/M (MiDAS)?

A

1.Fork cleavage. 2.RAD52 recruitment. 3. D-loop formation by RAD52 dependent strand annealing. 4. BIR by migrating D-loop.

41
Q

In HR what happens when synthesis takes too long?

A

Usually happens during S phase unless replication takes longer which goes into G2. We use the helicase to keep it going not the CMG helicase.

42
Q

What happens when a replication fork stalls?

A

Replication fork reversal can occur

43
Q

What happens during fork reversal?

A

BRCA1 and BRCA 2 aid in restarting reversed replication forks.

44
Q

What does BRCA2 do?

A

Loads RAD51

45
Q

What class are DNA-only transposons?

A

Class II

46
Q

What circular intermediate on DNA-only Transposons mediates cut-and-paste jumps?

A

Transposase

47
Q

What do DNA-only transposons contain at their ends?

A

Short inverted repeats

48
Q

For DNA-only transposons, how are previous insertion sites known?

A

Residual duplication of host sequence

49
Q

DNA-only transposons are less common in human genome than

A

Class I transposons

50
Q

DNA-only transposons have similar mechanism to

A

V(D)J recombination in antibodies

51
Q

What is an example of DNA-only transposons?

A

Antibiotic resistence genes

52
Q

what class are Retroviral-like transposons?

A

Class 1

53
Q

What two enzymes are required for Retroviral-like transposons?

A

RNA-dependent DNA Pol (reverse transcriptase) and Integrase (endocuclease)

54
Q

Retroviral-like transposons contain what at their ends?

A

Long terminal repeats (LTR) contain promoter for RNA

55
Q

What is an example for Retroviral-like transposons

A

HERVs (human endogenous retroviruses

56
Q

True or False? HERVs are not silent

A

True

57
Q

Where are HERV proteins expressed in?

A

Embryogenesis, Mothers placenta

58
Q

In Embryogenesis expression of HERV genes does what?

A

Protect stem cells from viral infection

59
Q

In the mother’s placenta, what HERV protein is necessary for placental development?

A

Syncytin-1

60
Q

How could HERV elements play a role in causing cancer?

A

elicits an immune response that could be anti-tumorigenic

61
Q

What class are Nonretroviral-like transposons?

A

Class I

62
Q

What two enzymes are required for Nonretroviral-like transposons?

A

RNA-dependent DNA pol (reverse transcriptase) and Integrase (endonuclease)

63
Q

What are two key features of Nonretroviral-like transposons?

A

No terminal repeats and has a poly A tail in DNA sequence

64
Q

What are some examples of Nonretroviral-like transposons?

A

SINEs and LINEs

65
Q

What are 3 implications of transposons?

A

Can insert into coding region of genes, deletions and inversions of significant portions of chromosomes and the insertion is random.

66
Q

What is Conservative Site-Specific Recombination?

A

a process that enables genetic recombination between DNA molecules that contain short DNA sequences, which are bound by specific recombinase proteins

67
Q

True or False? Conservative Site-Specific Recombination occurs in viruses, humans but not bacteria

A

False. Occurs in Viruses,Bacteria but not humans

68
Q

What are three characteristics of Conservative Site-Specific Recombination?

A

Its a reversible temporary process, Site-specific/homologous, and recombinases act like topoisomerases in reverse (they put stuff together)

COB Molecular (36 decks)

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