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Molecular Biology > DNA Repication, Repair And Recombination III > Flashcards

DNA Repication, Repair And Recombination III Flashcards

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1
Q

Does meiotic recombination involve a single or double strand break?

A

Single

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2
Q

During recombination, what complex is present as the double stranded DNA is cut? Is this complex found at the 3’ or 5’ end?

A

Mre11 nuclease complex.

It identifies the DNA damage and processes the ends of the break.

It is found at the 3’ end.

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3
Q

During meiotic recombination, what protein catalyzes strand exchange (e.g. Crossing over)?

A

RecA

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4
Q

During meiotic recombination, what occurs after a double stranded break?

A

Strand invasion and a double Holliday junction formation.

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5
Q

What does homologous recombination mean?

A

Generation of DNA molecules of novel sequence

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6
Q

What is a Holliday junction?

A

A DNA intermediate containing four DNA strands from two different helices.

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7
Q

What enzyme cleaves the strands of Holliday junctions?

A

Endonuclease (RuvC)

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8
Q

What are the two outcomes of the resolution of meiotic recombination?

A

Crossing over

Gene conversion

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9
Q

In order for chromosomes to cross over, how should strands in each Holliday junction be cut?

A

In opposite directions.

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10
Q

True or false: branch migration requires a protein.

A

False. Branch migration can occur spontaneously or with a protein.

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11
Q

During branch migration, what occurs?

A

An unpaired region of one single strand displaces a paired region on the other.

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12
Q

Recombination results in regions of _____ DNA

A

Heteroduplex

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13
Q

What is meant by “heteroduplex DNA”?

A

It is a region where a strand from the maternal homolog is base-paired with a strand from the paternal homolog.

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14
Q

True or false: in meosis, each parent should make an equal contribution to the genetic material of the offspring.

A

True.

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15
Q

In meiosis, each parent should make an equal contribution to the genetic material of the offspring. However, there are rare cases in which this did not occur. What is this due to?

A

Gene conversion

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16
Q

What is gene conversion?

A

A divergence from the expected distribution of alleles during meiosis.

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17
Q

How does gene conversion occur?

A

DNA synthesis during homologous recombination.

Repair of mismatches in regions of heteroduplex DNA - as a consequence of repair, one allele is lost, and the other duplicated, resulting in “conversion” of one to the other.

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18
Q

What are the three types of transposons used during transpositional recombination?

A

DNA-only transposons

Retroviral-like retrotransposons

Nonretroviral retrotransposons

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19
Q

True or false: transposons are mobile genetic elements.

A

True.

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

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20
Q

Do transposons have a unique set of genes?

A

Yes

21
Q

Does the transposon or another element encode the enzyme that catalyzes the movement of a transposon?

A

The transposon

22
Q

What is a benefit of transposons in bacteria?

A

Transposons provide antibiotic resistance in bacteria.

23
Q

True or false: transposons occasionally rearrange neighboring DNA of host and can insert anywhere in the genome.

A

True

24
Q

What is a transposase?

A

An enzyme encoded by the transposon itself. IT acts on specific DNA sequences on each end of the transposon and allows insertion into a target DNA site.

25
Q

What are the three large classes of transposons?

A

Transposase

Reverse transcriptase and integrase

Reverse transcriptase and endonuclease

26
Q

How does transposase move DNA?

A

Either by cut-and-paste or replicative pathways.

27
Q

How does reverse transcriptase and integrase move DNA?

A

Via an RNA intermediate whose production is driven by a promoter in the LTR.

28
Q

How do reverse transcriptase and endonuclease move DNA?

A

Via an RNA intermediate that is often synthesized from a neighboring promoter.

29
Q

What do DNA-only transposons contain?

A

Gene encoding transposase

Sequences recognized by the enzyme necessary for movement.

30
Q

What is the loop of transposase called created by two transposase molecules?

A

Transpososome

31
Q

Transposase removes an element at the base of a loop to form what?

A

A central intermediate.

The central intermediate catalyzes direct attack on random site of target DNA.

32
Q

Once a central intermediate attacks a random site of target DNA, what does it create?

A

A staggered break; this is created by breaking 2 phosphodiester bonds and creating new ones as it joints the central indermediate and DNA together.

33
Q

Staggered breaks created by central intermediates are repaired and sealed by what enzymes?

A

DNA polymerase and ligase

34
Q

As the central intermediate has attacked the target DNA, a hole is created in the donor chromosome from where the intermediate left. How will the hole created be repaired?

A

By double stranded break repair.

If the chromosome has ben replicated and there is an identical copy, the transposon will be restored.

If homologous recombination using a homologous chromosome occurred, the transposon will not be restored.

If nonhomologous ends joins, a mutation will be produced at the break site.

35
Q

What enzyme do viruses use in order to convert RNA into DNA?

A

Reverse transcriptase

36
Q

What are the steps in transposition?

A

Entire transposon is transcribed by the host

Reverse transcriptase makes DS DNA copy via hybrid DNA/RNA intermediate.

DS DNA integrates into a site on the host chromosome using integrase.

37
Q

How is viral DNA inserted into the target?

A

Via integrase.

It cose one strand at each of the viral sequences. Each exposed 3’ OH ends attacks a phosphodiester bond of target DNA.

This inserts viral DNA into target, leaving gaps to be filled/ligated.

38
Q

What type of transposons comprise a large portion of the human genome?

A

Nonretroviral transposons

The repeated sequences are mutated and truncated nonretroviral transposons.

39
Q

True or false: transposons are highly mobile.

A

False. They are largely immobile.

40
Q

What do nonretroviral transposons require to move?

A

Endonuclease and reverse transcriptase.

Transposons do not encode the enzymes.

41
Q

What are the steps of transposition by nonretroviral retrotransposon?

A

Endonuclease and reverse transcriptase bind to L1 RNA

Endonuclease nicks the target DNA at insertion point; this releases 3’OH to serve as primer in reverse transcripton step.

SS DNA copy of L1 links to target DNA.

DS DNA copy of L1 is inserted at the target site.

42
Q

What is the function of conservative site specific recombination?

A

It mediates rearrangements of other types of mobile DNA elements (not transposons).

43
Q

How does conservative site specific recombination work?

A

It breaks and joins two DNA double helices on each molecule. It can involve DNA integration, excision or inversion.

44
Q

How is conservative site specific recombination different from transposition?

A

CSSR needs special sites on each DNA that serve as recognition sites for recombinase. A transposon sequence does not require this.

A transient high energy covalent bond is used as energy to complete DNA rearrangement. This is not required in transposition.

Gaps must be filled by DNA polymerase and ligase.

45
Q

Many bacterial viruses move in and out of the host genome via what mechanism?

A

Conservative site specific recombination.

46
Q

What does a bacteria use to adjust to its host (control flagellin genes)?

A

Conservative-site specific recombination.

47
Q

What is a function of site-specific recombination?

A

It can be used to turn genes on and off.

It is a tool for knocking out gene function in specific tissues in mice.

48
Q

True or false: crossing over and gene conversion can occur in the same chromosome.

A

True

Molecular Biology (12 decks)

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