Molecular Bio chapter 16 dna repair and crossing over practice questions

how can gene conversion occur during repair of a double stranded break?

Gene conversion occurs when the homologous chromosome is used as a repair template and changes which allele is expressed at the loci.

What causes the size of the D loop to increase during the formation of a holliday junction

Holliday junction is a branched nucleic acid structure that contains four double-stranded arms joined together The D-loop gets larger because it has to allow the newly synthesized DNA to unpair from the template strand and pair with complementary damaged duplex strand.

What is homologoius recombination and what is required for its initiation

Homologous recombination is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. A double stranded single-stranded 3' extension of DNA and double stranded breaks in meiosis.

what influences how much sequence will be resected when a double stranded break is repaired by the single strand resection pathway

Single-strand annealing (SSA) occurs at double-strand breaks between direct repeats.- Requires only a single DNA duplex.- Resection of double-strand break endsresults in 3′-single-stranded tails.- Complementarity between the repeats allows for annealing of the single strands.- The sequence between the direct repeats is deleted after SSA is completed.- Deletions up to 100kb can be produced.

name the bacterial and eukaryotic strand exchange recombinases

The recombinase is RecA in bacteria and Rad51 in eukaryotes

Which of the following statements correctly describes why unintended double strand breaks can be severely damaging?

There is no intact complementary strand to use as a template for repair

what initiates homologous recombination and what are its outcomes

a DSB and the hopefully the exchange of genetic material, but depending on how it is resolved either a recombinant or non recombinant product can form.

during D loop formation, which of the following is true?

the non template duplex does not base pair with the damaged duplex

What mechanisms can resolve the structure of the replication fork.

1. Cleavage and fork restoration 2. degradation of paired newly synthesized strands 3. reversal of regression.

Briefly describe the way the ends are processed in the two main NHEJ pathways

1. When blunt ends are generated and nulceases or polymerases remove a few nucleotides on each side and then they are aligned and ligated. 2. the tails are trimmed back to the base paired DNA (microhomology) and the gaps are filled in by repair polymerases and the ends are ligated.

What are holliday junctions and how are they formed?

A Holliday junction is a branched nucleic acid structure that contains four double-stranded arms joined. They are formed from genetic recombination

What is the function of single-strand binding proteins

Attach to single-stranded DNA and prevent secondary structures from forming

When is homology directed repair most likely to be mutagenic

During G1, because repair template is usually a homologous chromosome

Describe how homology directed repair can restore a collapsed replication fork

1. Degradation to expose 3' ssdna 2. Strand invasion of the damaged arm into the undamaged arm to form a D-loop. 3. Invading strand acts a primer for DNA synthesis. 4. The other single strand of DNA of the damaged duplex also specifically interacts with the undamaged arm by binding to the displaced strand of the D-loop. 5. Single strands from each parental duplex are reciprocally exchanged between parental duplexes. 6. Replisome is assembled to resume dna synthesis on the lagging strand.

What is a D-loop

D-loop- three stranded structure contained the paired damaged ssDNA and its complementary strand of undamaged DNA along with the displaced template strand on the undamaged duplexStrand invasion- ssDNA from one end of the damaged duplex locates and pair with its complementary strand in the undamaged duplexHeteroduplex- region in which a single strand from one DNA molecule is base-paired with a single strand from a different DNA molecule

How can homologous recombination cause chromosomal rearrangements

Errors during homologous recombination (ectopic recombination) cause chromosomal abnormalities and these errors are primarily due to presence of repetitive DNA sequence.

why do double strand breaks lead to loss of heterozygousity

If a homologous chromosome is used (instead of a sister chromatid) to repair a double-strand break, one of the parental alleles of the affected gene can be replaced by the other allele, leading to loss of heterozygosity.

how does reca monomers induce d-loop formation

Invasion of a duplex DNA by RecA-coated ssDNA from another duplex that has suffered a DS-break - forms a D-loop.

Once a holliday junction forms what affects the size of the heteroduplex DNA. What enzymes resolve them

Strand invasion generates a Holliday junction that can then move along the DNA by branch migration. This migration increases the length of the DNA exchanged. Resolvases resolve the junctions.

Explain SDSA

Synthesis-dependent strand-annealing 3' OH of invading strand acts as a primer to initiate synthesis using the undamaged strand as a template, as D loop moves along the DNA the newly synthesized DNA is released from the template strand and base pairs with the complementary strand in the damaged duplex (the invading strand)

What are the two major strategies for double-stranded break repair? Briefly describe them and which is more likely to cause a mutation

The two main mechanisms by which cells can repair Double stranded breaks are are homologous recombination (HR) and nonhomologous end joining (NHEJ).In homologous recombination a segment of an undamaged sister chromatid is used as a template to repair a DSB in the damaged sister chromatid. [Here you need another chromosome]During nonhomologous end joining, the two broken ends of DNA are simply pieced back together (see Figure 19.22).This can lead to more mutations as it it chewd up and then just stuck together.

Where does a holliday junction get cleaved to form non recombinant and recombinant DNA

Vertical for recombinant horizontal for non recombinant

when is gene converison least likely to occur

g2

which key meiotic processes involve a modified homolgy directed repair process

homologous recombination

what correctly identifies when a D loop forms?

in homology directed repair

Where does NHEJ usually occur

non dividing cells

Briefly describe the four main phases of homologous DNA repair

● Generation of ssDNA at break ● Pairing of one single-stranded end with the intact duplex, forming heteroduplex ● Repair of the damaged duplex using the undamaged duplex as a template ● Separation of the two duplexes