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Biol200 > DNA repair and recombination > Flashcards

DNA repair and recombination Flashcards

1
Q

What are the different types of damage that DNA is constantly subject to? (4)

A

DNA is subject to
hydrolytic depurination,
cytosine deamination,
guanidine oxidation,
and methylation of adenine

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2
Q

What are mutations?

A

Mutations are permanent, transmissible changes to the genetic material of a cell or organism.

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3
Q

What are mutagens?

A

Mutagens are chemical compounds, ultraviolet (UV) radiation, or ionizing radiation that increase the frequency of mutations.

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4
Q

Mutations can occur… (3 ways)

A

spontaneously
by transposable elements
by errors during replication

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5
Q

What are carcinogens?

A

Carcinogens are agents that cause cancer, and many of them are mutagens.

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6
Q

What is the importance of DNA stability?

A

DNA stability is important because DNA is the information repository of the cell.

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7
Q

Which DNA polymerases have a proofreading activity in eukaryotes?

A

DNA polymerases e and d, but not a, have a 3’ to 5’ exonuclease or “proofreading” activity.

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8
Q

What is the mechanism of proof reading?

A

Incorporation of an incorrect base causes the polymerase to pause. The 3’ end of the new strand is free to move to the 3’ -> 5’ exonuclease site and the mispaired base is removed.

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9
Q

What is the most common point mutation?

A

The most common point mutation is a single base change from C to T.

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10
Q

How does the point mutation is change from C to T happen?

A

Deamination
(can also produce uracil from cytsine)
amino group not so stable and this reaction just happens.

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11
Q

At what step must the base excision repair occur?

A

After the deamination and before the replication

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12
Q

In a mismatched base pair,
which base is correct and which base is wrong?

A

T-G mismatches almost always result from deamination of C to U or 5mC to T, so T is wrong
and should be replaced by C.

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13
Q

What are the steps of the base excision repair? (4)

A
  1. The DNA glycosylase breaks the bond between T and the sugarphosphate backbone
  2. The APEI endonuclease cuts the DNA strand where it is missing a base
  3. AP lyase (part of DNA pol beta) removes deoxyribose phosphate
  4. A special DNA polymerase (beta) inserts C using G as template, DNA ligase repairs
    sugar-phosphate backbone
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14
Q

What is the difference between exonuclease vs endonuclease?

A

exo: cuts at the end of the strand
endo: cuts in the middle

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15
Q

What types of error does the process of Mismatch Excision Repair repair?

A

Mismatch excision repair fixes errors introduced during replication, including :
-basepair mismatches
-insertions or deletions of one or a few nucleotides.

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16
Q

During a Mismatch Excision Repair, which strand is the wrong one?

A

the newly synthesized strand is the wrong one, there are mechanisms to recognize which strand this is

17
Q

When does a Mismatch Excision Repair happen?

A

after DNA replication

18
Q

What are the steps for Mismatch Excision Repair? (4)

A
  1. MSH2 and MSH6 recognize the mismatch and distinguish the newly synthesized (daughter) strand.
  2. This triggers binding and activity of MLH1 endonuclease (dimerized with PMS2). MLH1 cuts the newly synthesized strand.
  3. DNA helicase unwinds and DNA exonuclease digests several nucleotides of the daughter strand.
  4. DNA polymerase (Pol d) fills in the missing nucleotides using the other strand as template and ligase repairs the sugar-phosphate backbone.
19
Q

What does Nucleotide Excision Repair fix?

A

DNA regions where chemically modified bases locally distort the double helix.

20
Q

What is the thymine-thymine dimer?

A

distortion of the helix caused by UV irradiation, where two adjacent thymine bases become chemically bonded to each other.

21
Q

Chemicals that can bind to DNA
________, including many carcinogens, also locally _______ the double _________.

A

bases
distort
helix

22
Q

What are the steps of Nucleotide Excision Repair?

A
  1. XP-C and 23B proteins recognize the distorted double helix.
  2. TFIIH, XP-G, and RPA unwind the helix to make a bubble of ~25 nucleotides.
  3. XP-F and XP-G cut the damaged strand.
  4. DNA polymerase fills in the missing nucleotides using the other strand as template and ligase repairs the sugarphosphate backbone.
23
Q

What are the names XP-n derive from ?

A

The names XP-n derive from xeroderma pigmentosum, a genetic disease that causes a high disposition to UV-induced cancer. Mutations that affect XP proteins cause this disease.

24
Q

What happens if a thymine-thymine dimer is not repaired and it enters a replication fork? (4)

A
  • Normal replicative DNA polymerases (Pol d and Pol e) stall when they reach a thymine-thymine dimer.
  • A special translesion polymerase (Pol eta n) can read through the thymine-thymine dimer, but this polymerase lacks proofreading activity.
  • So the region in the vicinity of the thymine-thymine dimer will be likely to contain mutations caused by replication errors.
  • Eventually Pol n will get replaced by one of the normal replicative DNA polymerases.
25
Q

What causes double-strand breaks in DNA ?

A

Radiation (X-rays, g-rays) and some anticancer drugs (bleomycin for example)

26
Q

What happens if a double-strand break is not repaired?

A

then the part of the chromosome distal to the break would be lost at the next cell
division, probably causing lethality.

27
Q

What does Double-Strand Break Repair End Joining do?

A

rejoins the broken chromosome ends but base pairs are usually
lost at the joining point, producing a small deletion

28
Q

What are the steps of Double-Strand Break Repair End Joining? (3)

A
  1. Ku and DNA-PK bind the end of a double-strand break (DSB).
  2. When two DSBs bound by these proteins come together, they recruit nucleases that remove several bases.
  3. The two double-stranded molecules are then ligated together.
29
Q

Does the mechanism of Double-Strand Break Repair End Joining ensure that what is ligated together originated from adjacent parts of the same chromosome?

A

No, it does not ensure that what is ligated together originated from adjacent parts of the same chromosome, so it can fuse DSBs originating from different chromosomes or far apart on the same one, producing chromosomal rearrangements.

30
Q

What happens during the process of Double-strand Break Repair by Homologous
Recombination?

A
  • The damaged DNA sequence is replaced with a copy of an undamaged copy of the same sequence on the homologous chromosome in diploid organisms.
  • This involves an exchange of strands between separate DNA
    molecules, a process known as recombination.
31
Q

What are the steps of Double-strand Break Repair by Homologous Recombination ? (7)

A
  1. Replication fork collapse
  2. 5’-exonuclease acts on broken end. Other daughter strand ligated to repaired parental strand in unbroken chromosome.
  3. RecA- or Rad51-mediated strand invasion
  4. Branch migration
  5. Cuts strands at crossover
  6. Ligate ends
  7. Rebuild replication fork and continue replication
32
Q
  • A similar mechanism can repair a double-strand break in a chromosome and can also produce an _________ of segments between two double-stranded DNA molecules.
  • The __________ structure that involves all four strands can be resolved in two alternative ways. One regenerates the original ____________,
    while the other produces two _____________ strands and two
    recombinant strands containing DNA from both parents.
A

exchange
Holliday
chromosomes
uniparental

Biol200 (12 decks)

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