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Molec and Cell > Chapter 5: DNA Replication, Repair, and Recombination > Flashcards

Chapter 5: DNA Replication, Repair, and Recombination Flashcards

1
Q

What is the error rate of P activity in DNA polymerase?

A

1 x 10^5

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2
Q

What is the error rate of E activity in DNA polymerase?

A

1 x 10^2

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3
Q

What is the combined error rate of total DNA polymerase activity?

A

1 x 10^7

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4
Q

This function occurs at the E site of DNA polymerase; identifies the polymerization of incorrect nucleic acids

A

exonucleolytic proofreading

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5
Q

This process occurs soon after DNA replication and before ligase activity seals the “nicks” of Okazaki fragments

A

Eukaryotic strand-directed mismatch repair

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6
Q

What is the error rate of eukaryotic strand-directed mismatch repair?

A

1 x 10^3

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7
Q

these are a common artifact after DNA synthesis that serve as markers to identify new strands

A

“nicks”

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8
Q

What is the total combined error rate of DNA synthesis/replication?

A

1 X 10^10 (1 in 10 billion)

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9
Q

What are the two challenges of maintaining chromosome ends

A
  1. break/error repairs
  2. shortening telomeres with replication
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10
Q

What are 3 things done to prevent the breakage-repair of chromosome ends?

A
  1. 5’ end removal (via nuclease)
  2. addition of protruding 3’ end (telomere)
  3. shelterin protein protection
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11
Q

What are the bases of the protruding 3’ repeat sequence added to the ends of chromosomes?

A

TTAGGG

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12
Q

about how many times are the telomere sequences repeated on a chromosome end?

A

~3000x

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13
Q

What are 3 outcomes of telomere shortening?

A
  1. loss of coding DNA
  2. triggering of cellular senescence
  3. telomerase restoration
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14
Q

What is cellular senescence?

A

the ceasing of cell division; not synonymous with cell death

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15
Q

How does telomerase extend the 3’ end of chromosomes?

A

uses RNA template to complete synthesis of the lagging strand (via DNA pol)

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16
Q

This is a method of DNA repair that excises ALL bases to look for errors (via 6 different enzymes)

A

Base excision repair

17
Q

What are the 5 steps of base excision repair?

A
  1. error base recognition
  2. base removal
  3. phosphate backbone removal
  4. nucleotide replacement (via DNA pol)
  5. nick sealing (via ligase)
18
Q

what are the most common DNA errors that are not caught during replication (via endonuclease activity/eukaryotic strand-directed repair)

A

deaminations

19
Q

This is a method of post-replication DNA repair that removes whole chunks of polynucleotides

A

nucleotide excision repair

20
Q

When does nucleotide excision repair occur most frequently? why?

A

during RNA transcription; RNA pol II gets stalled by bulky lesions

21
Q

What is the enzyme used in nucleotide excision repair?

A

excision nuclease

22
Q

Double-stranded break repair that occurs post-DNA replication is a subtype of what other DNA repair?

A

HDR (homology-directed repair)

23
Q

What are the only times double-stranded break repair can occur?

A

during cell division (after DNA replication, before nuclear division)

24
Q

what are the 3 additional methods of DNA repair that usually occur post-DNA replication?

A
  1. base excision repair
  2. nucleotide excision repair
  3. double-stranded break repair
25
Q

What are the 3 main classes of transposable elements?

A
  1. transposases
  2. reverse transcriptase (+integrase)
  3. reverse transcriptase (+endonuclease)
26
Q

What are the 3 methods of transposing elements?

A
  1. DNA-only transposons
  2. Retroviral-like transposons
  3. non-retroviral-like retrotransposons
27
Q

transposase is coded by DNA/RNA to move the transposable elements in which method of transposition?

A

DNA-only transposition

28
Q

DNA-only transposons are found in which organisms?

A

bacteria/prokaryotes ONLY

29
Q

What are the 5 steps of DNA-only transposons?

A
  1. coded transposase from DNA/RNA
  2. transposase binds to target DNA
  3. target DNA is looped + broken
  4. target DNA is integrated into a new location
  5. donor region is repaired
30
Q

What are the 4 steps of retroviral-like transposition?

A
  1. reverse transcriptase codes DNA from vRNA
  2. retrotransposon integrates DNA into new location
  3. copies of viral sequence are made
  4. protein synth from viral sequence (replication occurs)
31
Q

What are the 4 steps of nonretroviral retrotransposition?

A
  1. L1 RNA sequence synthesizes reverse transcriptase
  2. rt protein binds to 5’ of L1 + DNA target
  3. rt is primed
  4. sequence transcribes (+ is integrated into new location)
32
Q

about how many transposable elements are present in the human genome?

A

~3,000,000

33
Q

LINE elements compose about what percentage of the human genome?

A

~50%

34
Q

about how many nonretroviral retrotransposons are active in the human genome?

A

80-100

35
Q

What is the TATA box?

A

Molec and Cell (18 decks)

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