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Kaplan: Biochemistry Part I > Chapter 2: DNA Replication and Repair > Flashcards

Chapter 2: DNA Replication and Repair Flashcards

1
Q

Polymerases?

A

enzymes that synthesize nucleic acids by forming phosphodiester (PDE) bonds

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2
Q

Nucleases? (moreso MOA)

A

enzymes that hydrolyze PDE bonds

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3
Q

Exonucleases?

A

remove nucleotides from the 5’ or the 3’ end of a nucleic acid

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4
Q

Endonucleases?

A

cut within the nucleic acid and release nucleic acid fragments

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5
Q

Is the p arm of the chromosome the long or short arm?

A

short arm

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6
Q

Is the q arm of the chromosome the long or short arm?

A

long arm

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7
Q

High fidelity synthesis occurs with RNA polymerase or DNA polymerase?

A

DNA polymerase

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8
Q

Low fidelity synthesis occurs with DNA or RNA polymerase?

A

RNA polymerase

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9
Q

Do you need primer for RNA polymerase?

A

no primer needed

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10
Q

Compare and contrast require substrates for DNA or RNA polymerase?

A

dATP, dGTP, dCTP, dTTP (for DNA polymerase)
ATP, GTP, CTP, UTP (for RNA polymerase)

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11
Q

Do you require primer for RNA polymerase?

A

no

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12
Q

Is there proofreading activity with RNA polymerase? DNA polymerase?

A

no

yes

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13
Q

List the steps in DNA replication. (prokaryotes)

A
  1. Base sequence at the origin of replication is recognized
  2. Helicase breaks the H bonds holding the base pairs together. This allows the 2 parental strands of DNA to begin unnwinding and forms 2 replication forks
  3. ssDNA binding protein (SSB) binds to the single stranded portion of each DNA strand, preventing them from reassociating and protecting them from degradation by nucleases
  4. Primase synthesizes a short (about 10 nucleoties) RNA primer in the 5’ -> 3’ dir., beginning at the origin on each parental strand; parental strand is used as template.
  5. DNA polymerase III begins synthesizing DNA in the 5’ -> 3’ direction, beginning at the 3’ end of each RNA primer. Strand can be made continuously in one long piece (“leading strand”)
  6. RNA primers are removed by RNAase H in eukaryotes and an uncharacterized DNA polymerase fills in the gap with DNA; in prokaryotes, DNA polymerase I both removes primer (5’ exonuclease) and synthesizes new DNA, beginning at the 3’ end of the neighboring Okazaki fragment
  7. Both eukaryotic and prokaryotic DNA polymerases proofread
  8. DNA ligase seals the “nicks” between Okazaki fragments, converting them to. a continuous strand of DNA
  9. DNA gyrase (DNA topoisomerase II) provides a “swivel” in front of each replication fork. As helicase unwinds DNA at replication fork the DNA ahead of it becomes overwound and positive supercoils form. (DNA gyrase inserts negative supercoils be nicking both strands of DNA, passing DNA strands through the nick, and then resealing both strands.)
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14
Q

Why are RNA primers required for DNA polymerase?

A

because DNA polymerases are unable to initiate synthesis of DNA can only extend a strand from the 3’ end of a preformed “primer”

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15
Q

What is the lagging strand?

A

synthesized discontinuously as series of small fragments known as Okazaki fragments

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16
Q

Each Okazaki fragment is initiated by synthesis of an RNA primer by a primase, and then completed by synthesis of DNA using what enzyme?

A

DNA polymerase III

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17
Q

Purpose of RNAase H?

A

5’ exoribonuclease acivity

digest the RNA primer from fragment 1

In eukaryotic cells, DNA polymerase extends the next fragment to fill in the gap

In prokaryotic cells DNA polymerase 1 has both the 5’ exocnulease acitivity to remove primers, and the DNA polymerase acitivty to extend the next fragment to fill in the gap

In both types of cells DNA ligase connects fragments 1 and 2 by making a phosphodiester bond

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18
Q

What is telomerase?

A

completes replication of the telomere sequence at both ends of eukaryotic chromosome

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19
Q

Where is telomerase present?(What type of cells)

A

embryonic cells, fetal cells, and certain adult stem cells;

inappropriately present in many cancer cells

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20
Q

Where is telomerase not present?

A

in adult somatic cells

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21
Q

What are telomeres?

A

repeitive sequences at ends of linear DNA moelcules in eukaryotic chromsomes

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22
Q

Relate telomeres and aging of cells?

A

with each round of replication in most normal cells the telomeres are shortened because DNA polymerase cannot complete synthesis of the 5’ end of each strand

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23
Q

Compare and contrast origin of replication for prokaryotes and eukaryotes.

A

Prokaryotes:
one ori site per chromsome

Eukaryotes:
multiple ori sites per chromsome

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24
Q

Compare and contrast how unwinding of DNA double helix is performed in prokaryotes and eukaryotes?

A

helicase in both

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25
Q

Compare and contrast stabilization of unwound template strands in prokaryotes and eukaryotes?

A

single-stranded DNA-binding protein (SSB) in both

26
Q

Compare and contrast synthesis of RNA primers in prokaryotes and eukaryotes?

A

primase in both

27
Q

Compare and contrast synthesis of DNA leading strand, lagging strand (Okazaki fragments) in prokaryotes and eukaryotes?

A

Prokaryotes:
DNA polymerase III
DNA polymerase III

Eukaryotes:
DNA polymerase a + delta
DNA polymerase a + delta

28
Q

Compare and contrast removal of RNA primers in prokaryotes vs eukaryotes?

A

Prokaryotes:
DNA polymerase I
(5’ -> 3’) exonuclease)

Eukaryotes:
RNAase H
(5’ -> 3’ exonuclease)

29
Q

Compare and contrast replacement of RNA with DNA in prokaryotes and eukaryotes?

A

DNA polymerase I (prokaryotes)
DNA polymerase ð (eukaryotes)

30
Q

Compare and contrast joining of Okazaki fragments in prokaryotes and eukaryotes?

A

DNA ligase

31
Q

Compare and contrast removal of positive supercoils ahead of advancing replication forks?

A

Prokaryotes
DNA topoisomerase II (DNA gyrase)

Eukaryotes
DNA topoisomerase

32
Q

Compare and contrast synthesis of telomeres in prokaryotes and eukaryotes.

A

Prokaryotes:
none

Eukaryotes:
telomerase

33
Q

Some current uses of quinolones?

A

treatment of gonorrhea and upper and lower UTI in both sexes

34
Q

What is reverse transcriptase?

A

RNA dependent DNA polymerase that requires an RNA template to direct the synthesis of new DNA

35
Q

DNA synthesis by reverse transcriptase in retrovirusis can be inhibited by what?

A

AZT (zidovudine)
ddC (zalcitabine) 2’-3’ deoxycytidine
ddI (didanosine) 2’-3’ dideoxyinosine

36
Q

AZT full name?

A

3’-azido-2’, 3’-dideoxythymidine

37
Q

AZT MOA?

A

enters cell and can be converted to the triphosphate derivative and used as a substrate for the viral reverse transcriptase in synthesizing DNA from RNA genome

one replacement of an azide instead of normal hydroxyl group at the 3’ position of deoxyribose prevent further replication by effectively causing chain termination.

38
Q

Does reverse transcriptase have proofreading activity?

A

Although it is a DNA polymerase, reverse transcriptase lacks proofreading activity

39
Q

Cause of thymine dimers?

A

UV radiation

40
Q

What is the recognition/excision enzyme in thymine dimers? In what condition is this enzyme deficient?

A

excision endonuclease (deficient in xeroderma pigmentosum)

41
Q

Repair enzymes to fix thymine dimers?

A

DNA polymerase and DNA ligase

42
Q

What part of the cell cycle can thymine dimers be created?

A

G1

43
Q

What stage of the cell cycle can mismatched bases occur?

A

G2 and S

44
Q

Cause of mismatched bases?

A

DNA replication errors

45
Q

Examples of enzymes involved in pathogenesis of mismatched bases?

A

a mutation on one of two genes, hMSH2 or hMLH1, initiates defective repair of DNA mismatches, resulting ina condition known as hereditary nonpolyposis colorectal cancer- HNPCC

46
Q

Repair enzymes for mismatched bases?

A

DNA polymerase and DNA ligase

47
Q

Cytosine deamination occurs at what stage of the cell cycle?

A

G1

48
Q

Cytosine deamination is caused by what?

A

spontaneous/ heat

49
Q

What are the recognition/excision enzymes involved in cytosine deamination?

A

uracil glycosylase AP endonuclease

50
Q

What are the repair enzymes in cytosine deamination?

A

DNA polymrase and DNA ligase

51
Q

Name 3 tumor suppressor genes?

A

p53, ATM, Rb

52
Q

Li Fraumeni syndrome and many solid tumors are associated with inactivation or deletion of what gene?

A

p53

53
Q

MOA p53 gene?

A

encodes a protein that prevents a cell with damaged DNA from entering the S phase

54
Q

ATM gene MOA?

A

encodes a kinase essential for p53 acitivity

55
Q

ATM is inactivated in what condition?

A

ataxia telangiectasia, BRCA-1, and BRCA-2

56
Q

Ataxia telangiectasia characteristics.

A

Hypersensitivity to X-rays and predisposition to lymphomas

57
Q

Rb gene MOA?

A

negative regulator of the cell cycle through it ability to bind the transcription factor E2F and repress transcription of genes required for S phase.

58
Q

What are microsatellites also known as?

A

short tandem repeats

59
Q

What are microsatellites?

A

di, tri, or tetranucleotide repeats dispersed throughout the DNA, usu. (but not exclusively) in noncoding regions

for example, TGTGTGTG may occur at a particular locus. If cells lack mismatch repair, the replicated DNA will vary in the number of repeats at that locus e.g, TGTGTGTGTGTG or TGTGTG

60
Q

Characteristics of XP?

A

extreme sensitivity to sunlight, skin freckling, ulcerations, and skin cancer… carcinomas and melanomas appear early in life

61
Q

How can XP be diagnosed?

A

measurement of the relevant enzyme excision endonucleases in white cells of the blood

Kaplan: Biochemistry Part I (27 decks)

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