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Biochemistry - Victor > Qiao > Flashcards

Qiao Flashcards

0
Q

What does the Meselson Stahl experiment show?

A

When N15 DNA replicated in N14 broth, N15/N14 DNA found in generation 1, and N15/N14 AND N14/N14 DNA in generation 2. Showed semiconservative.

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1
Q

What does actinomycin D do?

A

Cytotoxic, intercalate with narrow groove of DNA, disrupt DNA RNA synthesis

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2
Q

T or F. Both in eukaryotes and prokaryotes, DNA replication is bidirectional.

A

True.

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3
Q

What does DNA pol 1 do?

A

(prokaryotes)
1. after primer removed, replacing it with DNTPs.
2. 3’-5’ exonuclease activity
3. primer removal. 5’-3’ exonuclease activity

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4
Q

What do the metal ions in the active site of DNA pol (palm) do?

A

Neutralizes charge, attracts DNTP to right position

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5
Q

What does DnaA do?

A

(prokaryotes) Binds to AT rich ori, melts AT (requires ATP)

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6
Q

What does DnaB do?

A

helicase, binds ssDNA near replication fork, unzips DNA, causing supercoiling. encircles DNA, continuous processivity

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7
Q

What does SSB protein do?

A

Single strand binding protein, cooperative binding, shifts equilibrium to ssDNA, protects it from nucleases

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8
Q

What does DNA primase do?

A

(prokaryotes) adds RNA primer for elongation.

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9
Q

What does type 1 topoisomerase do?

A

Cuts one strand of double helix, has nuclease and ligase activity. Uses energy of cut phosphodiester bond to ligate.

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10
Q

What does type II isomerase do?

A

Breaks both strands of duplex, causes other part of DNA strand to pass through break, reseals it. Also involved in daughter chromosome separation.

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11
Q

What does camptothecin do?

A

Targets Topo 1 DNA complex, cytotoxic in S phase.

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12
Q

What does DNA pol iii do?

A

alpha: polymerase activity
epsilon: 3’-5’ exonuclease activity
gamma/sigma: clamp loader
beta: sliding clamp

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13
Q

What does DNA pol i, ii, iii, iv, and v do?

A

i: RNA primer removal, DNA repair
ii: DNA repair
iii: main DNA replication enzyme
iv: DNA repair
v: DNA repair

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14
Q

What does cytosine arabinoside and zidovudine do?

A

Nucleoside analogs, blocks elongation.

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15
Q

What does pol a, e, s, b and y do for eukaryotes?

A

a: primase
e: lead strand elongation
s: lag strand elongation
b: gap filling in DNA repair, base excision repair
y: replicates mito DNA

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16
Q

Histones are positively charged due to which amino acids?

A

lys, arg.

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17
Q

What diseases are from CAG repeats?

A

Huntingtons, Kennedy’s, Spinocerebellar ataxia

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18
Q

What is the “end replication problem?”

A

missing nucleotides at the extreme 5’ end of lagging strand.

19
Q

What is the Hayflick limit?

A

normal times a human cell will divide until it stops

20
Q

What is ALT?

A

Alternative lengthening of telomeres, homology to create dsDNA, rolling circle to create it

21
Q

What is a nucleotide transversion? Transition?

A

Transversion: purine to pyrimidine
Transition: purine to purine

22
Q

What is a neutral mutation?

A

A change from one aa to a similar aa.

23
Q

Deaminations of cytosine to ________.

A

Uracil. Changes CG to AT.

24
Q

Which amino acid can’t be deaminated?

A

Thymine.

25
Q

UV damage can cause ________ dimers.

A

pyrimidine

26
Q

What is the Ames test?

A

determining if a chemical is a mutagen. Grow his dependent bacteria in his negative broth. add mutagen candidate, see if any growths occur. if they do, candidate is mutagen.

27
Q

What does photolyase do?

A

(not in humans) uses chromophore to excite itself, destabilizes pyrimidine dimer caused by uv light.

28
Q

What is an example of “direct reversal of damage?”

A

(non humans)O6 alkylguanine DNA Alkyltransferase (AGT) repair by taking abnormal methyl group of alkylation of guanine away.

29
Q

What is mismatch repair?

A

Mut protein recognizes mismatch, also recognizes newly synthesized strand vs parent strand (methylated)

  • endonuclease cleaves mutation with 5’ and 3’ around it
  • DNA pol 1 fills gap, ligase
30
Q

Can mismatch repair recognize O6meG-T pair?

A

Yes. but it can’t remove the methylated guanine. it can remove thymine. futile cycle of nucleotide removal and synthesis. leads to cell arrest and apoptosis.

31
Q

What is base excision repair?

A

Cytosine spontaneously deaminates/nitrous acid deaminates to uracil. GU pair.

  • glycosylase recognizes uracil, cleaves it out (AP site)
  • AP endonuclease nicks at 5’
  • Deoxyribose phosphate lyase removes backbone
  • DNA pol, ligase.
32
Q

What is nucleotide excision repair?

A

UV endonuclease recognizes dimer, cleaves strand on 5’ and 3’ end of pyrimidine dimers. Dimer released, DNApol, ligase

33
Q

Xeroderma pigmentosum: deficient in __________ repair. What other syndromes?

A

Nucleotide excision repair.
Cockayne’s syndrome
trichothiodystrophy.

34
Q

What are some origins of double strand breaks?

A

ionizing radiation
ROS followed by replication
during VDJ recombination
during meiosis

35
Q

________ uses normal sister chromatid as template for DNA repair.

A

DSB repair using Homologous recombination

36
Q

What happens during non homologous end joining?

A

Ku heterodimer and DNA activated protein kinase recruited. ends ligated or filled in with more shit and ligated.

37
Q

What are the general steps of eukaryotic homologous recombination?

A
  1. 5’ 3’ resection
  2. strand invasion
  3. new DNA synthesis on invading strand
  4. Strand annealing
38
Q

What enzyme makes the double strand break during homologous recombination?

A

spo 11

39
Q

T or F. Meiotic recombination can occur with or without crossover.

A

True.

40
Q

What is site specific recombination?

A

movement of mobile genetic elements (with transposase) to nonhomologous sites of a chromosome.

41
Q

VDJ recombination in B cell formation is an example of

A

site specific recombination.

42
Q

What is p53?

A

Genome guardian, germ line. Key in check point activation. Can block entry into S phase. Can receive many negative signals (hyperproliferation signals, dna damage, telomere shortening, hypoxia) and in response can arrest cell cycle, senescence, apoptosis.

43
Q

What recognizes broken DNA in checkpoint activation? Where in the cell cycle does this checkpoint regulate?

A

ATM, ATR, slows down replication in S phase, blocks entry into M phase.

44
Q

Name 3 disorders that affect ATM, one that affects BRCA2.

A

AT, ATLD, NBS.

FA.

Biochemistry - Victor (17 decks)

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