Qiao Flashcards by Victor Tran

What does the Meselson Stahl experiment show?

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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What does actinomycin D do?

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

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

True.

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What does DNA pol 1 do?

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

Neutralizes charge, attracts DNTP to right position

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What does DnaA do?

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

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What does DnaB do?

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

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What does SSB protein do?

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

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What does DNA primase do?

(prokaryotes) adds RNA primer for elongation.

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What does type 1 topoisomerase do?

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

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What does type II isomerase do?

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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What does camptothecin do?

Targets Topo 1 DNA complex, cytotoxic in S phase.

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What does DNA pol iii do?

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

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

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

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What does cytosine arabinoside and zidovudine do?

Nucleoside analogs, blocks elongation.

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

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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Histones are positively charged due to which amino acids?

lys, arg.

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What diseases are from CAG repeats?

Huntingtons, Kennedy’s, Spinocerebellar ataxia

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What is the “end replication problem?”

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

What is the Hayflick limit?

normal times a human cell will divide until it stops

What is ALT?

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

What is a nucleotide transversion? Transition?

Transversion: purine to pyrimidine
Transition: purine to purine

What is a neutral mutation?

A change from one aa to a similar aa.

Deaminations of cytosine to ________.

Uracil. Changes CG to AT.

Which amino acid can't be deaminated?

Thymine.

UV damage can cause ________ dimers.

pyrimidine

What is the Ames test?

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.

What does photolyase do?

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

What is an example of "direct reversal of damage?"

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

What is mismatch repair?

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

Can mismatch repair recognize O6meG-T pair?

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.

What is base excision repair?

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.

What is nucleotide excision repair?

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

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

Nucleotide excision repair. Cockayne's syndrome trichothiodystrophy.

What are some origins of double strand breaks?

ionizing radiation ROS followed by replication during VDJ recombination during meiosis

________ uses normal sister chromatid as template for DNA repair.

DSB repair using Homologous recombination

What happens during non homologous end joining?

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

What are the general steps of eukaryotic homologous recombination?

1. 5' 3' resection 2. strand invasion 3. new DNA synthesis on invading strand 4. Strand annealing

What enzyme makes the double strand break during homologous recombination?

spo 11

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

True.

What is site specific recombination?

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

VDJ recombination in B cell formation is an example of

site specific recombination.

What is p53?

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.

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

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

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

AT, ATLD, NBS. | FA.