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Mol Bio - Exam 1 > Basic Molecular Genetic Mechanisms 2 (L2) > Flashcards

Basic Molecular Genetic Mechanisms 2 (L2) Flashcards

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1
Q

mechanism of DNA replication?

A

semi-conservative (determined using heavy and light N isotopes?

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2
Q

direction of DNA replication?

A

bidirectional

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3
Q

function of helicase

A

unwinds DNA

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4
Q

leading strand

A

parent strand that runs 3’ to 5’ so that the daughter strand can be synthesized continuously as the fork unwinds

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5
Q

lagging strand

A

parent strand that runs 5’ to 3’ so that the daughter strand must be synthesized in fragments as the fork unwinds

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6
Q

ligation

A

when newly synthesized DNA strand portions are linked together

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7
Q

Okazaki fragments

A

fragments of DNA synthesized on the lagging strand

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8
Q

RNA primase

A

puts down about 10 bases of RNA onto the DNA to start replication

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9
Q

DNA polymerase alpha

A

recognizes and binds RNA primer then continues to replicate the next 30 bases of DNA

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10
Q

describe the primer for DNA pol alpha

A

hybrid of DNA + RNA

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11
Q

why does DNA replication require a primer?

A

DNA polymerases require a 3’ OH to begin synthesis, so you need RNA in a primer

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12
Q

does RNA require a primer to replicate?

A

no - already has 3’ OH

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13
Q

PCNA

A

proliferative cell nuclear antigen - locks polymerase complex on DNA so that the polymerase won’t fall off and so that the polymerase goes in one direction

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14
Q

DNA polymerase delta/epsilon

A

takes over majority of DNA synthesis after primer is laid down

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15
Q

replication protein A

A

binds ssDNA to maintain it in extended form - prevents secondary structures from forming before the polymerase has reached that segment

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16
Q

RNAse H

A

degrades RNA from RNA/DNA primer so that DNA can link together (ligation)

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17
Q

what is the fingers domain of DNA pol responsible for?

A

mediates polymerization

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18
Q

what is the exonucleanse domain of DNA pol responsible for?

A

proofreading activity in 3’ to 5’ direction

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19
Q

what happens after the error is removed by exonuclease?

A

strand goes back to pol domain and synthesis resumes

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20
Q

how much does exonuclease reduce error rate?

A

100,000 fold

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21
Q

what are the two ways that spontaneous mutation occurs?

A

deamination and depurination

22
Q

depurination

A

purines are less stable inside the cell - they tend to just go away, leaving a sugar + phosphate

23
Q

deamination

A

5-methylcytosine -> C4 amine replaced w/ carbonyl -> thymine - then during replication, the new strand is synthesized with an A where there was supposed to be a G (can also happen C deaminated to U)

24
Q

difference b/w repair of depurination and deamination

A

none - both repaired by same base excision repair b/c go through same intermediate

25
Q

three methods of DNA repair

A
  1. base excision repair
  2. mismatch excision repair
  3. nucleotide excision repair
26
Q

base excision repair

A
  1. DNA glycosylase chops off base from wrong nt - leaves phosphate + sugar
  2. endonuclease - cuts on either side of sugar + phosphate
  3. lyase (part of DNA pol beta) - puts in correct nt
  4. ligase - seals gap, forms phosphodiester bond
27
Q

difference b/w endonuclease and exonuclease

A

endonuclease chops from middle

exonuclease chops from end

28
Q

mismatch excision repair

A

enzymes remove larger stretch of DNA than just the one wrong nucleotide - then same repair mechanism (DNA pol beta + ligase)

29
Q

what proteins are often mutated in patients w/ colon cancer and what repair mechanism are they associated with?

A

MSH2 and MSH6 - part of mismatch excision repair

30
Q

effect of UV light on DNA

A

can cross link 2 T’s next to each other, creating a pouch in DNA (thymine dimer)

31
Q

what is the problem with thymine dimers?

A

they don’t replicate faithfully - more prone to cancer

32
Q

nucleotide excision repair

A

XP proteins recognize thymine dimers, open up dsDNA, cut small stretch that contains error, then DNA pol and ligase come fill the gaps and link the ends, respectively

33
Q

what causes double strand lesions?

A

too much ionizing radiation

34
Q

what are the two repair mechanisms for double strand lesions?

A
  1. nonhomologous end joining (NHEJ)

2. homologous recombination repair

35
Q

NHEJ

A
  1. KU proteins recognize broken ends, bring ends together, chop off any protruding nt’s to get a blunt end
  2. ligase comes in and joints blunt ends together
36
Q

limitation of NHEJ

A

can create frameshift mutations if only one or two nt’s are chopped off

37
Q

collapse of the replication fork is fixed by what mechanism?

A

homologous recombination repair

38
Q

basic idea of homologous recombination repair

A

borrows information from the intact homologous chromosome to fix the broken chromosome - maintains respective position of the nucleotides (faithful)

39
Q

Holliday structure

A

crossover made during homologous recombination repair strand invasion - made by ONE phosphodiester bond

40
Q

what enzyme mediates strand invasion in homologous recombination repair?

A

Rec A (bacteria) and Rad51 (human)

41
Q

link b/w homologous recombination repair enzymes and breast cancer?

A

Rad51 interacts w/ BRCA1 and BRCA2 (tumor suppressor genes) - homologous recombination repair doesn’t fxn properly in patients with breast cancer

42
Q

steps of homologous recombination repair

A
  1. 5’ exonuclease acts on broken end
  2. intact daughter strand ligated to repaired parental strand in unbroken chromosome
  3. Rad51-mediated strand invasion
  4. Branch migration (Holliday structure formation)
  5. Strands cut at crossover
  6. Ligate ends
  7. Rebuild replication fork and continue replication
43
Q

difference b/w ss and ds homologous recombination repair

A

ds: 2 Holliday structures and 2 strand invasions
ss: 1 Holliday structure and 1 strand invasion

44
Q

what is the Holliday structure also used for?

A

same mechanism for crossing over during meiosis

45
Q

resolution of Holliday structure in ds homologous recombination repair?

A

4 possible products - 2 parental, 2 recombinant

46
Q

difference b/w early and late viral proteins

A

early: replicate viral DNA
late: produce protein coat - capsid

47
Q

phage lytic cycle

A
  1. adsorption and injection of viral DNA in host cell
  2. expression of viral early proteins inside cell
  3. replication of viral DNA and expression of viral late proteins
  4. assembly
  5. lysis and release
48
Q

what does the plaque assay tell you?

A

each plaque represents cell lysis initiated by one viral particle - estimate how many infectious viruses were in the solution added to the lawn

49
Q

retrovirus

A

virus that contains ssRNA that is used to build DNA inside of the host cell (reverse transcriptase)

50
Q

retroviral life cycle

A
  1. fusion of virus w/ host cell
  2. reverse transcriptase makes DNA from viral ssRNA
  3. viral DNA transported to nucleus and incorporated into host genome
  4. transcription and translation - builds retrovirus proteins
  5. budding off of retroviruses

Mol Bio - Exam 1 (10 decks)

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