2 DNA Replication Flashcards

1
Q

what do a-helices have to do with protein interaction with DNA?

A

they can fit into the major groove and interact with the nitrogenous bases

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2
Q

when an ORC recognizes an origin site, what happens first?

A

unzipping of DNA via helicase, establishment of rep fork

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3
Q

what class of protein is T-Ag?

A

helicase

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4
Q

is helicase ATp dependent?

A

yes

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5
Q

what are the three major proteins needed to initiate replicaiton?

A
  • helicase (T-ag)
  • Humans single stranded binding protein (replication protein A)
  • topoisomerase 1
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6
Q

what is the function of SSB (RPA)?

A

required for replication, stabiliizes single stranded DNA

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7
Q

what is the cause of blooms disease and what are these patients at risk for?

A
  • deficient in helicase

- risk for malignancies

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8
Q

what is the cause of werners syndrome? what are the symptoms?

A
  • gene involved is a helicase

- premature aging, dwarfism, cataracts, scleroderma

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9
Q

what polymerase initiates DNA synthesis? how does it do so?

A

Pol alpha makes RNA/DNA primers

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10
Q

what polymerase synthesizes the lagging strand? what is this dependent on?

A

pol delta, PCNA (proliferating cell nuclear antigen) (clamp) dependent

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11
Q

what polymerase synthesizes the leading strand?

A

pol epsilon, PCNA dependent

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12
Q

what type of reaction occurs as nucleotides are added to the DNA chain?

A

nucleophilic attack, creating a phosphodiester bond

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13
Q

what is RF-C’s job in DNA synthesis?

A

this is a clamp loader, it is responsible for secruing PCNA which then recruits the pol delta or epsilon

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14
Q

the pieces of DNA that are synthesized piece meal on the lagging strand are called what?

A

okazaki fragments

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15
Q

what direction exonuclease activity does pol e and d have?

A

3’ to 5’ because it goes backwards to do this

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16
Q

what is necessary to join okazaki fragments?

A

DNA ligase

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17
Q

what is the function of dna pol gama?

A

mitochondrial DNA synthesis

18
Q

what is the function of DNA pol beta?

A

repair DNA synthesis

19
Q

what class of molecule do AZT (zidovudine) and acyclovir fall into?

A

nulceotide anologues, used to treat viral infections due to their lack of a 3’ OH

20
Q

why are the effects of AZT limited?

A
  • very toxic, it inhibits other polymerases

- eventually mutant forms of RT arise that have a lower affinity for the drug

21
Q

at what checkpoint in cell division does p53 function?

A

G1/S

22
Q

what class of protein is p53?

A

tumor supressor

23
Q

what happens when you have a mutant p53?

A

cell growth is not arrested if the DNA is damaged and genetic instability occurs leading to potential malignancies

24
Q

what is the molecular characterization of li fraumeni syndrome?

A

mutated p53, leading to multiple tumor sites

25
Q

what types of insults to DNA result in base-excision repair?

A

x rays, oxygen radicals, alkylating agents, spontaneous reactions

26
Q

what sorts of insults lead to nucleotide excision repair?

A

UV light, polycyclic aromatics, and hydrocarbons leading to PP, bulky adducts, and CPD

27
Q

what sorts of insults lead to recombinational repair?

A

x rays, anti-tumor agents, leaing to interstrand crosslink and ds breaks

28
Q

what sorts of insults to DNA lead to mismatch repair?

A

replication errors, leading to A-G or C-T mismatches, insertions, and deletions

29
Q

during mismatch repair in e coli, how is the parent strand recognized?

A

it is methylated

30
Q

what protein recognizes a mismatch in e coli?

A

Mut S

31
Q

what is the molecular cause of fragile X?

A

expansion of over 200 trinucleotide repeats

32
Q

what is the molecular function of myotonic dystrophy?

A

dramatic expansion of a trinucleotide repeat, over 1000

33
Q

what is the molecular cause of huntingtons

A

expansion of a trinucleotide repeat

34
Q

what areas of the genome are prone to insertions and deletions?

A

microsatellites

35
Q

name the basic 4 step process of excision repair and a primary reason it needs to be done?

A
  • incision
  • excision
  • resynthesis
  • ligation
  • UV light causes thymine dimers to form
36
Q

what is xeroderma pigmentosum caused by?

A

abnormal excision repair nuclease that is responsible for cleaving DNA near the pyrimidine dimers

37
Q

What enzyme is responsible for removing uracil from DNA when cytosine spontaneously deaminates?

A

uracil-DNA glycosidase

38
Q

cytosine is deaminated to form what in the presence of HNO2?

A

uracil

39
Q

Adenine deaminates to form what in the presence of HNO2?

A

hypoxanthine

40
Q

what does alkylation of N7 of gluanine do to DNA?

A

causes labilization

41
Q

what is the primary example of a DNA intercolator? why are these a problem?

A

ethidium bromide

-gives rise to insertions and deletions