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Biochem > DNA replication > Flashcards

DNA replication Flashcards

exam 1

1
Q

protein-dna interactions predominantly occur in the

A

major groove through hydrogen bonds between aa and bases

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2
Q

what does site specific recognition requires?

A

multiple DNA-protein interactions

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3
Q

in yeast ORC does what?

A

binds to initiate replication at the origin and unwinds DNA

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4
Q

true or false: exact dna sequence that mark human origins of replication have been determined

A

false, it has not

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5
Q

initially used to study human DNA replication

A

SV40

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6
Q

SV40 requires only one viral protein ____, the other proteins are supplies by the host cell

A

T-antigen (tag)

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7
Q

multifunctional protein that not only binds to the origin of replication but act as a DNA helicase

A

T-ag

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8
Q

class of enzymes that use energy released from hydrolysis of ATP to break the hydrogen bond that stabilize the double helical form of DNA, “unwinding” it

A

DNA helicase

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9
Q

SSB protein

A

human single strand binding protein also called RPA

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10
Q

required for dNA replication to stabilize the single stranded DNA once unwound

A

SSB

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11
Q

enzyme that helps to maintain the stability of DNA by relaxing the supercoils

A

Topo I

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12
Q

disorder in which cellular DNA helicase is deficient associated with a high risk of developing malignancy

A

Bloom’s synd

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13
Q

associated with mutation of a gene encoding a helicase.

A

Werner’s syndrome

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14
Q

characterized by premature aging

A

Werner’s syndrome

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15
Q

necessary for DNA synthesis (all 5–> 3)

A

DNA pol

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16
Q

needed to initiate DNA synthesis and makes an RNA primer

A

Pol alpha primase

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17
Q

required for lagging strand synthesis and generate okasaki fragments

A

Pol delta

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18
Q

dependent on PCNA and RF-C

A

Pol delta

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19
Q

DNA clamp that facilitates binding and it is loaded on using RF-C

A

PCNA

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20
Q

have 3 to 5 exonuclease activity contributing to their high fidelity through proofreading activity

A

pol delta and pol epsilon

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21
Q

required for leading strand synthesis and also PCNA dependent

A

pol epsilon

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22
Q

used in mitochondrial DNA synthesis

A

pol gamma

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23
Q

used in DNA synthesis repair

A

pol Beta

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24
Q

catalyzes the formation of a bond between two ends of DNA

A

DNA ligase

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25
Q

occurs through nucleophilic attack by 3 hydroxyl on the phosphate group of incoming nucleotide

A

DNA elongation

26
Q

AZT and acyclovir

A

nucleotide analogues

27
Q

Nucleotide analogues have structures like nucleotides, but lack the __________ to permit elongation, therefore leads to _____ ___ and this inhibits ______ ______

A

Nucleotide analogues have structures like nucleotides, but lack the 3’ hydroxyl required to permit elongation and therefore lead to chain termination and thus inhibits DNA replication

28
Q

therapeutic drug is limited because it blocks other pol such as DNA pol gamma causing adverse side effects

A

AZT

29
Q

Mutant forms of ______ ____ arise that have ______ affinity for AZT rendering it ineffective

A

Mutant forms of reverse transcriptase leading to lower affinity

30
Q

cell cycle composed of

A

G1, S, G2, and M

31
Q

DNA synthesis occurs during

A

S phase

32
Q

tumor suppressor that acts at the G1/S checkpoint

A

p53

33
Q

increased risk for malignant replication

A

mutated p53

34
Q

inherited disorder where a mutated p53 tumor suppressor gene leads tumors at multiple sites in the body because all cells carry the mutation

A

Li-Fraumeni

35
Q

DNA damage sense at one of the checkpoints it will undergo

A

apoptosis, cell death

36
Q

prokaryotes mismatch repair

A

MutL, MutS, MutH

37
Q

parental strand marked by

A

methylation

38
Q

recognizes the mismatched base pair in prokatyotes

A

MutS

39
Q

produces a nick at a GATC site in the daughter strand identified by lack of methylation upstream or downstream in prokaryotes

A

MutH

40
Q

facilitates an interaction between MutS and MutH

A

MutL

41
Q

___ and ___ have been isolate in humans

A

hMSH and hMLH

42
Q

mutations in genes encoding mismatch repair proteins leads to

A

hereditary non-polyposis colon cancer HNPCC

43
Q

also associated with trinucleotide repeats expansion

A

HNPCC

44
Q

x-linked dom characterized by CGG

A

fragile x

45
Q

autosomal dom characterized by CTG repeats

A

myotonic dystrophy

46
Q

autosomal dom characterized by CAG repeats

A

Huntington’s

47
Q

Many proteins required for replication are also required for

A

excision repair

48
Q

___ ___causes adjacent thymine bases to form ______ bonds forming a ______ ______

A

DNA UV causes adjacent thymine bases to form covalent bonds forming a thymine dimer

49
Q

thymine dimers removed by

A

excision repair

50
Q

disease caused by defective excision repair, leading to a greatly increased risk of developing skin lesions/ cancer

A

xeroderma pigmentosum

51
Q

_____ spontaneously deaminates to _____ which can be mutagenic as it changes base-pairing

A

cytosine to uracil

52
Q

removes uracil from dNA creating an AP site

A

uracil-DNA glycosidases

53
Q

AP site

A

apurinic or apyrimidine

54
Q

acts as a chemical mutagen that can deaminate cytosine to uracil or adenine to hypoxanthine leading to mutations

A

nitrous acid

55
Q

guanine may be alkylated on

A

N7

56
Q

gives rise to insertions and deletions in DNA

A

intercalators

57
Q

examples of intercalators

A

ethidium, proflavin, acridine orange

58
Q

excision repair marked by three phases of

A

enzyme activity

59
Q

excision repair (1)

A

in e coli, exonuclease recognizes the pyrimidine dimer and cleaves on both sides creating a fragment that contains the dimer. fragment is removed leaving a gap in DNA

60
Q

excision repair (2)

A

DNA pol I fills the gap using the 3’ OH end as a primer (resyntheis)

61
Q

excision repair (3)

A

DNA ligase rejoins the newly formed strand with the original DNA

Biochem (10 decks)

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