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Biochem > Lecture 16: Replication and Repair > Flashcards

Lecture 16: Replication and Repair Flashcards

1
Q

Human genome replication time

A

-8 hours
-200,000 bp per second
-multiple replication origins

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2
Q

Error rate of replication

A

one error per billion bps

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3
Q

DNA polymerases

A

-synthesize DNA
-add nucleotide
-conserve genetic info
-requires 3’-OH of primer
-delta

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4
Q

DNA synthesis direction

A

occurs in 5 to 3 while moving 3 to 5

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5
Q

dNTPs

A

-deoxyribonucleotides
-substrates for DNA synthesis
-not enough = replication STOPS

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6
Q

Phosphodiester bond

A

-3’OH group with a-phosphate of dNTP
-releases a pyrophosphate (ppi)

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7
Q

Leading strand

A

-new template sequence in front of the synthesis
-continuous

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8
Q

Lagging Strand

A

-new template behind the synthesis
-okazaki fragmentsl

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9
Q

ligase

A

link okazaki frgments

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10
Q

Unwinding

A

-helicase unwinds DNA
-exposed DNA stabilized by single-strand binding (SSB) proteins

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11
Q

Priming

A

-primase synthesizes short RNA primer

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12
Q

Strand elongation

A

DNA polymerases synthesize DNA

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13
Q

Primer removal

A

RNA primers digested by RNase H

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14
Q

Gap Filling

A

DNA polymerases synthesize DNA to end of okazaki fragment in front

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15
Q

Ligation

A

ligase seals nicks in DNA strand

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16
Q

Proofreading

A

-DNA polymerases has 3 to 5 exonuclease activity
-removes newly added nucleotide
-proofreads nucleotide at 3’ end

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17
Q

proper nucleotide at 3’ end

A

suppresses proofreading

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18
Q

mismatched nucleotide at 3’ end

A

supresses synthesis

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19
Q

processivity

A

-DNA polymerases may dissociate from DNA before completion of synthesis
-rebinding of DNA polymerase slows replication

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20
Q

enhanced processivity

A

increased rate of DNA synthesisS

21
Q

Sliding Clamp

A

-PCNA (proliferating cell nuclear antigen) holds down DNA polymerase
-suppresses dissociation
-increases processivity

22
Q

Replisome

A

complex of polymerases working on the leading and lagging strands

23
Q

Ending replication problem

A

-DNA linear
-5’ end of lagging strand cannot be replicated bc no primer can be made
-DNA shortened by 50-100 bp per replication

24
Q

telomere

A

-located at end of chromosomal DNAs
-repeat TTAGGG w/o genetic info
-lost after 40-60 replications = cell death

25
Q

Hayflick limit

A

-40-60 replications before telomere is lost
=cell death

26
Q

Telomerase

A

-ribonucleoprotein complex with RNA
-adds TTAGGG to 3’ end of telomere using RNA sequence as template
-enlongates telomere
-increases lifespan of cells

27
Q

Cancer cell immortality

A

-reactivation of telomerase

28
Q

Polymerase chain reaction (PCR)

A

-amplifies DNA fragment tagged by DNA primers in vitro
-3 step cycle repeats 25-30 times
-cloning and detection (PCR test for covid)

29
Q

PCR phases

A
  1. denaturing (94degrees)
  2. Anneling (50)
  3. extension. (72)

-each at different temp
-requires thermocycler and a heat-resistant polymerase

30
Q

DNA damage causes

A

-reactive oxygen
-deamidation
-depurination

31
Q

reactive oxygen species

A

-hydroxy radical (HO-)
-superoxide (O2-)

32
Q

Depurination

A

-several thousands of purine lost a day
-generates abasic (AP) sites
-missing bp

33
Q

Deamidation

34
Q

External causes of DNA damage

A

-carcinogens
-UV radiationca

35
Q

carcinogens

A

-mustard gas
-N-nitroso in meat
-chemo
-benzopyrene

36
Q

UV RADIATION

A

-pyrimadine dimers

37
Q

DNA repair

A

-base-excision
-nucleotide-excision
-mismatch
-demethylation
-photoreactivation
-double-strand breakssdessdessdeesdesdesdewsdesxcfdscgresxcvgrew

38
Q

base-excision repair

A

-damage base removed
-forms AP site
-AP site removed
-gap resynthesized

39
Q

nucleotide-excision repair

A

-stretch of nucleotides with damage is removed
-gap resynthesized

40
Q

Xeroderma Pigmentosum (XP)

A

-autosomal recessive genetic disease
-defect in nucleotide-excision repair
-photosensitive and susceptive to skin cancer

41
Q

mismatch repair

A

-fix mismatch pair
-similar to nucleotide-excision
-mutation occurs
-methylation may guide identification of parental strand

42
Q

direct demethylation

A

removes methyl group from O-methylguanine

43
Q

Photoreactivation

A

reverts pyrimidine dimer

44
Q

Double-strand break repair

A

-10 breaks per cycle
-homologous recombination (Accurate)
-non-homologous end-joining (error-prone)

45
Q

p53

A

-control DNA repair
-transcription factor responding to damages

45
Q

p53 functions

A

-activates DNA repair proteins
-arrests cell cycle
-may initiate programmed cell death if too much damage

45
Q

p53 tumor suppressor

A

-failure of programmed cell death may cause cancer
-frequently mutated in human cancer

Biochem (30 decks)

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