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MOL BIO Exam #1- Lo > Lec 04- DNA Replication, Repair, and Recombination 2 > Flashcards

Lec 04- DNA Replication, Repair, and Recombination 2 Flashcards

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1
Q

What are 2 main reasons DNA becomes damaged and needs repair?

A
  • replication errors

- accidental lesions that occur in the genome

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2
Q

How many accidental base changes result in a permanent mutation?

A

fewer than 1/1000 accidental base changes

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3
Q

What is the spontaneous reaction that causes 5000 purine bases to be lost every day?

A

depurination

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4
Q

What is the spontaneous reaction involving the conversion of C to U that occurs in 100 bases every day?

A

deamination

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5
Q

What does exposure to reactive forms of oxygen in the cell or chemicals in the environment do to DNA?

A

causes DNA damage

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6
Q

What does UV radiation exposure do to DNA?

A

produces a covalent linkage between 2 adjacent pyrimidies (pyrimidine dimers) such as T-T or C-T

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7
Q

What happens when unprepared DNA is replicated?

A

deletion or a base pair substitution occurs in the daughter strand

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8
Q

What are the 4 main types of DNA repair?

A

1) Base excision repair
2) Nucleotide excision repair
3) Transcription-coupled repair
4) Double-strand break repair

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9
Q

What are the 2 types of Double-strand break repair?

A
  • Non-homologous end joining

- Homologous recombination

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10
Q

What types of DNA repair occur only on one strand?

A
  • Base excision repair
  • Nucleotide excision repair
  • Transcription-coupled repair
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11
Q

How many different DNA glycosylases are there?

A

at least 6 different types

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12
Q

What is the function of DNA glycosylases?

A

each recognizes a specific type of altered base and catalyzes its removal

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13
Q

What happens when the DNA glycoslyase flips out of the base from the helix?

A

it probes for damage

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14
Q

What happens when the DNA glycoslyase finds an incorrect base?

A

it cleaves the glycosyl bond that connects the base with the sugar

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15
Q

What do AP endonuclease and phosphodiesterase do in base excision repair?

A

cut the phosphodiester backbone

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16
Q

What is the result of cutting the phosphodiester backbone during base excision repair?

A
  • damage is removed

- gap is repaired

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17
Q

When are depurinations repaired during base excision repair?

A

directly repaired beginning with AP endonuclease

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18
Q

What are the steps of base excision repair?

A

1) DNA glycosylases probe for damage
2) If incorrect base, glycosyl bond between base and sugar is cleaved by specific DNA glycosylase
3) AP endonuclease and phosphodiesterase cut phosphodiester backbone (damage removed)
4) DNA pol adds new nucleotides
5) DNA ligase seals the nick

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19
Q

How is nucleotide excision repair different from BER?

A

differ in how the damage is removed

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20
Q

What kind of lesions can be repaired by nucleotide excision repair?

A

bulky lesions:

  • chemically induced
  • thymine dimers
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21
Q

What does the multienzyme complex in the nucleotide excision repair do?

A

scans DNA for distortion in the double helix (instead of a specific base change)

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22
Q

Where does nucleotide excision repair cleave the DNA?

A

cleaves the phosphodiester backbone on both sides

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23
Q

What does DNA helicase do in nucleotide excision repair?

A

peels lesion-containing strand away

doesn’t remove any of the individual bases

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24
Q

How is the large gap created by nucleotide excision repair fixed?

A

repaired by DNA pol and ligase

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25
Q

How can cells preferentially direct DNA repair to sequences that are being actively transcribed (sequences that urgently need repair)?

A

by linking RNA pol with DNA repair

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26
Q

What stalls lesions and directs repair machinery there in transcription-coupled repair?

A

RNA pol

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27
Q

What does transcription-coupled repair work with to repair genes that are being expressed when the damage occurs?

A

BER
NER
others

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28
Q

What is transcription-coupled repair specific for?

A

the strand being transcribed

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29
Q

At what rate is the non-transcribed strand repaired in transcription-coupled repair?

A

non-transcribed strand is repaired at the same rate as the DNA not being transcribed

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30
Q

What is cockayne’s syndrome caused by?

A

defect in transcription-coupled repair

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31
Q

What are some of the results from cockayne’s syndrome?

A
  • growth retardation
  • skeletal abnormalities
  • sensitivity to sunlight
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32
Q

In Cockayne’s syndrome, what does the defect in transcription-coupled repair do to the genes?

A

permanently stalls RNA pol at the sites of damage in important genes

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33
Q

DNA molecules are __________ constructed for repair.

A

optimally

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34
Q

Two strands of DNA allows a __________

A

backup copy

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35
Q

What makes the distinction between damaged/undamaged DNA obvious?

A

the nature of the 4 bases

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36
Q

What does every deamination event form?

A

an unnatural base

works as a signal

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37
Q

What is a possible reason why RNA is not the hereditary information?

A

cannot distinguish between deaminated C and natural U

38
Q

What occurs at some CpG sequences?

A

special problem with methylated cytosines in vertebrate DNA

39
Q

What are associated with problems with methylated cytosines in vertebrate DNA?

A

inactive genes

40
Q

What does the deamination of methyl-C produce?

A

T mismatched with G

41
Q

What enzyme recognizes the mismatched T & G and removes the T?

A

DNA glycosylase

42
Q

The repair of T&G mismatch using DNA glycosylase is relatively __________.

A

ineffective

43
Q

What % of C nucleotides in the human genome are methylated?

A

3%

44
Q

How much do methylated C nucleotides account for all point mutations associated with inherited human diseases?

A

1/3 of all point mutations

45
Q

What are some of the causes of double-stranded breaks?

A
  • ionizing radiation
  • replication errors
  • oxidizing agents
  • other metabolites
46
Q

What happens if double-strand breaks are left unpaired?

A

chromosomes would break into smaller fragments and be lost

47
Q

What process brings broken ends of DNA together and rejoins them using DNA ligation in a double-strand break repair?

A

Non-homologous end joining

48
Q

What occurs as a result of the process of non-homologous end joining?

A

1 or more nucleotides will be lost

49
Q

Why does the double-strand break repair process predominate in humans?

A

because so little of the genome is protein coding

50
Q

How many DNA scars will a typical 70 year old have from double-strand break repair?

A

2000

51
Q

What are checkpoints?

A
  • an additional layer of regulation

- ensures the completion of one stage in the cell cycle before the next stage can begin

52
Q

What triggers checkpoints?

A

presence of DNA damage

53
Q

What are some of the checkpoints?

A
  • blocking entry from G1–>S phase
  • slowing down progression through S phase
  • blocking transition from G2–>M phase
54
Q

Checkpoints give the cell ____________ to repair DNA damage

A

extra time

55
Q

What is homologous recombination?

A

genetic exchange between a pair of homologous DNA sequences

56
Q

What are some of the functions of homologous recombination?

A
  • repair of double-strand breaks (at stalled or broken replication forks)
  • exchange of genetic information to create new combinations of genetic sequences (crossing over and gene conversion in meiosis)
57
Q

What mechanical role does homologous recombination play?

A

assuring accurate chromosome segregation

58
Q

What is the fundamental process of genetic exchange that is common to all organisms?

A

homologous recombination

59
Q

What is the location of homologous recombination repair?

A

at stalled or broken replication fork

60
Q

What kind of sequences does HR repair take place between?

A

similar sequences

61
Q

What does the process of HR require?

A

base pairing

but it doesn’t have to be a perfect match

62
Q

When a nick is encountered in the replication fork during HR, what will happen?

A

the replication fork will collapse and break

63
Q

What enzyme chews back the parental strand to prepare for strand invasion in HR repair?

A

5’ exonuclease

64
Q

In HR, what is strand invasion?

A

pairing of single-stranded DNA with complementary strand in a different double-stranded helix

65
Q

What does strand invasion form?

A

forms a region of heteroduplex DNA

66
Q

What happens after strand invasion in HR?

A
  • strands break and dissociate
  • DNA synthesis continues
  • replication fork restarts
67
Q

What guides homologous recombination?

A

base-pairing

68
Q

What do DNA duplexes do in HR?

A

sample each other to look for regions of homology

69
Q

What is hybridization?

A

DNA double helix reforming from its separated single strands

“zipper”

70
Q

What is another name for hybridization?

A

renaturation

71
Q

What happens during HR once a region of homology is found?

A

the single strands rapidly pair up

72
Q

What is the result of hybridization?

A

creates a double helix from strands that originate from different molecules

heteroduplex DNA

73
Q

What is heteroduplex DNA?

A

a double helix with strands that originate from different molecules

74
Q

What does DNA hybridization require?

A

a single-stranded DNA freed from pairing with complement so that it can pair with the second strand

75
Q

What directs the single-stranded invading strand?

A
  • RecA (PRO)
  • Rad51 (EUK)
  • other proteins
76
Q

What is the DNA synapsis reaction?

A
  • binds cooperatively to single stranded DNA

- holds it together with the double helix until homologous sequence is found

77
Q

How does the single strand search for the homologous sequence?

A

via an unknown mechanism

78
Q

What happens once a homologous sequence is identified?

A
  • strand invasion occurs

- heteroduplex is formed

79
Q

What does the point of exchange move through once strand invasion occurs?

A

branch migration

80
Q

What happens during branch migration?

A

unpaired region of one single strand displaces a paired region on another single strand

81
Q

Branch migration characteristics

A
  • happens spontaneously
  • both directions
  • catalyzed by special helicase to move in one direction (requires energy)
82
Q

How is non-homologous end joining different from homologous recombination?

A

Non-homologous end joining:

  • no template required
  • creates mutation at site of repair
  • can create translocation

Homologous recombination:

  • uses daughter DNA duplex as template
  • no loss/alteration of repair site DNA
  • can repair other DNA damage types (versatile)
  • mechanism and proteins conserved in all organisms
83
Q

In repair of double stranded breaks by HR, what are the 5’ ends degraded by?

A

exonuclease

84
Q

What invades the homologous template and primes repair DNA synthesis?

A

one 3’ end

85
Q

What strand can anneal to the other original 3’ overhang in the damaged chromosome through complementary base pairing?

A

the newly synthesized 3’ end of the invading strand

86
Q

What does the use of a non-functioning homolog to repair the other homolog do in HR?

A

Causes loss of heterozygosity

  • critical first step in cancer development
  • rare occurrence
87
Q

How is repair prevented in the absence of damage?

A
  • dispersed repair proteins throughout the cell

- repair occurs at the sites of damage in “factories” or “foci”

88
Q

BRCA2 maintains Rad51 (RecA) inactive. What happens if there is a mutation in BRCA2?

A

leads to increase of breast cancer

89
Q

To help demonstrate the localization of repair proteins to DNA damage, fibroblasts were x-rayed to produce ___________

A

double strand breaks

90
Q

What stain was used to show new DNA synthesis?

A

BrdU

91
Q

What does the Mre11 complex recognize in its localization to damage sites?

A

recognizes double-strand breaks and mobilized additional proteins to repair the damage

MOL BIO Exam #1- Lo (8 decks)

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