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Biochemistry > New: DNA Repair and Recombination > Flashcards

New: DNA Repair and Recombination Flashcards

1
Q

holoenzme responsible for the majority of DA synthesis in E.coli

A

DNA pol 3

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2
Q

highly processive polymerase that once it begins catalysis it rarely releases the DNA substrate (due to beta subunit grabbing on)

A

DNA polymerase 3

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3
Q

Okazaki fragments are joined by

A

DNA polymerase 1 and DNA ligase

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4
Q

Okazaki fragments are joined to produce a continuos strand of DNA in these 3 steps:

A
  1. removal of the RNA primer: the 5’ –> 3’ exonuclease activity of DNA pol 1
  2. Synthesis of replacement DNA - polymerase activity of DNA pol 1 synthesizes DNA in place of RNA
  3. sealing of adjacent DNA fragments - DNA ligase
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5
Q

Problem with joining of Okazaki fragments by DNA pol 1 and DNA ligase

A

after Okazaki fragment synthesis is complete, have a gap between end of Okazaki fragment and RNA primer (need to replace RNA primer)

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6
Q

nick translation

A

When DNA pol 1 extends the Okazaki fragment while its 5’–>3’ exonuclease activity removes the RNA primer

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7
Q

DNA ligase binds to the ____ when repairing gaps in DNA

A

nick

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8
Q

DNA ligase then catalyzes the formation of a _______ _______ between 3’ hydroxyl and 5’ phosphate of adjacent Okazaki fragments - then it dissociated from DNA

A

phosphodiester linkage

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9
Q

why cant DNA pol fill in the gap?

A

no free 3’ end

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10
Q

describe eukaryotic chromosomes

A

large linear, double stranded DNA molecules

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11
Q

replication of eukaryotic chromosomes is in what direction

A

bidirectional

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12
Q

compared to E.coli, eukaryotic replication has _____ sets of initiation of DNA synthesis

A

multiple

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13
Q

unique structures at the ends of linear chromosomes (the free end of linear DNA)

A

telomeres

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14
Q

what 2 problems do telomeres have

A
  1. they are susceptible to damage by nucleases

2. due to the nature of DNA synthesis, one strand will shorten upon each round of DNA Synthesis

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15
Q

telomeres have the job of

A

protecting the end from degradation by forming a loop from the guanine rich single stranded DNA - protects end of chromosome from nuclease

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16
Q

this enzyme can reverse transcribe DNA from RNA template; has DNA activity but is dependent on RNA

A

telomerase

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17
Q

telomerase unusual hairpin structure forms new primer to make

A

double stranded DNA

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18
Q

_____ of hairpin yields lengthened telomere

A

cleavage

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19
Q

why is telomerase called a reverse transcriptase when it is adding deoxynucleotides?

A

b/c it is a RNA-dependent DNA polymerase; it has its own RNA template complementary to the telomeric repeat sequence so, it REVERSE transcribes DNA from the RNA template

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20
Q

short telomeres cause

A

premature aging; bone marrow diseases; secondary hit + telomeres cause idiopathic pulmonary fibrosis

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21
Q

DNA pol 3 holoenzyme also

A

fixes mistakes

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22
Q

possesses 3’ –> 5’ exonuclease activity - “proofreading”

A

DNA polymerase 3 holoenzyme

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23
Q

pol 3 can catalyze both chain

A

elongation and degradation

24
Q

exonuclease activity removes mispaired nucleotide before

A

polymerization continues

25
Q

*most uncorrected replication errors are subsequently corrected by

A

the DNA repair enzymes

26
Q

____ is the only cellular macromolecule that can be repaired

A

DNA

27
Q

specific _____ ____ scan DNA to detect any alterations - recognize mismatched bases, modified nucleotides

A

repair enzymes

28
Q

repair that does not require breaking the phosphodiester backbone of DNA

A

direct repair

29
Q

mechanisms that do involve breaking the DNA backbone to repair

A

mismatch; base-excision; and nucleotide-excision

30
Q

repair of thymine dimers is done by

A

DNA photolyase - photoreactivation

31
Q

double-helical DNA is very sensitive to damage by

A

UV light; dimerization of adjacent pyrimidines in a DNA strand is common

32
Q

repair after photodimerization is _____ repair

A

direct

33
Q

mismatch-repair system corrects errors that

A

were not corrected by proofreading that cannot be directly repaired

34
Q

in Ecoli, MutS recongnizes the error, MutL reruits MutH to

A

cleave the DNA and the exonuclease activity of MutH excises the bases
MISMATCH-REPAIR

35
Q

parent strand may be marked by methylation or adenines so that repair machinery can

A

recognize the correct base

36
Q

_______ synthesizes new strand in mismatch repair and ____ ligates the pieces together

A

DNA pol 3; DNA ligase

37
Q

nucleotide deamination

A

hydrolytic deamination of C to U or G to A; DNA glycosylases hydrolyze base-sugar N glycosidic bonds; deaminated bases are then removed and replaced

38
Q

AlkA glycosylase does what?

A

hydrolyzes the glycosidic bond leaving an AP site

base -excision repair

39
Q

AP endonuclease detects AP site and

A

nicks the sugar-phosphate backbone (base excision repair)

40
Q

deoxyribose phosphodiesterase excises the

A

deoxyribose phosphate (base-excision repair)

41
Q

DNA pol 1 fills gap and DNA ligase

A

seals the nick

42
Q

what happens when excision repair does not function?

A

extreme sensitivity to the sun, greater risk of skin cancer, cancer growth, xeroderma pigmentosum

43
Q

carcinogens are detected using bacteria via what test

A

ames test

44
Q

simple, sensitive means of determining if a chemical is mutagenic

A

Ames test

45
Q

3 steps of the Ames test

A
  1. Salmonella bacteria that require histidine because of a mutation in its biosynthetic pathway are treated with the chemicals
  2. salmonella are plated on a plate lacking histidine
  3. salmonella growth suggest that the chemical caused a mutation which restored histidine synthesis
46
Q

exchange or transfer of pieces of DNA from on chromosome to another or within a chromosome

A

recombination

47
Q

occurs between pieces of DNA tat have closely related sequences (exchange between paired chromosomes during meiosis)

A

homologous recombination

48
Q

non-homologous recombination occurs between

A

unrelated sequences

49
Q

site specific recombination

A

recombination at a specific location

50
Q

why is recombination needed?

A

mutation gives new genetic variation; recombination created different combinations of mutations within a genome.

51
Q

recombination also plays an important role in the

A

repair of DNA

52
Q

how can recombination be used in repair

A

severe lesions in DNA can be repaired by strand exchange from intact daughter chromosome to defective daughter

53
Q

RAD51

A

key protein in double strand breaks repaired by recombination

54
Q

know steps of double strand breaks repaired by recombination!

A
  1. break recognized, 5’ end digested, single-strand regions are bound by RAD51
  2. strand inversion occurs-single strand form damaged DNA replaces a strand in undamaged DNA. This 3 stranded structure is called a DISPLACEMENT LOOP
  3. DNA synthesis occurs, using the undamaed DNA as a template
  4. a second strand invasion occurs to complete the repair, forming a HOLLIDAY JUNCTION
    5 cleavage and ligation yield two intact helices
55
Q

what happens when ds break repair doesn’t function?

A

human BRACA1 and BRACA2 - human breast cancer genes BRC repeats of BRACA2 interact directly with Rad51
BRCA2 may serve to deliver Rad51 to the site of DNA damage
conserved C-terminus appears to bind ssDNA and dsDNA

Biochemistry (6 decks)

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