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Quiz 2 > Q2-FUN10/DNA Replication > Flashcards

Q2-FUN10/DNA Replication Flashcards

1
Q

why is eukaryotic DNA replication so difficult?

A

there is a large amt of DNA to be replicated, chromosomes are strucutrally complex, need a lot of enzymes, takes a lot of time

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2
Q

how long is the cell cycle for yeast

A

1.4 hrs

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3
Q

how long is the cell cycle for cultured animal cells?

A

16-24 hrs

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4
Q

how long is the cell cycle for human cells

A

8hrs - 100 days or permanent (G0)

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5
Q

what does semiconservative replication mean?

A

two copies of the original dna molecule are produced, and each copy replicates the info from 1/2 of the original DNA molecule

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6
Q

what are the 4 DNA replication requirements?

A
  1. single stranded template
  2. nucleotides
  3. replisome
  4. a primer with a free 3’ hydroxyl group
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7
Q

what is a replisome?

A

large protein complex that carries out DNA replication, has a bunch of enzymes and proteins in it

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8
Q

what is the origin of replication?

A

a place where the separation of 2 complimentary strands occur

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9
Q

what moves outwards from the ori during initiation?

A

two replication forks

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10
Q

what are the unwinding proteins?

A

DNA helicase, single-strand binding proteins, and topoisomerase

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11
Q

what does DNA helicase do?

A

it separates the DNA strands, uses energy

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12
Q

what do SSB proteins do?

A

these proteins bind single stranded regions of DNA to prevent the strands from re-associating

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13
Q

what does topoisomerase do?

A

it regulates the twisting of DNA, prevents DNA supercoiling

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14
Q

What is primase?

A

it is a RNA polymerase enzyme

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15
Q

What does primase make?

A

it makes a primer, which is an RNA starter strand

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16
Q

the primer starts on the __’ to ___’ strand

A

5’ - 3’

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17
Q

Why do we need RNA polymerase to make a primer?

A

because DNA polymerase enzymes can only extend a chain, they cant make DNA from scratch

they require a free 3’ hydroxyl group to extend DNA (DNA is copied in the direction of 5’ to 3’)

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18
Q

once RNA primer is removed, what fills its gap?

A

DNA polymerase

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19
Q

what does DNA poly use as a template?

A

single stranded DNA

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20
Q

how does DNA poly read its template?

A

3’ to 5’

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21
Q

how does DNA poly MAKE new DNA?

A

5’ to 3’

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22
Q

DNA starts the formation of __________ bonds

A

phosphodiester

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23
Q

What does PCNA stand for?

A

proliferating cell nuclear antigen

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24
Q

what does PCNA do?

A

it acts as a sliding clamp. DNA polymerase attached nucleotides at abt 1000 per second so it needs something to keep it close to the template as it moves along.

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25
Q

What enzyme helps proofread the activity so that no errors occur?

A

DNA polymerase

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26
Q

what is substrate specificity in DNA replication?

A

the DNA poly active site can bind all 4 nucleotides, but catalysis only occurs when the correct one is bound

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27
Q

what is 3’ to 5’ exonuclease activity?

A

it is the proofreading of the strand. it removed nucleotides at the 3’ end of the new strand that is incorrectly matched.

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28
Q

which strand is made continuously and which strand is made discontinuously?

A

leading, lagging (DNA poly can only make DNA 5’ to 3’)

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29
Q

in the lagging strand, primase makes a new primer at ___________ intervals?

A

regular

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30
Q

what is an okazaki fragment?

A

fragments on the lagging strand

31
Q

what seals up the gaps between the okazaki fragments?

A

DNA ligase

32
Q

what are the 3 main enzymes in eukaryotic replication?

A

alpha, delta, epsilon

33
Q

Pol alpha is involved in starting ______

A

replication

34
Q

Pol alpha is strongly associated with _______.

A

primase, to make a Pol alpha/primase complex

35
Q

What does Pol alpha not have?

A

exonuclease activity, which means that there is no proofreading

36
Q

are Pol epsilon and Pol delta associated with primase?

A

no

37
Q

Pol alpha is _______ processive

A

moderately

38
Q

Pol epsilon and Pol delta are ________ processive

A

highly

39
Q

What does Pol epsilon and Pol delta have that Pol alpha doesnt?

A

3’ to 5’ exonuclease activity, these 2 enzymes can proofread

40
Q

Pol epsilon is involved in _______ synthesis and Pol delta is involved in ________ synthesis

A
41
Q

What is Pol beta involved in?

A

DNA repair

42
Q

What does Pol gamma do?

A

it replicates mitochondrial DNA

43
Q

What 2 enzymes remove RNA primase once it has made the primer?

A

Rnase H1 and Flap endonuclease 1

44
Q

what does Rnase H1 do?

A

it removes most of the RNA primer, leaving one 5’ ribonucleotide next to the DNA

45
Q

What does FEN1 (Flap endonuclease 1) do?

A

it removes the 5’ ribonucleotide

46
Q

What fills in the gaps once all the RNA primer is removed?

A

DNA Pol epsilon and delta

47
Q

Explain replication termination in eukaryotes.

A

eukaryotes do not have termination sequences. DNA replication keeps going until the replication fork collids with the fork from the adjacent replicon.

48
Q

what causes the problem in replicating the 2 ends of linear DNA strands?

A

telomeres

49
Q

explain termination in leading and lagging strand.

A

on the leading strand, DNA synthesis can occur to the end of the template, but on the lagging strand, the primer was removed so there is no OH group available for DNA poly to add nucleotides to.

50
Q

where are telomeres located?

A

on the 3’ end of each chromosome

51
Q

what are telomeres?

A

1000’s of tandem repeats (TTAGGG in humans)

52
Q

What is telomeric DNA made and maintained by?

A

telomerase

53
Q

What type of molecule is telomerase?

A

a Ribonucleoprotein (RNA + protein)

54
Q

during development as cells divide and differentiate, what happens to telomerase?

A

telomerase function declines, telomeres shorten

55
Q

the absence of telomerase causes _________

A

aging

56
Q

The proof-reading activity of DNA Polymerase reduces the error rate from 1 in __________ to approximately 1 in _____ bases replicated

A

10^4 -10^5, 10^7

57
Q

what things can cause damage to DNA?

A

radiation, high energy radiation, chemicals

58
Q

What are the types of damage that can occur to DNA?

A

base substitutions, insertions, deletions

59
Q

Explain mismatch repair.

A

When MSH proteins see a mismatch they recruit endonuclease. This endonuclease cuts out the mismatched nucleotide bonds from the DNA strand. Then exonuclease comes in and removes the severed piece of DNA. This leaves a gap which is filled by DNA polymerase. Then DNA ligase joins the backbone. Now, the damage is fully repaired.

60
Q

What is HNPC?

A

it is hereditary non polyposis cancer. it is when there is a defect in the genes that code for mismatch repair; it doesnt produce the Mut L proteins that help carry out mismatch repair.

61
Q

What damage causes a base excision repair to be used?

A

harmful chemicals and physical factors

62
Q

Explain base excision repair.

A

DNA glycosylases identifies and removes the damaged base. The site of removal is then called apurinic or apyrimidic, because there is no base left there. Then AP endonuclease cuts the backbone and exonuclease removes the sugar and several adjacent pairs. Then DNA polymerase adds the new nucleotides and DNA ligase seals the backbone.

63
Q

When would a nucleotide excision repair be used?

A

UV radiation

64
Q

Explain nucleotide excision repair.

A

UV radiation causes pyrimidine dimers, which are usually found between two adjacent thymines. The thymines forms bonds with one another, distorting the DNA strand in that region of the molecule.

Then, the endonucleases cleave the 3’ side of the damage and the 5’ side of the damage. This leaves a fragment of about 12-24 nucleotides long, that the exonucleases takes away.

DNA polymerase fills in the nucleotides and DNA ligase seals the gaps in the backbone.

65
Q
A
66
Q

What is xeroderma pigmentosum?

A

it is a rare human skin disease

67
Q

XP is __________ recessive

A

autosomal recessive

68
Q

XP is a deficiency in what?

A

nucleotide excision repair, there is a lack of enzymes necessary for repair of DNA damage induced by UV radiation

69
Q

What are symptoms of XP (xeroderma pigmentosum)?

A

extreme sensitivity to light, skin cancer, secondary tumours

70
Q

What are the 2 ways to fix double strand breaks?

A

nonhomologous end joining and recombination

71
Q

Explain nonhomologous end joining. (NHEJ)

A

First, the Ku protein (DNA Protein kinase) recognises the double stranded break. Another protein called artemis cuts off the single stranded parts. DNA ligase binds the 2 together.

72
Q

Why is NHEJ bad?

A

it is an error prone repair and it leads to a loss of genetic information

73
Q

Explain homologous recombination.

A

Homologous recombination uses a sister chromatid. A protein called MRN binds to the broken strand and calls in endonucleases to remove nucleotides from one strand of the DNA.

Now we have end 1 and end 2. end 1 is placed near a similar homologous sequence on the other chromatid, because its found in the same spot on the homologous sister chromatid.

End 1 then pairs up with the complementary strand of the intact homologous DNA region. This creates a loop in the homologous DNA.

Then DNA polymerase makes nucleotides to extend end 1, until it reaches a sequence that is complimentary to end 2.

then end 1 releases the homologous DNA and the last few nucleotides bind to the last nucleotides of end 2.

Then DNA polymerase fills in the gaps of both sides of the broken strand, and DNA ligase seals it up.

Quiz 2 (18 decks)

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