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STRUC+FUNC 1 (vet) > Genetics - DNA replication > Flashcards

Genetics - DNA replication Flashcards

1
Q

what important tasks do cells need to complete before they divide?

A

grow
copy its genetic material (DNA)
physically split into two daughter cells

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2
Q

what two major phases is the cell cycle divided into?

A

interphase and mitosis (M) phase

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3
Q

what happens during interphase?

A

G1, S, G2
the cell grows and makes a copy of its DNA

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4
Q

During the mitotic phase, what happens?

A

the cell separates its DNA into two sets and divides its cytoplasm, forming two new cells

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5
Q

at each cell division, what must a cell do?

A

it must copy its genome
it is essential that this process occurs accurately

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6
Q

Semi-conservative replication?

A

DNA acts as a template for its own replication

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7
Q

what type of replication does DNA replicate by?

A

semi-conservative replication

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8
Q

what does DNA helicase do?

A

unwinds the DNA

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9
Q

What does DNA polymerase do?

A

synthesises DNA 5’-3’ direction

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10
Q

what does DNA topoisomerase do?

A

relieves the tension in DNA

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11
Q

What does DNA primase do?

A

synthesises RNA primers

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12
Q

what do ribonucleases do?

A

degrades RNA primers

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13
Q

what does DNA ligase do?

A

joins DNA fragments

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14
Q

what does telomerase do?

A

replicates the ends of the chromosome

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15
Q

DNA unwinding?

A

DNA helicase
SSB
DNA topoisomerase

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16
Q

DNA helicase function?

A

unwinds the DNA
uses ATP to propel itself along the DNA

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17
Q

SSB? Function?

A

SSB - single-stranded DNA binding protein
Binds and keep the strands apart

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18
Q

DNA topoisomerase function?

A

relieves the tension

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19
Q

DNA synthesis process?

A

DNA polymerase requires a template
DNA polymerase requires a primer
A new strand of DNA is always synthesised in a 5’ to 3’ direction
it elongates from a free 3’OH
Synthesis begins at an origin replication

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20
Q

DNA primase?

A

synthesises short RNA primer

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21
Q

primer?

A

short segment of RNA complementary to the template with a 3’OH

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22
Q

3’OH?

A

3 prime hydroxyl group

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23
Q

DNA replication progresses in the –>

A

5’-3’ so replication on the leading strand is continuous

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24
Q

As DNA replication cannot progress in the opposite direction…

A

replication on the lagging strand is discontinuous

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25
Q

Okazaki fragments?

A

the short DNA sequences (100-1000 nucleotides) synthesised on the lagging strand

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26
Q

DNA helicase results in the formation of a…

A

replication fork

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27
Q

exonuclease?

A

removes all of the RNA primers –> another DNA polymerase molecule fills these gaps with DNA nucleotides

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28
Q

How does the DNA polymerase remain attached to the DNA template?

A

by interaction with a protein called sliding clamp

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29
Q

when does a new sliding clamp come in?

A

a new clamp has to be loaded on the lagging strand as each Okazaki fragment is synthesised

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30
Q

What happens with the lagging strand?

A

DNA primase attaches RNA to template
DNA polymerase III adds nucleotides until it reaches the previous primer
RNase H digests the RNA primer, leaving a gap
DNA polymerase I fills in the gaps
DNA ligase then joins the fragments together

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31
Q

telomerase?

A

elongates parental strand
end problem

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32
Q

what are telomeres?

A

repetitive regions at the very ends of chromosomes are called telomeres

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33
Q

what do telomeres act as?

A

act as caps that protect the internal regions of the chromosomes, and they’re worn down a small amount in each round of DNA replication

34
Q

Depurination?

A

no DNA breaks
removal of purines
removal of guanine or adenine base to leave sugar-phosphate group

35
Q

Deamination?

A

no DNA breaks
results in a C to U transition
e.g. conversion of cytosine to uracil

36
Q

What is a gain of function mutation?

A

A DNA sequence change that leads to increased or alternative activity

37
Q

What is a loss of function mutation?

A

A DNA sequence change that leads to decreased activity

38
Q

silent mutation?

A

when a nucleotide substitution results in a different codon that still encodes the same amino acid - therefore the protein is unaffected in function and the phenotype of the organism is not significantly altered

39
Q

Missense mutation?

A

when a nucleotide substitution results in a codon that encodes a different amino acid - therefore the primary protein sequence is altered which may be conservative or radical

40
Q

what is a conservative substitution?

A

similar amino acid R group size and charge
similar protein shape and function
e.g. Gly –> Ala

41
Q

radical substitution?

A

new amino acid R group different in charge or size
protein may have altered secondary or tertiary structure affecting function

42
Q

consequences of missense mutation?

A

conservative substitution
radical substitution
disrupting functional or structurally important residues

43
Q

Nonsense mutations?

A

when a nucleotide substitution results in a stop codon that stops translation, therefore the protein truncated and may not function properly or even at all

44
Q

what is protein truncation?

A

shortening due to change of sequence resulting in stop codon

45
Q

NMD?

A

nonsense mediated decay
a process during translation that detects transcripts with premature stop codons and degrades them

46
Q

3 mechanisms for DNA repair

A

Excision
Repair
Joining

47
Q

excision?

A

recognition and removal of damage
exonuclease

48
Q

repair?

A

re-synthesis of missing DNA
DNA polymerase

49
Q

Joining?

A

sealing the nick
DNA ligase

50
Q

Mismatch repair?

A

DNA replication makes a mistake 1 in 10(7) nucleotides copied - mismatch repair reduces this to 1 in 10(9)

51
Q

What do RNA primers provide when we are creating the lagging strand?

A

the 3’ OH groups at regular intervals along the lagging strand template

52
Q

when does the lagging strand stop?

A

it stops short of the end of the lagging strand template

53
Q

why do chromosomes get progressively shorter during each replication cycle?

A

because there is an inability to replicate the ends as there is
no 3’ OH group available to prime DNA synthesis

54
Q

what solves the end replication problem?

A

solved by the enzyme telomerase

55
Q

telomere?

A

G-rich series of repeats

56
Q

where is a telomere found?

A

in the ends of chromosomes

57
Q

what does telomerase do?

A

recognises the tip of an existing repeat sequence, using an RNA template within the enzyme
telomerase elongates the parental strand in the 5’ to 3’ direction and adds additional repeats as it moves down the parental strand

58
Q

how is the lagging strand completed?

A

by DNA polymerase alpha, carries a DNA primase as one of its subunits - allows the ends to be completely copied in the new DNA

59
Q

What is the problem in the lagging strand?

A

Okazaki fragments cannot cover the end of the chromosome

60
Q

Why can the other primers throughout the lagging strand be replaced, apart from the end one?

A

there is no way to get the fragment started because the primer would fall beyond the chromosome end

61
Q

What happens in each round of replication because of the problem in the telomeres?

A

part of the DNA at the end of a eukaryotic chromosome goes uncopied in each round of replication

62
Q

part of the DNA at the end of a eukaryotic chromosome goes uncopied in each round of replication - what does this result in?

A

leaves a single-stranded overhang.

63
Q

part of the DNA at the end of a eukaryotic chromosome goes uncopied in each round of replication - what happens over multiple rounds of cell division?

A

the chromosome will get shorter as this process repeats

64
Q

what is telomerase?

A

an enzyme which is an RNA-dependent DNA polymerase, meaning an enzyme that can make DNA using RNA as a template

65
Q

what is the solution for the problem caused in telomeres?

A

the enzyme binds to a special RNA molecule that contains the sequence complementary to the telomeric repeat

66
Q

telomere solution, the enzyme binds to a special RNA molecule that contains the sequence complementary to the telomeric repeat - what happens after this?

A

telomerase recognises the tip of an existing repeat sequence and uses the RNA template within the enzyme to add additional repeats to the telomere DNA

67
Q

Telomere - solution, telomerase recognises the tip of an existing repeat sequence and uses the RNA template within the enzyme to add additional repeats to the telomere DNA - what happens after this?

A

when the overhang is long enough, a matching strand can be made by DNA polymerase alpha, which has its own primase subunit - so DOESN’T NEED A PRIMER

68
Q

how does the active site help with ‘proof-reading’ and ‘fidelity’?

A

active site geometry only accommodates A-T & G-C base pairs

69
Q

How is the ‘proof-reading’ carried out?

A

3’ to 5’ exonuclease activity

70
Q

what can cause damage to DNA?

A

can be damaged as a result of UV light, ionising radiation exposure, toxic chemical agents, reactive oxygen species

71
Q

What can DNA damage result in?

A

results in mutations in genes that can lead to altered coding for proteins resulting in loss or gain of functions

72
Q

how many errors does a typical mammalian cell accumulate in its DNA every 24 hours?

A

many thousands of errors

73
Q

What type of damage arises from UV light exposure?

A

Thymidine Dimers

74
Q

What are the types of damages to the DNA?

A

Double stranded breaks, thymidine dimers, depurination, deamination

75
Q

What kind of damage are we talking about when we say ‘thymidine dimers’?

A

two adjacent thymine bases become covalently attached to each other –> leads to stalling of the replication machinery

76
Q

Failure to repair thymidine dimer leads to?

A

this is the problem in xeroderma pigmentosum

77
Q

what causes double stranded breaks?

A

some environmental factors such as high energy radiation

78
Q

what happens during double stranded breaks?

A

chromosomes are literally split in two

79
Q

In double stranded breaks, what depends on where the break is and how extensive the damage is?

A

depending on these two factors, large numbers and the information they encode can be lost

80
Q
A

STRUC+FUNC 1 (vet) (19 decks)

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