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Molecular and Cellular Biology: > DNA Mechanisms- Replication and Repair: > Flashcards

DNA Mechanisms- Replication and Repair: Flashcards

1
Q

What is DNA replication?

A

The process by which a copy of DNA is made

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2
Q

What happens to the DNA before cell division?

A

The DNA is duplicated

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3
Q

List the two main stages of the cell cycle:

A
  • Interphase

- Mitosis (division)

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4
Q

Which of the two stages of the cell cycle are the longest?

A

Interphase

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5
Q

List the phases in Interphase:

A
  • G1 phase
  • G0 phase
  • S phase
  • G2 phase
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6
Q

What cells undergo the G0 phase?

A

Cells that have stopped dividing

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7
Q

What happens in the S phase?

A

DNA synthesis

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8
Q

By what process is DNA replicated?

A

Semi-conservative replication

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9
Q

What is produced from semi-conservative replication of DNA?

A

A DNA molecule consisting of one original strand of DNA, and a new complementary strand

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10
Q

What protein is responsible for separating the strands of DNA?

A

DNA helicase

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11
Q

How does DNA helicase separate DNA strands?

A

It breaks the hydrogen bonds between base pairs, using energy produced from the hydrolysis of ATP

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12
Q

What enzyme is responsible for the synthesis of new DNA?

A

DNA polymerase

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13
Q

How does DNA polymerase synthesis new DNA?

A

It adds nucleotides to the 3’ (3 prime) end of the previous nucleotide, so the strand is made from the 5’ (5 prime) end to the 3’ end

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14
Q

What is required for DNA polymerase to synthesis a new DNA strand?

A
  • Template DNA strand
  • Oligonucleotide primer
  • Supply of deoxynucleotide triphosphates (dNTPs)
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15
Q

What are oligonucleotides?

A

A short sequence of DNA or RNA molecules

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16
Q

Why do DNA polymerase enzymes require oligonucleotide primers?

A

They are required to bind (via hydrogen bonds between complementary base pairs) to the template DNA strand, from which DNA polymerase attaches nucleotide (acts as a start point)

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17
Q

What is the name of the process by which DNA polymerase synthesises new DNA strands?

A

Chain Elongation

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18
Q

What is a deoxyribonucleoside triphosphate?

A

A nucleotide containing 3 phosphates attached to the 5’ prime carbon atom of the deoxyribose sugar of DNA nucleotides

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19
Q

What happens to the innermost phosphorus atom of the incoming deoxyribonucleoside triphosphate?

A

The phosphate (negatively charged) atom undergoes nucleophilic attack by the 3’-hydroxyl group

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20
Q

What is nucleophilic attack?

A

Where a nucleophile attacks a region of positive charge

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21
Q

What is a nucleophile?

A

A negatively charged substance which is attracted to an area of positive charge

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22
Q

What happens once the phosphorus atom is attacked by the 3’-hydroxyl group?

A

A phosphodiester bridge is formed, releasing pyrophosphate

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23
Q

What enzyme is responsible for the synthesis of RNA primers?

A

DNA primase ??

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24
Q

What are primases?

A

RNA polymerases

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25
Q

What do primases do?

A

Synthesis short RNA sequences complementary to a single-stranded piece of DNA template

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26
Q

What does DNA primase do?

A
  • Start new polynucleotide chains
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27
Q

Why do primers contain a high frequency of errors?

A

DNA primase enzymes do not proofread their work

28
Q

What makes DNA replication a highly accurate process?

A

Most DNA polymerase enzymes can proofread their work

29
Q

Describe how DNA polymerase proofreads its work:

A

Before adding another nucleotide, DNA polymerase checks whether the previous nuceotide is correctly base paired with the template strand. If correctly paired, it will add the next nucleotide. If not, the DNA polymerase clips off the mispaired nucleotide

30
Q

Which way does the DNA polymerase proofread the new DNA strand?

A

From the 3’ end to the 5’ end ???

31
Q

How does the DNA polymerase enzyme proofread the DNA?

A

Through it’s exonuclease activity which cleaves the phosphodiester backbone

32
Q

Why does synthesis and proofreading of DNA strands by DNA polymerase have to be tightly coordinated?

A

Proofreading and synthesis happen at the same time

33
Q

Why is it important that DNA is not synthesised by DNA polymerase from the 3’ end to the 5’ end?

A

DNA polymerase would be unable to proofread the DNA molecule if it was made this way

34
Q

What would DNA polymerase do if it removed an incorrectly paired molecule on a DNA molecule that is made from the 3’ end to the 5’ end?

A

It would create a chemically dead chain end which could no longer be elongated

35
Q

How would DNA polymerase create a chain that is chemically dead?

A

DNA polymerase would remove an incorrect nucleotide that would block the addition of the correct nucleotide and prevent further chain elongation

36
Q

What is the replication fork?

A

The point at which DNA replication takes place

37
Q

Why is it more difficult to replicate one DNA strand over the other?

A

The strands of a single DNA molecule run anti-parallel to each other, which means DNA polymerase would not be able to move in the 5’ to 3’ along the second strand

38
Q

What do cells form in order to counter-act the problem of one of the strands being harder to replicate?

A

Asymmetric replication fork

39
Q

What happens at the asymmetric replication fork?

A

The leading strand in the DNA molecule is synthesised continuously in the 5’ to 3’ direction, while the lagging strand (whose 5’ end must grow) is made discontinuously in successive separate small pieces

40
Q

What are the names of the successive separate small pieces making up the lagging strand?

A

Okazaki Fragments

41
Q

What needed to start the replication of the leading strand of DNA?

A

A single RNA primer is needed to start replication.

42
Q

How are primers used by DNA polymerase to synthesis the lagging strand? How does this affect the way the lagging strand is synthesised?

A

New primers are added continually- making DNA synthesis discontinuous. DNA polymerase will use the primers to start new DNA fragments and continue to elongate it unil it runs into the next RNA primer

43
Q

How is a continuous new DNA strand made from separate Okazaki fragments made on the lagging strand?

A
  • A DNA repair system acts to quickly erase the RNA primer and replace it with DNA
  • DNA ligase enzyme joins the 3’ end of the new DNA fragment to the 5’ end of the previous one to complete the process
44
Q

What three enzymes work on the lagging strand and what are their roles?

A
  • Nuclease: Break apart the RNA primer
  • Repair Polymerase: Replaces RNA with DNA
  • DNA ligase: Joins the 5’- phosphate end of one new DNA fragment to the adjacent 3’- hydroxyl end of the next
45
Q

Describe how the leading strand is synthesised:

A
  • An RNA primer is required to start of replication at the replication orgin
  • This leaves the 3’ hydroxyl group end of RNA primer free to allow for chain elongation
  • DNA polymerase copies the DNA sequence of the template strand in a continuous manner

-

46
Q

Describe how the lagging strand is synthesised?

A
  • For synthesis, RNA primers are needed at many points along the template strand
  • A new RNA primer is made by DNA primase
  • There is an exposed hydroxyl group on the 3’ end of the RNA primer
  • DNA polymerase adds to the RNA primer from this exposed hydroxyl group, synthesising new Okazaki fragments
  • Ribonuclease erases the old RNA primer used previously in the sequence, leaving a space between Okazaki fragments
  • The gap is filled by repair DNA polymerase
  • DNA ligase joins the new Okazaki fragment to the growing chain

-

47
Q

What problem is reached when the replication fork reaches the end of a chromosome?

A

There is no template sequence for synthesising a new RNA primer ???

48
Q

What would happen if, when the replication fork reached the end of a chromosome, DNA was synthesised without a new RNA primer?

A

DNA would be lost from the ends of a DNA molecule each time it replicated

49
Q

How do bacteria solve the problem of having no template sequence for synthesising new RNA primers when the replication fork reaches the end of the chromosome?

A

By having circular DNA molecules as chromosomes

50
Q

How often and fast does DNA replication occur?

A

Every time a cell divides, at a rate of 50 nucleotides per second

51
Q

What is the effect of DNA polymerase (used in replication) and DNA repair not being 100% efficient?

A

Incorrectly paired nucleotides that remain following DNA repair become permanent changes after the next cell division- and the cell will no longer recognise these as errors

52
Q

What does the inefficiency of DNA polymerase and DNA repair lead to?

A

Mutations and variants

53
Q

What precautions are made to prevent mutations in the base sequence from becoming permanent?

A
  • Polymerases have intrinsic proofreading activity

- DNA is constantly monitored for damage and base mismatches

54
Q

What is the overall error rate?

A

1-2 bases per genome

55
Q

What is an alternatie word for a variant?

A

Polymorphism ??

56
Q

What are mutations?

A

All random changes to the base DNA sequence from that of the orginial template

57
Q

What can arise from DNA mutation?

A

Variance (variant individuals)

58
Q

Why might we never know the orginal true sequence of DNA in a population?

A
  • DNA bases changes occur very frequently in a general population
  • Genes spread throughout the population
59
Q

What are variants?

A

Differences in physical and physiological characteristics between members of a population

60
Q

Why would it be useful to know the particular combination of mutations that each individual has?

A
  • It can give insight on possible effective treatments

- Help figure out the risk of individual’s getting a certain disease, given certain environmental exposures

61
Q

Which enzyme catalyses the separation of DNA strands, and where does it get the energy to do this?

A

DNA helicase breaks hydrogen between DNA bases, separating the two strands, using energy from ATP hydrolysis

62
Q

Describe the structure of DNA helicase:

A
  • It has a hexagonal arrangement of six identical sub-units, which is slightly squished.
  • It has six available ATP binding sites, two of which bind to ATP very tightly, other two are more likely to bind ADP and inorganic phosphate and the ,fast two are empty
63
Q

How are the ATP binding sites used in DNA helicase?

A

The state of each ATP binding site rotates around as ATP is hydrolysed, creating a ripple effect that continuous around the ring (one that binds DNA or nothing may bind ADP and phosphate instead, and vice versa)

64
Q

Why do the loops that extend into the centre hole of the ring of DNA helicase oscillate up and down?

A

Due to the conformational changes of the DNA helicase, which helps pull DNA through the central hole- helping to split the strands of DNA

65
Q

What is the role of the loops extending into the centre hole of DNA helicase?

A

To bind DNA

Molecular and Cellular Biology: (4 decks)

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