Replication of DNA Flashcards

1
Q

1) Describe the initiation of DNA replication in prokaryotes

A
  • Proteins interact at the origin of replication on DNA
  • Double helix is opened up with aid of helicase enzymes (initiator proteins) and 2 replication forks are formed, exposing single stranded templates for DNA synthesis
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2
Q

2) How is the rest of the DNA strand affected when helicase opens up the double helix?

A
  • When opened, torsion is sent down the double helix (twisting)
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3
Q

3) Which enzymes must act on the supercoiled DNA strands before initiation and what do they do?

A
  • Topoisomerase enzymes which uncoil the supercoiled DNA strands, ahead of replication
    > Type I relaxes the supercoiled DNA
    > Type I (gyrase) cuts and releases the DNA strand to relieve supercoiling (loosens twist -> straightens)
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4
Q

4) Which direction is new DNA synthesized?

A

From the 5’ -> 3’ end

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5
Q

5) What is the leading strand and the lagging strand in DNA replication?

A
  • Leading strand: strand of DNA from which the new DNA strand is synthesized continuously
  • Lagging strand: the other strand of DNA from which the new strand is synthesized as a series of short [Okazaki] fragments (discontinuously)
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6
Q

6) Why can the lagging strand not be used to synthesize a new DNA strand continuously? [Polarity problem]

A
  • This would be synthesized from 3’ to 5’ end which contradicts the 5’ -> 3’ end rule
  • Replication machinery must move from the 5’ -> 3’ end, as the parent strands are unwound
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7
Q

7) How is the lagging strand still able to produce a new strand of DNA despite initially running in the 3’ -> 5’ direction?

A
  • Lagging strand template is looped to allow synthesis (so is running in the opposite direction to itself, parallel)
  • DNA polymerase III makes new DNA on both strands simultaneously and moves in the same direction as the replication fork
  • Loop enlarges as RNA primers move along the strand
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8
Q

8) Name the 3 enzymes involved in the initiation stages of DNA replication

A
  • Helicase - unwind DNA strands at replication fork
  • Topoisomerases - release supercoils in DNA
  • Single strand binding proteins - stabilise single stranded DNA in separate strands
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9
Q

9) Which enzyme attaches DNA polymerase III firmly to the DNA strand?

A
  • beta protein (sliding clamp)
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10
Q

10) What are the functions of DNA polymerase III and primase in DNA replication of the leading and lagging strand?

A
  • Leading : requires primase(makes RNA primer to begin DNA synthesis) only at the beginning of the synthesis of the new strand
  • Lagging: Requires primase at the beginning of each new Okazaki fragment (RNA primers needed for each)
  • Both strands need DNA Polymerase III to synthesize the new DNA strand
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11
Q

11) What are the functions of DNA polymerase I and DNA ligase in DNA replication of the leading and lagging strand?

A
  • DNA polymerase I : transfers complementary deoxy nucleotides to the leading and lagging strand
  • removes the nucleotides of the RNA primer and adds deoxynucleotides to fill the gap with DNA
  • Ligase : joins discontinuous Okazaki DNA fragments by making a phosphodiester bond (in lagging strand) and joins nucleotides with the same bond (in leading)
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12
Q

12) How can mutations be created in the new DNA strand?

A
  • Incorporation of incorrect nucleotides into the new DNA chain
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13
Q

13) Which 2 enzymes have a proof-reading ability and how is mutated DNA repaired?

A
  • Polymerase I and III can detect incorrect base pairs
  • 3’ -> 5’ (reverse) exonuclease activity removes the incorrect base and polymerase inserts the correct base instead
  • Errors that escape this proof reading are also repaired in E.Coli
    [Another protein group can removes a section of newly formed DNA and PolyIII resynthesizes the new strand]
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14
Q

14) What does it mean DNA has a high ‘fidelity’ and why is this so important?

A
  • low error rate
  • as consequences of a single base mutation are serious
    ( mutated gene -> abnormal protein -> loss of important function/gain of toxic function (e.g.cancers) )
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15
Q

15) Give 8 ways in which DNA can be damaged (and may be repaired by DNA repair complexes)

A
  • UV light : thymine dimer formation
  • Ionising radition : strand breaks
  • Nitrous acid : cytosine converted to uracil
  • Alkylating agents : guanine modification (GC->AT)
  • Free radicals : strand breaks, base modification
  • Bulky chemicals : distorts double helix
  • Spontaneous : cytosine -> uracil, CG becomes T, loss of purines
  • Carcinogenic chemicals (smoke) -> various base modifications
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16
Q

16) How does mitochondrial DNA replicate?

A
  • Have its own single circular chromosome

- Needs to be replicated independantly from nuclear chromosomes, as eukaryotic cells divide

17
Q

17) Give differences between DNA replication in eukaryotes and prokaryotes

A
  • Eukaryotes: more enzymes, named differently
  • different polymerases involved -> alpha, beta, gamma, delta, epsilon
  • have mitochondria which replicates independantly
  • dna is part of a cell cycle in eukaryotes (G1,S,G2,M)
  • formation of numerous replicons in chromosomal DNA
18
Q

18) Define replicons in chromosomal DNA

A
  • Nucleic acid molecules which replicate as a unit, beginning at a specific site within the molecule