DNA replication Flashcards

1
Q

DNA replication is ________ and __________

A

semi-conservative

bidirectional

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2
Q

Origin of replication

A
  • sequence specific site recognized by replication proteins

- hundreds of origins per chromosome in euk (only 1 in prok)

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3
Q

Replication fork

A

where DNA helicases have unwound the double helix and the replication machinery sits and synthesizes complementary strands

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4
Q

Origin binding proteins

A
  • Recognize replication origin

- Proteins bind to origin and become part of the complex, also recruits Polymerase

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5
Q

Helicase

A

enzymes that catalyze the breaking of H-bonds between base pairs and the subsequent ‘unwinding’ of the helix.

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6
Q

Single-Stranded Binding Proteins

A

bind to the melted strands of original DNA to prevent them from re-annealing or getting attacked by nucleases

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7
Q

Primase

A

Enzyme that catalyzes the addition of the RNA primer to begin replication
(RNA primer required for DNA pol)

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8
Q

DNA polymerase I (3 different activities)

A

Removes RNA primer, replace with DNA

1) 5’–>3’ exonuclease activity: removes RNA primer
2) 3’–>5’ exonuclease activity: proof-reading
3) 5’–>3’ DNA synthesis: fills gap once RNA is removed

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9
Q

_________ is distributive and falls on and off the DNA easily and _______ is processive

A

DNA polymerase I

DNA polymerase III

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10
Q

DNA Polymerase III (2 activities)

A
  • Elongation of DNA from RNA primer
  • uses sliding clamp (processive)
  • multi-protein complex

1) 5’–>3’ DNA synthesis
2) 3’–>5’ Exonuclease activity (proofreading)

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11
Q

DNA polymerase III determines the correct base to input based on ________ and _________

A

H-bonds and geometry

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12
Q

DNA ligase

A
  • enzyme responsible for sealing Okazaki fragments together once the RNA primers have been replaced by Pol I
  • Uses cofactors (ATP-euk, NAD+ - prok)
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13
Q

Sliding clamp

A
  • Holds on to DNA and allows DNA pol III to hold on to DNA strongly, but enables it to move
  • PCNA (euk), Beta clamp (prok)
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14
Q

Telomere

A
  • sequence at the ends of chromosomes, consisting of a large number of repeating segments
  • gets consistently shorter with every chromosome replication
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15
Q

Dysteratosis congenita

A

telomere shortening syndrome

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16
Q

Topoisomerase/gyrase

A
  • Enzyme responsible for relieving torsional strain in the DNA helix in the region ahead of the replication fork
  • Does so by breaking and rejoining dsDNA
  • topogyrase for prok
17
Q

Exonucleases

A

chews from the end

18
Q

Endonuclease

A

cuts within a DNA strand - breaks phosphodiester bond between sugar and phosphate

19
Q

DNA polymerase requires that the deoxyribonucleotide to have a _________ group for phosphodiester bond synthesis

A

3 hydroxy group

20
Q

DNA synthesis requires a ______ and proceeds in the _______ direction

A

RNA primer

Proceeds in the 5’–>3’ direction

21
Q

Errors in replication are corrected by the __________ activity of the DNA polymerase

A

3’–>5’ exonuclease proofreading

22
Q

7 Steps of DNA synthesis on leading strand

A

1) origin binding proteins bint to origin
2) DNA melted apart by helicases
3) Topoisomerase relieves tension ahead of replication fork
4) ssbinding proteins protect unwound ssDNA
5) RNA primer synthesized by RNA primase
6) Pol III elongats DNA from RNA primer, complementary to leading strand
7) New and old strands annealed

23
Q

DNA synthesis on lagging strand (5 steps - after DNA unwound)

A

1) primase attaches RNA primer to lagging strand segment
2) Pol III elongates DNA from RNA primer back a short ways, forming an Okazaki fragment
3) RNA primer removed and replaced with DNA by Pol I
4) Fragments sealed together with DNA ligase
5) new and old strands annealed

24
Q

In eukaryotes: DNA pol E synthesizes on the _________ strand and DNA pol d synthesizes on the _______ strand

A

leading

lagging

25
Q

In Prokaryotes: DNA pol III synthesizes leading and lagging strands concurrently via ___________ in the _________ polymerase complexes

A

looping of the lagging strand

2 core

26
Q

End replication problem

A

progressive shortening of chromosomal ends during rounds of DNA replication

27
Q

Telomerase

A
  • Reverse transcriptase that uses RNA template to copy DNA repeats onto the ends of telomeres
  • can be a target for treating cancer
28
Q

AZT

A

targets reverse transcriptase

29
Q

Acyclovir

A

targets viral DNA polymerase

30
Q

Quinolones

A

targets bacterial DNA gyrase