DNA Replication Flashcards

1
Q

What type of replication is DNA replication?

A

Semi-conservative:

2 parent -> 1parent/1new + 1parent/1new -> 1parent/1new + 2new + 2new + 1parent/1new

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2
Q

How was semi-conservative DNA replication found?

A
  • Matthew Meselson and Franklin Stahl, 1958 experiment
  • Grew bacteria with 15N media, then switched to 14N media (any new bacteria made has to use 14N)
  • Looked at the distribution of 14N and 15N in the DNA molecules after multiple replications (each subsequent generation became more and more 14N with less and less 15N, but 15N still present)
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3
Q

How is DNA replicated?

A

DNA polymerase catalyzes addition of deoxyribonucleotides to a DNA strand

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4
Q

DNA Polymerase I (of E. coli)

A

Function: Primer removal and DNA repair

Additional enzyme activities: 5’ -> 3’ exonuclease

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5
Q

DNA Polymerase III (of E. coli)

A

Function: Replication, catalyzes the strand-elongation reaction, uses hydrolysis of PPi + H2O -> 2Pi to make even more favourable, uses induced fit (conformational change)
Addition enzyme activities: 3’ -> 5’ exonucleoase

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6
Q

What is the function of MG2+ in strand-elongation reaction?

A

Helps incorporate incoming nucleotides

- Required for catalysis!

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7
Q

DNA Polymerase Requirements/Facts??

A

1) Requires dNTPs and Mg2+
2) New DNA strand is assembled on an existing template
3) Requires a primer to begin synthesis
4) Elongation is in 5’ to 3’ direction
5) Can correct mistakes using 3’ to 5’ exonuclease activity (proofreading)

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8
Q

How are mistakes corrected by polymerase?

A
  • DNA Pol I 3’-5’ exonuclease removes incorrect nucleotides from 3’ end by hydrolysis
  • A mismatch results in a “stall” = pause gives enough time for incorrect region to flop into exonuclease active site where it is removed
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9
Q

How is DNA separated into single strands?

A

Helicase: ring-like hexamers that use ATP to unwind DNA

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10
Q

Building of the pre-priming complex

A

1) DnaA binds to the origin of replication locus (AT-rich areas, with consensus sequence)
2) DnaAs oligomerize (wrapping origin around themselves)
3) DnaB joins DnaA
4) DnaB is a helicase -> uses ATP hydrolysis to unwind the duplex, including AT-rich regions
5) Single-strand-binding proteins (SSB) bind to newly generated single-strand regions (prevents reformation of the double helix)
Result: pre-priming complex (makes single-stranded DNA accessible to other enzymes for the beginning of the synthesis of complementary strands)

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11
Q

Priming

A

RNA polymerase called primase makes an RNA primer

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12
Q

Synthesis of the leading and lagging strand

A

At the replication fork
Leading strand: continuous
Okazaki fragments: discontinuous
Due to antiparallel, always synthesized 5’ to 3’

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13
Q

DNA polymerase III holoenzyme structure:

A
Clamp loader (in centre under DnaB): feeds DNA through and keeps the enzyme attached to DNA
DnaB (just on top of clamp loader): helicase 
2 Polymerase cores (on either side of clamp loader): contain B2 and exonuclease regions
Sliding clamps (B2): help polymerase "stay on task"
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14
Q

Leading strand in trombone model

A

Made continuously by Pol III in 5’-3’ direction

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15
Q

Lagging strand in trombone model:

A
  • Is looped out
  • Pol III adds ~1000 nucleotides in 5’-3’ direction
  • Releases sliding clamp
  • New loop formed, sliding clamp added
  • Primase adds RNA primer
  • Pol III makes new Okazaki fragment
  • Pol I fills gaps between fragments and removes RNA primer with 5’-3’ exonuclease activity
  • Ligase seals fragments
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16
Q

Ligase Seals Okazaki Fragments by:

A

Joining the 3’OH group and the 5’phosphate group of two fragments
- Hydrolyzes ATP