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Physiology of the Prokaryotic Cell > Macromolecular Synthesis-DNA Replication > Flashcards

Macromolecular Synthesis-DNA Replication Flashcards

1
Q

Characteristics of DNA replication (3)

A
  1. bacterial genomes are circular
  2. DNA synthesis is semi-conservative
  3. proved by Meselson and Stahl experiment
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2
Q

Fidelity in DNA replication

A
  • base selection
  • 3’ to 5’ exonuclease
  • mismatch repair
  • involved multiple DNA pol.
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3
Q

Key Points of DNA rep. (5)

A
  • DNA pol. add nucleotides to 3’ end
  • DNA pol can only extend existing nucleic acid chains (can’t make new ones)
  • DNA synthesis begins at the origin and proceeds bidirectionally
  • DNA synthesis is continuous on leading strand
  • lagging strand is made in pieces that are ligated together
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4
Q

Key Players of Replication-Primase (DnaG)

A
  • RNA pol

- makes RNA primer

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5
Q

Key Players of Replication-Polymerase III

A
  • DNA pol
  • the workhorse pol
  • has proofreading activity
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6
Q

Key Players of Replication-SSB

A
  • single stranding binding proteins

- binds DNA to maintain in ss form

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7
Q

Key Players of Replication-Polymerase I

A

-replaces RNA primer ribonucleotides w/ deoxyribonucleotides

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8
Q

Early Steps in Replication-formation of open complex (2)

A
  1. DnaA binds specific sequences in OriC (w/help from histone like protein HU
  2. DNA unwinds (strands separate) in an ATP-dependent manner
  3. SSBs bind to keep open complex open
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9
Q

Early Steps in Replication-Prepriming complex (2)

A
  1. DnaB (helicase) binds to both ends of open complex

2. gives 2 replication forks going in opposite directions

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10
Q

Key Players of Replication-DNA ligase

A

-links okazaki fragments together

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11
Q

Key Players of Replication-Helicase (DnaB)

A

-unwinds the DNA ahead of the replication fork

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12
Q

Key Players of Replication-Tus

A
  • binds Ter

- blocks replisome until the other one shows up

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13
Q

Key Players of Replication-Replisome

A

-complex of proteins that make up the replication fork

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14
Q

Key Players of Replication-HU

A

histone-like protein that helps DnaA bind the ori

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15
Q

Priming (4)

A
  1. Primase binds and makes 12 nt piece of RNA
  2. DNA pol III can initiate DNA synthesis, adding deoxyribonucleic acids one at a time to the 3’ end
  3. extension occurs continuously on the leading strand
  4. synthesis of lagging strand is made in pieces called okazaki fragments
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16
Q

Okazaki Fragments (5)

A
  • same steps as for synthesis of leading strand
  • usually 1000 bp
  • Pol III stops when it reaches last RNA primer
  • RNA primer is removed by Pol I (5’ to 3’ exonuclease activity)
  • break sealed by DNA ligase
17
Q

Termination

A
  1. Tus binds Ter
  2. Ter allows one way replication
  3. Ter stops replisome, thought to stop the helices DnaB
  4. other replisome shows up and dislodges Tus
  5. replication is done
  6. chromosomes end up tangled, resolved by recombination or decantation by Topo IV
18
Q

Chromosome Dimer formation and resolution

A
  • chromosomes get tangled during replication and form dimers
  • dimers resolved by site specific recombination at dif sites
  • the dif sites are lined up by FtsK, which is localized to the septum
  • XerC/D is activated-the recombinase that acts on dif sites
19
Q

DNA Supercoiling (5)

A
  • DNA duplex is a right handed helix
  • 10.5 bases/ turn
  • overwinding=positive supercoiling, Underwinding=negative supercoiling
  • supercoiling is energy stored in DNA molecules as twist/writhe
  • superhelical tension can be used to aid processes (packaging, open complex formation)
20
Q

Topoisomerases (3)

A
  • enzymes that introduce or relieve supercoils by breaking the phosphate bond of DNA
    1. topo I removes supercoils
    2. Gyrase-introduces supercoils
    3. topo IV-removes catenations
21
Q

Histone like proteins

A
  1. compact DNA
  2. small and abundant
  3. some are site specific and some bind in a more general way
  4. can serve as accessory factors to help initiate processes (replication, recombination)
  5. can be general repressors (e.g. HNS can repress pol binding by occupying space on DNA)

Physiology of the Prokaryotic Cell (11 decks)

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