Unit 3: DNA Replication Flashcards

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1
Q

Why is our DNA semi-conservitive?

A

Each DNA strand serves as a template strand to produce a new complementary one

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2
Q

What do the 2 Mg2+ ions held in Pol do?

A

1st Mg2+: Deprotonates the primer 3’-OH hydroxly to 3’-O- nucleophile
2nd Mg2+: Binds PPi and facilitates its departure

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3
Q

What are the DNA polymerase reaction steps?

A
  1. Synthesis of the RNA primer
  2. Incorporation of the 1st nucleotide
  3. Translocation of polymerase
  4. Incorporation of 2nd nucleotide
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4
Q

How does the DNA polymerase know which dNTP to incorporate?

A

Binding of a dNTP causes a conformational change of Pol Active site in closed form

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5
Q

What kind of proofreading activity does DNA polymerase have?

A

A 3’ - 5’ exonuclease to get rid of incorrect nucleotides added

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6
Q

What does Pol III contain?

A

Pol III core x3
Sliding Clamp x3
Clamp loader

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7
Q

What is the role of the Pol III core?

A

Add the nucleotides & proofreading

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8
Q

What is the role of the Pol III beta sliding clamp?

A

Increase speed of replication by not letting polymerase fall off of DNA

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9
Q

What is the role of the clamp loader?

A

Loads beta sliding clamp onto DNA

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10
Q

What does the DNA helicase do? Where is it located?

A

DNA “unzipping”
In bacteria: located on lagging strand
In eukaryotes: located on leading strand

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11
Q

What does the Topoisomerase do?

A

Works ahead of the Helicase to untwist DNA

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12
Q

What does the Primase do?

A

RNA polymerase that adds RNA primer as the first nucleotides

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13
Q

What does a ligase do?

A

Seals DNA nicks, “glues the Okazaki fragments together”

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14
Q

What is a nick in DNA?

A

A place where the phosphdiestar bond is not made between fragments

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15
Q

What occurs during nick translation?

A

The Pol I exonuclease works 5’ to 3’ to remove RNA primers and replace with DNA

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16
Q

What happens after Pol I is done?

A

After Pol I, beta clamp stays on to recruit ligase

17
Q

How is the beta clamp removed?

A

Delta subunit of clamp loader

18
Q

What is 1 difference between bacteria and eukaryotic DNA replication structures?

A

Eukaryotic replisome has 2 DNA polymerases (1 for each strand) as opposed to 3 so it is much slower

19
Q

How does replication initiation begin in bacteria?

A

A long bp sequence with repeating bp sites is recognized by DnaA and the DnaA binds to these R-repeats. An A&T rich repeat unwinds the DNA

20
Q

What happens after the A-T region is destabilized?

A

DnaC loads helicase onto each strand

21
Q

What prevents the origin from initiating again?

A

DAM sites are methylated in old strands, but new strands are not allowing SeqA to bind to the unmethylated strand and prevent DnaA from binding to origin.

22
Q

How do eukaryotes orchestrate chromosomal replication? What are the steps?

A

Through cell cycle phases

  • # 1 G1: Assembly of pre-replication complexes
  • # 2 S: Degradation of preRC
  • # 3 S: Replication
  • # 4: S-G2-M: no pre-RC assembly = no initiation