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Bioc2201 > DNA Replication ll > Flashcards

DNA Replication ll Flashcards

1
Q

What 7 proteins and their functions are required for replication in E. coli?

A

Helicase - unwinds DNA

DNA gyrase - aids in unwinding

Single Strand Binding proteins - ensure DNA doesn’t form secondary structure while unwinding

Primase - adds RNA primer

DNA pol lll - elongation of DNA strand by DNA synthesis

DNA pol l - remove of RNA primer and filling gap with DNA

DNA ligase - links fragments in new DNA strand

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2
Q

What sequence properties are present at the origins of DNA replication? What proteins assists with this?

A

AT-rich. There are 3 OH bonds (compared to 2 in other pairs). Protien DnaA

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3
Q

What does helicase do? What is its structure? What is another name for it?What is its process driven by?

A
  • DnaB
  • Hexameric complex
  • Further separates the DNA strands, breaks H-bonds
  • Driven bt the free energy of ATP hydrolysis
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4
Q

What protein further facilitates DNA unwinding? What does it prevent?

A
  • DNA gyrase
  • A type ll topoisomerase
  • prevents DNA supercoiling ahead of the replication fork
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5
Q

What are type l and type ll topoisomerase?

A

Both work to uncoil DNA as it unwinds. Topoisomerase l cuts a strand uncoils and sticks together. Topoisomerase can cut both strands.

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6
Q

What is a nuclease?

A

An enzyme that cleave phosphodiester bonds between nucleotides of nucleic acids

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7
Q

When does a Single-stranded binding protein need to stripped away?

A

Before the ssDNA can be replicated by. DNA polymerase

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8
Q

What does an SSB do?

A

Single-stranded binding protein has a high affinity to ssDNA and binds to it preventing it from forming a secondary structure, protecting from nucleases

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9
Q

Draw the initiation of replication in E. coli. include; SSB, ATP, Helicase, Gyrase, DNA pol lll, primase

A
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10
Q

What is a primasome? What are 2 examples?

A

proteins in E.coli that mediate primer synthesis

  • kinds
  • Helicase (DnaB)
  • Primase (DnaG)
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11
Q

What does primase catalyse? How long is it?

A
  • Polymerisation of RNA segment
  • approx 5 - 15 nucleotides in length
  • provides the free 3’ OH group
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12
Q

How does the primosome work in the lagging strand?

A

The primasome is propelled toward the opening of the replication fork (5’ - 3’). It reverses in direction momentarily to synthesise complementary RNA primers for each Okazaki fragment in the lagging strand.

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13
Q

What is the replisome?

A
  • The replisome is a large protein complex that carries out DNA replication, starting at the replication origin.
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14
Q

Why does the replisome have a special “looping arrangement?

A

allows the replisome to move as a single unit in the direction of the advancing replication fork

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15
Q

Draw the process of the replisome.

A
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16
Q

What is a holoenzyme?

A

Enzyme with a whole.

17
Q

What are the 3 components of DNA pol lll?

A
  • Core enzyme (Pol lll)
  • Clamp loader
  • B Sliding Clamp
18
Q

What does the DNA pol lll sliding clamp do? What is its processivity? Draw a diagram of how it works.

A
  • Pol lll not functional until combined with the other components.
  • processivity of > 5000
  • B subunit forms a ring around the DNA
  • sliding clamp can move along it
  • keeps pol lll holoenzyme from dissociating
  • without would dissociate after 12 residues
19
Q

What enzymatic activities does DNA Pol l have?

A
  • three different enzymatic activities of DNA pol l
  • polymerase domain
  • 3-5’ exonuclease
  • 5-3’ exonuclease
20
Q

What does DNA pol l have that DNA pol lll does not?

A

5’ - 3’ exonuclease domain

21
Q

What is “Nick Translation”? How are RNA primers removed?

A
  • Single nucleotide removal
  • removed and replaced with DNA through the DNA pol l “nick translation” process
  • nicks are sealed together by DNA ligase
22
Q

How does DNA replication stop? What are the 10 Ter terminator sites and how do they act? What protein arrests the replication fork?

A
  • Stop when the terminator sequence reached.
  • Requires binding of Tus protein.

Sites start with Ter. A-J

23
Q

Compare bacterial and eukaryotic DNA replication

A
  • Eukaryotic is similar but much more complex.
  • more protein required
  • several different modes of replication occur
  • have several different DNA pol

Bioc2201 (8 decks)

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