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Undeleted > DNA Replication > Flashcards

DNA Replication Flashcards

1
Q

How is replicating DNA conserved

A 
Semi-conserved.
One parent (original) strand, one daughter (new) strand.
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2
Q

What is different about the origin of DNA replication in Prokaryotes and Eukaryotes

A

Prokaryotes - Only one origin

Eukaryotes - Multiple origins

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3
Q

Why is necessary for a DNA replication origin to occur

A

Binding sites for initiator proteins/origin recognition proteins
Something to unwind/distort the DNA
Sometimes need binding sites for transcription activation proteins.
Overall sequence is AT rich

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4
Q

What is the mechanism by which DNA polymerase makes a polymer

A

DNA strand separation exposes the hydrogen bond donor/acceptor groups on each base.
DNA pol uses this to add free nucleotides to the 3’ OH end of the chain.
The new nucleotide loses 2 phosphate groups in this.

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5
Q

What is semi-discontinuous DNA replication and why does it occur

A

Antiparallel strands of DNA.
DNA pol can only code in the 3’ direction.
The 5’-3’ (leading) strand can be synthesised straight away.
The 3’-5’ (lagging) strand is semi-discontinuous. Requires specialist bits to recruit DNApol to site further ahead, and it codes backwards. Creates Okazaki fragments which are stuck together by DNA ligase.

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6
Q

What is the main structural difference between prokaryote and eukaryote DNA

A

Prokaryote - naked DNA

Eukaryote - as chromatin, wrapped around a histone.

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7
Q

What proteins are involved in the initial stages of DNA replication

A 
Initiator proteins (P) / ORC complex (E). 
Helicase
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8
Q

How does a helicase function

A

Unwinds DNA by breaking the hydrogen bonds that hold the two strands together (hydrolysis)

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9
Q

How can a helicase be identified in vitro

A

Radioactively label DNA (if helicase present DNA will unwind)(observed in gel electrophoresis)
Fragment displacement assay. radioactively labelled DNA is hybridised to ss circular DNA (complementary). If helicase present DNA unwinds and fragment dissociates from the circular DNA.

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10
Q

What is the importance of single strand (ss) DNA binding proteins in DNA replication

A

They assist in helix-opining processes, then stabilise the unwound DNA.
They bind to DNA without shielding bases.

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11
Q

What is the point of a priming event

A

To provide a 3’ OH group on the template DNA strand. Allows DNA pol to work.
Single primer for leading strand; multiple needed on the lagging strand.
Carried out by a primase enzyme (DNAG in prokaryotes)

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12
Q

What is the structure of a eukaryotic primase enzyme

A

4 subunits.

1 alpha primase subunit which has DNA polymerase activity

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13
Q

What is required to catalyse primase activity

A 
A template to bind to
Nucleotide binding
Synthesis initiation
Extension to a functional primer
Transfer to DNA pol.
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14
Q

What is the process of DNA replication (in prokaryotes/eukaryotes)

A

ABF1 binds to origin (E)
Initiator complex binds (DNA(A/C)/ ORC)
Helicase binds (DNAB/ MCMs)
Replication initiated (SSB, Gyrase/ R(P/F)A, Topo 2)
Replication elongation (DNAG, RNA primer / DNA pol 1, RNA primer, Initiator DNA)
Elongation stage 2 (DNA pol 3/DNA pol 2)

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15
Q

How accurate is DNA replication

A

Very. Replicases have proofreading activity. Mutations occur in ~ 1 in 10^-8/10.

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16
Q

How does DNA polymerase act as a proof-reader

A

Nucleotide enters vacant site of DNA pol.
DNA pol advances 1 nucleotide.
If nucleotide is not correct, polymerase activity is inactivated; DNA pol goes back. Exonuclease activity activated. Removes nucleotide.
DNA pol tries again

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17
Q

Describe the three types of DNA polymerase present in e.coli

A

DNA pol I (most common);
Monomer, polymerase, exonuclease (both direction). Involved in DNA replication and repair.
DNA pol II;
Monomer, polymerase, 3’-5’ exonuclease activity. Involved in DNA repair
DNA pol III;
Multimer, polymerase, 3’-5’ exonuclease. Involved in DNA replication.

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18
Q

What is the structure of DNA pol III

A

An asymmetric dimer.

19
Q

What roles do specific DNA pol III subunits have

A

Alpha - polymerase (DNA synthesis)
Beta - DNA Clamp
Epsilon - 3’-5’ exonuclease (proofreading)
Gamma - displaces primase from the RNA primer

20
Q

What roles do specific higher eukaryotic DNA polymerase subunits have

A 
Alpha - DNA replication
Beta - DNA repair
Delta - DNA replication
Gamma - mitochondrial DNA replication
Epsilon - DNA replication and repair
21
Q

How are the alpha, delta and gamma subunits of eukaryotic DNA pol involved in DNA replication

A

Alpha (complex with primase; initiator), Delta (links lagging strand primer region), Epsilon (leading strand) synthesise DNA at the replication fork.

22
Q

What is the mechanism by which DNA ligase joins okazaki fragments

A

Catalyses the formation of a phosphodiester bond between 3’ OH and 5’ P on adjacent nucleotides.

23
Q

Why is a clamp (accessory protein) required for DNA replication

A

It keeps the polymerase on the DNA when it is synthesising, then facilitates polymerase release when replication is finished

24
Q

What is the structure of the beta subunit of DNA pol III in e.coli

A

Ring shaped dimer

25
Q

What is the eukaryotic homologue of the beta subunit clamp in e.coli

A

PCNA

26
Q

Suggest a way that the leading and lagging strand can be coordinated as one action

A

Lagging strand template may be looped. Would enable polymerase at replication fork to synthesise both strands. (lagging strand would be in reverse 5’-3’ )

27
Q

What is the purpose of telomeres

A

They fill the ‘primer gap’ at the end of a lagging strand.

To attempt to maintain DNA length

28
Q

What is the function of telomerase

A

To resynthesise telomeric sequences - extend the 3’ end of a DNA strand.
Acts as a reverse transcriptase (makes DNA from RNA)
Less telomerase leads to telomere shortening.

29
Q

How is DNA replication and the cell cycle linked

A

Replication MUST only occur once per cell cycle.

Replication initiation commits the cell to division (which occurs after replication is complete)

30
Q

What are the main stages of the eukaryotic cell cycle

A

Mitosis (Pro/Meta/Ana/Telo) <- DNA replication

31
Q

At what point in the cell cycle are the origins (of replication) active

A

S-phase (once)

32
Q

What factor regulates origin (of replication) activation, and how

A

Licensing factor.

Present at origins that haven’t fired; absent from origins that have.

33
Q

When in the cell cycle is DNA replication initiated

A

As soon as a G1 nucleus enters S-phase

34
Q

How is DNA re-replication blocked

A

Either; An inhibitor binds to the DNA after replication

Or; A licence factor required for DNA replication is removed when replication is complete

35
Q

How does a licencing factor become attached to DNA

A

Its a component of the pre-replicative complex that assembles at origins (ORC)

36
Q

What does ORC stand for

A

Origin Recognition Complex

37
Q

Name proteins involved in formation of the pre-initiation complex

A

Cdc 6/18 , Cdt1 (which recruit:)
MCM2-7
ORC

38
Q

How do CDC6/18 and CDT1 act as licencing factors

A

CDC6 is phosphorylated/degraded after it has recruited MCM2-7/ORC to the origin.
CDT1 undergoes ubiquitin-mediated degradation. Activity is inhibited by geminin.

39
Q

How can the MCM complex act as a licencing factor

A

Required for DNA replication.
Can be phosphorylated and dissociate from chromatin. This correlates with the removal of the licence for chromosomes to replicate.

40
Q

How can the MCM complex act as a replicative helicase

A

Possess DNA-dependent ATPase motifs.
Similar structure to other known helicases
Shown to leave origins when ssDNA binding protein does. Appears to move with the replication fork.

41
Q

How are CDK and DDK involved in replicative helicase activation

A

CDK required for formation of pre-loading complex and its association with pre-replicative complex at the origin.
DDK phosphorylates MCM complex. Results in conformational change. Helps convert inactive MCM complex into an active helicase.

42
Q

At which point in the cell cycle do CDK and DDK both act as a checkpoint

A

Initiation of DNA replication - beginning of S-phase.

43
Q

What role does cdc45 have in DNA replication

A

Binds to the pre-replicative complex.
Stimulates helicase activity of the MCM complex.
Interacts with DNA pol delta/epsilon and bridges with helicase; important in elongation.

44
Q

What role does GINS have in DNA replication

A

Required for formation of active helicase CMG

Stabilises the MCM complex

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