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Biol200 > DNA replication > Flashcards

DNA replication Flashcards

1
Q

What is the principle of DNA replication? (the fundamentals)

A

During replication, the double helix denatures, each parental strand is used as a template for the formation of a new daughter strand that is complementary to the parental strand.

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2
Q

What is the chemical reaction that makes DNA synthesis unidirectional?

A

The alpha-phosphate group in the incoming deoxy nucleotide triphosphate (dNTP) reacts with the 3’ hydroxyl group (OH) in the growing DNA chain.

(unidirectional bcz the 3’ hydroxyl must be free and the 5’ phosphate can’t attack a phosphate.)

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3
Q

What is the role of DNA helicases in DNA
replication?

A

They participate in separating the strands of duplex DNA.

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4
Q

What is the function of a primer in DNA replication?

A

DNA polymerases cannot initiate synthesis of a new strand, they can only elongate an existing strand. Therefore they require a primer to initiate synthesis of a new strand.

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5
Q

What is the function of a primase in DNA replication?

A

A specialized RNA polymerase, called a primase, forms a short RNA molecule complementary to a single-stranded region of the unwound duplex DNA. DNA polymerase extends the primer to eventually form a new daughter duplex DNA.

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6
Q

What is the direction of DNA synthesis during replication?

A

5’ to 3’

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7
Q

What is the difference between leading and lagging strand DNA synthesis?

A

The leading strand can be replicated 5’ to 3’ by DNA
polymerase following the movement of the replication fork, while the lagging strand is
synthesized in short fragments called Okazaki fragments.

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8
Q

What is the mechanism of action of topoisomerase
in DNA replication?

A

It relieves supercoils in the DNA

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9
Q

What are Okazaki fragments?

A

Okazaki fragments are short, discontinuous fragments consisting of RNA and DNA.

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10
Q

What replaces the RNA component of Okazaki
fragments?

A

The RNA component of Okazaki fragments is replaced by DNA.

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11
Q

What is the function of DNA ligase in DNA replication?

A

DNA ligase ligates together the two adjoining DNA molecules.

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12
Q

Much of what we know about DNA replication has been obtained from studies using: (3)

A

-prokaryotes (like E. coli)
-viruses (like SV40 that
infects monkeys and humans),
-budding yeast.

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13
Q

What is Large T-antigen?
What is the function of large T-antigen in DNA synthesis?

A

-hexamer
-helicase
-encoded by the viral genome
-Unwinds double helix at replication fork

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14
Q

What is the function of Replication Protein A (RPA)
in DNA replication?

A

RPA binds single-stranded DNA and keeps the single-stranded DNA template in optimal conformation for DNA polymerase.

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15
Q

What is the function of DNA Polymerase Epsilon in
DNA replication?

A

DNA Polymerase Epsilon carries out leading strand DNA synthesis.

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16
Q

What is the function of PCNA in DNA replication?

A

PCNA is a homotrimeric protein. Prevents the Pol e (or d) complex from disassociating from the template.

17
Q

What is the function of Primase/Polymerase a in
DNA synthesis?

A

Primase forms the RNA component of the primer,
and DNA polymerase a (Pol a) extends the primer with DNA.

18
Q

What is the function of the Pol delta /Rfc/PCNA complex
in DNA synthesis?

A

It replaces the Pol alpha/primase complex and completes the synthesis of an Okazaki fragment.

19
Q

What is the function of RFC/PCNA complex in DNA
synthesis?

A

RFC is the PCNA loader, it opens the PCNA ring and loads it at a primer on DNA.

20
Q

What is the function of Ribonuclease H and FEN-1
in DNA synthesis?

A

They displace the RNA component at the 5’ ends of
the Okazaki fragments.

21
Q

What is the function of Pol delta in DNA synthesis?

A

Synthesis of lagging strand

22
Q

What is the function of DNA ligase in DNA
synthesis?

A

It ligates DNA fragments together.

23
Q

What are replication origins?

A

They are specific regions in duplex DNA where unwinding of DNA is initiated.

24
Q

Why do the replication origins tend to be AT-rich ?

A

because the breakage of two hydrogen bonds between A and T requires less energy than G-C rich sites which have three hydrogen bonds between G and C

25
Q

Is leading strand synthesis continuous or discontinuous?

A

continuous

26
Q

Is lagging strand synthesis continuous or discontinuous?

A

discontinuous

27
Q

Explain the step of Unwinding in replication ?

A

Unwinding is catalyzed by large T-antigen (helicase) driven by the hydrolysis of ATP. RPA binds and stabilizes singlestranded regions.

28
Q

Explain the step of Primer Synthesis in replication?

A

Primase-Pol alpha complexes synthesize primer sequences that are base-paired to the parental templates.

29
Q

Explain the step after the Extension in replication?

A

(pol alpha extends the primer only)

Leading: pol Epsilon carries out leading strand synthesis. (With PCNA that was loaded with RFC)
Lagging: Pol delta/Rfc/PCNA complexes replace the primase-Pol alpha complexes and complete synthesis of Okazaki fragment.

30
Q

Explain the step of Further Unwinding in replication?

A

Further unwinding and binding of RPA to single-stranded regions.
Pol Epsilon/Rfc/PCNA complexes continue to synthesize the leading strands.

31
Q

Explain the step of Lagging-strand primer synthesis in replication?

A

Primase-Pol alpha complexes form primers for lagging-strand synthesis.

32
Q

Explain the step of Primer Extension, Primer Removal, and
Strand Ligation in replication? (4) (lagging strand)

A

-Pol delta /Rfc/PCNA complexes replace the primase-Pol alpha complexes and extend the primer sequence.
-Removal of the primers is performed by FEN-1 and ribonuclease H.
-Pol delta /Rfc/PCNA complexes replace the primer sequences with DNA.
-Strands are ligated together by DNA ligase.

Biol200 (12 decks)

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