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BIOL 200 > PL1 > Flashcards

PL1 Flashcards

1
Q

When is information stored in DNA copied (replicated)

A

Whenever a cell divides

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2
Q

What is the difference between transcription and replication in terms of DNA polymerase and RNA polymerase

A

DNA pol can’t start a strand from scratch (only elongate whereas RNA polymerase can

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3
Q

What strand of the double helix, once denatured, is used as a template for daughter strand

A

Both

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4
Q

What is the relationship between the daughter strand and the template strand of DNA

A

Daughter is complementary to parental strand

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5
Q

What does the alpha (first) phosphate group in the dNTP react with and what kind of bond is it

A

3’ hydroxyl group in the growing DNA chain

High energy bond

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6
Q

What does DNA helicase do

A

Unwinds the duplex DNA for access

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7
Q

What does DNA topoisomerase do

A

Relieves the supercoils after unwinding

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8
Q

Which strand is the leading strand

A

5’ to 3’ (3’ end) so DNA is synthesized 5’ to 3’ in direction of replication fork

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9
Q

Which strand is the lagging strand

A

3’ to 5’ end

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10
Q

Which way does DNA synthesis always proceed

A

5’ to 3’

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11
Q

Why is a primer necessary in DNA replication

A

DNA polymerases can’t initiate synthesis of a new strand, they can only elongate an existing strand

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12
Q

What is primase

A

A specialized RNA polymerase

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13
Q

What does primase do in replication

A

Forms a short RNA molecule complementary to a single-stranded region of the denatured and unwound duplex DNA

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14
Q

What does DNA polymerase do in replication

A

Extends the primer to eventually form a new daughter duplex DNA

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15
Q

Why does synthesis only occur in 5’ to 3’

A

Because you need a 3’ hydroxyl group to add the next nucleotide

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16
Q

What is the relationship between the two strands on duplex DNA

A

They are antiparallel

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17
Q

What are Okazaki fragments and where are they found

A

Short discontinuous fragments consisting of RNA and DNA found on the lagging strand

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18
Q

How do the Okazaki turn from fragments to a daughter strand

A

The RNA components of the Okazaki fragments are replaced by DNA and the two adjoining DNA molecules are ligated together

19
Q

What ligates the Okazaki fragments

A

DNA ligase

20
Q

What is much of what we know about DNA replication obtained from

A

Studies using prokaryotes, viruses and from budding yeast

21
Q

What is the large t-antigen and what does it do

A

It’s a hexamer, helicase encoded by the viral genome and unwinds the double helix at the replication fork

22
Q

What does replication protein A do

A
  1. Binds single-stranded DNA
  2. Keeps single-stranded DNA in optimal conformation for DNA polymerase
  3. Increases accuracy of reaction
23
Q

What does DNA polymerase epsilon do

A

Carries out leading strand DNA synthesis

24
Q

What is PCNA and what does it do

A

Homotrimetric protein

Prevents polymerase epsilon complex from disassociating from the template

25
Q

What is the function of primase with polymerase alpha

A

Primase forms the RNS component of the primer and DNA polymerase alpha extends the primer with DNA

26
Q

What is the function of Pol s, RFC, PCNA complex

A

Replaces the polymerase alpha/primase complex and completes the synthesis of an Okazaki fragment

27
Q

What is the function of the Rfc/PCNA complex

A

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

28
Q

What do ribonuclease H and FEN-1 do

A

They displace the RNA component and the 5’ ends of the Okazaki fragments

29
Q

What does Pol S do

A

Replaces the RNA with DNA

30
Q

What are replication origins

A

Unwinding of DNA is initiated at specific regions in duplex DNA

31
Q

What is an important quality of replication origins and why

A

They tend to be AT rich as those base pairs only have 2 hydrogen bonds which takes less energy to denature them

32
Q

What are the general steps of replication

A
  1. Loading of the replisome at the replication origin
  2. Unwinding
  3. Primer synthesis
  4. Extension
  5. Further unwinding
  6. Further extension
  7. Lagging-strand primer synthesis
  8. Primer extension, primer removal and strand ligation
33
Q

How is unwinding catalyzed

A

By large T-antigen (helicase) driven by the hydrolysis of ATP

34
Q

What happens during unwinding

A

RPA binds and stabilizes single-stranded regions

35
Q

What happens during primer synthesis

A

Primase Polymerase Alpha complexes synthesize primer sequences that are base-paired to the parental templates

36
Q

What happens during extension

A

Pol epsilon / Rfc / PCNA complexes replace the primase/pol alpha complexes and extend the primer sequences

37
Q

What happens during further unwinding

A

Further unwinding and binding of RPA to single stranded regions

38
Q

What happens during further extension

A

Pol Episilon / Rfc / PCNA complexes continue to synthesize the leading strands

39
Q

What happens during lagging-strand primer synthesis

A

Primase / pol alpha complexes form primers for lagging strand synthesis

40
Q

What happens during primer extension, primer removal and strand ligation

A
  1. Pol S / RFC / PCNA complexes replace the primase - pol alpha complexes and extend the primer sequence
  2. Removal of primers performed by FEN-1 and ribonuclease H
  3. Pol s / RFC / PCNA complexes replace the primer sequences with DNA
  4. Strands are ligated together by DNA ligase
41
Q

Why is synthesis done from 5’ to 3’

A

Because 3’ hydroxy has to react with incoming phosphate

42
Q

What are the characteristics of the bonds between the 3 phosphates

A

They are high energy meaning that when they are broken, energy is released

43
Q

Why does RPS make base pairing more accurate

A

Makes it so that it’s not just energy that decides which base pair goes in but also the geometry of the protein is such that the wrong one won’t have access to the base

44
Q

What does PCNA ultimately help with

A

It speeds up the reaction

BIOL 200 (13 decks)

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