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B3 Biochem > DNA Replication > Flashcards

DNA Replication Flashcards

1
Q

DNA replication is _____________ and ________________

A

Bidirectional and semiconservative

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2
Q

How is DNA replication bidirectional?

A

Replication begins in the interior of a DNA molecule, and proceeds in both directions

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3
Q

How is DNA replication semiconservative?

A

Each copy of the DNA molecule, after replication, contains on strand from the original template and one newly synthesized strand

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4
Q

DNA replication in Prokaryotes

A

One origin of replication, circular DNA

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5
Q

DNA replication in Eukaryotes

A

Multiple origins of replication, in order to replicate in a reasonable amount of time

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6
Q

What needs to happen to the origin of replication for the separation of the two complementary strands to occur?

What are they composed of?

What is this accomplished by?

A

It needs to be ‘melted’

Usually almost exclusively composed of A-T bases

Accomplished by 20-50 monomers of DnaA protein

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7
Q

What binds to single strands to prevent reannealing and protect DNA from nuclease degradation?

A

SSBs, single strand binding proteins.

They bind after the DNA helicase start unwinding the helix.

Part of the Formation of the Replication Fork

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8
Q

What do DNA helicases do?

A

Unwind the double helix.

They move towards the DS region, or toward the replication fork, and force the strands apart.

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9
Q

Why does supercooling occur?

A

When the helicases separate the strands of DNA, supercooling occurs ahead of the replication fork.

Because of DNA being a helix and stuff.

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10
Q

What alleviates supercoiling? (Ahead of the replication fork)

A

Topoisomerases.

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11
Q

Creates a nick in one strand which allows the DNA to swivel around the intact strand, then seals the nicked strand

A

Type 1 isomerase

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12
Q

Cuts both strands to relieve the supercoil, then re-ligates the two strands

A

Type 2 isomerase

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13
Q

What’s a special type 2 topoisomerase that introduces negative supercoiling? What inhibits this enzyme?

A

DNA gyrase, inhibited by quinolones **

Also important for separation of circular chromosomes after replication

Found in bacteria

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14
Q

Topoisomerases are directly involved with..

Type 1 vs Type 2

A

Supercoiling.

1- cleaves one strand of a DNA molecule to relieve supercoiling, then religates the strand

2- cleaves BOTH strands of a DNA molecule to relieve supercoiling, then religates the strand

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15
Q

All polymerases that synthesize nucleic acids only catalyze synthesis in what direction

A

5’ to 3’

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16
Q

Template readings are in what direction

A

3’ to 5’, since DNA is antiparallel

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17
Q

What is the strand called that is continuously replicated as the replication fork advances?

A

The leading strand

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18
Q

The strand that is discontinuously synthesized, is called what? And what are it’s sections called?

A

Lagging strand

Okazaki fragments, later joined together as a continuous segment of DNA

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19
Q

DNA polymerases require what to begin synthesis?

What enzyme makes this happen?

A

A free 3’ OH group

Primases copy the first ~10 nucleotides to “prime synthesis” that allow DNA polymerases access to a free 3’ OH group

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20
Q

A primase is a..

A

RNA polymerase

Don’t require a free 3’ OH to begin synthesis

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21
Q

Each new DNA fragment on the lagging strand begins with the action of _______ laying down an ____ ________

A

Primase

Rna primer

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22
Q

What do DNA polymerases do?

A

Catalyze a reaction between the 3’ OH of the strand being synthesized and the 5’ triphosphate of an incoming nucleotide specified by the template being copied

23
Q

Net reaction of DNA polymerase action

A

Addition of a nucleotide to a growing DNA stand, and the release of a pyrophosphate

24
Q

What is pyrophosphate released by?

What is it cleaved into? Why?

A

DNA polymerase

Inorganic phosphate, to make the reaction irreversible and drive the reaction in the forward direction

25
Q

What type of reaction does DNA polymerase create?

A

A coupled irreversible reaction

26
Q

In a growing DNA chain, how many high energy bonds are cleaved for each added nucleotides?

A

2

27
Q

What enzyme elongates both the leading and lagging strands in prokaryotes?

A

DNA polymerase III

28
Q

What enzyme has proofreading activity? What does that entail?

A

Pol III

Making sure DNA replication is as accurate as possible, since a single nucleotide mutation can have devastating consequences

29
Q

How does Pol III proofread?

A

It checks each added nucleotide and makes sure its correctly base-paired with the template strand.

When it detects a mistake, it shifts backward one nucleotide, and excises the misincorporated nucleotide.

Called “3’ to 5’ exonuclease activity”

30
Q

To complete replication of circular DNA and the joining of Okazaki fragments, the RNA primer must be removed and replaced with:

A

dNTPs

31
Q

What removes the RNA primer?

A

Pol I

32
Q

‘Seals’ the nicks that remain after the RNA primer is removed and replaced with dNTPs

A

DNA lipase

33
Q

Eukaryotic cell cycle

A

G1, G0, S, G2, M phase

34
Q

Gap 1 (G1)

A

Most variable in terms of time, growth and metabolism.

G0- semipermanent

G1- appropriate signals can cause reentry into cell cycle

35
Q

S Phase

A

DNA synthesis

36
Q

G2 Phase, gap 2

A

Cell prepares to divide

37
Q

M Phase

A

Cell division (mitosis)

38
Q

Primase + DNA polymerase (begins strand synthesis)

A

Pol α (alpha)

39
Q

DNA polymerase + proofreading (extends strands)

A

Pol δ (delta)

40
Q

DNA repair enzymes

A

Pol β and Pol ε (beta and epsilon

41
Q

Mitochondrial DNA polymerase

A

Pol γ (gamma)

42
Q

Eukaryotic chromosomes are ________

A

Linear

43
Q

At the end of the DNA molecule, the lagging strand will have a gap once the ____________ is removed. This is fixed by what enzyme?

A

RNA primer

Telomerase.

44
Q

Extends the ends of linear chromosomes, as a template, acts on a telomere

A

Telomerase

45
Q

The ends of eukaryotic chromosome contain repeated sequences called..

A

Telomeres

6-nucleotide repeats

46
Q

Telomerase also contains a ________ _________ that does what?

A

Reverse transcriptase

Copies its own template (RNA) into DNA extending the 3’ overhand on the chromosome

Repeated many times

47
Q

After telomerase extends the repeat many times, the overhang is filled in by the action of ________ and ___ __________.

A

Primase

DNA polymerase

48
Q

There will always be a section of DNA left that is single stranded.

T/F

A

True.

This overhand assumes a special structure with the dsDNA and certain proteins to protect the end of the DNA

49
Q

Telomerase is only expressed in what cells?

Cells that don’t express telomerase have what fault?

A

Cells that continually divide.

If they don’t have telomerase, their chromosomes become shortened at each cell division. Aging, cancer.

50
Q

Process of polymerases copying RNA into DNA

A

Reverse transcription, via reverse transcriptase

HIV

Lack proofreading, high mutation rate

51
Q

What is HNPCC?

A

Hereditary nonpolyposis colorectal cancer.

One of the most common inherited cancers

A defect in mismatch repair, failure of DNA repair

52
Q

things that cause damage to DNA… need DNA repair….

IDK im sleepy

A

Cig smoke

Exposure to chemicals, radiation

UV light (causes pyrimidine dimers/thymine dimers)

53
Q

a rare genetic disorder called xeroderma pigmentosum most often results from:

A

A deficiency in excision endonuclease

B3 Biochem (4 decks)

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