DNA Replication Flashcards by Jeremy Penn

DNA replication is _____________ and ________________

Bidirectional and semiconservative

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How is DNA replication bidirectional?

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

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How is DNA replication semiconservative?

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

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DNA replication in Prokaryotes

One origin of replication, circular DNA

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DNA replication in Eukaryotes

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

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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?

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

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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What do DNA helicases do?

Unwind the double helix.

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

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Why does supercooling occur?

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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What alleviates supercoiling? (Ahead of the replication fork)

Topoisomerases.

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

Type 1 isomerase

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

Type 2 isomerase

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

DNA gyrase, inhibited by quinolones **

Also important for separation of circular chromosomes after replication

Found in bacteria

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Topoisomerases are directly involved with..

Type 1 vs Type 2

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

5’ to 3’

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Template readings are in what direction

3’ to 5’, since DNA is antiparallel

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

The leading strand

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

Lagging strand

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

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DNA polymerases require what to begin synthesis?

What enzyme makes this happen?

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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A primase is a..

RNA polymerase

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

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

Primase

Rna primer

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What do DNA polymerases do?

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

Net reaction of DNA polymerase action

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

What is pyrophosphate released by?

What is it cleaved into? Why?

DNA polymerase

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

What type of reaction does DNA polymerase create?

A coupled irreversible reaction

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

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

DNA polymerase III

What enzyme has proofreading activity? What does that entail?

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

How does Pol III proofread?

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"

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

dNTPs

What removes the RNA primer?

Pol I

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

DNA lipase

Eukaryotic cell cycle

G1, G0, S, G2, M phase

Gap 1 (G1)

Most variable in terms of time, growth and metabolism. G0- semipermanent G1- appropriate signals can cause reentry into cell cycle

S Phase

DNA synthesis

G2 Phase, gap 2

Cell prepares to divide

M Phase

Cell division (mitosis)

Primase + DNA polymerase (begins strand synthesis)

Pol α (alpha)

DNA polymerase + proofreading (extends strands)

Pol δ (delta)

DNA repair enzymes

Pol β and Pol ε (beta and epsilon

Mitochondrial DNA polymerase

Pol γ (gamma)

Eukaryotic chromosomes are ________

Linear

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

RNA primer Telomerase.

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

Telomerase

The ends of eukaryotic chromosome contain repeated sequences called..

Telomeres 6-nucleotide repeats

Telomerase also contains a ________ _________ that does what?

Reverse transcriptase Copies its own template (RNA) into DNA extending the 3' overhand on the chromosome Repeated many times

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

Primase DNA polymerase

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

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

Telomerase is only expressed in what cells? Cells that don't express telomerase have what fault?

Cells that continually divide. If they don't have telomerase, their chromosomes become shortened at each cell division. Aging, cancer.

Process of polymerases copying RNA into DNA

Reverse transcription, via reverse transcriptase HIV Lack proofreading, high mutation rate

What is HNPCC?

Hereditary nonpolyposis colorectal cancer. One of the most common inherited cancers A defect in mismatch repair, failure of DNA repair

things that cause damage to DNA... need DNA repair.... IDK im sleepy

Cig smoke Exposure to chemicals, radiation UV light (causes pyrimidine dimers/thymine dimers)

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

A deficiency in excision endonuclease