DNA Replication and Repair Flashcards
New DNA has a parent strand that serves as a template for the synthesis of one daughter strand. Founded by Meselson-Stahl with their experiment.
Semi conservative replication.
Both strands of DNA are replicated simultaneously, with two replication forks. The initiation site is called the “origin” of relocation.
Bidirectional replication
Addition of new nucleotides to the 3’ end. The leading strand is made continuously as the replication fork advances. The lagging strand is made discontinuously in short pieces (Okazaki fragments) that are later joined together.
Semi-discontinuous (proceeds 5’ –> 3’) replication
What does the (3’ - OH) primer do when it comes to the characteristics and mechanisms of DNA polymerase?
The nucleophilic OH group at the 3’ end of the growing chain attacks the alpha-phosphate of the incoming trinucleotide. Primer = short strand complementarity to the template, which contains a 3’-OH required for the first DNA polymerase-catalyzed reaction, and can be made of DNA for RNA which is more common.
What does the Mg2+ ion residues in the active site do when it comes to the characteristics and mechanisms of DNA polymerase?
The 3’-OH is made a more powerful nucleophile by nearby Mg2+ ions. It shields for unfavorable (-) charges from each other. One of them helps to deprotonate the 3’-hydroxyl group, rendering it a more effective nucleophile. The other binds to the incoming dNTP and facilitates departure of the pyrophosphate.
What does the Asp residues do when it comes to the characteristics and mechanisms of DNA polymerase?
The Asp helps coordinate the two active Mg2+ in the active site.
What is the inorganic pyrophosphate (PPi) when it comes to the characteristics and mechanisms of DNA polymerase?
The PPi is made up of the beta and gamma phosphates and is released during during the reaction.
What is the dNTP (nucleoside triphosphate) when it comes to the characteristics and mechanisms of DNA polymerase?
They are building blocks used for synthesis. dNTPs are used to add complementary nucleotides to the growing DNA strand.
What is processivity?
DNA polymerase can add nucleotides or dissociate. The number of nucleotides added before dissociation is called processivity. Each specific nucleotide has its own processivity and polymerization rate. (If there is low processivity than DNA replication would be slow).
What is high fidelity?
Replicative DNA polymerase active site excludes base pairs with incorrect geometry. Most DNA polymerases have 3’ –> 5’ -exonuclease activity (exo- meaning that it only takes off the nucleotides at the very end (3’ end)). “Proofreads synthesis for mismatched base, pair, and correct errors made during replication.
What is the origin recognition complex (ORC)?
This complex loads a helicase onto the DNA. The origins are often A-T rich regions. Used in initiation.
What is a helicase?
A hexamer (six units) of minichromosome maintenance proteins (MCM 2-7) which helps open up DNA and then goes on like a sliding clamp. Used in initiation.
What does Pol alpha (primase) do in DNA elongation.
It is a primase (adds a nucleotide opposite a template strand without anything) and polymerase (extend beyond one nucleotide). Can add RNA complementary to template DNA. Does not have 3’ –> 5’ proofreading (RNA primer gets removed before DNA replication is over, and if there is mismatch there will just be a slower start).
What does Pol epsilon do in elongation?
This is a replicative polymerase on the leading strand, that is highly processive and has high fidelity, and is continuous synthesis.
What does Pol delta do in elongation?
This is a replicative polymerase on the lagging strand. It is highly processive and has high fidelity. It requires Okazaki fragments.
