Basics of DNA Replication

DNA

5 carbon sugar, Phosphate Group, Nitrogenous Base, Free hydroxyl group, and Anti-parallel

Nitrogenous Base

2 ringed group purine = Adenine (A) or Guanine (G)

single ringed group pyrimidine (thymine (T) or cytosine (C))

RNA has Uracil (U) instead of thymine (T)

Phosphodiester bond

chain of nucleotides in a 5’ phosphate group to 3’ hydroxyl orientation. Bond by adj nucleotides.

phosphate group is linked to 2 sugar making the ester bond.

Phosphodiester backbone

made up of long polymers of nucleotides and they wrap around an axis to make the double helix

major and minor groove are connected by H+ bond

Major groove

interacts with proteins

Double Helix dimensions

Diameter/ Width of 2nm and a complete turn every 3.4 nm

distance btwn the bases of 0.34 and held by hydrogen bonds

Chargaff rules

5’ AGGCTATGCTAA 3”

5’ TTAGCATAGCCT 3’ A pairs w/ T and C pairs w/ G

Watson-Crick model

amount of A = T and the amount G = C because they are complementary

Ex: A= 24% T = 24% then G = 26% C= 26%

Conservative Model

both strands of the parental DNA would remain intact (conserved), and new DNA copies would consist of a all new molecules.

Semiconservative (correct version)

Daughter strands each consist of one parental strands and one newly synthesized strand

Dispersive model

copies of DNA could consist of mixtures of parental and newly synthesized strands

Replication

semi discontinuous

something to copy (template) → parental DNA

something to do the copying → enzymes

building blocks to make the copy → nucleotides.

Stages of DNA Replication

Initiation → replication begins

Elongation → new strand DNA are synthesized by DNA polymerase

Termination → replication terminates.

Dna Polymerase

an enzyme that synthesizes from the original template and only goes in 5’to 3’ direction and requires a primer to extend.

RNA polymerase

makes the Primer for DNA polymerase to synthesize from.

Replicon

DNA controlled by origin

Chromosomes + origin = single ?

DNA Polymerase I

Acts on lagging strands to remove primers and replace w/DNA

5’-3’ exonuclease activity to remove RNA primer

DNA Polymerase II

involved in DNA repair processes

DNA Polymerase III

main replication enzyme or Synthesizes DNA

Endonuclease

an enzyme located internally in a DNA strand that cleaves phosphodiester bonds btwn nucleotides

Exonuclease

An enzyme located at the end of a DNA strand and removes nucleotides from the ends of DNA

DNA Polymerase I, II, and III

3’-5’ exonuclease activity that proofreads the DNA replication

Helicase

enzyme w/DNA unwinding activity using ATP

Single-Strand Binding Proteins (SSB)

coat the strands to keep them apart so replication takes place

Topoisomerase or DNA gyrase

enzymes that prevent supercoiling

Lagging vs Leading Strand

Leading → continuous from 1 primer

Lagging → discontinuous from multiple primers

Okazaki Fragment

DNA fragments on lagging strand

Primase

Synthesizes RNA primers

DNA ligase

joins the ends of DNA segments; DNA repair

Processivity

ability of a polymerase to remain attached to the template

Ex: DNA polymerase III

Beta subunit

high processivity makes this subunit of the enzyme.

Sliding Clamp → clamp made up of Beta subunit to hold the DNA Pol III to DNA

Replication fork

partial opening of helix formed where the doubled stranded FNA is being unwounded.

Replisome

macromolecular assembly of enzymes involved in DNA replication