DNA Replication

Semi-conservative: both strands will serve as a template for new strand synthesis
Starts at an origin
Synthesis always in the 5🡪3’ direction b/c the DNA polymerase needs a 3’ hydroxyl end
Can be unidirectional but as a rule it’s bidirectional
Semi-discontinuous: one DNA strand is replicated in fragments
RNA primers required

Origin of replication: provides an opening called a replication bubble that forms two replication forks. * DNA replication proceeds outward from forks

DNA polymerase: covalently links nucleotides together * Deoxynucleoside triphosphates: free nucleotides with three phosphate groups * Breaks covalent bonds to release pyrophosphate (two phosphates) and provides energy to connect nucleotides

DNA polymerase cannot begin synthesis on a bare template strand * Requires a primer to get started * DNA primase makes the primer from RNA * The RNA primer is removed and replaced with DNA later
DNA polymerase only works 5’ to 3’

Leading strand * DNA synthesized in as one long molecule (continuous) * DNA primase makes a single RNA primer * DNA polymerase adds nucleotides in a 5’ to 3’ direction as it slides forward
Lagging strand * DNA synthesized 5’ to 3’ but as Okazaki fragments (discontinuous) * Okazaki fragments consist of RNA primers plus DNA
In both strands * RNA primers are removed by DNA polymerase and replaced with DNA * DNA ligase joins adjacent DNA fragments

Three mechanisms for accuracy * Hydrogen bonding between A and T, and between G and C is more stable than mismatched combinations * Active site of DNA polymerase is unlikely to form bonds if pairs mismatched * DNA polymerase can proofread to remove mismatched pairs * DNA polymerase backs up and digests linkages * Other DNA repair enzymes as well

E. coli has 5 DNA polymerases * DNA Polymerase II: multiple subunits, responsible for majority of replication * DNA Polymerase I: a single subunit, rapidly removes RNA primers and fills in DNA * DNA Polymerase II, IV, and V: DNA repair and can replicate damaged DNA * DNA polymerases I and III stall at DNA damage * DNA polymerases II, IV, and V don’t stall but go slower and make sure replication is complete
Humans have 12 or more DNA polymerases * Designated with Greek letters * DNA polymerase α: its own built in primase subunit * *DNA polymerase* δ and 𝜀: extend DNA at a faster rate * DNA polymerase 𝛾: replicates mitochondrial DNA * When DNA polymerases α, δ, and 𝜀 encounter abnormalities, they may be unable to replicate * Lesion-replicating polymerases may be able to synthesize complementary strands to the damaged area

Series of short nucleotide sequences repeated at the ends of chromosomes in eukaryotes
Specialized form of DNA replication only in eukaryotes in the telomeres
Telomere at 3’ does not have a complementary strand and is called a 3’ overhang