# DNA Replication ## Enzymes of Replication ### DNA Polymerase Rather than detecting the exact nucleotide that enters the active site, DNA polymerase will monitor the incoming dNTP’s ability to form the AT/GC pair. ![[Pasted image 20240330011319.png|200]] rNTPs are sterically selected against because the 2’-OH cannot fit into the active site due to two amino acids already interacting with the sugar. #### Mechanism of DNA Synthesis Two highly conserved aspartate residues contribute to the formation of two metal ion coordinate groups (Mg or Zn). - Sn2 nucleophilic reaction #### Proofreading Mechanism **Single Stranded DNA Binding Proteins (SSBs)** - Coat single-stranded DNA to protect it from damage **Topoisomerase** **DNA Helicase** - Movement is powered by ATP - Disrupts the hydrogen bonds holding dsDNA together as it travels (denaturing) **RNA Primase** - Synthesizes a short strand of RNA (~10 bp) to provide a starting point for DNA polymerase III - Synthesize an RNA primer → Discard old beta clamp proteins → Load new beta clamps to the next spot on the DNA to be replicated → Tether the template to the core enzyme ## Initiation of Replication - Melting of 13-mer region (made easier ) - RNA Polymerase assists process by binding and causing superhelical tension - - SSBs bind to ssDNA and protect it - The initiation of replication is complete when two forks have been assembled - Newly replicated DNA is hemimethylated for a short period of time - Making sure the replication Cell Cycle Timing - Cyclin Dependent Kinases (CDKs) - Cell Division Control (CDCs) ### Origins of Replication In eukaryotes: - replication begins at thousands of replication origins simultaneously ### S-Phase Initiation > See also: > - [[The Cell Cycle]] ### Signaling Cascade - Melting of 13-mer region (made easier ) - RNA Polymerase assists process by binding and causing superhelical tension - - SSBs bind to ssDNA and protect it - The initiation of replication is complete when two forks have been assembled - Newly replicated DNA is hemimethylated for a short period of time - Making sure the replication **Cell Cycle Timing** - Cyclin Dependent Kinases (CDKs) - Cell Division Control (CDCs) ## The Replisome > See also: > - [[Epigenetics]] > - [[Chromosomes]]