BMSC 220 Lec 5

-means one strand of parental DNA is conserved as one half of each new progeny DNA molecule

-DNA polymerase

• -synthesize DNA in only the 5' to 3' end 
• -means that the new strand created is built from 3' to 5' 
• -polymerases add a new dNTP(deaoxyribonucleotide triphosphate) only to a preformed primer strand that is H bonded to the template

-3' to 5' direction

• -region of DNA synthesis where the parental strands separate and two new daughter strands elongate
• -location of active DNA replication containing the macromolecular complex

-synthesized in a continuous manner in the direction of overall DNA replication

-synthesized in a discontinuous manner in the direction opposite of movement of the DNA fork

-small pieces of newly synthesized DNA that are joined to form an intact new DNA strand on the lagging strand

-short fragments of RNA serve as primers for DNA replication which are added by Primase

• -enzyme that makes short RNA primers complementary to lagging strand 
• -3-10 nucleotides
• -does not require a 3'OH group be already attached to the chain

-enzymes that degrade(hydrolyzes) DNA or RNA molecules from their ends

-enzyme that degrades the RNA strand(primer) of RNA-DNA hybrids in eukaryotes

• -enyzme that seals breaks in DNA strands following removal of the RNA primer by RNase H and insertion of new DNA base pairs by DNA polymerase 
• -joins Okazaki fragments together

-loads clamp proteins onto replication fork at primer

-load and hold polymerase onto template

-enzymes that catalyze the unwinding of parental DNA (in ATP dependent manner)

-stabilize the unwound single stranded template DNA

• -enzymes that catalyze the reversible breakage and rejoining of DNA strand to relieve torsion caused by unwinding of DNA by replication fork
• -like spinning the garden hose when you coil it up

• -ori
• -DNA sequences that serve as binding sites for the protein complex that initiates the DNA replication process 
• -single origins can suffice for simple organisms, but humans have about 30,000 ori sequences

• -autonomously replicating sequence is an origin of DNA replication in yeast
• -100 bp with bp common core

• -origin recognition complex 
• -recognizes core sequence and bind to initiate formation of replication bubble
• -bind to ori/ARS

• -unique enzyme that maintains the ends of the eukaryotic chromosomes
• -possesses reverse transcriptase activity

-DNA polymerase that uses RNA template

• -repeats of a simple sequence DNA that maintain the ends of linear chromosomes 
• -needed because DNA polymerase cannot replicate the extreme 5' end of linear molecules

• -free energy differences in H bonding leads to an incorrect base every 100-1000 pairs
• -polymerase makes a mistake 1 in every 10⁵-10⁶ 
• -proofreading by polymerase improves the fidelity to a mistake in 1 in every 10⁸-10⁹
• -DNA repair mechanisms increase fidelity further

• -selective removal of mismatched bases by DNA polymerase 
• -made possible by fundamental properties of DNA polymerases, that they require primers and only go from 5' to 3'