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DNA Replication Chapter 8 DNA Replication is a very complex process Must unwind helix and energy is normally required pyrophosphatase driven ssDNA tends to form intra strand base pairs that can halt the process cruciform structures A single enzyme can realistically only catalyze a limited number of different types of reactions replication complexes are typically among the most complex enzymatic associations that exist in any organism Safeguards have evolved to recognize and prevent errors and to repair most of those that do occur Circularity in prokaryotes and largely linear molecules in eukaryotes in concert with the great size of the genomes of many organisms add physical constraints to replication systems No particular mode of replication is suitable for all organisms or viruses Replication is always invariably a double stranded event Deoxy Nucleotide triphosphates Primer template junction Substrates for Replication Fig 8 1 The replicating enzyme monitors ability to base pair not the exact nucleotide Fig 8 3 Correct base pairing is essential Ribonucleotides are sterically not tolerated for incorporation 1000 fold lower rate into DNA Change glu ala discrimination lost Binding site is too small to allow OH at ribose position 2 Fig 8 4 DNA Pol III the paradigm palm of the hand is largely sheet it is site of catalysis and monitors accuracy of base pairing Fig 8 8 Hand model for DNA polymerase O helix is in the finger domain of most DNA polymerases DNA polymerase grips template and incoming NTP when base pairing is correct Fig 8 7 Thumb domain is not directly involved in catalysis It maintains proper orientation of primer and active site Helps maintain strong association between DNA Pol and the substrates increases processivity DNA polymerase processivity is what allows replication to proceed rapidly up to 1000 NTP sec it is basically how long the Pol stays on template Rate limiting step is binding of polymerase to primer template junction Fig 8 9 Proofreading

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