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York University
BIOL 2020
K Wheaton

What helps to copy and preserve DNA DNA polymerase How many polymerases do E coli have? 5 (roman numeral numbering) DNA polymerase requires what precursors? 5: deoxynuclcleoside 5’-triphosphate, dATP, And what 2 other things dGTP, dCTP, dTTP as well as Mg2+ ...and primer and proof reader DNA polymerase is what type of enzyme? Also Template directed enzyme included in what DNA polymerase needs Where must the primer be bound? And what Free 3’-OH, bound to template strand, made does it bind to? of RNA Chain elongation is a? Nucleophilic attack by the 3’-OH on the innermost phosphorous atom of the deoxynucleoside triphosphate, phosphodiester bond is created and releases pyrophosphate, this then yields 2 orthophosphates (by pyrophosphatase) occurs in the 5’3’ end DNA polymerase I active sites? (3) Polymerase , 3’5’ exonuclease ( high fidelity, less than 10^-8 error, from induced fit mechanism) and 5’3’ exonuclease site How does proof reading occur DNA polymerase close down around (dNTP), triggers conformational change (active site binding in polymerase), finger domain rotates to form tight pocket, base pair can now readily fit. What does helicase do? Using ATP hydrolysis power to separate strands. Domain A1 and B1 of PcrA bind single stranded DNA, when ATP binds the cleft between these 2 closes, domain A1 slides along DNA, when ATP is hydrolyzed the cleft opens, DNA goes toward A1. Repeated over and over, and DNA is unwound. Naturally occurring DNA is what type of Negative supercoiled coiled? What does topoisomerase do? Elimate supercoils by temporarily cleaving DNA What does bacterial topoisomerase do? Called DNA gyrase. Target of antibiotics, Called? Novobiocin blocks the binding of ATP to gyrase, Nalidixic acid and ciprofloxacin (also prevents anthrax) interfere with the breakage and rejoining of DNA chains (used for urinary tract infections) , In E coli where does replication start? Origin of replication (oriC), contains 4 repeats of a sequence that act as binding site for initiation protein called DnaA, uses DnaB as a helicase (uses ATP), SSB prevents it from forming double helix Describe primase RNA polymerase (primase) joins with prepriming complex (primosome), makes short strand of RNA, complementary to DNA strand, removed by 5’3’ exonuclease, in E coli exo. Is in the third active site of DNA polymerase I What is the replication fork ? Site of DNA synthesis, both daughter strands appear to grow in the same direction How to synthesize with okazaki fragments New DNA exist in small fragments called okazaki fragments, they become covalently linked through DNA ligase (uses ATP), termed the lagging strand made in 5’3’ direction the discontinuous assembly makes it go in the 3’5’ direction What is DNA polymerase II used for? Forms a ring around DNA duplex, polymerase can move without falling off DNA substrate Describe ligase Catalyzes the formation of a phosphodiester linkage between 3’OH at the end and 5’ phosphate group, uses ATP , in bacteria NAD+ is used for energy Replication of human genome requires how 30,000, replication must be complete before many origins of replication? the cell cycle progresses. Licensing factors permit the formation of the DNA synthesis initiation complex by binding to the origin or
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