Ch11 | DNA Replication Flashcards
DNA Replication
Duplication of the cellular genome
Semiconservative Replication
Duplicaton of DNA where each daughter duplex conserves only one strand of parental DNA
The three proposed models of DNA replication examined and tested by Meselson & Stahl
(1) Conservative
(2) Semiconservative
(3) Dispersive
Replication Fork
Point where parental duplex separates and daughter duplexes arise via DNA synthesis
Origin of Replication
Specific sequence where DNA synthesis begins
DNA polymerase
Enzymes that synthesize DNA (always extending in the 5’ —> 3’ direction)
Leading strand
Continuously synthesized daughter strand
Lagging strand
Discontinuously synthesized daughter strand
Okasaki fragments
Discontinuous base-pair segments of lagging strand primed by even shorter segments of RNA at 5’ end that are bridged (primer removed) via nuclease action and sealed by ligase
Template strand
Requirement for action of any polymerase that acts as a guide for nucleotide base-pairing (or polymerization reaction)
Primer strand
Secondary requirement of polymerase action the contains the vacant 3’-OH end to which subsequent nucleotides may be added
Primer terminus
Free (vacant) 3’-OH end of primer strand to which additional nucleotides are added
Primed template
Double-stranded DNA product of primer
Steps of DNA Polymerase Reaction (4)
(1) dNTP approaches primer terminus
(2) If dNTP is complimentary to template strand insertion occurs
(3) By-product of insertion pairing reaction is pyrophosphate
(4) Translocation of both strands provides alignment, in relation to DNA poly, for subsequent dNTP additions
DNA nuclease
Class of enzymes that degrades DNA
Exonuclease
Enzymes that shorten DNA from the ends
Endonuclease
Enzymes that cuts/shortens DNA from internal position
Proofreading
A 3’ –> 5’ exonuclease action that removes improperly placed nucleotides providing second opportunity for proper complimentary base-pairing. This process is NOT the reverse of polymerization reaction as it does not involve pyrophosphate.
Nick translation
The cooperative repair mechanism involving:
(1) Excision by 5’ –> 3’ exonuclease and, simultaneously;
(2) Polymerization via DNA polymerase I
Useful in radio-tagging for molecular biology research
Bacterial DNA Polymerases (Name & Function)
I: Okazaki processing & DNA repair II: Translesion synthesis III: Chromosome replication IV: Translesion synthesis V: Translesion synthesis
Translesion synthesis
DNA damage tolerance mechanism that allows replication machinery to continue past certain DNA lesions and the subsequent use of specialized Translesion Polymerases to perform repair with placement of proper nucleotides.
DNA Polymerase “Open Form” vs “Closed Form”
Conformational change that allows for correct binding of dNTP to the fingers domain and subsequent placement of correct base-pair
Distributive synthesis
One of two paths taken by DNA polymerase whereby newly synthesized DNA is shifted to the post-insertion position involving disassociation and immediate rebinding mechanism.
Processive synthesis
One of two paths taken by DNA polymerase whereby newly synthesized DNA is shifted to the post-insertion position without disassociation through multiple catalytic cycles.
Pol III core
Heterotrimer of α, ε and θ subunits
Pol III haloenzyme
Protein assembly that replicates both leading and lagging strand
DNA helicases
Class of enzymes that separate parental strands of DNA
Topoisomerase
Enzymes that unwinds condensed DNA
Primases
Specialized RNA polymerases that synthesize RNA primers
RnaseH
Ribonuclease which can remove RNA base paired to DNA
Single-Stranded DNA Binding Protein (SSDBP)
Produced by helicase during separation as a place-holder protecting DNA from endonucleases and prompting DNA polymerase action
Trombone model
Common name for the process of repeated loop growth and disassembly on the lagging strand during synthesis of Okasaki fragments
Collision release
The beta clamp release upon completion of an Okasaki fragment
