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Bacterial DNA replic
Uni of Notts, Structure Function & Analysis of Genes, year 2, topic 2
| Term | Definition |
|---|---|
| Direction of DNA polymerase relative to DNA extension | DNA polymerase reads the strand 3'-5' but DNA extends 5'-3' |
| Direct trans-esterification in DNA synthesis | 3'-OH acts as a nucleophile, attacking the α-phosphate of a dNTP forming a new isoenergetic phosphodiester bond & hydrolysing the one connecting to the PPi, which is hydrolysed by pyrophosphatase driving the reaction forward, no water produced |
| Why DNA can only be extended 5'-3' | Only the breaking of the NTP phosphodiester bond with the 3'-OH acting as an nucleophile can provide enough free energy to drive the reaction, Le Chatellier's principle |
| Difference between ligation & direct trans-esterification | Fusing 2 backbones by ligation rather than synthesising a new strand requires energy investment & forming a new ester bond rather than recycling an old one which is a condensation reaction generating H2O |
| E. Coli origin of replication (OriC) | ~245bp, contains structural regions of 9mer boxes for factors (such as DnaA) to bind & three 13mers rich in AT in order to melt & form the replication forks |
| DnaA | Bacterial replication initiation factor, melts the 13mer consensuses using ATP hydrolysis & tortional strain then recruits other replication factors, such as helicase |
| Minimal origin point | The smallest possible sequences within OriC that still retain the ability to initiate replication, this is where replication starts |
| DnaC & DnaB | DnaC - chaperone to help load DnaB DnaB - hexameric helicase |
| Why DnaB needs loading | Active DnaB is a closed-circle hexamer that can't pass through dsDNA, DnaC-ATP binds & keeps it in an open inactive conformation which clamps it around ssDNA in the melted 13mer section & hydrolyses ATP to dissociate |
| Bidirectional replication | Replication forks flow bidirectionally in opposite directs before colliding at the terminus, forming 2 identical sister chromatids |
| Torsional stress generated from replication & topoisomerases | Unwinding the helix by helicases generates positive supercoils to balance out torsional strain ahead of the replication fork which can halt synthesis, topoisomerases negates these supercoils |
| Catenation & topoisomerase II | sister chromatids formed from 2 replication forks can interlock, forming a catenane just after fork convergence which can be separated by topoisomerase II before separation |
| Catenane | 2 interlocked macrocyclic molecules which cannot be separated without breaking covalent bonds |
| How lagging & leading strand synthesis are coupled | DNA Pol III is dimerized, mediated by τ-subunits of clamp-loading complex. One protein synthesises the lagging & the other the leading strand to ensure the replisome progresses evenly |
| Trombone model of DNA synthesis | The formation of a loop from the lagging strand of DNA to better orient replisome enzymes to add Okazaki fragments & extend the strand. The loop is released once a fragment is added |
| DNA Primase | DnaG, DNA-dependent RNA-synthesis, forms 10-12bp RNA fragments from lagging strand. These are reverse transcribed using RNaseH to form Okazaki fragments to extend the lagging strand |
| DNA primosome | Complex formed from primase (DnaG) binding with helicase (DnaB) in order to be loaded onto the lagging strand at the replication fork |
| How cells only produce Okazaki fragments for the leading strand | Opportunistically rather than signalling. Leading ssDNA can be synthesised normally, so it will have DNA Pol III bound however, the lagging strand won't & will have a loop for DnaG to bind |
| Sliding clamp | Grommet-like hexamer which slides over dsDNA (using loading & unloading proteins) to increase processivity of replication forks |
| How sliding clamps increase processivity | Topologically tether DNA Pol to their surface to keep them close to DNA to prevent dissociation & enable much quicker rebinding. They don't need energy to slide & there is low friction |
| Stem loops in termination | Ter sites can form 2' structure loops & bind a terminus utilisation substance protein (Tus) which forms a locked stable structure with hydrogen bonds when approached by helicase causing it to stop & dissociate |
Created by:
Denny12
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