DNA REPLICATION: Parallel One-Way Streets

a) DNA polymerases extend a 3' end by adding nucleotides. DNA polymerases can only add nucleotides when there is a primer/template duplex.  DNA replication begins with the formation of short RNA primers, synthesized by primase. This is because DNA polymerases can not add nucleotides unless there is a pre-existing 3' end to add nucleotides to. Once the primer is in place, polymerase can elongate it. Finally, RNAase removes the primers, and DNA polymerase fills in the resulting gaps by extending the growing strand that is upstream. When the last nucleotide is filled in, the resultant gap is closed by ligase. b) As the helix continues to open up, enough room is available to allow synthesis of a primer, and its subsequent elongation, on the opposite strand. c) Elongation of the leading strands proceeds both leftward and rightward. The leading strands undergo continuous elongation. As the helix opens up, new primers can be added to the lagging strands, and the primers elongated by DNA polymerase. d) Each leading/lagging strand pair constitutes a "replication fork". Thus, the replication forks migrate leftward and rightward, opening up the helix and allowing for new primers to be inserted on the lagging strands.

e) Each DNA polymerase complex either reaches the end of the molecule, or the 5' end of a primer. f) When DNA polymerase reaches a primer, its 5'->3' exonuclease activity deletes the primers, leaving short gaps upstream from each primer. g)Finally, DNA polymerase fills in the gaps, and ligase forms phosphodiester bonds between adjacent nucleotides. Note that the excision of primers at each end of the molecule leaves unrepaired gaps. DNA polymerase can only add nucleotides to 3' ends, and not to 5' ends. Since there are no primers upstream from these terminal gaps, the gaps can not be filled in.

With the exception of some viruses, DNA replication proceeds in a  bidirectional fashion, with two replication forks per replicon. Each replication fork has a  leading and lagging strand. As forks proceed in both directions, the leading strand grows continuously. On the lagging strand, each new segment of DNA synthesis begins when enough DNA has been "peeled apart" to allow replication enzymes to bind.

3D Structure of Replication Fork editing complex at PDB
http://www.rcsb.org/pdb/explore/jmol.do?structureId=1CLQ&bionumber=1

Eukaryotic Chromosomes have Multiple origins of Replication

Eukaryotes have enormous chromosomes, ranging in size from 105 to 108 bp. To allow for efficient replication, most eukaryotic chromosomes have multiple replication origins. Replication initiates independently at each replication origin. Each pair of replication forks is referred to as a "replicon". Replicons can be visualized as bubbles of replicated DNA that expand in both directions. Eventually, all replicons merge into a single large bubble, until replication terminates at the telomeres. Note: Do not be misled by this figure. Each replicon has two replication forks, and each replication fork has both leading and lagging strands. If this figure was more accurately-drawn, the lagging strands would be drawn to show Okazaki fragments.

from http://faculty.ccbcmd.edu/~gkaiser/biotutorials/dna/fg21.html

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