Prokaryotic Elongation

A nice diagram of a replication fork from Nature can be found at this link.

You should understand the roles of the following proteins:

• Dna PolIII: This is the DNA polymerase that is responsible for chromosome replication in E. coli. As seen in the diagrams that are at the links above, each replication fork in E. coli has two DNA PolIII enzymes, one for the lagging strand and one for the leading strand. The two enzymes are held together by the tau subunit and each PolIII is clamped to the DNA molecule by a Beta clamp. During elongation the alpha subunit of PolIII incorporates nucleotides and the epsilon subunit proofreads it. If the incorrect nucleotide was incorporated, epsilon removes it so that alpha subunit can then redo that site.

• DNA Primase must be present to synthesize the RNA primers as needed for lagging strand replication. DNA Primase is present as part of a Primosome which also contains DnaB which, remember, is a helicase.


• Single-stranded binding protein (SSB) binds to the two single strands once they have been separated by the helicase. This prevents them from re-annealing so that they are available to serve as templates for DNA PolIII

Lagging strand synthesis: As shown in the videos below, the lagging strand is synthesized discontinuously in short segments referred to as Okazaki fragments, each on the order of 1000 nucleotides in length. A single Okazaki fragment is composed of the RNA primer and the DNA added by DNA PolIII. Once the fork has passed and a region of the lagging strand has released (see the video below), DNA PolI finishes the process. This enzyme has 5' to 3' exonuclease activity that it uses to remove the RNA primer and 5' to 3' polymerase activity that it uses to replace the primer with DNA - by extending the adjacent Okazaki fragment. Once this is complete, DNA ligase seals the gap between adjacent Okazaki fragments, something that DNA Polymerases cannot do since they only synthesize the formation of a phosphodiester bond with an incoming trinucleotide.

A video about the basic replication process:

A video that is a good illustration of how the lagging strand is looped around: