(21)
3. Beskrive hvordan polymeriseringsprocessen (DNA-synthese) foregår fra 5' imod 3'
Stryer, s.760-1, fig.27.27
Stryer, s.763-4, fig. 27.33
Devlin, s.166-7, fig.4.5

Both strands of parental DNA serve as templates for synthesis of new DNA. The site of DNA synthesis is called the replication fork. There are two replication forks created from each origin of replication, going in two oppsite directions.  

Replication fork - complex formed by the newly synthesized daugther strands arising from the parental duplex. DNA polymerase III moves in the direction of the fork opening. Therefor there are also two DNA polymerases III that go in oppsite directions from one origin of replication.

The two strands are antiparallel, meaning they run in opposite direction. One of the daughter strands has its 3`-end towards the replication fork, which is fine because the DNA polymerase III adds nucleotides to the free 3´-OH group of the previous nucleotide in the sequence.

DNA polymerase III only adds nucleotides in the 5´-3´direction.

The polymerisation reaction - The phosphodiester bond of the dNTP connecting the first ( α ) phosphate attached to 5`-carbon of the deoxyribose and the two other ( β, γ ) phosphates undergoes a nucleophillic attack from the free 3`-OH group of the previous nucleotide attached to the DNA. That way, a new bond is created between the a  phosphate of dNTP and the  3`-OH group of deoxyribose.The terminal two phosphates are released as inorganic phosphate and hydrolyzed in the cells. This makes the reaction irreversible.

This process is, as already mentioned, catalysed by DNA polymerase III.  

However, the strand that has its 5´-end towards the replication and this presents a problem. The mode of synthesis of the lagging strand is therefore more complex.

A looping of the template for the lagging strand places it in position for 5`-3` polymerization. The looped lagging strand template passes through the polymerase site in one subunit of a dimeric DNA polymerase III, while the leading strand passes through the other subunit.

DNA polymerase lets go of the lagging strand after adding about 1000 nucleotides. The synthsiezed fragment is called an Okazaki fragment. A new loop is then formed and primase again synthesizes a short RNA primer to initiate for another Okazaki fragment.

This way all synthesis goes on in the 5`-3` direction.

The gaps between these fragments are filled up by DNA polymerase I. This enzyme also has a 5´-3´ endonuclease activity to remove the RNA primer. In the end, DNA ligase connects the fragments.

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