Why is the Okazaki fragment necessary?

Answer 1

When the lagging strand is being replicated on the original strand, the 5'-3' pattern must be used; thus a small discontinuity occurs and an Okazaki Fragment forms. These fragments are processed by the replication machinery to produce a continuous strand of DNA and hence a complete daughter DNA helix.

In dealing with the synthesis of complementary DNA strands the leading strand always reads 5' to 3'. Its antiparallel complement strand, the lagging strand reads from 3' to 5'. Because the original strands of DNA are antiparallel, and only one continuous new strand can be synthesised at the 3' end of the leading strand due to the intrinsic 5'-3' polarity of DNA polymerases, the other strand must grow discontinuously in the opposite direction. Regarding the lagging strand, the result of this strand's discontinuous replication is the production of a series of short sections of DNA called Okazaki fragments.

Each Okazaki fragment is initiated near the replication fork at an RNA primer created by primase, and extended by DNA polymerase III. In eukaryotes, lagging strand synthesis is carried out by the DNA polymerase α-primase complex. The primer is later removed by enzymes that have endonucleolytic activity such as Ribonuclease H (RNAse H), flap endonucleases (FENs) and Dna2 helicase/nucleases. In prokaryotes the FEN nuclease is a domain of DNA polymerase I while in eukaryotes FENs are separate enzymes. The excised RNA bases are replaced with DNA by DNA polymerase I in prokaryotes or DNA polymerase δ in eukaryotes. Adjoining fragments are then linked together by DNA ligase, using phosphodiester bonds, to create a continuous strand of DNA.

Answer 2

When DNA replicates it's strands are open up (forks). Replication takes place on both strands, one side is 3' --> 5' so the new strand is complementary (5' -->3') and since the DNA polymerase adds to the 3' end of the growing complement strand it can extend it easily.

However, the other template side is 5' -->3' this causes problems since to replicate it DNA polymerase would have to run in reverse. It would have to add to the 5' side of a 3' --> 5' strand. It can't do this, so to cope the DNA polymerase lets fork open up a bit, start a piece of the compliment near the replication fork split and run it backwards toward the already duplicated DNA strand where it last left off. It stops when it runs out of DNA to duplicate and goes back toward the fork to do it again. This repeating process makes a series of short fragments of DNA on the newly replicated side(Okazaki Fragments) , they later get ligated together. This way both sides of the replication fork get duplicated and have polymerase running 5' --> 3' (the only way it can) laying down new DNA.

Answer 3

The two sides of the DNA molecule are antiparallel, so the nucleotides are joined in opposite directions.