What Are Okazaki Fragments And Why Are They Necessary?

Okazaki fragments are short sequences of DNA nucleotides that are synthesized discontinuously. They are formed during the process of duplication of DNA. The other strand is produced as one continuous piece of DNA.

The fragments were identified by Reiji Okazaki (1930 to 1975) and his wife who was a famous Japanese molecular biologist. 

These fragments are important because they allow for replication of the 3′ to 5′ strand.

The Double-Helix Uncoils

When a cell is replicating its DNA, the double-helix is uncoiled like undoing a zipper. The unzipped parent DNA chain which runs in the 3′ to 5′ direction can be copied by polymerase III. All new DNA is synthesized in the 5′ to 3′ direction. It cannot produce a new strand which itself is in the 3′ to 5′ direction.  DNA polymerase III is used here and forms a continuous strand. It only requires one primer. 

The new strand formed is called the leading strand. 

DNA replication is more tricky when it comes to copying the opposite parent strand. This is the other strand  that starts running from the 5′ to 3′ direction. This parent strand that is now unzipped as it were has no 3′ site at the beginning of the unzipped DNA for the enzyme polymerase III to work off. Given polymerase III can only work in a 5′ to 3′ direction it means that DNA copied off the original 5′ to 3′ strand must be produced in discrete amounts.

Duplication of this strand is discontinuous, not continuous. The new strand formed from the parent DNA is known as the lagging strand. It requires a number of RNA primers to generate these fragments of DNA which then need to be joined together.

The Okazaki fragments as they are known are just short, newly synthesized DNA fragments. These are formed then on the template strand during DNA replication.

The Okazaki fragments are 1000 to 2000 nucleotides long in prokaryotes. They are much shorter in eukaryotes being usually just 150 nucleotides long. All these fragments are separated by RNA primers which are 10 nucleotides long.

Each Okazaki fragment is connected to form a continuous newly synthesized complementary strand, catalysed using the enzyme ligase. 

When the synthesis of the lagging strand is completed, the RNA primers are removed from the fragments using DNA polymerase I. This enzyme also fills in the gaps left by the primer but a nick is left. So, DNA polymerase I cannot join two nucleotide chains together.

Another enzyme called DNA ligase is required to repair the nick. It joins the two polynucleotide chains together by catalyzing the formation of a phosphodiester bond sealing the Okazaki fragments together.