Okazaki Fragments definition
Okazaki Fragments refers to small single stranded DNA fragments, formed upon DNA replication, more specifically, the back strand.
DNA Replication/Duplication
For normal cell growth and division in organisms, an initial step called DNA replication is required. This process is based on semi-conservative copy of DNA in the nucleus of a growing cell.
DNA replication then begins with distortion of double helix by topoisomerase, followed by separation of two DNA strands by helicase. Separation of DNA single strands leads to formation of replication fork, where the replication machinery (protein and enzyme complex) will bind. An RNA polymerase is the constituent of this complex that adds small primers to the beginning of DNA single strand to be copied. Then another enzyme, DNA polymerase, recognizes the primers added by RNA polymerase and starts copying the DNA strands. At the end of replication there are two DNA molecules, each of the double strand containing one strand originating from cell and one copied (hence the name semi-conservative replication).
However, a major hindrance to DNA replication comes from the fact that DNA polymerase enzyme can only perform its function of nucleic acid polymerization (addition of nucleic acids to the growing strand) in 5 ‘→ 3’ sense. Since the two strands of DNA molecule are antiparallel and replication fork separates the two strands at the same site, strand in the 5 ‘→ 3’ direction is easily replicated towards the opening of replication fork. For this reason, this chain is called ‘leader chain’. The problem lies in the other strand, which is oriented in 3 ‘← 5’ direction, in which DNA polymerase cannot bind and perform its function because the opening of replication fork occurs in the opposite direction to replication.
Okazaki Fragments’ formation
To work around this problem, cell makes copies the strand that is oriented 3 ‘← 5’ in a discontinuous manner. This chain is called a ‘delayed chain’.
In this process, several small fragments of the delayed chain are replicated as replication fork advances (5 ‘→ 3’) and further separates the double helix from DNA molecule. The fragments resulting from this discontinuous replication are called ‘Okazaki Fragments’. Thus, although backward chain is growing in the 3 ‘→ 5’ direction, in fact Okazaki Fragments are being synthesized in the 3 ‘← 5’ direction.
After the primers are removed, nucleic acid gaps between Okazaki Fragments are filled and a final enzyme, DNA ligase, binds fragments to form a single, single strand of continuous DNA.
Figure 1 – Representative schematic image of DNA replication and consequent formation of Okazaki Fragments.
Okazaki Fragments were named after the scientist who discovered them in 1969, Reiji Okazaki. In bacteria such fragments have a size of 1000 to 2000 nucleic acids; on the other hand, in eukaryotes have a size smaller than 200 nucleic acids.
References:
Alberts B., Johnson A., Lewis J., Raff M., Keith R., Walter P. (2007). Molecular Biology of the Cell (5th edition). Garland Science, New York.
Berg J.M., Tymoczko J.L., Stryer L. (2002). Biochemistry (5th edition). W. H. Freeman, New York.
Cooper G.M. (2000). The Cell: A Molecular Approach (2th edition). Sinauer Associates, Sunderland (MA).
Griffiths A.J.F., Miller J.H., Lewontin R.C., Gelbart W.M. (1999). Modern Genetic Analysis (2nd edition). W. H. Freeman, New York.
Griffiths A.J.F., Miller J.H., Suzuki D.T., Lewontin R.C., Gelbart W.M. (2000). An Introduction to Genetic Analysis (7ª edição). W. H. Freeman, New York.
Lodish H., Berk A., Zipursky S.L., Matsudaira P., Baltimore D., Darnell J. (2000). Molecular Cell Biology (4th edition). W. H. Freeman, New York.
