Okazaki fragments are short, newly synthesized DNA segments formed during the replication of a cell’s genetic material. These fragments specifically appear on one of the two template strands, known as the lagging strand. They are later joined together to create a continuous DNA molecule.
The DNA Replication Process
DNA replication is the process by which a cell creates an exact copy of its entire DNA content before cell division. This ensures that each new daughter cell receives a complete set of genetic instructions. The process begins with the unwinding of the double helix structure of DNA, where the two complementary strands separate, much like a zipper opening.
Each of these separated strands serves as a template for the synthesis of a new, complementary DNA strand. This method of copying is known as semi-conservative replication, meaning each new DNA molecule consists of one original strand and one newly synthesized strand. As the DNA unwinds, a Y-shaped structure called a replication fork forms, which is the active site of DNA synthesis.
At this replication fork, DNA synthesis proceeds differently on the two exposed template strands. One strand, termed the leading strand, is synthesized continuously. The other, the lagging strand, is synthesized in a discontinuous manner.
The Antiparallel Challenge
The necessity for Okazaki fragments arises from a characteristic of DNA and the enzymes that build it. DNA strands are antiparallel, meaning they run in opposite directions. One strand has a 5′ (five-prime) end and a 3′ (three-prime) end, while its complementary partner runs in the opposite orientation, with a 3′ end paired with the 5′ end of the first strand.
DNA polymerase, the enzyme responsible for synthesizing new DNA, can only add new nucleotides in one direction: from the 5′ end to the 3′ end of the growing strand. This means it always builds a new strand by extending the 3′ end. This directionality is determined by the chemical structure of the DNA molecule itself.
Because of this directional limitation, DNA synthesis can proceed continuously on only one of the template strands, the leading strand, which is oriented to allow 5′ to 3′ synthesis directly towards the unwinding replication fork. However, the other template strand, the lagging strand, is oriented in the opposite direction. For DNA polymerase to synthesize on this strand, it must work discontinuously, moving away from the replication fork.
Creating Okazaki Fragments
The discontinuous synthesis on the lagging strand involves the formation of short DNA segments known as Okazaki fragments. Each fragment begins with a short RNA primer, which is synthesized by an enzyme called primase. This RNA primer, typically 10-12 nucleotides long, provides the necessary starting point for DNA polymerase.
Once the RNA primer is in place, a DNA polymerase binds and begins to add DNA nucleotides. This enzyme extends the RNA primer by adding nucleotides in the 5′ to 3′ direction, forming the DNA portion of the Okazaki fragment.
As the replication fork continues to unwind, new sections of the lagging strand template become available. This leads to the repeated initiation of new RNA primers and subsequent DNA synthesis, resulting in multiple, distinct Okazaki fragments along the lagging strand.
Finalizing the New DNA Strand
After the Okazaki fragments have been synthesized, several steps are required to convert these discontinuous segments into a complete, continuous DNA strand. The initial RNA primers, which are temporary starting points, must first be removed.
Following primer removal, the gaps that remain are filled with the appropriate DNA nucleotides. DNA polymerase fills these gaps by synthesizing new DNA.
The final step involves joining the newly synthesized DNA segments together. An enzyme called DNA ligase forms phosphodiester bonds between the adjacent Okazaki fragments. This action effectively seals the nicks and creates a seamless, continuous DNA strand, completing the replication of the lagging strand.