The replication fork is the point at which DNA replication occurs , it is also called the growth point. It is Y-shaped, and as replication takes place, the hairpin moves through the DNA molecule.
DNA replication is the cellular process that involves the duplication of genetic material in the cell. The structure of DNA is a double helix, and in order to replicate its content it must be opened. Each of the strands will be part of the new DNA chain, since replication is a semi-conservative process.
The replication fork forms precisely between the junction between the newly separated template or template strands and the duplex DNA that has not yet been duplicated. When initiating DNA replication, one of the strands can be easily duplicated, while the other strand faces a polarity problem.
The enzyme in charge of polymerizing the chain – DNA polymerase – only synthesizes the DNA strand in the 5′-3 ‘direction. Thus, one strand is continuous and the other undergoes discontinuous replication, generating Okazaki fragments.
DNA replication and replication fork
DNA is the molecule that stores the necessary genetic information for all living organisms – with the exception of some viruses.
This huge polymer composed of four different nucleotides (A, T, G and C) resides in the nucleus of eukaryotes , in each of the cells that make up the tissues of these beings (except in the mature red blood cells of mammals , which lack core).
Each time a cell divides, DNA must replicate in order to create a daughter cell with genetic material.
One-way and two-way replication
Replication can be unidirectional or bidirectional, depending on the formation of the replication fork at the point of origin.
Logically, in the case of replication in one direction, only one hairpin is formed, while in bidirectional replication, two hairpins are formed.
For this process, a complex enzymatic machinery is necessary, which works quickly and can replicate DNA precisely. The most important enzymes are DNA polymerase, DNA primase, DNA helicase, DNA ligase, and topoisomerase.
Start of replication and hairpin formation
DNA replication does not start at any random place in the molecule. There are specific regions in DNA that mark the start of replication.
In most bacteria, the bacterial chromosome has a single AT-rich start point. This composition is logical, since it facilitates the opening of the region (the AT pairs are linked by two hydrogen bonds , while the GC pair by three).
As DNA begins to open, a Y-shaped structure forms: the replication fork.
Fork elongation and movement
DNA polymerase cannot start daughter chain synthesis from scratch. You need a molecule that has a 3 ‘end so that the polymerase has a place to start polymerizing.
This free 3 ‘end is offered by a small nucleotide molecule called the primer or primer. The first acts as a kind of hook for the polymerase.
In the course of replication, the replication fork has the ability to move along the DNA. The passage of the replication fork leaves two single-band DNA molecules that direct the formation of the double-band daughter molecules.
The hairpin can move forward thanks to the action of helicase enzymes that unwind the DNA molecule. This enzyme breaks the hydrogen bonds between the base pairs and allows the displacement of the hairpin.
Replication is complete when the two hairpins are at 180 ° C from the origin.
In this case, we are talking about how the replication process flows in bacteria and it is necessary to highlight the entire torsion process of the circular molecule that replication implies. Topoisomerases play an important role in the unwinding of the molecule.
DNA replication is semi-conservative
Have you ever wondered how replication occurs in DNA? In other words, another double helix must emerge from the double helix, but how does it happen? For several years, this was an open question among biologists. There could be several permutations: two old strands together and two new strands together, or one new strand and one old to form the double helix.
In 1957, this question was answered by researchers Matthew Meselson and Franklin Stahl. The replication model proposed by the authors was the semi-conservative.
Meselson and Stahl argued that the result of replication is two DNA double helix molecules. Each of the resulting molecules is made up of an old strand (from the parent or initial molecule) and a newly synthesized new strand.
The problem of polarity
How does polymerase work?
The DNA helix is made up of two chains that run antiparallel: one goes in the 5′-3 ‘direction and the other 3′-5’.
The most prominent enzyme in the replication process is DNA polymerase, which is responsible for catalyzing the union of the new nucleotides that will be added to the chain. DNA polymerase can only extend the chain in the 5′-3 ‘direction. This fact hinders the simultaneous duplication of the chains in the replication fork.
Why? The addition of nucleotides occurs at the free end 3 ‘where there is a hydroxyl group (-OH). Thus, only one of the strands can be easily amplified by the terminal addition of the nucleotide to the 3 ‘end. This is called a conductive or continuous strand.
Production of Okazaki Shards
The other strand cannot be elongated, because the free end is the 5 ‘and not the 3’ and no polymerase catalyzes the addition of nucleotides to the 5 ‘end. The problem is solved with the synthesis of multiple short fragments (from 130 to 200 nucleotides), each one in the normal direction of replication from 5´ to 3´.
This discontinuous synthesis of fragments ends with the union of each of the parts, a reaction catalyzed by DNA ligase. In honor of the discoverer of this mechanism, Reiji Okazaki, the small synthesized segments are called Okazaki fragments.
- Alberts, B., Bray, D., Hopkin, K., Johnson, AD, Lewis, J., Raff, M.,… & Walter, P. (2015). Essential cell biology . Garland Science.
- Cann, IK, & Ishino, Y. (1999). Archaeal DNA replication: identifying the pieces to solve a puzzle. Genetics , 152 (4), 1249-67.
- Cooper, GM, & Hausman, RE (2004). The cell: Molecular approach . Medicinska naklada.
- Garcia-Diaz, M., & Bebenek, K. (2007). Multiple functions of DNA polymerases. Critical reviews in plant sciences , 26 (2), 105-122.
- Lewin, B. (2008). genes IX . Mc Graw-Hill Interamericana.
- Shcherbakova, PV, Bebenek, K., & Kunkel, TA (2003). Functions of eukaryotic DNA polymerases. Science’s SAGE KE , 2003 (8), 3.
- Steitz, TA (1999). DNA polymerases: structural diversity and common mechanisms. Journal of Biological Chemistry , 274 (25), 17395-17398.
- Watson, JD (2006). Molecular biology of the gene . Panamerican Medical Ed.
- Wu, S., Beard, WA, Pedersen, LG, & Wilson, SH (2013). Structural comparison of DNA polymerase architecture suggests a nucleotide gateway to the polymerase active site. Chemical Reviews , 114 (5), 2759-74.