DNA POLYMERASE: TYPES, FUNCTION AND STRUCTURE - BIOLOGY - 2025

The DNA polymerase is an enzyme that is responsible for catalyzing the polymerization of the new DNA strand during replication of this molecule. Its main function is to pair the triphosphate deoxyribonucleotides with those of the template chain. It is also involved in DNA repair.

This enzyme allows the correct pairing between the DNA bases of the template chain and the new one, following the scheme of A pairs with T, and G with C.

Structure of DNA polymerase beta in humans.

Source: Yikrazuul, from Wikimedia Commons

The DNA replication process must be effective and must be carried out quickly, so DNA polymerase works by adding about 700 nucleotides per second and only makes one mistake every 10 ⁹ or 10 ¹⁰ nucleotides incorporated.

There are different types of DNA polymerase. These vary in both eukaryotes and prokaryotes, and each has a specific role in DNA replication and repair.

It is possible that one of the first enzymes to appear in evolution was polymerases, since the ability to precisely replicate the genome is an intrinsic requirement for the development of organisms.

The discovery of this enzyme is credited to Arthur Kornberg and his colleagues. This researcher identified DNA polymerase I (Pol I) in 1956, while working with Escherichia coli. Similarly, it was Watson and Crick who proposed that this enzyme could produce faithful copies of the DNA molecule.

Types

Prokaryotes

Prokaryotic organisms (organisms without a true nucleus, bounded by a membrane) possess three main DNA polymerases, commonly abbreviated as pol I, II, and III.

DNA polymerase I participates in DNA replication and repair and has exonuclease activity in both directions. The role of this enzyme in replication is considered to be secondary.

II participates in DNA repair and its exonuclease activity is in the 3'-5 'sense. III participates in the replication and revision of DNA, and like the previous enzyme, it exhibits exonuclease activity in the 3'-5 'sense.

Eukaryotes

Eukaryotes (organisms with a true nucleus, delimited by a membrane) have five DNA polymerases, named with letters of the Greek alphabet: α, β, γ, δ and ε.

Polymerase γ is located in the mitochondria and is responsible for the replication of genetic material in this cell organelle. In contrast, the other four are found in the nucleus of cells and are involved in nuclear DNA replication.

The α, δ and ε variants are the most active in the cell division process, suggesting that their main function is associated with the production of DNA copies.

DNA polymerase β, for its part, exhibits peaks of activity in cells that are not dividing, so it is assumed that its main function is associated with DNA repair.

Different experiments have been able to verify the hypothesis that they mostly associate α, δ and ε polymerases with DNA replication. Types γ, δ and ε show 3'-5 'exonuclease activity.

Arches

New sequencing methods have succeeded in identifying a huge variety of DNA polymerase families. In archaea, specifically, a family of enzymes, called the D family, has been identified that are unique to this group of organisms.

Functions: DNA replication and repair

What is DNA replication?

DNA is the molecule that carries all the genetic information of an organism. It is made up of a sugar, a nitrogenous base (adenine, guanine, cytosine, and thymine) and a phosphate group.

During the processes of cell division, which are constantly occurring, DNA must be copied quickly and accurately - specifically in the S phase of the cell cycle. This process where the cell copies DNA is known as replication.

Structurally, the DNA molecule is made up of two strands, forming a helix. During the replication process, these separate and each acts as a template for the formation of a new molecule. Thus, the new strands pass to the daughter cells in the process of cell division.

Since each strand serves as a template, DNA replication is said to be semi-conservative - at the end of the process, the new molecule consists of a new and an old strand. This process was described in 1958 by researchers Meselson and Stahl, using isopotes.

DNA replication requires a series of enzymes that catalyze the process. Among these protein molecules, DNA polymerase stands out.

Reaction

For DNA synthesis to occur, the substrates necessary for the process are required: deoxyribonucleotide triphosphate (dNTP)

The reaction mechanism involves a nucleophilic attack by the hydroxyl group at the 3 'end of the growing strand on the alpha phosphate of the complementary dNTPs, eliminating a pyrophosphate. This step is very important, since the energy for polymerization comes from the hydrolysis of the dNTPs and the resulting pyrophosphate.

The pol III or alpha binds to the primer (see properties of polymerases) and begins to add nucleotides. The epsilon elongates the lead chain, and the delta elongates the retarded strand.

Properties of DNA polymerases

All known DNA polymerases share two essential properties associated with the replication process.

First, all polymerases synthesize the DNA strand in the 5'-3 'direction, adding the dNTPs to the hydroxyl group of the growing chain.

Second, DNA polymerases cannot start synthesizing a new strand from scratch. They need an additional element known as a first or primer, which is a molecule made up of a few nucleotides that provides a free hydroxyl group, where the polymerase can anchor itself and begin its activity.

This is one of the fundamental differences between DNA and RNA polymerases, since the latter is capable of initiating the synthesis of a de novo chain.

Fragments of Okazaki

The first property of DNA polymerases mentioned in the previous section represents a complication for semi-conservative replication. As the two DNA strands run antiparallel, one of them is synthesized discontinuously (the one that would need to be synthesized in the 3'-5 'sense).

In the delayed strand, discontinuous synthesis occurs through normal polymerase activity, 5'-3 ', and the resulting fragments - known in the literature as Okazaki fragments - are linked by another enzyme, ligase.

DNA repair

DNA is constantly exposed to factors, both endogenous and exogenous, that can damage it. These damages can block replication and accumulate, affecting the expression of genes, causing problems in the various cellular processes.

In addition to its role in the DNA replication process, polymerase is also a key component of DNA repair mechanisms. They can also act as sensors in the cell cycle that prevent entry into the division phase if DNA is damaged.

Structure

Currently, thanks to crystallography studies, the structures of various polymerases have been elucidated. Based on their primary sequence, polymerases are grouped into families: A, B, C, X, and Y.

Some aspects are common to all polymerases, particularly those related to the catalytic centers of the enzyme.

These include two key active sites that possess metal ions, with two aspartate residues and one variable residue - either aspartate or glutamate, which coordinates the metals. There are another series of charged residues that surround the catalytic center and are conserved in the different polymerases.

In prokaryotes, DNA polymerase I is a 103 kd polypeptide, II is an 88 kd polypeptide, and III consists of ten subunits.

In eukaryotes, the enzymes are larger and more complex: α consists of five units, β and γ of one subunit, δ of two subunits, and ε of 5.

Applications

PRC

The polymerase chain reaction (PRC) is a method used in all molecular biology laboratories, thanks to its utility and simplicity. The goal of this method is to massively amplify a DNA molecule of interest.

To achieve this, biologists use a DNA polymerase that is not damaged by heat (high temperatures are essential for this process) to amplify the molecule. The result of this process is a large number of DNA molecules that can be used for different purposes.

One of the most outstanding clinical utilities of the technique is its use in medical diagnosis. PRC can be used to check patients for pathogenic bacteria and viruses.

Antibiotics and antitumor drugs

A significant number of drugs aim to truncate the mechanisms of DNA replication in the pathogenic organism, be it a virus or a bacterium.

In some of this, the target is inhibition of DNA polymerase activity. For example, the chemotherapeutic drug cytarabine, also called cytosine arabinoside, disables DNA polymerase.

References

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