The polymerases are enzymes whose function is related to the processes of replication and transcription of nucleic acids. There are two main types of these enzymes: DNA polymerase and RNA polymerase.
DNA polymerase is responsible for synthesizing the new DNA chain during the replication process, adding new nucleotides. They are large, complex enzymes, and differ in structure depending on whether they are found in a eukaryotic or a prokaryotic organism.
Similarly, RNA polymerase acts during DNA transcription, synthesizing the RNA molecule. Like DNA polymerase, it is found in both eukaryotes and prokaryotes and its structure and complexity vary depending on the group.
From an evolutionary perspective, it is plausible to think that the first enzymes must have had polymerase activity, since one of the intrinsic requirements for the development of life is the replication capacity of the genome.
The central dogma of molecular biology
The so-called “dogma” of molecular biology describes the formation of proteins from genes encrypted in DNA in three steps: replication, transcription and translation.
The process begins with the replication of the DNA molecule, where two copies of it are generated in a semi-conservative manner. The message from the DNA is then transcribed into an RNA molecule, called messenger RNA. Finally, the messenger is translated into proteins by the ribosomal machinery.
In this article we will explore two crucial enzymes involved in the first two processes mentioned.
It is worth noting that there are exceptions to the central dogma. Many genes are not translated into proteins, and in some cases the flow of information is from RNA to DNA (as in retroviruses).
DNA polymerase is the enzyme responsible for the exact replication of the genome. The work of the enzyme must be efficient enough to ensure the maintenance of genetic information and its transmission to the next generations.
If we consider the size of the genome, it is quite a challenging task. For example, if we set ourselves the task of transcribing a 100-page document on our computer, we would surely have one error (or more, depending on our concentration) for each page.
The polymerase can add more than 700 nucleotides every second, and it is only wrong every 10 9 or 10 10 incorporated nucleotides, an extraordinary number.
The polymerase must have mechanisms that allow the information of the genome to be copied exactly. Therefore, there are different polymerases that have the ability to replicate and repair DNA.
Characteristics and structure
DNA polymerase is an enzyme that works in the 5′-3 ‘direction, and works by adding nucleotides to the terminal end with the free -OH group.
One of the immediate consequences of this feature is that one of the strands can be synthesized without any inconvenience, but what about the strand that needs to be synthesized in the 3′-5 ‘direction?
This chain is synthesized in what is known as Okazaki fragments. Thus, small segments are synthesized in the normal direction, 5′-3 ‘, which are subsequently joined by an enzyme called ligase.
Structurally, DNA polymerases have in common two active sites that possess metal ions. In them we find aspartate and other amino acid residues that coordinate metals.
Traditionally, in prokaryotes three types of polymerases have been identified that are named with Roman numerals: I, II and III. In eukaryotes, five enzymes are recognized and are named with letters of the Greek alphabet, namely: α, β, γ, δ and ε.
The most recent investigations have identified five types of DNA in Escherichia coli, 8 in the yeast Saccharomyces cerevisiae and more than 15 in humans. In the plant lineage, the enzyme has been less studied. However, about 12 enzymes have been described in the model organism Arabidopsis thaliana .
One of the most used techniques in molecular biology laboratories is PCR or polymerase chain reaction. This procedure takes advantage of the polymerization capacity of DNA polymerase to amplify, by several orders of magnitude, a DNA molecule that we wish to study.
In other words, at the end of the procedure we will have thousands of copies of our target DNA. The uses of PCR are very varied. It can be applied to scientific research , to the diagnosis of some diseases or even in ecology.
RNA polymerase is responsible for generating an RNA molecule starting from a DNA template. The resulting transcript is a copy that complements the DNA segment that was used as a template.
Messenger RNA is responsible for carrying information to the ribosome , to generate a protein. They also participate in the synthesis of the other types of RNA.
This cannot act alone, it needs proteins called transcription factors to be able to carry out its functions successfully.
Characteristics and structure
RNA polymerases are large enzyme complexes. They are more complex in the eukaryotic lineage than in the prokaryotic.
In eukaryotes, there are three types of polymerases: Pol I, II and III, which are the central machinery for the synthesis of ribosomal, messenger, and transfer RNA, respectively. In contrast, in prokaryotes all of their genes are processed by a single type of polymerase.
Differences between DNA and RNA polymerase
Although both enzymes use DNA annealing, they differ in three key ways. First, DNA polymerase requires a primer to initiate replication and connect nucleotides. A first or primer is a molecule consisting of a few nucleotides, whose sequence are complementary to a specific site in the DNA.
The primer gives a free –OH to the polymerase to start its catalytic process. In contrast, RNA polymerases can start their work without the need for a primer .
Second, DNA polymerase has multiple binding regions on the DNA molecule. RNA polymerase can only bind to promoter sequences of genes.
Lastly, DNA polymerase is an enzyme that does its job with high fidelity. RNA polymerase is susceptible to more errors, introducing a wrong nucleotide every 10 4 nucleotides.
- 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. (1975). Gene expression . UMI Books on Demand.
- Lodish, H., Berk, A., Darnell, JE, Kaiser, CA, Krieger, M., Scott, MP,… & Matsudaira, P. (2008). Molecular cell biology . Macmillan.
- Pierce, BA (2009). Genetics: A conceptual approach . Panamerican Medical Ed.
- 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.
- 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.