NITROGEN BASES: CLASSIFICATION AND FUNCTIONS - BIOLOGY - 2025

The nitrogenous bases are organic compounds heterocyclically rich in nitrogen. They are part of the building blocks of nucleic acids and other molecules of biological interest, such as nucleosides, dinucleotides and intracellular messengers. In other words, nitrogenous bases are a part of the units that make up nucleic acids (RNA and DNA) and the other molecules mentioned.

There are two main groups of nitrogenous bases: purine or purine bases and pyrimidine or pyrimidine bases. Adenine and guanine belong to the first group, while thymine, cytosine and uracil are pyrimidine bases. These bases are generally denoted by their first letter: A, G, T, C, and U.

Different nitrogenous bases in DNA and RNA.

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The building blocks of DNA are A, G, T and C. In this ordering of bases all the information necessary for the construction and development of a living organism is encoded. In RNA, the components are the same, only T is replaced by U.

Structure and classification

Nitrogen bases are flat molecules, of the aromatic and heterocyclic type, which are generally derived from purines or pyrimidines.

Pyrimidine ring

Chemical structure of pyrimidine.

The pyrimidine ring are six-membered heterocyclic aromatic rings with two nitrogen atoms. The atoms are numbered in a clockwise direction.

Purine ring

Chemical structure of purine.

The purine ring consists of a two-ring system: one is structurally similar to the pyrimidine ring and the other is similar to the imidazole ring. These nine atoms are fused into a single ring.

The pyrimidine ring is a flat system, while the purines deviate somewhat from this pattern. A slight crease or wrinkle has been reported between the imidazole ring and the pyrimidine ring.

Properties of nitrogenous bases

Aromaticity

In organic chemistry, an aromatic ring is defined as a molecule whose electrons from the double bonds have free circulation within the cyclic structure. The mobility of the electrons within the ring gives stability to the molecule -if we compare it with the same molecule-, but with the electrons fixed in the double bonds.

The aromatic nature of this ring system gives them the ability to experience a phenomenon called keto-enol tautomerism.

That is, purines and pyrimidines exist in tautomeric pairs. Keto tautomers are predominant at neutral pH for the bases uracil, thymine, and guanine. In contrast, the enol form is predominant for cytosine, at neutral pH. This aspect is essential for the formation of hydrogen bonds between the bases.

UV light absorption

Another property of purines and pyrimidines is their ability to strongly absorb ultraviolet light (UV light). This absorption pattern is a direct consequence of the aromaticity of its heterocyclic rings.

The absorption spectrum has a maximum close to 260 nm. Researchers use this standard to quantify the amount of DNA in their samples.

Water solubility

Thanks to the strong aromatic character of the nitrogenous bases, these molecules are practically insoluble in water.

Nitrogen bases of biological interest

Although there are a large number of nitrogenous bases, we only find a few naturally in the cellular environments of living organisms.

The most common pyrimidines are cytosine, uracil, and thymine (5-methyluracil). Cytosine and thymine are the pyrimidines typically found in the DNA double helix, while cytosine and uracil are common in RNA. Note that the only difference between uracil and thymine is a methyl group at carbon 5.

Similarly, the most common purines are adenine (6-amino purine) and guanine (2-amino-6-oxy purine). These compounds are abundant in both the DNA and RNA molecules.

There are other derivatives of purines that we find naturally in the cell, among them xanthine, hypoxanthine and uric acid. The first two can be found in nucleic acids, but in a very rare and specific way. In contrast, uric acid is never found as a structural component of these biomolecules.

How do they mate?

The structure of DNA was elucidated by researchers Watson and Crick. Thanks to their study, it was possible to conclude that DNA is a double helix. It is made up of a long chain of nucleotides linked by phosphodiester bonds, in which the phosphate group forms a bridge between the hydroxyl groups (-OH) of the sugar residues.

The structure that we have just described resembles a ladder together with its respective handrail. The nitrogenous bases are the analogues to the stairs, which are grouped in the double helix by means of hydrogen bonds.

In a hydrogen bridge, two electronegative atoms share a proton between the bases. For the formation of a hydrogen bond, the participation of a hydrogen atom with a slight positive charge and an acceptor with a small negative charge is necessary.

The bridge is formed between an H and an O. These bonds are weak, and they must be, since DNA must open easily to replicate.

Chargaff rule

The base pairs form hydrogen bonds by following the following purine-pyrimidine pairing pattern known as Chargaff's rule: guanine pairs with cytosine and adenine pairs with thymine.

The GC pair forms three hydrogen canisters to each other, while the AT pair is linked only by two bridges. Thus, we can predict that a DNA with a higher GC content will be more stable.

Each of the chains (or the handrails in our analogy), run in opposite directions: one 5 ′ → 3 ′ and the other 3 ′ → 5 ′.

Features

Building blocks of nucleic acids

Organic beings present a type of biomolecules called nucleic acids. These are very large polymers made up of repeating monomers - nucleotides, joined by a special type of bond, called a phosphodiester bond. They are classified into two basic types, DNA and RNA.

Each nucleotide is made up of a phosphate group, a sugar (deoxyribose type in DNA and ribose in RNA), and one of the five nitrogenous bases: A, T, G, C and U. When the phosphate group is not present, the molecule is called a nucleoside.

In DNA

DNA is the genetic material of living beings (with the exception of some viruses that use RNA mainly). Using the 4-base code, DNA has the sequence for all proteins that exist in organisms, as well as elements that regulate their expression.

The structure of DNA must be stable, since organisms use it to encode information. However, it is a molecule prone to changes, called mutations. These changes in the genetic material are the basic material for evolutionary change.

In the RNA

Like DNA, RNA is a nucleotide polymer, with the exception that the base T is replaced by the U. This molecule is in the form of a single band and fulfills a wide range of biological functions.

In the cell, there are three main RNAs. Messenger RNA is an intermediary between DNA and protein formation. It is in charge of copying the information in the DNA and taking it to the protein translation machinery. Ribosomal RNA, a second type, is a structural part of this complex machinery.

The third type, or transfer RNA, is responsible for carrying the appropriate amino acid residues for the synthesis of proteins.

In addition to the three “traditional” RNAs, there are a series of small RNAs that participate in the regulation of gene expression, since all the genes encoded in DNA cannot be expressed constantly and in the same magnitude in a cell.

Organisms must have pathways to regulate their genes, that is, to decide whether they are expressed or not. Similarly, the genetic material consists only of a dictionary of Spanish words, and the regulatory mechanism allows the formation of a literary work.

Building blocks of nucleoside triphosphates

Nitrogen bases are part of nucleoside triphosphates, a molecule that, like DNA and RNA, is of biological interest. In addition to the base, it is made up of a pentose and three phosphate groups linked together by means of high-energy bonds.

Thanks to these bonds, nucleoside triphosphates are energy-rich molecules and are the main product of metabolic pathways that seek the release of energy. Among the most used is ATP.

ATP or adenosine triphosphate is made up of the nitrogenous base adenine, linked to the carbon located at position 1 of a pentose-type sugar: ribose. In position five of this carbohydrate, all three phosphate groups are linked.

In general, ATP is the energy currency of the cell, since it can be used and regenerated quickly. Many common metabolic pathways among organics use and produce ATP.

Its "power" is based on high-energy bonds, formed by phosphate groups. The negative charges of these groups are in constant repulsion. There are other causes that predispose hydrolysis in ATP, including resonance stabilization and solvation.

Autacoid

Although most nucleosides lack significant biological activity, adenosine is a marked exception in mammals. This works as an autacoid, analogous to a "local hormone" and as a neuromodulator.

This nucleoside circulates freely in the bloodstream and acts locally, with various effects on the dilation of blood vessels, smooth muscle contractions, neuronal discharges, neurotransmitter release, and fat metabolism. It is also related to heart rate regulation.

This molecule is also involved in the regulation of sleep patterns. The adenosine concentration increases and promotes fatigue. This is why caffeine helps us stay awake: it blocks neuronal interactions with extracellular adenosine.

Structural blocks of regulatory elements

A significant number of common metabolic pathways in cells have regulatory mechanisms based on the levels of ATP, ADP and AMP. These last two molecules have the same structure as ATP, but have lost one and two phosphate groups, respectively.

As we mentioned in the previous section, ATP is an unstable molecule. The cell should only produce ATP when it needs it, as it must use it quickly. ATP itself is also an element that regulates metabolic pathways, since its presence indicates to the cell that it should not produce more ATP.

In contrast, its hydrolyzed derivatives (AMP), warn the cell that ATP is running out and must produce more. Thus, AMP activates metabolic pathways for energy production, such as glycolysis.

Similarly, many hormonal signals (such as those involved in glycogen metabolism) are mediated intracellularly by cAMP molecules (c is for cyclic) or by a similar variant but with guanine in its structure: cGMP.

Building blocks of coenzymes

At multiple steps in the metabolic pathways, enzymes cannot act alone. They need additional molecules to be able to fulfill their functions; These elements are called coenzymes or cosubstrates, the latter term being more appropriate, since coenzymes are not catalytically active.

In these catalytic reactions, there is a need to transfer the electrons or group of atoms to another substrate. The auxiliary molecules that participate in this phenomenon are coenzymes.

Nitrogen bases are structural elements of these cofactors. Among the most recognized are the pyrimidine nucleotides (NAD ⁺, NADP ⁺), FMN, FAD and coenzyme A. These participate in very important metabolic pathways, such as glycolysis, the Krebs cycle, photosynthesis, among others.

For example, pyrimidine nucleotides are very important coenzymes of enzymes with dehydrogenase activity, and are responsible for the transport of hydride ions.

References

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