Proteinogenic amino acid

Proteinogenic amino acids are the fundamental building blocks of life. The term "proteinogenic" literally means "protein creating." These molecules are incorporated biosynthetically into proteins during a cellular process called translation. During translation, a cell reads instructions from RNA to assemble amino acids into long chains. While many different types of amino acids exist in nature, only a small fraction are used to build proteins.

The mechanism of protein synthesis relies on a highly specific genetic code. Most known life forms use a standard set of 20 proteinogenic amino acids. However, two additional amino acids can be incorporated through specialized translation mechanisms. These are selenocysteine and pyrrolysine. In many eukaryotes and prokaryotes, selenocysteine is added when a specific nucleotide sequence called a SECIS element is present. This element directs the cell to treat a UGA codon as a signal for selenocysteine instead of a stop signal. In certain methanogenic prokaryotes, the UAG codon can also be translated to include pyrrolysine.

Amino acids can be categorized by how they are produced and used. Proteinogenic amino acids are those encoded by genes to build proteins. In contrast, non-proteinogenic amino acids are not used in this standard way. Some, like GABA or L-DOPA, are simply not incorporated into proteins. Others, such as hydroxyproline, are created through post-translational modification after a protein is already made. Some non-proteinogenic amino acids are instead used to build nonribosomal peptides. These are synthesized by a different system called non-ribosomal peptide synthetases.

Evolutionary history likely shaped the specific set of amino acids we see today. Some scientists suggest these molecules were selected from the "primordial soup" of early Earth. They may have been chosen because they incorporate into polypeptide chains more effectively than other molecules. Other amino acids may have been excluded because they are chemically unstable. For example, ornithine and homoserine can cause a protein backbone to fragment. Other molecules, such as the arginine analog canavanine, are toxic because they can be mistakenly incorporated into proteins.

In humans, the variety of proteinogenic amino acids is specifically organized. Humans use 21 proteinogenic amino acids, which includes the 20 standard ones plus selenocysteine. Our bodies can synthesize 12 of these from other molecules or metabolic intermediates. The remaining nine must be obtained through our diet. These are known as essential amino acids. They include histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

Each amino acid possesses unique chemical properties that determine its function. These properties include the mass of the molecule and the behavior of its side chain. For instance, side chains can be hydrophobic, which means they repel water, or polar, which means they interact with water. Some are acidic, while others are basic. The mass of a protein is calculated by adding the masses of its amino acids and then subtracting 18.01524 Da for every peptide bond formed. This subtraction occurs because forming a peptide bond results in the elimination of a water molecule.

Understanding these molecules connects biology to complex chemical systems. The way amino acids interact determines how a protein folds into its final shape. This shape is vital for the protein to perform its biological role. The specific side-chain properties, such as the aromatic rings in phenylalanine or the sulfur in cysteine, allow for diverse chemical reactions. These reactions include the formation of disulfide bonds, which stabilize protein structures in harsh environments. By studying these tiny building blocks, scientists can understand the very foundation of biological complexity.