Amino acids: Monomers that make up proteins
Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group (see image below).
Amino acids have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group) are attached. Image Attribution: OpenStax Biology
The name “amino acid” comes from the fact that they contain both amino group and carboxyl-acid-group in their basic structure. As mentioned, there are 20 amino acids present in proteins. Ten of these are essential amino acids in humans because the human body cannot produce them. Actually, humans can only obtain them from their diet. For each amino acid, the R group (or side chain) is different (see image below).
There are 20 common amino acids commonly found in proteins, each with a different R group (variant group) that determines its chemical nature. Image Attribution: OpenStax Biology
Nature of Amino Acids
The chemical nature of the side chain determines the nature of the amino acid (that is, whether it is acidic, basic, polar, or nonpolar). For example, the amino acid glycine has a hydrogen atom as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or hydrophobic in nature. On the other hand, amino acids such as serine, threonine, and cysteine are polar and have hydrophilic side chains.
The side chains of lysine and arginine are positively charged. Therefore, we refer to these amino acids as basic amino acids. Proline has an R group linked to the amino group, forming a ring-like structure. Proline is an exception to the standard structure of an amino acid since its amino group is not separate from the side chain (see image above).
Representing Amino Acids
Amino acids are represented by a single uppercase letter or a three-letter abbreviation. For example, valine is known by the letter V or the three-letter symbol val. Just as some fatty acids are essential to a diet, some amino acids are necessary as well. We refer to them as essential amino acids. In humans they include isoleucine, leucine, and cysteine. Essential amino acids refer to those necessary for construction of proteins in the body, although not produced by the body. However, essential amino acids vary from organism to organism.
How Amino Acids Determine Protein’s Shape, Size and Function
The sequence and the number of amino acids ultimately determine the protein’s shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond. A dehydration reaction is responsible for forming this bond. The carboxyl group of one amino acid and the amino group of the incoming amino acid combine, releasing a molecule of water. The resulting bond is the peptide bond (see image below).
Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of one amino acid links to the amino group of the incoming amino acid. In the process, there is a release of one water molecule. Image Attribution: OpenStax Biology
The products formed by such linkages are called peptides. As more amino acids join to this growing chain, the resulting chain is known as a polypeptide. Each polypeptide has a free amino group at one end. This end is called the N terminal, or the amino terminal. Furthermore, the other end has a free carboxyl group, which we refer to as the C terminal or carboxyl terminal.
Sometimes, the terms polypeptide and protein are used interchangeably. Nevertheless, a polypeptide is technically a polymer of amino acids. On the other hand, the term protein is used for a polypeptide or polypeptides that have combined together, often have bound non-peptide prosthetic groups, have a distinct shape, and have a unique function.
After protein synthesis (translation), most proteins are modified. We refer to this as post-translational modifications. They may undergo cleavage, phosphorylation, or may require the addition of other chemical groups. Only after these modifications is the protein completely functional.
Evolution and Proteins
The Evolutionary Significance of Cytochrome c protein
Cytochrome c is an important component of the electron transport chain, a part of cellular respiration. It is normally found in the cellular organelle, the mitochondrion. This protein has a heme prosthetic group, and the central ion of the heme gets alternately reduced and oxidized during electron transfer. Because this essential protein’s role in producing cellular energy is crucial, it has changed very little over millions of years.
Protein sequencing has shown that there is a considerable amount of cytochrome c amino acid sequence homology among different species. In other words, evolutionary kinship can be assessed by measuring the similarities or differences among various species’ DNA or protein sequences.
Scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule from different organisms that has been sequenced to date, 37 of these amino acids appear in the same position in all samples of cytochrome c. This indicates that there may have been a common ancestor.
On comparing the human and chimpanzee protein sequences, no sequence difference was found. When human and rhesus monkey sequences were compared, the single difference found was in one amino acid. In another comparison, human to yeast sequencing shows a difference in the 44th position.
Video Animation Showing Protein Synthesis
This 3D animation below by yourgenome.org shows how proteins are made in the cell from the information in the DNA code.