Proteins and amino acids

Proteins, the most common large molecules in living things, make up about 50 per cent of all organic matter. They are important structural parts of the tissues of cells and of the substances between cells and also play an essential role in controlling chemical reactions in the body. Enzymes and many hormones are proteins.

Hemoglobin contains four heme groups. Each heme has an iron atom at its center, linked to two nitrogen atoms. Oxygen, which bonds reversibly to the iron, is transported through the bloodstream, and taken up by various cells. This explains the vital role of hemoglobin in cell metabolism.

Amino acids

Just as carbohydrates and lipids are made of simpler molecules, all proteins are constructed of amino acids. There are about 20 common types of amino acids, and they form a kind of alphabet from which ail the words and sentences in an almost infinitely large book can be made. In addition to these 20, there are a few other simple derivatives of the common types of amino acids which are occasionally found as part of a specific protein in a particular species.

With two exceptions, all the amino acids contain just four elements: carbon, hydrogen, oxygen, and nitrogen. (The two important exceptions are methionine and cysteine, each of which contains a single sulfur atom.) The molecular architecture, or stereochemistry, of the atomic components gives each amino acid its special properties. Small chains of amino acids are known as peptides. Two amino acids form a dipeptide by joining together and losing a molecule of water. Repeated several times, the linking process forms a polypeptide. When such chains reach lengths of more than 100 units, they are known as proteins.

In every amino acid, one carbon atom carries four important bonds. Attached to it are an amino group, a carboxylic acid group, a hydrogen atom, and a side chain, the nature of which defines the particular amino acid. Thus, the carbon atom at the center of an amino acid has four different groups attached to it, which renders it asymmetric. (Asymmetric means that the four groups can be attached to carbon in two different mirror-image forms.) Glycine is the only exception because its side chain is a second hydrogen atom.

Polypeptides and proteins are formed from amino acids by a condensation reaction (red arrows). This reaction forms a dipeptide connected by a peptide bond. Repetition of this reaction (polymerization) converts dipeptides to polypeptides and these in turn to proteins. A standard formula for an amino acid, with the variable group R, has been used in the diagram on the right Breakdown of proteins to polypeptides to amino acids is the reverse process, called hydrolysis (blue arrows).

Structures of proteins

Proteins are very large molecules—many have molecular weights in the tens of thousands.

(By contrast, a molecule of hydrogen, the lightest element, has a molecular weight of just under 2.) Proteins fall into two main categories: the highly folded and roughly spherical globular proteins, such as globulin, which are generally soluble in water; and the long fibrous proteins, such as the keratin of human hair, which are insoluble in water.

The primary structure of proteins is determined by the sequence of the amino acids, like the beads in a necklace. The amino acid sequence in proteins that have the same functions tends to be similar even in very different species. But with 20 different amino acids to choose from, the possibilities for variation are enormous. Some proteins are unique to a particular species.

The secondary structure of a protein is a result of the attraction between the amino acid units in neighboring sections of the polypeptide chain. Attractive forces within a protein can be maximized when a coiled structure like a telephone cord is formed. This is called the alpha helix. A different pleated form called the beta structure, in which the protein chains line up side by side, occurs in some proteins.

These regular structures can, however, be distorted by the influence of the side chains of some amino acids, which can form hydrogen bonds with other parts of the molecule, or with other side chains. The folding of the chains into a three-dimensional shape as a result of these distortions in the helix is called the tertiary structure.

Some large proteins also possess a quaternary structure. This results from the shape that results when two or more smaller protein subunits are assembled in a specific way.

Protein can have great structural strength. It can be formed rapidly, as in the keratin of the antlers of a red deer. Antlers are shed annually and have to be grown again every year.

Specialized proteins

Hemoglobin, the red substance that carries oxygen in the blood, is an example of a protein with a quaternary structure. It consists of four nearly spherical protein subunits, each of which contains a heme group. Each of the four heme groups contains an iron atom that bonds temporarily with oxygen. Hemoglobin is classified as a conjugated protein like the related compound myoglobin in muscle. Conjugated proteins also contain nonprotein groups and they are important in a number of biological functions. Chlorophyll, the green pigment found in plants, is closely related to heme, but contains magnesium instead of iron.

Antibodies, another type of specialized protein, form part of the body’s defense against disease. By binding to a foreign protein or carbohydrate in the blood, they cause the foreign bodies to clump together (agglutinate). By combining with a particular point on the surface of a foreign body (called the antigen), antibodies also tag” foreign bodies, triggering a set of processes that destroy the invaders.

Proteins in food can be used by the body as a source of energy. The body’s own protein is used up only during starvation. Amino acids cannot be made from inorganic materials but must be obtained from food (though some so-called nonessential amino acids can be synthesized from other amino acids; others, called essential amino acids, cannot be synthesized.) A diet deficient in protein will retard growth.

Amino acids fall into two categories. Those such as arginine are called essential amino acids (pink box shown below). These must be absorbed from food because the body cannot synthesize them. Other amino acids such as alanine are called nonessential (green box shown below). The adult body can synthesize these amino acids.