Protein

I

Introduction

Protein, one of a large group of nitrogen-rich compounds of high molecular weight that are essential and abundant constituents of living organisms. Proteins make up over 50 per cent of the dry weight of most cells and only plant cells with their high cellulose content are less than half protein. There are many different kinds of proteins, including enzymes, hormones, storage proteins such as those in the eggs of birds and reptiles and in seeds, transport proteins such as haemoglobin, contractile proteins found in muscle, proteins involved in blood clotting and immune defence (antibodies), membrane proteins, and many different types of structural proteins. Despite this overwhelming diversity all proteins are made in the same general manner, as linear chains of amino acids. Each chain of amino acids, which might contain several hundred amino acids in a precise sequence, folds up into a unique three-dimensional shape in which its atoms (mainly carbon, hydrogen, nitrogen, oxygen, and sulphur) adopt precise locations. The astronomical number of possible structures that can be generated in this way produces a huge diversity of properties and functions. From a chemical standpoint, proteins are by far the most structurally complex and functionally sophisticated molecules known.

II

Historical Background

The term “protein” (from the Greek “pre-eminent” or “first”) was first used by the Swedish chemist Jöns Berzelius in 1838 for the complex organic nitrogen-rich substance found in the cells of all animals and plants. Over the following century these were found to be built from 20 different amino acids and to be linked together in linear polymers, known as polypeptide chains. For many years proteins were thought to be amorphous substances with variable compositions. Progress came with the separation of individual proteins from complex mixtures and the preparation of crystals of pure proteins, such as haemoglobin and the enzyme urease. In the late 1930s, Linus Pauling and Robert Corey in the United States used x-ray diffraction (a technique in which a beam of X-rays is passed through a crystal of the substance and the scattered rays measured) to determine the structures of amino acids and peptides. They also correctly predicted that many amino acid chains would fold into a stable conformation rather like a spiral staircase, now known as an a- (alpha-) helix. Another milestone occurred in 1955 when the Cambridge scientist Fred Sanger chemically analysed insulin, a small protein hormone, and showed that it was built from a defined set of amino acids linked together in a unique linear sequence. Everyone now accepts that each kind of protein molecule has its own unique sequence of amino acids.

In 1955 the American Christian Anfinsen reported that the small protein ribonuclease (an enzyme) could spontaneously refold into an active form after being 'opened up' by harsh chemicals—evidence that the amino acid sequence of a protein specifies its function. At the same time, on the other side of the Atlantic, scientists were probing the three-dimensional structure of protein molecules. In 1960, John Kendrew and Max Perutz used X-ray diffraction to determine the three-dimensional structures of the oxygen-carrying molecules myoglobin and haemoglobin. These studies led to the concept that linear chains of amino acids fold up to give protein molecules that have always precisely the same structure and function.

III

Amino Acids

Amino acids are the basic structural units of proteins and, like chocolates, come in many different “flavours”. Each is made to the same design, with an amino group, a carboxyl group, a hydrogen atom, and a distinct R group (or side chain) all of which are bonded to an a-carbon atom. Amino acids are linked together in proteins by a peptide bond, made by the reaction of the carboxyl group of one amino acid with the amino group of the next.

Twenty kinds of side chains varying in size, shape, charge, bonding capacity, and chemical reactivity are commonly found in proteins. Indeed, all proteins in all species from bacteria to humans are constructed from the same set of 20 amino acids. This fundamental “alphabet” of proteins is at least two billion years old, the remarkable range of functions mediated by proteins resulting from the chemical diversity of these 20 kinds of building blocks. We will see below how this alphabet is used to create the intricate three-dimensional structures that enable proteins to carry out so many biological processes.

The amino acid side chains (the part that projects from the polypeptide chain) range in size from a single hydrogen (in glycine) to a large, nitrogen-containing aromatic ring (in tryptophan). Five of the amino acids have side chains that can form ions in solution and can thereby carry a charge. The others are uncharged, and may be water-loving or water-hating, acidic or alkaline. The sequence in which amino acids are linked together determines the way in which the polypeptide chain folds up, and hence the three-dimensional structure of the protein. In broad terms, the chemistry of the amino acid side chains, especially those exposed on the protein's surface, specify its interactions with other molecules and hence the protein's function in the cell.

IV

Conjugated Proteins

Amino acids are the primary determinant of protein structure, but cannot always provide the full range of chemical properties needed. Consequently, many proteins recruit additional groups of atoms, either as chemical modifications of their amino acid chains or as molecules so tightly bound to the protein that they can be considered part of its structure. For example, a surprisingly high proportion of proteins inside the cytoplasm of cells undergo the reversible addition of phosphate groups at specific locations, used to trigger changes in structure and hence activity. Other proteins are linked to sugars or lipids, or are cleaved and trimmed after being made in the cell. Many enzymes become linked to small molecules, known as cofactors that extend their chemical repertoire and enhance their catalytic abilities. The ability of the blood protein haemoglobin to carry oxygen depends on an iron-containing haeme group, which is made separately in the cell and then binds tightly to a crevice on the protein surface.