Proteins are linear polypeptides that have distinguishable ends (Figure 1). On one end, called the N-terminus, is an unreacted –NH2 group. The other end, with an unreacted –COOH group, is the C-terminus. At physiological pH, these groups are usually charged: –NH3+ and –COO–. The remarkable, and extremely important, characteristic of proteins is that each has a defined and unique sequence of amino acid residues. This sequence is, by convention, written from the N-terminus to the C-terminus, using either the three-letter or one-letter abbreviated codes given in Figure 2. This sequence of amino acid residues constitutes the primary structure of the protein. The primary sequences of myoglobin from the muscles of humans and sperm whales are shown as an example in Figure 3. If myoglobins from mil lions of people are sampled, most will have exactly the same sequence, although an occasional mutant variety, differing in one or more residues, might turn up. On the other hand, myoglobins from other animal species will have significantly different sequences. Other proteins, with completely different functions, will have very different sequences. There are examples, however, of proteins that have quite different sequences carrying out the same function in different organisms. An example is myohemerythrin from certain primitive invertebrates. Like myoglobin, myohemerythrin stores oxygen in tissues, but its sequence is altogether different from that of myoglobin. Evolution has sometimes found different routes to achieve the same function. Conversely, there are also many examples of proteins that have similar sequences but carry out quite different functions.
Fig1. Extended polypeptide chain showing typical backbone bond lengths and angles. Rn–2 , Rn–1 , and Rn represent different side chains. [Adapted from Petsko GA & Ringe D (2004) Protein Structure and Function. With permission from Oxford University Press.]
Fig2. Classical amino acids found in proteins. The amino acids are grouped according to the chemical properties of their side chains. Each amino acid is presented by its full name, its three-letter abbreviation, and its one-letter code.
Fig3. Amino acid sequences of myoglobin from two sources: human and sperm whale. Single-letter abbreviations are used. Numbering of amino acid residues along the polypeptide chain conventionally starts at the N-terminus. Myoglobin is highly con served between these two species: 84% of the residues are identical. Another 16 of the amino acid substitutions are conservative, meaning an amino acid is replaced by an amino acid of the same chemical type; these are shown by blue boxes. Only nine substitutions are non conservative, designated by red letters. There are no insertions or deletions.
Myoglobin, with only 153 residues, is a small protein. Most proteins contain about 200–300 residues, and some are as large as 4,000 residues. The number of possible proteins is almost infinite; theoretically, 200 residues can be arranged into 20200 different polypeptides. In the 1920s, the discovery that proteins were indeed large, covalently linked molecules (Box 3.1) came as a shock to many scientists, who were accustomed to the small molecules of organic chemistry. The later discovery that proteins have unique sequences was of equal or even greater significance. A number of methods were originally used to sequence proteins directly, whereas today, almost all protein sequences are deduced from their encoding gene sequences. One technique that remains of importance in analyzing proteins is gel electrophoresis (Box 3.2 and Box 3.3). Box 3.4 illustrates another set of widely used techniques, those that rely on specific interactions between proteins and antibody molecules.
