▲ FIGURE 3-2 Structure of a tripeptide. Peptide bonds (yellow) link the amide nitrogen atom (blue) of one amino acid (aa) with the carbonyl carbon atom (gray) of an adjacent one in the linear polymers known as peptides or polypeptides, depending on their length. Proteins are polypeptides that have folded into a defined three-dimensional structure (conformation). The side chains, or R groups (green), extending from the a carbon atoms (black) of the amino acids composing a protein largely determine its properties. At physiological pH values, the terminal amino and carboxyl groups are ionized.
The primary structure of a protein is simply the linear arrangement, or sequence, of the amino acid residues that compose it. Many terms are used to denote the chains formed by the polymerization of amino acids. A short chain of amino acids linked by peptide bonds and having a defined sequence is called a peptide; longer chains are referred to as polypeptides. Peptides generally contain fewer than 20-30 amino acid residues, whereas polypeptides contain as many as 4000 residues. We generally reserve the term protein for a polypeptide (or for a complex of polypeptides) that has a well-defined three-dimensional structure. It is implied that proteins and peptides are the natural products of a cell.
The size of a protein or a polypeptide is reported as its mass in daltons (a dalton is 1 atomic mass unit) or as its molecular weight (MW), which is a dimensionless number. For example, a 10,000-MW protein has a mass of 10,000 daltons (Da), or 10 kilodaltons (kDa). In the last section of this chapter, we will consider different methods for measuring the sizes and other physical characteristics of proteins. The known and predicted proteins encoded by the yeast genome have an average molecular weight of 52,728 and contain, on average, 466 amino acid residues. The average molecular weight of amino acids in proteins is 113, taking into account their average relative abundance. This value can be used to estimate the number of residues in a protein from its molecular weight or, conversely, its molecular weight from the number of residues.
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