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Modern Genetic Analysis Chapter 3. Gene Function
Protein Structure

A protein is a polymer composed of monomers called amino acids. In other words, it is a chain of amino acids and is sometimes referred to as a polypeptide. Amino acids all have the general formula

The side chain, or R (reactive) group, can be anything from a hydrogen atom (as in the amino acid glycine) to a complex ring (as in the amino acid tryptophan). There are 20 amino acids known to occur in proteins (see Table 3-1 on the following page), each having a different R group that gives the amino acid its unique properties. In proteins the amino acids are linked together by covalent bonds called peptide bonds. A peptide bond is formed through a condensation reaction during which one water molecule is removed (Figure 3-15). Because of the way in which the peptide bond forms, a polypeptide chain always has an amino end (NH2) and a carboxyl end (COOH), as shown in this figure.

Proteins have a complex structure that has four levels of organization (Figure 3-16). The linear sequence of the amino acids in a polypeptide chain constitutes the primary structure of the protein. Several types of weak bonds (hydrogen, electrostatic, and van der Waals) acting between atoms within a polypeptide chain, or between different polypeptide chains, cause the protein to take on a specific shape. The secondary structure of a protein arises from the interactions of amino acids that are close together in the linear sequence, most commonly forming an a helix. Tertiary structure is produced by folding the helix or other secondary structure. In some proteins, two or more tertiary structures come together to form a quaternary structure. The quaternary association can be between different types of polypeptides or between identical polypeptides.

Many proteins are compact structures and are called globular proteins. Enzymes and antibodies are among the most important globular proteins. Proteins with linear shape, called fibrous proteins, are important components of such structures as hair and muscle.

Shape is all-important to a protein because its specific shape enables it to do its specific job in the cell. For example, an enzyme has a specific pocket (the active site) into which its substrate can fit (see Figure 3-17 on the next page). Shape is largely determined by the primary amino acid sequence. Ultimately, even the quaternary structure of a protein is determined by the primary structures of its component amino acid chains. However, at present, we don't fully understand the rules by which primary structure is converted into higher-order structure. The amino acid sequence also determines which R groups are available to enable the protein to bind to other specific cellular components.

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