*In some common analyses, such as acid hydrolysis, Asp and Asn are not readily distinguished from each other and are together designated Asx (or B). Similarly, when Glu and Gln cannot be distinguished, they are together designated Glx (or Z). In addition, Trp is destroyed. Additional procedures must be employed to obtain an accurate assessment of complete amino acid content.

and tyrosine are also lost. When a precise amino acid composition is required, biochemists use additional procedures to resolve the ambiguities that remain from acid hydrolysis.

Some Proteins Contain Chemical Groups Other Than Amino Acids

Many proteins, for example the enzymes ribonuclease A and chymotrypsinogen, contain only amino acid residues and no other chemical constituents; these are considered simple proteins. However, some proteins contain permanently associated chemical components in addition to amino acids; these are called conjugated proteins. The non-amino acid part of a conjugated protein is usually called its prosthetic group. Conjugated proteins are classified on the basis of the chemical nature of their prosthetic groups (Table 3-4); for example, lipoproteins contain lipids, glycoproteins contain sugar groups, and metalloproteins contain a specific metal. A number of proteins contain more than one prosthetic group. Usually the prosthetic group plays an important role in the protein's biological function.

There Are Several Levels of Protein Structure

For large macromolecules such as proteins, the tasks of describing and understanding structure are approached at several levels of complexity, arranged in a kind of conceptual hierarchy. Four levels of protein structure are commonly defined (Fig. 3-16). A description of all co-valent bonds (mainly peptide bonds and disulfide bonds) linking amino acid residues in a polypeptide chain is its primary structure. The most important element of primary structure is the sequence of amino acid residues. Secondary structure refers to particularly stable arrangements of amino acid residues giving rise to recurring structural patterns. Tertiary structure describes all aspects of the three-dimensional folding of a polypeptide. When a protein has two or more polypeptide subunits, their arrangement in space is referred to as quaternary structure. Primary structure is the focus of Section 3.4; the higher levels of structure are discussed in Chapter 4.

SUMMARY 3.2 Peptides and Proteins

■ Amino acids can be joined covalently through peptide bonds to form peptides and proteins. Cells generally contain thousands of different proteins, each with a different biological activity.

■ Proteins can be very long polypeptide chains of 100 to several thousand amino acid residues. However, some naturally occurring peptides have only a few amino acid residues. Some proteins are composed of several noncovalently

Primary structure

Secondary structure

Tertiary structure tt

Quaternary structure


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