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Protein Structure and Genetics Help (page 2)

By — McGraw-Hill Professional
Updated on Aug 21, 2011

Structural Levels

The linear sequence of amino acids forms the primary structure of proteins (Fig. 3-6).

Protein Structure

Some portions of many proteins have a secondary structure in the form of an alpha helix in which the carbonyl group (C=O) next to one peptide bond forms a hydrogen bond with an imino group (NH) flanking a peptide bond a few amino acids further along the polypeptide chain. The protein chain may fold back upon itself, forming weak internal bonds (e.g., hydrogen bonds, ionic bonds) as well as strong covalent disulfide bonds that stabilize its tertiary structure into a precisely and often intricately folded pattern. Two or more tertiary structures may unite into a functional quaternary structure. For example, hemoglobin consists of four polypeptide chains (two identical α-chains and two identical β-chains). A protein cannot function until it has assumed its full tertiary or quaternary configuration. Any disturbance of its normal co nfiguration may inactivate the function of the protein. For example, if the protein is an enzyme, heating may destroy its catalytic activity because weak bonds that hold the protein in its secondary or higher structural forms are ruptured. The shape of an active enzyme molecule fits its substrate (the substance that is catalyzed by the enzyme) in a manner analogous to the way a key fits a lock (Fig. 3-7). An enzyme that is altered, either genetically (by mutation of the respective gene), physically (e.g., heat), or chemically (e.g., pH change) may not fit the substrate and therefore would be incapable of catalyzing the conversion of substrate to normal product.

Protein Structure

Factors Governing Structural Levels

Relatively weak bonds such as hydrogen bonds and ionic bonds (attraction of positively and negatively charged ionic groups) are mainly responsible for the secondary and higher structural levels of protein organization. Enzymes are not involved in the formation of weak bonds. The extent to which a protein contains alpha-helical regions is dependent upon at least three factors. The most important factor governing tertiary protein structure involves formation of the most favorable energetic interactions between atomic groupings in the side chains of the amino acids. A second factor is the presence of proline, which cannot participate in alpha-helical formation because it is an imino acid rather a true amino acid. Proline is therefore often found at the "corners," or "hairpin turns," of polypeptide chains. Finally, the formation of intrastr and (on the same chain) disulfide bridges tends to distort the alpha helix.

Formation of Quaternary Structure

The ionized side chains of some amino acids readily interact with water and therefore are called hydrophilic ("water-loving") amino acids. Hydrophobic ("water-fearing") amino acids contain nonionized side chains that tend to avoid contact with water. When a polypeptide chain folds into its tertiary shape, these forces cause amino acids with hydrophilic groups to predominate on the outside and hydrophobic segments of the chain to predominate in the interior of globular proteins. The multiple polypeptide chains of quaternary proteins are usually joined by hydrophobic forces. Nonpolar groups of the individual polypeptide chains come together as a way of excluding water. Hydrogen bonds, ionic bonds, and possibly interstr and (between chains) disulfide bonds may also participate in forming quaternary protein structures. Some quaternary proteins consist of two or more identical polypeptide chains (e.g., the bacterial enzyme β-galactosidase consists of four identical polypep ide chains). Such proteins are called homopolymers.Other quaternary proteins (such as hemoglobin) consist of non-identical chains and are called heteropolymers. In order to become functional proteins, some polypeptide chains must be subject to modifications after they have been synthesized. For example, the protein chymotrypsinogen must be cleaved at one specific position by an enzyme to produce the active split-product chymotrypsin.

Practice problems for these concepts can be found at:

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