28.3 Amino Acids, Proteins, and Enzymes

Proteins are compounds of high molar mass consisting largely or entirely of chains of amino acids. Because of their great complexity, protein molecules cannot be classified on the basis of specific structural similarities, as carbohydrates and lipids are categorized. The two major structural classifications of proteins are based on far more general qualities: whether the protein is (1) fiberlike and insoluble or (2) globular and soluble. Some proteins, such as those that compose hair, skin, muscles, and connective tissue, are fiberlike. These fibrous proteins are insoluble in water and usually serve structural, connective, and protective functions. Examples of fibrous proteins are keratins, collagens, myosins, and elastins. Hair and the outer layer of skin are composed of keratin. Connective tissues contain collagen. Myosins are muscle proteins and are capable of contraction and extension. Elastins are found in ligaments and the elastic tissue of artery walls.

Globular proteins, the other major class, are soluble in aqueous media. In these proteins, the chains are folded so that the molecule as a whole is roughly spherical. Familiar examples include egg albumin from egg whites and serum albumin in blood. Serum albumin plays a major role in transporting fatty acids and maintaining a proper balance of osmotic pressures in the body. Hemoglobin and myoglobin, which are important for binding oxygen, are also globular proteins.

Levels of Protein Structure

The structure of proteins is generally described as having four organizational levels. The first of these is the primary structure, which is the number and sequence of amino acids in a protein’s polypeptide chain or chains, beginning with the free amino group and maintained by the peptide bonds connecting each amino acid to the next. The primary structure of insulin, composed of 51 amino acids, is shown in figure 283k.

A protein molecule is not a random tangle of polypeptide chains. Instead, the chains are arranged in unique but specific conformations. The term secondary structure refers to the fixed arrangement of the polypeptide backbone. On the basis of X ray studies, Linus Pauling and Robert Corey postulated that certain proteins or portions of proteins twist into a spiral or a helix. This helix is stabilized by intrachain hydrogen bonding between the carbonyl oxygen atom of one amino acid and the amide hydrogen atom four amino acids up the chain (located on the next turn of the helix) and is known as a right-handed α-helix. X ray data indicate that this helix makes one turn for every 3.6 amino acids, and the side chains of these amino acids project outward from the coiled backbone (Figure 28.3l.). The α-keratins, found in hair and wool, are exclusively α-helical in conformation. Some proteins, such as gamma globulin, chymotrypsin, and cytochrome c, have little or no helical structure. Others, such as hemoglobin and myoglobin, are helical in certain regions but not in others.

Another common type of secondary structure, called the β-pleated sheet conformation, is a sheetlike arrangement in which two or more extended polypeptide chains (or separate regions on the same chain) are aligned side by side. The aligned segments can run either parallel or antiparallel—that is, the N-terminals can face in the same direction on adjacent chains or in different directions—and are connected by interchain hydrogen bonding (Figure 28.3m.). The β-pleated sheet is particularly important in structural proteins, such as silk fibroin. It is also seen in portions of many enzymes, such as carboxypeptidase A and lysozyme.

Tertiary structure refers to the unique three-dimensional shape of the protein as a whole, which results from the folding and bending of the protein backbone. The tertiary structure is intimately tied to the proper biochemical functioning of the protein. Figure 28.3n. shows a depiction of the three-dimensional structure of insulin.

Four major types of attractive interactions determine the shape and stability of the tertiary structure of proteins. These are shown in Figure 28.3o.

1. Ionic bonding. Ionic bonds result from electrostatic attractions between positively and negatively charged side chains of amino acids. For example, the mutual attraction between an aspartic acid carboxylate ion and a lysine ammonium ion helps to maintain a particular folded area of a protein (part (a) of Figure 28.3o.).
2. Hydrogen bonding. Hydrogen bonding forms between a highly electronegative oxygen atom or a nitrogen atom and a hydrogen atom attached to another oxygen atom or a nitrogen atom, such as those found in polar amino acid side chains. Hydrogen bonding (as well as ionic attractions) is extremely important in both the intra- and intermolecular interactions of proteins (part (b) of Figure 28.3o.).
3. Disulfide linkages. Two cysteine amino acid units may be brought close together as the protein molecule folds. Subsequent oxidation and linkage of the sulfur atoms in the highly reactive sulfhydryl (SH) groups leads to the formation of cystine (part (c) of Figure 28.3o. and figure 28.3p.). Intrachain disulfide linkages are found in many proteins, including insulin (yellow bars in Figure 28.3k.) and have a strong stabilizing effect on the tertiary structure.

4. Dispersion forces. Dispersion forces arise when a normally nonpolar atom becomes momentarily polar due to an uneven distribution of electrons, leading to an instantaneous dipole that induces a shift of electrons in a neighbouring nonpolar atom. Dispersion forces are weak but can be important when other types of interactions are either missing or minimal (part (d) of Figure 28.3o.). This is the case with fibroin, the major protein in silk, in which a high proportion of amino acids in the protein have nonpolar side chains. The term hydrophobic interaction is often misused as a synonym for dispersion forces. Hydrophobic interactions arise because water molecules engage in hydrogen bonding with other water molecules (or groups in proteins capable of hydrogen bonding). Because nonpolar groups cannot engage in hydrogen bonding, the protein folds in such a way that these groups are buried in the interior part of the protein structure, minimizing their contact with water.

When a protein contains more than one polypeptide chain, each chain is called a subunit. The arrangement of multiple subunits represents a fourth level of structure, the quaternary structure of a protein. Hemoglobin, with four polypeptide chains or subunits, is the most frequently cited example of a protein having quaternary structure (Figure 28.3q.). The quaternary structure of a protein is produced and stabilized by the same kinds of interactions that produce and maintain the tertiary structure.

A schematic representation of the four levels of protein structure is shown in Figure 28.3r. The primary structure consists of the specific amino acid sequence. The resulting peptide chain can twist into an α-helix, which is one type of secondary structure. This helical segment is incorporated into the tertiary structure of the folded polypeptide chain. The single polypeptide chain is a subunit that constitutes the quaternary structure of a protein, such as hemoglobin that has four polypeptide chains.

Denaturation of Proteins

The highly organized structures of proteins are truly masterworks of chemical architecture. But highly organized structures tend to have a certain delicacy, and this is true of proteins. Denaturation is the term used for any change in the three-dimensional structure of a protein that renders it incapable of performing its assigned function. A denatured protein cannot do its job. (Sometimes denaturation is equated with the precipitation or coagulation of a protein; our definition is a bit broader.) A wide variety of reagents and conditions, such as heat, organic compounds, pH changes, and heavy metal ions can cause protein denaturation (Table 28.3f.).

Source: “18.4: Proteins” In Basics of GOB Chemistry (Ball et al.), CC BY-NC-SA 4.0.

Anyone who has fried an egg has observed denaturation. The clear egg white turns opaque as the albumin denatures and coagulates. No one has yet reversed that process. However, given the proper circumstances and enough time, a protein that has unfolded under sufficiently gentle conditions can refold and may again exhibit biological activity (Figure 28.3s.). Such evidence suggests that, at least for these proteins, the primary structure determines the secondary and tertiary structure. A given sequence of amino acids seems to adopt its particular three-dimensional arrangement naturally if conditions are right.

The primary structures of proteins are quite sturdy. In general, fairly vigorous conditions are needed to hydrolyze peptide bonds. At the secondary through quaternary levels, however, proteins are quite vulnerable to attack, though they vary in their vulnerability to denaturation. The delicately folded globular proteins are much easier to denature than are the tough, fibrous proteins of hair and skin.

Enzymes

Hundreds of enzymes have been purified and studied in an effort to understand how they work so effectively and with such specificity. The resulting knowledge has been used to design drugs that inhibit or activate particular enzymes. An example is the intensive research to improve the treatment of or find a cure for acquired immunodeficiency syndrome (AIDS). AIDS is caused by the human immunodeficiency virus (HIV). Researchers are studying the enzymes produced by this virus and are developing drugs intended to block the action of those enzymes without interfering with enzymes produced by the human body. Several of these drugs have now been approved for use by AIDS patients.

The first enzymes to be discovered were named according to their source or method of discovery. The enzyme pepsin, which aids in the hydrolysis of proteins, is found in the digestive juices of the stomach (Greek pepsis, meaning “digestion”). Papain, another enzyme that hydrolyzes protein (in fact, it is used in meat tenderizers), is isolated from papayas. As more enzymes were discovered, chemists recognized the need for a more systematic and chemically informative identification scheme. In the current numbering and naming scheme, under the oversight of the Nomenclature Commission of the International Union of Biochemistry, enzymes are arranged into six groups according to the general type of reaction they catalyze (Table 28.3g.), with subgroups and secondary subgroups that specify the reaction more precisely.

Source: “18.5: Enzymes” In Basics of GOB Chemistry (Ball et al.), CC BY-NC-SA 4.0.

Each enzyme is assigned a four-digit number, preceded by the prefix EC—for enzyme classification—that indicates its group, subgroup, and so forth. This is demonstrated in Table 28.19b. for alcohol dehydrogenase. Each enzyme is also given a name consisting of the root of the name of its substrate or substrates and the –ase suffix. Thus urease is the enzyme that catalyzes the hydrolysis of urea.

Example 28.3b

Alcohol dehydrogenase has an Enzyme Classification Number of EC 1.1.1.1.  What does this mean?

Solution:

The first digit indicates that this enzyme is an oxidoreductase; that is, an enzyme that catalyzes an oxidation-reduction reaction. The second digit indicates that this oxidoreductase catalyzes a reaction involving a primary or secondary alcohol. The third digit indicates that either the coenzyme NAD⁺ or NADP⁺ is required for this reaction. The fourth digit indicates that this was the first enzyme isolated, characterized, and named using this system of nomenclature. The systematic name for this enzyme is alcohol:NAD⁺ oxidoreductase, while the recommended or common name is alcohol dehydrogenase.

[latex]S + E \rightarrow E–S \tag{1}[/latex]

[latex]E–S \rightarrow P + E \tag{2}[/latex]

Hydrogen bonding and other electrostatic interactions hold the enzyme and substrate together in the complex. The structural features or functional groups on the enzyme that participate in these interactions are located in a cleft or pocket on the enzyme surface. This pocket, where the enzyme combines with the substrate and transforms the substrate to product is called the active site of the enzyme (Figure 28.3t.).

The active site of an enzyme possesses a unique conformation (including correctly positioned bonding groups) that is complementary to the structure of the substrate, so that the enzyme and substrate molecules fit together in much the same manner as a key fits into a tumbler lock. In fact, an early model describing the formation of the enzyme-substrate complex was called the lock-and-key model (Figure 28.3u.). This model portrayed the enzyme as conformationally rigid and able to bond only to substrates that exactly fit the active site.

Working out the precise three-dimensional structures of numerous enzymes has enabled chemists to refine the original lock-and-key model of enzyme actions. They discovered that the binding of a substrate often leads to a large conformational change in the enzyme, as well as to changes in the structure of the substrate or substrates. The current theory, known as the induced-fit model, says that enzymes can undergo a change in conformation when they bind substrate molecules, and the active site has a shape complementary to that of the substrate only after the substrate is bound, as shown for hexokinase in Figure 28.3v. After catalysis, the enzyme resumes its original structure.

The structural changes that occur when an enzyme and a substrate join together bring specific parts of a substrate into alignment with specific parts of the enzyme’s active site. Amino acid side chains in or near the binding site can then act as acid or base catalysts, provide binding sites for the transfer of functional groups from one substrate to another or aid in the rearrangement of a substrate. The participating amino acids, which are usually widely separated in the primary sequence of the protein, are brought close together in the active site as a result of the folding and bending of the polypeptide chain or chains when the protein acquires its tertiary and quaternary structure. Binding to enzymes brings reactants close to each other and aligns them properly, which has the same effect as increasing the concentration of the reacting compounds.

One characteristic that distinguishes an enzyme from all other types of catalysts is its substrate specificity. An inorganic acid such as sulfuric acid can be used to increase the reaction rates of many different reactions, such as the hydrolysis of disaccharides, polysaccharides, lipids, and proteins, with complete impartiality. In contrast, enzymes are much more specific. Some enzymes act on a single substrate, while other enzymes act on any of a group of related molecules containing a similar functional group or chemical bond. Some enzymes even distinguish between D- and L-stereoisomers, binding one stereoisomer but not the other. Urease, for example, is an enzyme that catalyzes the hydrolysis of a single substrate—urea—but not the closely related compounds methyl urea, thiourea, or biuret (Figure 28.3w.). The enzyme carboxypeptidase, on the other hand, is far less specific. It catalyzes the removal of nearly any amino acid from the carboxyl end of any peptide or protein.

Enzyme specificity results from the uniqueness of the active site in each different enzyme because of the identity, charge, and spatial orientation of the functional groups located there. It regulates cell chemistry so that the proper reactions occur in the proper place at the proper time. Clearly, it is crucial to the proper functioning of the living cell.