The Chemistry of Biology: Proteins

Proteins

Proteins are organic compounds that contain the element nitrogen as well as carbon, hydrogen, and oxygen. Proteins are the most diverse group of biologically important substances and are often considered to be the central compound necessary for life. In fact, the translation from the Greek root word means “first place.” Skin and muscles are composed of proteins; antibodies and enzymes are proteins; some hormones are proteins; and some proteins are involved with digestion, respiration, reproduction, and even normal vision, just to mention a few.

Amino Acids

There are obviously many types of proteins, but they are all made from amino acids bonded together by the dehydration synthesis. By continually adding amino acids, called peptides, two amino acids join together to form dipeptides; as more peptides join together, they form polypeptides. Proteins vary in length and complexity based on the number and type of amino acids that compose the chain. There are about 20 different amino acids, each with a different chemical structure and characteristics; for instance, some are polar, others are nonpolar. The final protein structure is dependent upon the amino acids that compose it. Protein function is directly related to the structure of that protein. A protein's specific shape determines its function. If the three-dimensional structure of the protein is altered because of a change in the structure of the amino acids, the protein becomes denatured and does not perform its function as expected.

Protein Structure

The three-dimensional geometry of a protein molecule is so important to its function that four levels of structure are used to describe a protein. The first level, or primary structure, is the linear sequence of amino acids that creates the peptide chain. In the secondary structure, hydrogen bonding between different amino acids creates a three-dimensional geometry like an alpha helix or pleated sheet. An alpha helix is simply a spiral or coiled molecule, whereas a pleated sheet looks like a ribbon with regular peaks and valleys as part of the fabric. The tertiary structure describes the overall shape of the protein. Most tertiary structures are either globular or fibrous. Generally, nonstructural proteins such as enzymes are globular, which means they look spherical. The enzyme amylase is a good example of a globular protein. Structural proteins are typically long and thin, and hence the name, fibrous. Quaternary structures describe the protein's appearance when a protein is composed of two or more polypeptide chains. Often the polypeptide chains will hydrogen bond with each other in unique patterns to create the desired protein configuration.

Enzymes

Most enzymes are proteins and therefore their function is specific to their structure. Enzymes function as a catalyst to increase the rate of virtually all the chemical reactions that take place in a living system. The enzymes, like all catalysts, are not consumed but are constantly reused to catalyze the same specific reaction. Enzymes depend on the correct structural alignment and orientation at the active site of the protein and the appropriate site of the reactants, or substrate, before the reaction can proceed. This geometric interaction between the enzyme and the substrate is referred to as the “lock-and-key model” because the enzyme's action parallels the action of a lock into which is fitted the key (substrate). If the key and lock do not match, the action does not work.

It is the same with enzymes and substrates. The active site for the enzyme and the appropriately matched site of the substrate must physically join before the reaction can occur. That is why the structure of the enzyme is so important. The enzyme binds with the appropriate substrate only in the correct alignment and orientation to connect the molecules. The resulting enzyme-substrate complex enables the reaction to occur. Finally, the products are formed and the enzyme is released to catalyze the same reaction for another substrate of the same type of molecule. Enzymes may fail to function if they are denatured. Remember the model simplifies your understanding of the process; in reality they are three-dimensional molecules.

Hormones

Hormones are chemical messengers produced in one part of the body to function in a different part of the body. Although fat-soluble hormones are made from steroids, water-soluble hormones such as the growth hormone are made from amino acids. Hormones function similarly to enzymes in that both require a specific receptor and perform a specific function. After a hormone is created and secreted by a cell, it travels—usually via the bloodstream—to its target cell. The target cell is the point of action that the hormone recognizes, binds to, and thereby delivers the chemical message. The hormone identifies the target cell by its receptor protein and employs the same lock-and-key process.