Proteins and Enzymes: Structure and Function

A peptide bond links the carboxyl group of one amino acid to the amino group of the next. Chains of amino acids held together this way are called polypeptides.

Proteins are built from 20 standard amino acids that differ only in their side chain (R group); glycine has the simplest one, a single hydrogen atom. Nine of them are essential: the body cannot make them, so they must come from food.

Breaking the bond adds a water molecule back (hydrolysis). It is the reverse of dehydration synthesis, in which the bond forms and a water molecule is released.

Each bond links two neighbors, so a chain always has one bond fewer than it has amino acids: 50 − 1 = 49.

Primary structure is the sequence of amino acids, secondary structure is local coiling or folding held by hydrogen bonds, and tertiary structure is the 3D shape of a whole chain. Quaternary structure has no pair, because it needs several chains and every example here is a single chain.

An antibody (IgG) is made of four chains (two heavy and two light), and catalase of four identical chains, so both have quaternary structure like hemoglobin. Myoglobin, which stores oxygen in muscles, and pepsin are each a single folded chain.

Insulin is a hormone, collagen is a structural protein, myosin is a motor protein in muscle, and antibodies defend the body. Carrying oxygen has no pair: that is the job of hemoglobin, which is not on the list.

A gene stores the amino acid order of each protein, and every amino acid contains nitrogen. The body has no store for extra amino acids (it breaks them down), and a protein's job depends on its shape as much as on its building blocks.

Enzymes lower the activation energy, so a reaction runs faster, and they come out of it unchanged, ready for the next molecule. They only speed up reactions that would happen anyway, just very slowly; most are proteins, but some RNA molecules (ribozymes) also catalyze reactions.

Catalase is the enzyme, hydrogen peroxide is the substrate it acts on, and water and oxygen are the products. The substrate binds in the active site. Nothing in this reaction is an inhibitor.

Enzymes are specific: only a molecule with a matching shape fits the active site. That is why each type of food molecule needs its own enzymes.

In the induced fit model, the active site is flexible and molds itself around the substrate. The older lock-and-key model pictured a rigid active site that matches the substrate exactly.

Each enzyme works best at the pH of the place where it works. The stomach is strongly acidic, while the small intestine, where pancreatic trypsin acts, is slightly alkaline.

A competitive inhibitor competes with the substrate for the active site, so extra substrate can push it out. A noncompetitive inhibitor binds to the enzyme somewhere else and changes its shape; many drugs, such as aspirin, are enzyme inhibitors.

Fresh pineapple contains bromelain, an enzyme that breaks down proteins, including gelatin (made from collagen). Canning heats the fruit, and the heat destroys the enzyme.

Heat, acid or other stress unfolds a protein's shape, but the peptide bonds stay intact, so the amino acid sequence is kept. In most cases, such as a cooked egg, the change cannot be undone.