CONCEPTS IN BIOLOGY
PART II. CORNERSTONES: CHEMISTRY, CELLS, AND METABOLISM
5. Enzymes, Coenzymes, and Energy
5.2. How Enzymes Speed Chemical Reaction Rates
As the instructions for the production of an enzyme are read from the genetic material, a specific sequence of amino acids is linked together at the ribosomes. Once bonded, the chain of amino acids folds and twists to form a molecule with a particular three-dimensional shape.
Enzymes Bind to Substrates
It is the nature of its three-dimensional shape, size, and electric charge that allows an enzyme to combine with a reactant and lower the activation energy. Each enzyme has a specific size and three-dimensional shape, which in turn is specific to the kind of reactant with which it can combine. The enzyme physically fits with the reactant. The molecule to which the enzyme attaches itself (the reactant) is known as the substrate. When the enzyme attaches itself to the substrate molecule, a new, temporary molecule—the enzyme-substrate complex—is formed (figure 5.2). When the substrate is combined with the enzyme, its chemical bonds are less stable and more likely to be altered and form new bonds. The enzyme is specific because it has a particular shape, which can combine only with specific parts of certain substrate molecules (Outlooks 5.1).
FIGURE 5.2. Enzyme-Substrate Complex Formation
During an enzyme-controlled reaction, the enzyme and substrate come together to form a new molecule—the enzyme-substrate complex molecule. This molecule exists for only a very short time. During that time, the activation energy is lowered and bonds are changed. The result is the formation of a new molecule or molecules, called the end products of the reaction. Notice that the enzyme comes out of the reaction intact and ready to be used again.
You can think of an enzyme as a tool that makes a job easier and faster. For example, the use of an open-end crescent wrench can make the job of removing or attaching a nut and bolt go much faster than doing the same job by hand. To do this job, the proper wrench must be used. Just any old tool (screwdriver or hammer) won’t work! The enzyme must also physically attach itself to the substrate; therefore, there is a specific binding site, or attachment site, on the enzyme surface. Figure 5.3 illustrates the specificity of both wrench and enzyme. Note that the wrench and enzyme are recovered unchanged after they have been used. This means that the enzyme and wrench can be used again. Eventually, like wrenches, enzymes wear out and have to be replaced by synthesizing new ones using the instructions provided by the cell’s genes. Generally, only very small quantities of enzymes are necessary, because they work so fast and can be reused.
Both enzymes and wrenches are specific in that they have a particular surface geometry, or shape, which matches the geometry of their respective substrates. Note that both the enzyme and the wrench are flexible. The enzyme can bend or fold to fit the substrate, just as the wrench can be adjusted to fit the nut. This is called the induced fit hypothesis. The fit is induced because the presence of the substrate causes the enzyme to mold or adjust itself to the substrate as the two come together.
The active site is the place on the enzyme that causes a specific part of the substrate to change. It is the place where chemical bonds are formed or broken. (Note in the case illustrated in figure 5.3 that the active site is the same as the binding site. This is typical of many enzymes.) This site is where the activation energy is lowered and the electrons are shifted to change the bonds. The active site may enable a positively charged surface to combine with the negative portion of a reactant. Although the active site molds itself to a substrate, enzymes cannot fit all substrates. Enzymes are specific to certain substrates or a group of very similar substrate molecules. One enzyme cannot speed the rate of all types of biochemical reactions. Rather, a special enzyme is required to control the rate of each type of reaction occurring in an organism.
FIGURE 5.3. It Fits, It's Fast, and It Works
(a) Although removing the wheel from this bicycle could be done by hand, using an open-end crescent wrench is more efficient. The wrench is adjusted and attached, temporarily forming a nut-bolt-wrench complex. Turning the wrench loosens the bonds holding the nut to the bolt and the two are separated. Using the wrench makes the task much easier. (b) An enzyme will “adjust itself” as it attaches to its substrate, forming a temporary enzyme-substrate complex. The presence and position of the enzyme in relation to the substrate lowers the activation energy required to alter the bonds.
Passing Gas, Enzymes, and Biotechnology
Certain foods like beans and peas will result in an increased amount of intestinal gas. The average person releases about a liter of gas every day (about 14 expulsions). As people shift to healthier diets which include more fruits, vegetables, milk products, bran and whole grains, the amount of intestinal gas (flatus) produced can increase, too.
The major components of intestinal gas are:
• Nitrogen: 20-90%
• Hydrogen: 0-50%
• Carbon dioxide: 10-30%
• Oxygen: 0-10%
• Methane: 0-10%
The other offensive gases are produced when bacteria (i.e., Escherichia coli) living in the large intestine hydrolyze complex carbohydrates that humans cannot enzymatically break down. The enzyme alpha-galactosidase breaks down the complex carbohydrates found in these foods. When E. coli metabolizes these smaller carbohydrates, they release hydrogen and foulsmelling gases. Some people have more of a gas problem than others do. This is because the ratios of the two types of intestinal bacteria—those that produce alpha-galactosidase and those that do not—vary from person to person. This ratio dictates how much gas will be produced.
Biotechnology has been used to genetically engineer the fungus Aspergillus niger. By inserting the gene for alpha galactosidase into the fungus and making other changes, Aspergillus is able to secrete the enzyme in a form that can be dissolved in glycerol and water. This product is then put into pill form and sold over the counter. Since the flavor of alpha-galactosidase is similar to soy sauce, it can be added to many foods without changing their flavor.
Because an enzyme is specific to both the substrate to which it can attach and the reaction it can encourage, a unique name can be given to each enzyme. The first part of an enzyme’s name is usually the name of the molecule to which it can become attached. The second part of the name indicates the type of reaction it facilitates. The third part of the name is “-ase,” the ending that indicates it is an enzyme. For example, DNA polymerase is the name of the enzyme that attaches to the molecule DNA and is responsible for increasing its length through a polymerization reaction. Some enzymes (e.g., pepsin and trypsin) were identified before a formal naming system was established and are still referred to by their original names. The enzyme responsible for the dehydration synthesis reactions among several glucose molecules to form glycogen is known as glycogen synthetase. The enzyme responsible for breaking the bond that attaches the amino group to the amino acid arginine is known as arginine aminase. When an enzyme is very common, its formal name is shortened: The salivary enzyme involved in the digestion of starch is amylose (starch) hydrolase; it is generally known as amylase. Other enzymes associated with the human digestive system are noted in table 24.2.
5.2. CONCEPT REVIEW
3. Would you expect a fat and a sugar molecule to be acted upon by the same enzyme? Why or why not?
4. Describe the sequence of events in an enzyme-controlled reaction.
5. What is meant by the term binding site? Active site?