Worked Example 19.1 Classifying Enzymes

1. Worked Example 19.1 Classifying Enzymes To what class does the enzyme that catalyzes the following reaction belong? Analysis First, identify the type of reaction that has occurred. An amino group and a carbonyl group have changed places. Then, determine what class of enzyme catalyzes this type of reaction. Solution The reaction is a transfer of an amino functional group; therefore, the enzyme is a transferase.

2. Worked Example 19.2 Identifying active site side-chain functions Look at the hydrolysis of a peptide bond by chymotrypsin in Figure 19.4. (a) Which amino acids have side chains that could provide stabilization to the aromatic ring shown in the substrate? (b) What does the serine side chain do in the reaction and why can it do this? (c) What does the histidine side chain do in the reaction and why can it do this? Analysis Look critically at the diagrams of the reaction in Figure 19.4. Consider each part of the question separately, using the diagrams as an aid. (a) Note that the aromatic ring of phenylalanine fits into a “hydrophobic pocket.” Therefore, the side chains of the amino acids surrounding this pocket in chymotrypsin must be nonpolar. (b) In the second diagram, note that serine has donated a hydrogen ion to histidine. Remember that acids are proton donors. (c) Also in the second diagram, note that histidine has accepted a proton from serine. Remember that bases are proton acceptors. Solution (a) Any of the following nonpolar amino acids could be part of the hydrophobic pocket in chymotrypsin: alanine, leucine, isoleucine, methionine, proline, valine, phenylalanine, or tryptophan (see Table 18.3). (b) Serine is a polar amino acid and can donate a proton from the —OH group on the side chain, functioning as an acid. The RO– remaining can interact with the substrate, initiating cleavage of the substrate. (c) Histidine is a basic amino acid and can accept a proton until needed to complete the cleavage reaction. In this example, nonpolar amino acids held the substrate in place while amino acids that could act as acids or bases carried out the reaction

3. Worked Example 19.3 Enzymatic Activity: Determining Optimum pH Enzymatic activity is shown for three different enzymes as a function of pH in the graph below. What is the optimum pH for pepsin (curve A), for urease (curve B), and for alanine dehydrogenase (curve C)? Analysis Recall that the optimum pH is the pH at which the enzyme shows the highest activity; therefore, the highest point on the curve, representing maximum activity, is the optimum pH for the enzyme. Solution Find the correct curve for each enzyme, then find the apex of the activity curve. Drop a vertical line to the pH axis and read the optimum pH directly from the axis scale. The optimum pH for pepsin is approximately 4.0, that for urease approximately 6.0, and that for alanine dehydrogenase approximately 9.5.

4. Worked Example 19.4 Enzymatic Activity: Determining Optimum Temperature Consider the temperature activity curve below. Enzymatic activity is shown for muscle lactate dehydrogenase from 0 °C to 60 °C. Suppose you wish to test a sample for lactate dehydrogenase activity; what is the best temperature for the test? Analysis An enzyme shows its highest catalytic activity at a certain temperature, with less activity at temperatures below and above the optimum temperature. Look at the curve of activity versus temperature and find the highest point on the curve—that point represents the optimum activity. Solution From the highest point on the curve of activity versus temperature, drop a vertical line down to the x-axis (the one that reads “Temperature”) to find the optimum temperature. The temperature optimum for lactate dehydrogenase is 40 °C.

5. Worked Example 19.5 Determining Feedback Control Points Look at the three-step pathway for the conversion of 3-phosphoglycerate to serine: When the cell has plenty of serine available, which enzyme in the pathway, 1, 2, or 3, is most likely to be inhibited? Analysis This is a simple, linear pathway. The pathway is most likely controlled by feedback control of the final product. Solution Assuming that feedback control is the simplest control mechanism for this linear pathway, serine, the product of the pathway, will inhibit the first enzyme in the pathway when sufficient serine is available in the cell.

6. Worked Example 19.6 Identifying Coenzymes Identify the substrate, product, and coenzyme in the reaction shown below. The reaction is catalyzed by the enzyme alcohol dehydrogenase. Analysis Identify which molecules have been changed and how, starting from the left side of the arrow (the beginning of the reaction) to the right side of the arrow (the end of the reaction). In this case, ethanol is oxidized to acetaldehyde and NAD+ is reduced to NADH/H+. Recognize that nicotinamide adenine dinucleotide (NAD+) is a coenzyme involved in oxidation/reduction reactions. Solution Since NAD+ is a coenzyme involved in oxidation/reduction reactions, ethanol (the other molecule on the left side of the equation) is the substrate and acetaldehyde (on the right side of the arrow) is the product of the reaction. NADH+ H+ is the reduced form of nicotinamide adenine dinucleotide and is considered to be reduced coenzyme only—not a product of the reaction.