BioChem Ch. 15: Enzymes

Lyases add water across a double bond or removes water from a molecule, thereby generating a double bond. Hydrolases use water to break ester or amide bond, thereby generating two molecules.

Both the lyases and hydrolases catalyze reactions involving water molecules. What is the difference in the types of reactions that these two enzymes catalyze?

The regulation process described in the problem is called feedback inhibition and is a common mechanism for controlling metabolic reactions. Consider the reaction sequence: A ->B->C->D->E->F The letters refer to metabolites or intermediates that are produced in the pathway to synthesize compound F. In feedback inhibition, compound F acts as an inhibitor for the enzyme that converts A to B. This type of inhibition becomes important when enough F has been produced for the cell.

Can the product of a reaction that is a part of a sequence act as an inhibitor for another reaction in the sequence? Explain.

The activation energy in an enzyme-catalyzed reaction is lower than the activation energy in an uncatalyzed reaction, which is why a catalyzed reaction proceeds at a faster rate.

Compare the activation energy in uncatalyzed reactions and in enzyme-catalyzed reactions.

As an example, consider an enzyme that has an aspartic acid and a glutamic acid in the active site. If we know that the pH optimum of the enzyme is near 4, which is the pKa range for the side chain carboxyls, we might predict a mechanism that involves one of the amino acids being protonated and the other one not. If the pH optimum is closer to 7, then we know that whatever mechanism we propose must have the side chain carboxyls of the two amino acids fully deprotonated.

How can the pH profile of an enzyme tell you something about the reaction mechanism if you know the amino acids at the active site?

This may work for some enzymes, but not for most. Each enzyme has a distinctive temperature profile (see Figure 23.5) that would have to be known before one tries to increase the rate of the reaction by increasing the temperature. For example, with the enzyme in Figure 23.5, one could increase the rate of the reaction within the range of 30°- 38° C. However, notice that the enzyme is not even active at temperatures below 20° and above 50°.

If we wish to double the rate of an enzyme-catalyzed reaction, can we do so by increasing the temperature by 10° C? Explain.

If the enzyme concentration, on a molar basis, is twice the maximum substrate concentration, no saturation curve is obtained. There would always be many more open active sites available on the enzyme than there are substrate molecules to fill them.

In most enzyme-catalyzed reactions, the rate of reaction reaches a constant value with increasing substrate concentration. This relationship is described in a saturation curve diagram. If the enzyme concentration on a molar basis is twice the maximum substrate concentration, would you obtain a saturation curve?

(a) The protein portion of the enzyme is called the apoenzyme. (b) The organic molecule portion is called a coenzyme.

In the citric acid cycle, an enzyme converts succinate to fumarate. The enzyme consists of a protein portion called FAD. What terms do we use to refer to (a) the protein portion and (b) the organic molecule portion?

Substrates for the monoamine oxidases usually have only one amino group. Therefore, based only on the name of the enzymes, both (a) and (b) should be active substrates. Compound (c) contains a nitro group, not an amino group. In actuality, the monoamine oxidases also prefer primary and secondary amines and aromatic compounds as substrates, so it is expected that (a) is the best substrate.

Monoamine oxidases are important enzymes in brain chemistry. Judging from the name, which of the following would be a suitable substrate for this class of enzymes (please see images in book on page 386, 15.8):

(a) isomerase (b) hydrolase (c) oxidoreductase (d) lyase

On the basis of the classification given in section 15.2, decide to which group each of the following belong (please see images in book on page 386, 15.9):

Trypsin, a protease, is a digestive enzyme that catalyzes the hydrolysis of peptide bonds in dietary proteins in the small intestines. The enzyme is produced in the pancreas in an inactive, zymogen form. If it were produced here in its active form, it would degrade proteins that are essential for normal cell function. It is converted to active trypsin when it is secreted into the small intestines.

The enzyme trypsin is synthesized by the body in the form of a long polypeptide chain containing 235 amino acids (trypsinogen), from which a piece must be cut before the trypsin can be active. Why does the body . not synthesize trypsin directly?

When lactate dehydrogenase is heated to 85° C, it becomes denatured (irreversibly inactivated). Cooling the denatured enzyme will not recover enzyme activity. When the enzyme is cooled to -10° C, the activity is very low, but the enzyme molecule is not denatured. Optimum enzyme activity would be recovered if the enzyme were warmed to 36° C.

The optimal temperature for the action of lactate dehydrogenase is 36° C. It is irreversibly inactivated at 85° C, but a yeast containing this enzyme can survive for months at -10° C. Explain how this can happen.

Trypsin and chymotrypsin are enzymes that catalyze the hydrolysis of amide bonds in proteins. Trypsin is more specific in its action because it hydrolyzes amide bonds on the carboxyl sides of the basic amino acid residues, Lys and Arg. Chymotrypsin works at amide bonds that are on the carboxyl sides of all aromatic amino acids, such as phe, try, and trp, but also has a minor reaction with other non polar amino acids, such as leu and ile.

Trypsin cleaves polypeptide chains at the carboxyl side of a lysine or arginine residue. Chymotropsin cleaves polypeptide chains on the carboxyl side of an aromatic amino acid residue or any other nonpolar, bulky side chain. Which enzyme is more specific? Explain.

Ribozymes are biological catalysts that are composed of ribonucleic acid (RNA). It was previously thought that all enzymes were protein molecules, but molecules of RNA that catalyze biochemical reactions were discovered in the early 1980s.

What are ribozymes made of?

A catalyst is any substance that speeds up the rate of a reaction and is not itself changed by the reaction. An enzyme is a biological catalyst, which is either a protein or an RNA molecule.

What is the difference between a catalyst and an enzyme?

In competitive inhibition, the maximum reaction rate achieved is the same with or without an inhibitor (Figure 23.11). However, in the presence of a competitive inhibitor, a higher substrate concentration is required to reach the maximum rate. The maximum rate for a noncompetitive inhibitor is always lower at any substrate concentration and can never equal the rate of the uninhibited reaction.

What is the maximum rate that can be achieved in competitive inhibition compared with noncompetitive inhibition?

A survey of the amino acids present at enzyme active sites has shown an abundance of amino acid residues with acidic and basic side chains. The most prominent amino acid include His, Asp, Arg, and Glu. The properties of these amino acids lead one to the conclusion that acid-base chemistry (proton transfer) is an important chemical process during enzyme action.

What kind of chemical reaction occurs most frequently at the active site?

(a) Deaminases catalyze the removal of amino groups from substrates. (b) Hydrolases catalyze the cleavage of bonds, usually esters and amides, with water. These are called hydrolysis reactions. (c) Dehydrogenases catalyze oxidation/reduction reactions. Sometimes these reactions involve removal of hydrogen atoms from a substrate, but not always. (d) Isomerases catalyze isomerization reactions. These are reactions where there is no net change in empirical formula, but the atoms are arranged differently in the products.

What kind of reaction does each of the following enzymes catalyze? (a) Deaminases (b) Hydrolases (c) Dehydrgenases (d) Isomerases

Because enzymes are very specific and thousands of reactions must be catalyzed in an organism.

Why does the body need so many different enzymes?

Yes, lipases are not very specific.

Would a lipase hydrolyze two triglycerides, one containing only oleic acid and the other containing only palmitic acid, with equal ease?