Enzymes

Enzymes are proteins that speed up the rate of chemical reactions. During these reactions, the enzyme molecules are not changed in any way, meaning they are biological catalysts. Without enzymes, most chemical reactions in a cell would go so slowly that the cell would be unable to live. Because an enzyme is not permanently changed or used up in the reaction it catalyzes, we might write it in a reaction equation this way:

A + B + enzyme C + D + enzyme

This way of writing the reaction shows that the enzyme participates with reactants A and B but is unchanged at the end of the reaction. A more common shorthand for enzymatic reactions shows the name of the enzyme above the reaction arrow, like this:

A + B e n z y m e C + D

In enzymatically catalyzed reactions, the reactants A and B are called substrates.

Enzymes Are Proteins

Most enzymes are large proteins with complex three-dimensional shapes, although recently researchers discovered that RNA can sometimes act as a catalyst. Like other proteins that bind to substrates, protein enzymes exhibit specificity, competition, and saturation [here].

A few enzymes come in a variety of related forms (isoforms) and are known as isozymes {iso-, equal} of one another. Isozymes are enzymes that catalyze the same reaction but under different conditions or in different tissues. The structures of related isozymes are slightly different from one another, which causes the variability in their activity. Many isozymes have complex structures with multiple protein chains.

For example, the enzyme lactate dehydrogenase (LDH) has two kinds of subunits, named H and M, that are assembled into tetramers—groups of four. LDH isozymes include H4, H2M2, and M4. The different LDH isozymes are tissue specific, including one found primarily in the heart and a second found in skeletal muscle and the liver.

Isozymes have an important role in the diagnosis of certain medical conditions. For example, in the hours following a heart attack, damaged heart muscle cells release enzymes into the blood. One way to determine whether a person’s chest pain was indeed due to a heart attack is to look for elevated levels of heart isozymes in the blood. Some diagnostically important enzymes and the diseases of which they are suggestive are listed in Table 4.3.

Table 4.3 Diagnostically Important Enzymes

Elevated blood levels of these enzymes are suggestive of the pathologies listed.

Enzyme Related Diseases
*A newer test for a molecule called prostate specific antigen (PSA) has replaced the test for acid phosphatase in the diagnosis of prostate cancer.
Acid phosphatase* Cancer of the prostate
Alkaline phosphatase Diseases of bone or liver
Amylase Pancreatic disease
Creatine kinase (CK) Myocardial infarction (heart attack), muscle disease
Lactate dehydrogenase (LDH) Tissue damage to heart, liver, skeletal muscle, red blood cells

Reaction Rates Are Variable

We measure the rate of an enzymatic reaction by monitoring either how fast the products are synthesized or how fast the substrates are consumed. Reaction rate can be altered by a number of factors, including changes in temperature, the amount of enzyme present, and substrate concentrations [here]. In mammals, we consider temperature to be essentially constant. This leaves enzyme amount and substrate concentration as the two main variables that affect reaction rate.

In protein-binding interactions, if the amount of protein (in this case, enzyme) is constant, the reaction rate is proportional to the substrate concentration. One strategy cells use to control reaction rates is to regulate the amount of enzyme in the cell. In the absence of appropriate enzyme, many biological reactions go very slowly or not at all. If enzyme is present, the rate of the reaction is proportional to the amount of enzyme and the amount of substrate, unless there is so much substrate that all enzyme binding sites are saturated and working at maximum capacity [here].

This seems simple until you consider a reversible reaction that can go in both directions. In that case, what determines in which direction the reaction goes? The answer is that reversible reactions go to a state of equilibrium, where the rate of the reaction in the forward direction (A + B→C + D) is equal to the rate of the reverse reaction (C + D→A + B) At equilibrium, there is no net change in the amount of substrate or product, and the ratio [C][D]/[A][B] is equal to the reaction’s equilibrium constant, Keq [here].

If substrates or products are added or removed by other reactions in a pathway, the reaction rate increases in the forward or reverse direction as needed to restore the ratio [C][D]/[A][B]. According to the law of mass action, the ratio of [C] and [D] to [A] and [B] is always the same at equilibrium.

Enzymes May Be Activated, Inactivated, or Modulated

Enzyme activity, like the activity of other soluble proteins, can be altered by various factors. Some enzymes are synthesized as inactive molecules (proenzymes or zymogens) and activated on demand by proteolytic activation [here]. Others require the binding of inorganic cofactors, such as Ca2+ or Mg2+ before they become active.

Organic cofactors for enzymes are called coenzymes. Coenzymes do not alter the enzyme’s binding site as inorganic cofactors do. Instead, coenzymes act as receptors and carriers for atoms or functional groups that are removed from the substrates during the reaction. Although coenzymes are needed for some metabolic reactions to take place, they are not required in large amounts.

Many of the substances that we call vitamins are the precursors of coenzymes. The water-soluble vitamins, such as the B vitamins, vitamin C, folic acid, biotin, and pantothenic acid, become coenzymes required for various metabolic reactions. For example, vitamin C is needed for adequate collagen synthesis.

Enzymes may be inactivated by inhibitors or by becoming denatured. Enzyme activity can be modulated by chemical factors or by changes in temperature and pH. Figure 4.6 shows how enzyme activity can vary over a range of pH values. By turning reactions on and off or by increasing and decreasing the rate at which reactions take place, a cell can regulate the flow of biomolecules through different synthetic and energy-producing pathways.

FIG. 4.6 pH affects enzyme activity

Figure Question: If the pH falls from 8 to 7.4, what happens to the activity of the enzyme?

Concept Check

  1. What is a biological advantage of having multiple isozymes for a given reaction rather than only one form of the enzyme?

  2. The four protein chains of an LDH isozyme are an example of what level of protein structure? (a) primary (b) secondary (c) tertiary (d) quaternary

Enzymes Lower Activation Energy of Reactions

How does an enzyme increase the rate of a reaction? In thermodynamic terms, it lowers the activation energy, making it more likely that the reaction will start (Fig. 4.7). Enzymes accomplish this by binding to their substrates and bringing them into the best position for reacting with each other. Without enzymes, the reaction would depend on random collisions between substrate molecules to bring them into alignment.

FIG. 4.7 Enzymes lower the activation energy of reactions

The rate of a reaction catalyzed by an enzyme is much more rapid than the rate of the same reaction taking place without the enzyme. For example, consider carbonic anhydrase, which facilitates conversion of CO2 and water to carbonic acid. This enzyme plays a critical role in the transport of waste CO2 from cells to lungs. Each molecule of carbonic anhydrase takes one second to catalyze the conversion of 1 million molecules of CO2 and water to carbonic acid. In the absence of enzyme, it takes more than a minute for one molecule of CO2 and water to be converted to carbonic acid. Without carbonic anhydrase and other enzymes in the body, biological reactions would go so slowly that cells would be unable to live.

Enzymatic Reactions Can Be Categorized

Most reactions catalyzed by enzymes can be classified into four categories: oxidation-reduction, hydrolysis-dehydration, exchange-addition-subtraction, and ligation reactions. Table 4.4 summarizes these categories and gives common enzymes for different types of reactions.

Table 4.4 Classification of Enzymatic Reactions

Reaction Type What Happens Representative Enzymes
*Enzyme classes as defined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology, www.chem.qmul.ac.uk/iubmb/enzyme .

1. Oxidation-reduction

(a) Oxidation

(b) Reduction

Add or subtract electrons

Transfer electrons from donor to oxygen

Remove electrons and H+

Gain electrons

Class:* oxidoreductase

Oxidase

Dehydrogenase

Reductase

2. Hydrolysis-dehydration

(a) Hydrolysis

(b) Dehydration

Add or subtract a water molecule

Split large molecules by adding water

Remove water to make one large molecule from several smaller ones

Class:* hydrolase

Peptidases, saccharidases, lipases

Dehydratases

3. Transfer chemical groups

(a) Exchange reaction

(b) Addition

(c) Subtraction

Exchange groups between molecules

Add or subtract groups

Phosphate

Amino group (transamination)

Phosphate (phosphorylation)

Amino group (amination)

Phosphate (dephosphorylation)

Amino group (deamination)

Class:* transferases

Class:* lyases

Kinase

Transaminase

Phosphorylase

Aminase

Phosphatase

Deaminase

4. Ligation Join two substrates using energy from ATP

Class:* ligases

Synthetase

An enzyme’s name can provide important clues to the type of reaction the enzyme catalyzes. Most enzymes are instantly recognizable by the suffix -ase. The first part of the enzyme’s name (everything that precedes the suffix) usually refers to the type of reaction, to the substrate upon which the enzyme acts, or to both. For example, glucokinase has glucose as its substrate, and as a kinase it will add a phosphate group [here] to the substrate. Addition of a phosphate group is called phosphorylation.

A few enzymes have two names. These enzymes were discovered before 1972, when the current standards for naming enzymes were first adopted. As a result, they have both a new name and a commonly used older name. Pepsin and trypsin, two digestive enzymes, are examples of older enzyme names.

Oxidation-Reduction Reactions

Oxidation-reduction reactions are the most important reactions in energy extraction and transfer in cells. These reactions transfer electrons from one molecule to another. A molecule that gains electrons is said to be reduced. One way to think of this is to remember that adding negatively charged electrons reduces the electric charge on the molecule. Conversely, molecules that lose electrons are said to be oxidized. Use the mnemonic OIL RIG to remember what happens: Oxidation Is Loss (of electrons), Reduction Is Gain.

Hydrolysis-Dehydration Reactions

Hydrolysis and dehydration reactions are important in the breakdown and synthesis of large biomolecules. In dehydration reactions {de-, out + hydr-, water}, a water molecule is one of the products. In many dehydration reactions, two molecules combine into one, losing water in the process. For example, the monosaccharides glucose and fructose join to make one sucrose molecule [here]. In the process, one substrate molecule loses a hydroxyl group -OH and the other substrate molecule loses a hydrogen to create water, H2O. When a dehydration reaction results in the synthesis of a new molecule, the process is known as dehydration synthesis.

In a hydrolysis reaction {hydro, water + lysis, to loosen or dissolve}, a substrate changes into one or more products through the addition of water. In these reactions, the covalent bonds of the water molecule are broken (“lysed”) so that the water reacts as a hydroxyl group OH- and a hydrogen ion H+. For example, an amino acid can be removed from the end of a peptide chain through a hydrolysis reaction.

When an enzyme name consists of the substrate name plus the suffix -ase, the enzyme causes a hydrolysis reaction. One example is lipase, an enzyme that breaks up large lipids into smaller lipids by hydrolysis. A peptidase is an enzyme that removes an amino acid from a peptide.

Addition-Subtraction-Exchange Reactions

An addition reaction adds a functional group to one or more of the substrates. A subtraction reaction removes a functional group from one or more of the substrates. Functional groups are exchanged between or among substrates during exchange reactions.

For example, phosphate groups may be transferred from one molecule to another during addition, subtraction, or exchange reactions. The transfer of phosphate groups is an important means of covalent modulation [here], turning reactions on or off or increasing or decreasing their rates. Several types of enzymes catalyze reactions that transfer phosphate groups. Kinases transfer a phosphate group from a substrate to an ADP molecule to create ATP, or from an ATP molecule to a substrate. For example, creatine kinase transfers a phosphate group from creatine phosphate to ADP, forming ATP and leaving behind creatine.

The addition, subtraction, and exchange of amino groups [here] are also important in the body’s use of amino acids. Removal of an amino group from an amino acid or peptide is a deamination reaction. Addition of an amino group is amination, and the transfer of an amino group from one molecule to another is transamination.

Ligation Reactions

Ligation reactions join two molecules together using enzymes known as synthetases and energy from ATP. An example of a ligation reaction is the synthesis of acetyl coenzyme A (acetyl CoA) from fatty acids and coenzyme A. Acetyl CoA is an important molecule in the body, as you will learn in the next section.

Concept Check

  1. Name the substrates for the enzymes lactase, peptidase, lipase, and sucrase.

  2. Match the reaction type or enzyme in the left column to the group or particle involved.

    1. kinase

    2. oxidation

    3. hydrolysis

    4. transaminase

    1. amino group

    2. electrons

    3. phosphate group

    4. water