Biochemistry and Human Nutrition

Module 2. Enzymes

Lesson7
ENZYME CATALYSIS AND CLASSIFICATION

7.1 Introduction

Enzymes are biologic polymers that catalyze the chemical reactions. With the exception of a few catalytic RNA molecules, or ribozymes, the vast majority of enzymes are proteins.

• The enzymes catalyze the conversion of one or more compounds (substrates) into one or more different compounds (products).
• They enhance the rates of the corresponding non-catalyzed reaction. Catalysts do not affect reaction equilibria.
• Like all catalysts, enzymes are neither consumed nor permanently altered as a consequence of their participation in a reaction.
• Their catalytic activity depends on the integrity of their native protein conformation. If an enzyme is denatured or dissociated into its subunits, catalytic activity is usually lost. If an enzyme is broken down into its component amino acids, its catalytic activity is always destroyed.
• The primary, secondary, tertiary, and quaternary structures of protein enzymes are essential to their catalytic activity.

7.2 Enzymes are Highly Specific Catalysts

Enzymes are also extremely selective catalysts. Unlike most catalysts used in synthetic chemistry, enzymes are specific both for the type of reaction catalyzed and for a single substrate or a small set of closely related substrates.

• Enzymes are substrate specific or group specific Conformation of complex proteins and uniqueness of active site of enzymes make them substrate specific or absolute group specific. For example glucokinase recognize glucose as absolute substrate while hexokinase recognizes aldohexose (Glucose or mannose etc) as substrate. Similarly, trypsin, chymotrypsin and elastase cleaves proteins or polypeptides on carboxyl side of positively charged (Lysine, Arginine), aromatic amino acids (Tyrosine, Phenylalanine) and small group side chains (alanine, glycine) amino acids respectively. (Fig. 7.1 Substrate specificity of enzymes)
  

• Enzymes are also stereospecific catalysts and typically catalyze reactions only of specific stereoisomers of a given compound—for example, D- but not L-sugars, L- but not D-amino acids.
  

• Enzymes show geometric specificity

Fig. 7.2 Geometric Specificity of Enzymes

• Enzyme Since they bind substrates through at least “three points of attachment,” enzymes can even convert nonchiral substrates to chiral products.

7.3 Enzyme Active Site

7.3.1 Common features of enzyme active site

• The active site of an enzyme is generally a pocket or cleft that is specialized to recognize specific substrates and catalyze chemical transformations. Hence, the enzyme and substrate should have complementary shapes.
• The active site takes up a relatively small part of the total volume of an enzyme.
• It is formed in the three-dimensional structure by a collection of different amino acids (active-site residues) that may or may not be adjacent in the primary sequence.
• The interactions between the active site and the substrate occur via the same forces that stabilize protein structure: hydrophobic interactions, electrostatic interactions (charge–charge), hydrogen bonding, and Vander Waals interactions.
• Enzyme active sites do not simply bind substrates; they also provide catalytic groups to facilitate the chemistry and provide specific interactions that stabilize the formation of the transition state for the chemical reaction. (Fig. 7.3 Active site)

During a chemical reaction, the structure of the substrate changes into the structure of the product. Somewhere in between, some bonds are partly broken; others are partly formed. The transition state is the highest- energy arrangement of atoms that is intermediate in structure between the structure of the reactants and the structure of the products. The diagram shows the free energy of the reactants, transition state, and product. The free-energy difference between the product and reactant is the free-energy change for the overall reaction. The free-energy change between the products and reactants tells you how favorable the reaction is thermodynamically. It does not tell you anything about how fast it is. Reactions don’t all occur with the same rate. Some energy must be put into the reactants before they can be converted to products. This activation energy provides a barrier to the reaction—the higher the barrier, the slower the reaction. The difference in free energy between the transition state and the reactant(s) is called the free energy of activation. (Fig. 7.4)

Reaction rates can be increased by raising the temperature, thereby increasing the number of molecules with sufficient energy to overcome the energy barrier. Alternatively, the activation energy can be lowered by adding a catalyst (Fig.). Catalysts enhance reaction rates by lowering activation energies. The role of enzymes is to accelerate the interconversion of S and P. The enzyme is not used up in the process, and the equilibrium point is unaffected. However, the reaction reaches equilibrium much faster when the appropriate enzyme is present, because the rate of the reaction is increased.

7.4 Enzyme Classification

Many enzymes have been named by adding the suffix “-ase” to the name of their substrate or to a word or phrase describing their activity. Thus urease catalyzes hydrolysis of urea, and DNA polymerase catalyzes the polymerization of nucleotides to form DNA. Some enzymes were named by their discoverers for a broad function, before the specific reaction catalyzed was known. For example, lysozyme was named for its ability to lyse bacterial cell walls. Sometimes the same enzyme has two or more names, or two different enzymes have the same name. Because of such ambiguities, and the ever increasing number of newly discovered enzymes, biochemists, by international agreement, have adopted a system for naming and classifying enzymes. This system divides enzymes into six classes, each with subclasses, based on the type of reaction catalyzed . Each enzyme is assigned a four-part classification number and a systematic name, which identifies the reaction it catalyzes. As an example, the formal systematic name of the enzyme catalyzing the reaction

is ATP:glucose phosphotransferase, which indicates that it catalyzes the transfer of a phosphoryl group from ATP to glucose. Its Enzyme Commission number (E.C.number) is 2.7.1.1. The first number (2) denotes the major class name (transferase); the second number (7), the subclass (phosphotransferase); the third number denotes sub-subclass (1), a phosphotransferase with a hydroxyl group as acceptor; and the fourth number (1) denotes the enzyme number in the sub-subclass.

7.4.1 International classification of enzymes

Table 7.1 International classification of enzymes

7.5 Cofactors

Enzymes, like other proteins, have molecular weights ranging from about 12,000 to more than 1 million. Some enzymes require no chemical groups for activity other than their amino acid residues. Others require an additional chemical component called a cofactor—either one or more inorganic ions, such as Fe²⁺, Mg²⁺, Mn²⁺, or Zn²⁺, or a complex organic or metalloorganic molecule called a coenzyme. Some enzymes require both a coenzyme and one or more metal ions for activity. A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein is called a prosthetic group. A complete, catalytically active enzyme together with its bound coenzyme and/or metal ions is called a holoenzyme. The protein part of such an enzyme is called the apoenzyme or apoprotein. Coenzymes act as transient carriers of specific functional groups. Most are derived from vitamins, organic nutrients required in small amounts in the diet.

7.6 Some Inorganic Elements as Cofactors for Enzymes

7.7 Coenzymes as Transient Carriers of Specific Atoms or Functional Group

Table 7.2 Coenzymes as transient carriers of specific atoms or functional group