____________________________________________________________________________________________________ Subject Chemistry Paper No and Title 16; Bioorganic and Biophysical Chemistry Module No and Title 8; Introduction to Enzymes, their classification and nomenclature Module Tag CHE_P16_M8 Chemistry PAPER No. 16: BIO-ORGANIC AND BIOPHYSICAL CHEMISTRY MODULE No. 8: Introduction to Enzymes, their nomenclature & classification ____________________________________________________________________________________________________ TABLE OF CONTENTS 1. Learning Outcomes 2. Introduction 3. Introduction to Enzymes 3.1 Enzymes are biocatalysts 3.2 History of Enzymology 3.3 Interaction of Enzyme with substrate 3.4 Cofactors and coenzymes 4. Nomenclature and classification of enzymes 4.1 Common names 4.2 IUBMB classification and nomenclature 5. Summary Chemistry PAPER No. 16: BIO-ORGANIC AND BIOPHYSICAL CHEMISTRY MODULE No. 8: Introduction to Enzymes, their nomenclature & classification ____________________________________________________________________________________________________ 1. Learning Outcomes After studying this module, you shall be able to: • Know what are enzymes and how they are different from chemical catalysts • Learn history f discovery of enzymes • How to enzymes recognize their substrates? • Know enzymes require cofactors and coenzymes beyond amino acids which it is made of. • Learn how enzymes are named. 2. Introduction Enzymes are biological catalysts Mostly enzymes are proteins which possess catalytic activity. Enzymes were discovered in 18th century. They recognize their specific substrate and bind to them via a cleft termed as substrate binding site. Once they bind the substrate, they carry out the reaction and release products. For this binding, they require structural as well as electronic complementarity with the substrate. They mediate the reactions at physiological pH and temperature at rates much higher than the uncatalyzed reactions. Some enzymes carry out catalysis by virtue of amino acids that they are made of, while some require additional cofactors and coenzymes for full catalytic activity. Enzymes are named by four digit nomenclature as well as common names. This chapter also discusses the history of enzymology. 3. Introduction to Enzymes 3.1 Enzymes are biocatalysts The term enzyme was coined by Wilhelm Friedrich Kuhne in 1878. Enzymes are biological catalysts that differ from chemical catalysts in following features: (a) They work milder reaction conditions unlike chemical catalysts. Enzymes work physiological temperature and pH for their activity. (b) Enzymes have higher reaction specificity. They bind to specific substrate, carry the catalytic reaction and release specific products. (c) Enzymes enhance the rates of reaction they catalyze by several orders of magnitude when compared with uncatalysed reactions. The rates of enzyme catalyzed reactions are much higher than the reactions catalyzed by chemical catalysts. Chemistry PAPER No. 16: BIO-ORGANIC AND BIOPHYSICAL CHEMISTRY MODULE No. 8: Introduction to Enzymes, their nomenclature & classification ____________________________________________________________________________________________________ Table 1: Enzyme enhance the rates of reactions compared to uncatalyzed reactions. Name of the Enzyme Fold enhancement in rate Carboxypeptidase A 1011 Urease 1014 Triose phosphate isomerase 109 (d) Enzyme catalyzed reactions are well regulated. These reaction rates are not only influenced by substrate or product concentrations but also can be regulated by covalent modifications of enzymes etc. Most enzymes are proteinecous in nature but RNA enzymes also exist. RNA enzymes are ribozymes. 3.2 History of Enzymology Research work on fermentation by Joseph Gay Lussac determined that yeast decomposes sugar into carbon dioxide and ethanol. Jacob Berzelius proposed that the malt extract (diastase) catalyzes starch hydrolysis much efficiently than chemical catalyst H2SO4. However, in mid nineteenth century, Louis Pasteur proposed that fermentation can only take place in living cells. The term enzyme was coined by W.H. Kuhne in 1878. Eduard Buchner in 1897 showed fermentation in cell free extracts illustrating that fermentation can occur outside the living cells. He named the enzyme responsible for fermentation of sucrose ‘zymase’. In 1907, he received Nobel Prize in Chemistry for his pioneer work on discovery of cell free fermentation. In 1926, James Sumner gave identity to the enzymes. His work on jack bean urease (which catalyzes hydrolysis of urea to ammonia and carbon dioxide) proved that enzymes are pure proteins. He crystallized urease. The crystals consisted entirely of proteins. But his work was not accepted till John Northrop and Moses Kunitz showed correlation of activities of enzymes— pepsin, trypsin and chymotrypsin with the amount of protein. In 1946, these three scientists were then awarded Nobel Prize in Chemistry. In 1963, the amino acid sequence of the first enzyme bovie pancreatic ribonuclease A was given and in 1965, the first enzyme whose X-ray structure was worked out was that of hen egg white lysozyme by David Phillips. 3.3 Interaction of Enzyme with Substrate Chemistry PAPER No. 16: BIO-ORGANIC AND BIOPHYSICAL CHEMISTRY MODULE No. 8: Introduction to Enzymes, their nomenclature & classification ____________________________________________________________________________________________________ 3.3.1 Geometric and Electronic complementarity Van der Waals forces, hydrophobic interactions and H-bonding are the noncovalent forces driving interactions between substrate and product. Substrate binding site in enzyme is a cleft in the enzyme in which the substrate fits. This is called the geometric or physical complementarity (Figure 1). Figure 1. Depiction of geometric and electronic complementarity between substrate and enzyme. The amino acids that form the substrate binding site of the enzyme form attractive interaction with the substrate. This is termed as electronic complementarity (Figure 1). 3.3.2 Models of substrate binding to enzyme Two models have been proposed for substrate binding to enzyme: (a) Lock and key model In 1894, Emil Fischer proposed that both enzyme and substrate possess geometric shapes complementary to each other such that substrate perfectly fits the substrate binding site of the enzyme just like a key fits into the lock. Most importantly, enzyme possesses the substrate binding site even in the absence of the substrate. Chemistry PAPER No. 16: BIO-ORGANIC AND BIOPHYSICAL CHEMISTRY MODULE No. 8: Introduction to Enzymes, their nomenclature & classification ____________________________________________________________________________________________________ A B Figure 2. (A) The lock and key model of substrate binding to enzyme. (B) induced fit model. (b) Induced fit model Induced fit model was proposed by Daniel Koshland in 1958. He suggested that the substrate binding site is not rigid but reshapes or moulds itself after initial interaction with the substrate (Figure 2B) to bind the substrate perfectly. 3.4 Cofactors and Coenzymes Most enzymes are proteins composed entirely of amino acids. Few enzymes require additional chemical moieties other than amino acids. These chemical moieties are termed as cofactors. For example: Hexokinase requires Mg2+ for its catalytic activity. These cofactors can be inorganic or organic moieties. If they are organic in nature, they are termed as ‘coenzymes’. These coenzymes are derived from vitamins. Few examples of cofactors and coenzymes have been listed in Table 1. Cofactor/ Coenzymes Enzymes Mg2+ Hexokinase Zn2+ Carbonic anhydrase Ni2+ Urease Biotin (Coenzyme form-Biocytin) Pyruvate carboxylase Vitamin B / Riboflavin (Flavin adenine 2 Succinate dehydrogenase dinucleotide) Vitamin B12 (Coenzyme B12) Methionine synthase Vitamin B /Thiamin (Thiamine 1 Pyruvate dehydrogenase pyrophosphate) Chemistry PAPER No. 16: BIO-ORGANIC AND BIOPHYSICAL CHEMISTRY MODULE No. 8: Introduction to Enzymes, their nomenclature & classification ____________________________________________________________________________________________________ Some enzymes can require both metal ions and coenzymes for their activity. If the metal ion or coenzyme is tightly bound to the enzyme, it is termed as prosthetic group. The enzyme without the prosthetic group is called the apoenzyme. Along with the prosthetic group, it is called holoenzyme. Holoenzyme is thus the complete catalytically active form of the enzyme. ���������� → ��������� + �������� 4. Nomenclature and Classification of Enzymes 4.1 Common names The enzymes are named by adding suffix ‘-ase’ to the name of the substrate or their activity. For example: Hexokinase mediates phosphorylation of hexoses; Urease catalyzes the hydrolysis of urea. RNA polymerase catalyzes the polymerization of ribonucleotides to form RNA. 4.2 IUBMB classification and nomenclature With the increasing number of enzymes, common names became less popular to avoid same names of two enzymes and one enzyme carrying different names. Hence, to avoid this confusion, International Union of Biochemistry and Molecular Biology (IUBMB) adopted a systematic classification and nomenclature of enymes. According to this classification, enzymes are functionally classified into six classes (Table 3). Class 1 belongs to all the oxidoreductases, Class 2 to transferases and so on. These classes have been subdivided into subclasses and sub- subclasses. Each enzyme has been allotted two names and four digit classification.