1.2 Enzyme Classification.pptx

Enzymes activity 8/21/2024 Diagnostic Clinical chemistry-II 1 Enzymes nomenclature and classification The human body is composed of different types of cells, tissues and other complex organs. For efficient functioning, the body releases some chemicals to accelerate bi...

Enzymes activity 8/21/2024 Diagnostic Clinical chemistry-II 1 Enzymes nomenclature and classification The human body is composed of different types of cells, tissues and other complex organs. For efficient functioning, the body releases some chemicals to accelerate biological processes such as respiration, digestion, excretion and few other metabolic activities to sustain a healthy life. Hence, enzymes are pivotal in all living entities which govern all the biological processes. 8/21/2024 Diagnostic Clinical chemistry-II 2 Enzyme nomenclature Enzymes were assigned various trivial names as they were discovered, which are convenient to use. For example, sucrase, lactase and urease are the commonly used names for the enzymes that catalyze hydrolysis of sucrose, lactose and urea, respectively. These enzymes have been named by attaching the suffix-ase to the respective substrates 8/21/2024 Diagnostic Clinical chemistry-II 3 Ambiguity of adding (suffix –ase) The nomenclature by adding suffix – ase may lead to ambiguities; For example, fumarase, a citric acid cycle enzyme, does not catalyze hydrolysis of its substrate, fumarate. Rather, it catalyzes addition of a water molecule to fumarate. 8/21/2024 Diagnostic Clinical chemistry-II 4 Standard enzyme nomenclature To remove ambiguities associated with use of such trivial names and to establish a uniform system for enzyme nomenclature and classification the Enzyme Commission (EC) of the IUB (International union of Biochemistry) adopted a classification system in 1961; the standards were revised in 1972 and 1978. The IUB system assigns a systematic name to each enzyme, defining the substrate acted on, the reaction catalyzed, and, possibly, the name of any coenzyme involved in the reaction. 8/21/2024 Diagnostic Clinical chemistry-II 5 IUB System of Enzyme Classification In addition to naming enzymes, the IUB system identifies each enzyme by an EC numerical code containing four digits separated by decimal points. As per this system, the name starts with EC (enzyme class) followed by 4 digits. First digit: represents the class, Second digit: stands for the subclass (group) Third digit: is the sub-subclass or subgroup, Fourth digit: gives the serial number of the particular enzyme 8/21/2024 Diagnostic Clinical chemistry-II 6 IUB System of Enzyme Classification EC numbers are four digits, for example a.b.c.d, where “a” is the class, “b” is the subclass, “c” is the sub-subclass, and “d” is the sub-sub-subclass. The “b” and “c” digits describe the reaction, while the “d” digit is used to distinguish between different enzymes of the same function based on the actual substrate in the reaction. 8/21/2024 Diagnostic Clinical chemistry-II 7 Enzymes Classification According to the International Union of Biochemists (I U B), enzymes are divided into six functional classes and are classified based on the type of reaction in which they are used to catalyze. The six kinds of enzymes are oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases. 8/21/2024 Diagnostic Clinical chemistry-II 8 EC 1.Oxidoreductases Biochemical Activity: Catalyse Oxidation/Reduction Reactions Act on many chemical groupings to add or remove hydrogen atoms. Example: Lactate dehydrogenase (EC 1.1.1.27) EC 2: Transferases Biochemical Activity: Transfer a functional groups (e.g. methyl or phosphate) between donor and acceptor molecules. Examples:Alanine transaminase (EC 2.6.1.2) 8/21/2024 Diagnostic Clinical chemistry-II 9 EC 3. Hydrolases Biochemical Activity: Catalyse the hydrolysis of various bonds Add water across a bond. Examples: Triacylglycérol lipase (EC 3.1.1.3) EC4. Lyases Biochemical Activity: Catalyze removal of groups from substrates without hydrolysis; the product contains double bonds. Examples: Pyruvate decarboxylase (EC 4.1.1.1) 8/21/2024 Diagnostic Clinical chemistry-II 10 EC 5. Isomerases Biochemical Activity: Catalyze the inter-conversion of geometric, optical, or positional isomers Examples: Alanine racemase (EC 5.1.1.1) EC6. Ligases Biochemical Activity: Catalyze the joining of two substrate molecules, coupled with breaking of the pyrophosphate bond in adenosine triphosphate (ATP) or a similar compound. Examples: Pyruvate carboxylase(EC 6.4.1.1) 8/21/2024 Diagnostic Clinical chemistry-II 11 Review Question Match the type of reaction with the following classes of enzymes: (1) Aminase (2) lLyase (3) Isomerase (4) Synthetase 3 A. Converts a cis-fatty acid to trans. 2 B. Removes 2 H atoms to form a double 4 bond C. Combine two molecules using ATP 1 D. Adds NH3 8/21/2024 Diagnostic Clinical chemistry-II 12 Catalytic activity of enzymes The amount of an enzyme in a given solution or tissue extract can be assayed in terms of the catalytic effect it produces. In an enzyme-catalyzed reaction, the catalytic activity of the enzyme is reflected by the rate at which the substrate is transformed into the product. The greater the rate of transformation, the more enzyme activity, and vice versa. Rate of transformation may be estimated from the rate of appearance of product and/or the rate of disappearance of the substrate. 8/21/2024 Diagnostic Clinical chemistry-II 13 Catalytic activity of enzymes Enzymes are characterized by two fundamental properties: First, they increase the rate of chemical reactions without themselves being consumed or permanently altered by the reaction. Second, they increase reaction rates without altering the chemical equilibrium between reactants and products, 8/21/2024 Diagnostic Clinical chemistry-II 14 Enzyme catalysis Enzyme catalysis is the increase in the rate of reaction which is occurs at a localized site, called the active site. Mechanisms of enzyme catalysis vary but are all similar in principle to other types of chemical catalysis in that the crucial factor is a reduction of energy barrier(s) separating the reactants from the products. The reduction of activation energy (Ea) increases the fraction of reactant molecules that can overcome this barrier and form the product. Enzymes always catalyze reactions in both directions and cannot drive a reaction forward or affect the equilibrium position - only the speed with which is it achieved. the enzyme is not consumed or changed by the reaction (as a substrate is) but is recycled. 8/21/2024 Diagnostic Clinical chemistry-II 15  Transition state 8/21/2024 Diagnostic Clinical chemistry-II 16 Enzymatic reactions energy The single most important property of enzymes is the ability to increase the rate of chemical reactions occurring in living organisms, a property known as catalytic activity. Enzymes speed up the rate of reactions because they lower the energy required to get to the transition state of the reaction. The transition state of the reaction is an unstable intermediate structure formed during the reaction process. 8/21/2024 Diagnostic Clinical chemistry-II 17 Enzymatic reactions energy The transition state has the highest energy of the reaction and is noted on the Gibbs Free Energy Diagram as the pinnacle of the ‘hill’ that occurs between the reactant and product energies. When enzymes or catalysts are present, the transition state energy is lowered, which in turn has an exponential effect on the reaction rate. Thus, enzymes can increase the reaction rate by many orders of magnitude. 8/21/2024 Diagnostic Clinical chemistry-II 18 Components of enzymatic reaction Substrate: the molecule upon which an enzyme acts. Product: the molecule obtained as a result of the enzyme’s action. Active site: part of the enzyme that binds to the substrate during a chemical reaction. Reaction rate: how an enzyme works. It is measured by changes in concentration of either the substrate or Diagnostic 8/21/2024 the product as Clinical chemistry-II 19 Components of enzymatic reaction 8/21/2024 Diagnostic Clinical chemistry-II 20 Enzyme and Substrate specificity Enzymes bind with chemical reactants called substrates. There may be one or more substrates for each type of enzyme, depending on the particular chemical reaction. In some reactions, a single-reactant substrate is broken down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction, both become modified and leave the reaction as two products. 8/21/2024 Diagnostic Clinical chemistry-II 21 Enzyme active site The enzyme’s active site binds to the substrate. Since enzymes are proteins, this site is composed of a unique combination of amino acid residues (side chains or R groups). The positions, sequences, structures, and properties of these residues create a very specific chemical environment within the active site. Each amino acid residue can be large or small; weakly acidic or basic; hydrophilic or hydrophobic; and positively charged, negatively charged, or neutral. 8/21/2024 Diagnostic Clinical chemistry-II 22 Enzyme and Substrate specificity 8/21/2024 Diagnostic Clinical chemistry-II 23 Active Sites and Environmental Conditions Environmental conditions can affect an enzyme’s active site and, therefore, the rate at which a chemical reaction can proceed. Increasing the environmental temperature increases reaction rates because the molecules are moving more quickly and are more likely to come into contact with each other. 8/21/2024 Diagnostic Clinical chemistry-II 24 Active Sites and Environmental Conditions However, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the enzyme and change its shape. If the enzyme changes shape, the active site may no longer bind to the appropriate substrate and the rate of reaction will decrease. Dramatic changes to the temperature and pH will eventually cause enzymes to denature. 8/21/2024 Diagnostic Clinical chemistry-II 25 Induced Fit and Enzyme Function This model asserted that the enzyme and substrate fit together perfectly in one instantaneous step. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme’s structure that confirms an ideal binding arrangement between the enzyme and the substrate. This dynamic binding maximizes 8/21/2024 Diagnostic Clinical chemistry-II 26 The general mechanism is Explanation: that an enzyme acts by Enzymes catalyse the A. Reducing the activation biochemical reactions by energy participating as a catalyst they are simply responsible for B. Increasing activation increasing the rate of reaction. energy Enzymes catalyse a reaction by binding substrate to the active C. Decreasing pH value site and various non-covalent D. Increasing the pH value interactions are formed and broken which provides energy. Answer is: This energy from bond formation and breakage counteracts the A. Reducing the activation activation barrier thus lowering energy the activation energy. 8/21/2024 Diagnostic Clinical chemistry-II 27 The coenzyme is: Explanation: Coenzymes are chemical A. Often a metal molecules that are required for catalytic activity by numerous B. always a protein enzymes. C. often a vitamin Vitamins or vitamin D. always an inorganic compounds are often used. compound In the absence of enzymes, they can operate as catalysts, Answer is: although not as effective as C. Often a vitamin when used in combination with an enzyme. 5-Deoxyadenosylcobalamin (coenzyme B12), flavin adenine dinucleotide, and lipoate are examples of 8/21/2024 common coenzymes. Diagnostic Clinical chemistry-II 28 Enzyme catalysing rearrangement of atomic grouping without altering molecular weight or number of atom is: Explanation: Isomerases are enzymes that A. Ligase aid in the conversion of a chemical substance from one B. Isomerase isomeric form to another by C. Oxidoreductase catalysing isomerization modifications in a molecule. D. Hydrolase Isomerization is the process of Answer is: converting one isomer into another. Any of two or more B. Isomerase versions of a molecule having the same chemical formula but a distinct stereochemical arrangement of the atoms is referred to as an isomer. 8/21/2024 Diagnostic Clinical chemistry-II 29 This statement about Explanation: enzymes is true: Enzymes catalyze the A. Enzymes accelerate reactions by lowering the activation energy biochemical reaction, they B. Enzymes are proteins whose three- increase the rate of dimensional form is key to their reaction by lowering the function activation barrier. C. Enzymes do not alter the overall change in free energy for a reaction They are generally tertiary D. All of these and quaternary proteins, Answer is: they are not consumed in D. All of these the reaction. 8/21/2024 Diagnostic Clinical chemistry-II 30 Which among them is Explanation: a cofactor: A cofactor is an apoprotein A. Inorganic ion that has a metal ion or one or more inorganic ions linked to B. Organic molecule it. Mg2+, Fe2+, Zn2+, and Mn2+ C. Both A and B are examples of common cofactors. D. None of these Metallic cofactors are used by Answer is: enzyme examples including C. Both A and B Cytochrome oxidase, catalase, peroxidase, pyruvate kinase, hexokinase, and glucose 6- phosphatase. In conclusion of the article, we have discussed multiple questions that will help in 8/21/2024 understanding the enzyme. 31 Diagnostic Clinical chemistry-II