YIJC [H2] CI1.3 Enzymes (N)

2024 JC1 H2 Biology Lecture Notes 1 CORE IDEA 1: THE CELL AND BIOMOLECULES OF LIFE TOPIC 1.3: ENZYMES Learning Outcomes: (p) Explain the mode of action of enzymes in terms of an active site, enzyme-substrate complex, lowering of activation energy and enzyme specificity using lock -and-key and induced -fit hypotheses. (q) Investigate and explain the effects of temperature, pH, enzyme concentration and substrate concentration of an enzyme-catalysed reaction by measuring rates of formation of products (e.g. measuring gas produced using catalase) or rate of disappearance of substrate (e.g. using amylase, starch and iodine). (r) Describe the structure of competitive and non-competitive inhibitors with reference to the binding sites of the inhibitors. (s) Explain the effects of competitive and non-competitive inhibitors (including allosteric inhibitors) on the rate of enzyme activity. References Campbell, Urry, Cain, Wasserman, Min orsky, Reece (2018) Biology – A Global Approach (11 th Edition)(Global Edition) Chapter 6: Energy and Life pg. 151 – 161 (Pearson Publication) ISBN- 10 1-292-17043-3 Lecture Outline: 1 Introduction 2 Properties of Enzymes 3 Mode of Action of Enzymes 4 Enzyme Kinetics 5 Factors Affecting Enzyme Activity 6 Enzyme Inhibition 7 Allosteric Regulation H2

2 1 INTRODUCTION Enzymes are biological catalysts which speed up the rate of metabolic reactions while remaining unchanged at the end of the reaction. Metabolic reactions are spontaneous (can occur without enzymes) but they occur at a very slow rate. Thus, enzymes are needed to speed up the se reactions. They are involved i n almost all biochemical reactions in living organisms including respiration, photosynthesis, digestion and biosynthesis of macromolecules. Fig. 1.1: Overview of metabolic reactions in a generalised animal cell Metabolic reactions can be classified into catabolic and anabolic reactions: Anabolic Reactions Catabolic Reactions Synthesis of complex molecules from simpler molecules Breakdown of complex molecules into simpler molecules Energy required Energy released E.g. Formation of glycogen from glucose, catalysed by glycogen synthase E.g. Breakdown of sucrose to glucose and fructose, catalysed by sucrase (a) Anabolic reaction via condensation (b) Catabolic reaction via hydrolysis Fig. 1.2: Anabolic and catabolic reactions

3 DID YOU KNOW? Not all enzymes are pro tein in nature. Molecules like RNA can also have catalytic functions. RNA that functions as enzymes are known as ribozymes. E.g. An RNA molecule found in ribosome, called peptidyl transferase, catalyses formation of peptide bond between amino acids during protein synthesis. (Details will be covered in Core Idea 2) 2 PROPERTIES OF ENZYMES 2.1 Enzymes are specific Enzymes have a specific active site which recognises and binds to specific groups of atoms or type of bond present in the substrates. Thus, most enzymes are specific to one particular type of substrate molecule e.g. amylase hydrolyses amylose but not cellulose. 2.2 Enzymes are effective in minute amounts Enzymes can catalyse a reaction repeatedly without unde rgoing permanent chemical changes itself i.e. it remains unchanged at the end of the chemical reaction. 2.3 Some enzymes require the aid of cofactors to perform their functions Cofactors are non-protein components that are required for the functioning of the enzyme. Types of cofactors include: 1. Inorganic ions E.g. Zn2+ acts as a cofactor for carbonic anhydrase 2. Coenzymes Coenzymes are organic molecules (contains C and H) that are loosely bound to enzymes. E.g. Nicotinamide adenine dinucleotide (NAD+) is a coenzyme for dehydrogenase involved in cellular respiration. (Details will be covered in Core Idea 3) 3. Prosthetic groups Prosthetic groups are organic molecules that remain tightly bound to enzymes. E.g. haem is an iron -containing porphyrin ring found in catalases and peroxidases, which catalyse the decomposition of hydrogen peroxide into water and oxygen.

4 3 MODE OF ACTION OF ENZYMES Enzymes are mostly globular proteins, each having a specific three-dimensional conformation. Fig. 3.1: 3D conformation of amylase Amino acids that make up the enzyme have different functions (Ref. to Fig. 3.2): 1. Contact residues. Amino acids that recognise and bind substrate(s) to active site via multiple weak non-covalent interactions. 2. Catalytic residues. Amino acids that catalyse the conversion of substrate to product. Contact and catalytic residues are found in the active site of the enzyme. 3. Structural residues. Amino acids are involved in maintaining the overall three-dimensional conformation of the enzyme. 4. Non-essential residues are generally found on the surface of the protein. They are a mino acids which do not play specific functions. Learning Outcome (p): Explain the mode of actions of enzymes in terms of active site, enzyme-substrate complex, lowering of activation energy and enzyme specificity using lock-and-key and induced-fit hypothesis.

5 Fig. 3.2: Folding of a linear polypeptide chain to form the 3D conformation of an enzyme. 3.1 Active Site Although the enzyme molecule is usually a relatively large molecule, only a small part of the enzyme, known as the active site, actually comes into direct contact with the substrate. Fig. 3.3: Active site of enzyme that binds to the substrate

6 The active site is formed by small number of amino acids from different parts of a single polypeptide chain brought together through the precise folding of the polypeptide chain. REMEMBER: Contact and catalytic residues are found in the active site of the enzyme. It has a specific three-dimensional conformation that is complementary to its substrate in terms of shape, size, charge and orientation. 3.2 Enzyme-Substrate Complex The s ubstrate binds t o active site of enzyme to form an enzyme-substrate complex (ES complex). The substrates are held in active site by contact residues via non -covalent bonds such as hydrogen bonds, ionic bonds and hydrophobic interactions. enzyme + substrate(s) → enzyme-substrate complex → enzyme + product(s) The R groups of the of the catalytic amino acid residues catalyse the conversion of substrate to product. Once the products are formed, they are no longer complementary to the active site and thus will leave the enzyme. The enzyme is then available to act on other substrates. Fig. 3.4: Enzymatic reaction 3.3 Mode of Action There are two hypotheses as to how an enzyme recognises and binds to its substrate: 1 Lock-and-key hypothesis 2. Induced fit hypothesis (i) Lock-and-key hypothesis The enzyme’s active site is perfectly complementary to the substrate in terms of sha pe, size, charge and orientation. The substrate binds to enzyme’s active site precisely to form the enzyme-substrate complex. This mode of activation is more probable for enzymes that work on only one type of substrate. Fig. 3.5: Lock-and-key hypothesis

7 (ii) Induced fit Hypothesis The enzyme’s active site is not perfectly complementary to the substrate in terms of shape, size, charge and orientation. Upon forming some bonds with the substrate, the enzyme undergoes a conformational change, which leads to a precise fit to form the enzyme-substrate complex. This mode of action is more probable for enzymes that work on a group of closely -related substrates, e.g. lipases. Fig. 3.6: Induced fit hypothesis 3.4 Lowering Activation Energy Activation energy (EA) is the initial investment of energy that reactant molecules must possess to overcome an energy barrier, for a reaction to begin. For uncatalysed reactions, EA is usually in the form of thermal energy (heat) t hat