Topic C Enzymes H1H2 2015

NANYANG JUNIOR COLLEGE H1 / H2 Biology Enzymes J1/2015 1 TOPIC C: ENZYMES Learning Outcomes Core Topic 1: Cellular Functions Candidates should be able to: (h) Explain the mode of action of enzymes in terms of an active site, enzyme/ substrate complex, lowering of activation energy and enzyme specificity. (i) Follow the time course of an enzyme -catalysed reaction by measuring rates of formation of products (e.g. using catalase) or rate of disappearance of substrate (e.g. using amylase). (j) Investigate and explain the effects of temperature, pH, enzyme concentration and substrate concentration on the rate of enzyme catalysed reactions, and explain these effects. (k) Explain the effects of competitive and non -competitive inhibitors (including allosteric inhibitors) on the rate of enzyme activity. Content Outline 1. Introduction 2. Characteristics of Enzymes (a) Common Properties of Enzymes 3. Mode of Action of Enzymes (a) Active Site (b) Enzyme specificity (c) Enzyme-Substrate Complex (d) Activation Energy 4. Enzyme Kinetics (a) Measurement of Enzyme Kinetics (b) Measurement of Enzyme Affinitiy 5. Factors Affecting Enzyme Activity (a) Substrate Concentration (b) Enzyme Concentration (c) Temperature (d) pH 6. Enzyme Inhibition (a) Competitive Inhibition (b) Non-competitive Inhibition (c) Reversible Inhibition (d) Irreversible Inhibition

NANYANG JUNIOR COLLEGE H1 / H2 Biology Enzymes J1/2015 2 References 1. Boyle, M. and Senior, K. (200 2) Biology. Chapter 5: Enzymes and Metabolism . Harper Collins Publishers Limited. 2. Campbell, N. A. and Reece J.B. (2008) Biology. Chapter 8: An Introduction to Metabolism . Eighth Edition. Pearson Education, Inc. 3. Jones, M. and Jones, G. (2004) Advanced Biology. Chapter 2 : Enzymes . Cambridge University Press. 1. Introduction Enzymes catalyse biological reactions. Thus, they are also called biological catalyst s. Most biological catalysts are globular proteins. However, some enzymes are RNA molecules known as ribozymes. For example, peptidyl transferase activity found in ribosome is mediated by the ribosomal RNA in the large subunit. They are important as many metabolic reactions, though spontaneous, occur at a very slow rate. Thus, enzymes are needed to speed up the se reactions. They are involved in almost all biochemical reactions in living organisms including respiration, photosynthesis, digestion and biosynthesis of macromolecules. Enzymes are usually classified according to the type of reaction they catalyse and they can be named according to their substrates (i.e. reactants that enzymes act on). Classification of Enzymes Class of Enzyme Type of Reaction Catalysed Examples Oxidoreductase Transfers electrons, oxygen atom or hydrogen atom between molecules, i.e. oxidation-reduction reactions Dehydrogenases Oxidases Transferase Transfers a functional group from one molecule to another molecule e.g. phosphate group Kinases Phosphorylases Hydrolase Carries out hydrolysis reactions Sucrase Lipases Proteases Lyase Removes a functional group from one molecule without hydrolysis Decarboxylases Isomerase Rearranges groups of atoms within a molecule Isomerases Ligase Forms bonds between two molecules using energy derived from the breakdown of ATP Synthetases Ligases Note: The names of enzymes usually ends with ‘-ase’.

NANYANG JUNIOR COLLEGE H1 / H2 Biology Enzymes J1/2015 3 2. Characteristics of Enzymes Enzymes are defined as biological catalyst s which speed up the rate of metabolic reactions (both catabolic and anabolic) while remaining chemically unchanged at the end of the reaction. Metabolic reactions can be classified into catabolic and anabolic reactions. (i) Anabolic reactions refer to reactions where complex molecules are built from simpler molecules using energy (e.g. photosynthesis). (ii) Catabolic reactions refer to reactions where complex molecules are broken down into simpler molecules and energy is usually released (e.g. respiration). Diagram showing anabolic reaction and catabolic reaction

NANYANG JUNIOR COLLEGE H1 / H2 Biology Enzymes J1/2015 4 (a) Common Properties of Enzymes (i) Enzymes are highly specific. • Most enzymes are highly specific to one particular type of substrate molecule, e.g. amylase hydrolyses amylose but not cellulose. • This is due to the specificity of enzyme’s active site which recognises specific groups of atoms or particular type of bond / linkage present in the substrates. (ii) Enzymes are effective in small amounts as they have high turn-over rates. • The turn-over rates of enzymes is the amount of substrate that a unit of enzyme can convert into its products over a period of time when enzyme is saturated. • E.g. one molecule of catalase can break down 6 x 105 molecules of hydrogen peroxide into oxygen and water per second. (iii) Enzymes remain chemically unchanged at the end of the chemical reaction. • Enzymes can be used repeatedly without undergoing permanent chemical damage. Therefore, enzymes can be reused. • A small amount of enzymes can effect a great change in the rate of the chemical reaction. (iv) Enzymes are affected by factors such as substrate concentration, enzyme concentration, temperature and pH. (v) 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. • They may vary from simple inorganic ions to complex organic molecules. • They may either remain chemically unchanged at the end of a reaction or be regenerated by a later process. • The enzyme-cofactor complex is called a holoenzyme. • The enzyme portion, without its cofactor, is called an apoenzyme. Apoenzyme and Holoenzyme

NANYANG JUNIOR COLLEGE H1 / H2 Biology Enzymes J1/2015 5 • There are three types of cofactor: inorganic ions, coenzymes and prosthetic groups. ➢ Inorganic ions o E.g. Zn2+ acts as a cofactor for carbonic anhydrase. ➢ Coenzymes are organic molecules which bind loosely to enzyme. o E.g. Nicotinamide adenine dinucleotide (NAD +), derived from vitamin niacin, is a coenzyme to dehydrogenase involved in cellular respiration. ➢ Prosthetic groups are organic molecules which remain tightly bound to enzymes. o 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. (vi) The activity of enzymes is tightly regulated. • Enzyme activity may be enhanced or reduced. (vii) Some enzymes allow reactions to reach equilibrium within a shorter period of time. • Some enzymes are able to catalyse both the forward and backward reactions of a reversible reaction. • Enzymes do not affect the position of the equilibrium.

NANYANG JUNIOR COLLEGE H1 / H2 Biology Enzymes J1/2015 6 3. Mode of Action of Enzymes (a) Active Site Enzymes have a unique three dimensional conformation with an active site (i.e. catalytic site and substrate-binding site) of the enzyme. Active site of hexokinase • The active site is formed by 3 to 12 amino acids from different parts of a single polypeptide chain held together by hydrogen bonds, ionic bonds, disulfide bonds and/or hydrophobic interactions. • Other amino acids are involved in maintaining the overall three dimensional structure of the enzyme. Structure of an enzyme • The active site comprises substrate binding site and catalytic site. ➢ Substrate binding site o Amino acid residues that recognise and bind to substrate thus determining enzyme specificity. ➢ Catalytic site o Amino acid residues that catalyse the reaction when substrate is bound. Maintain the three dimensional structure of protein. Substrate-binding site that recognises and binds to substrate. C