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UNIT 18: Enzymes and Metabolism Essential Idea(s): Living Organisms control their composition by complex web of chemical reactions. Metabolic reactions are regulated in response to the cell’s needs. Enzymes control the metabolism of the cell. IB Syllabus Statements Unit Objectives. Students will be able to: 2.1.U4 Metabolism is the web of all the enzyme-catalyzed reactions in a cell or organism. 8.1.U1 Metabolic pathways consist of chains and cycles of enzymecatalyzed reactions. 2.5.U1 Enzymes have an active site to which specific substrates bind. 2.5.U2 8.1.U2 Enzyme catalysis involves molecular motion and the collision of substrates with the active site. Enzymes lower the activation energy of the chemical reactions that they catalyze. 8.1.S2 Calculating and plotting rates of reaction from raw experimental results. 2.5.U3 Temperature, pH, and substrate concentration affect the rate of activity of enzymes. 2.4.A2 Denaturation of proteins by heat or by deviation of pH from the optimum. 2.5.U4 Enzymes are denatured. 8.1.U3 Enzyme inhibitors can be competitive or noncompetitive. 8.1.U4 Metabolic pathways can be controlled by end-product inhibition. 8.1.A1 8.1.S1 8.1.NOS End-product inhibition of the pathway that converts threonine is isoleucine. Distinguishing different types of inhibition from graphs at specified substrate concentrations. Developments in scientific research follow improvements in computing-developments in bioinformatics, such as the interrogation of databases have facilitated research into metabolic pathways. Define metabolism and catalysis. State the role of enzymes in metabolism. Contrast metabolic chain reactions pathways with cyclical reaction pathways. State the relationship between enzyme substrate and enzyme product. Explain the relationship between enzyme structure and enzyme specificity, including the role of the active site. Outline the three stages of enzyme activity. Explain the role of random collisions in the binding of the substrate with the enzyme active site. Describe the induced-fit model of enzyme action. Define activation energy. Explain the role of enzymes in lowering the activation energy of a reaction. State two methods for determining the rate of enzyme controlled reactions. State the unit for enzyme reaction rate. Given data, calculate and graph the rate of an enzyme catalyzed reaction. Explain how temperature affects the rate of enzyme activity. Draw a graph depicting the effect of temperature on the rate of enzyme activity. Explain how pH affects the rate of enzyme activity. Draw a graph of depicting the effect of pH on the rate of enzyme activity. Identify the optimum temperature or pH for enzyme activity on a graph. Explain how substrate concentration affects the rate of enzyme activity. Draw a graph of depicting the effect of substrate concentration on the rate of enzyme activity. Define denaturation. Outline the effect of heat and pH on protein structure and function. Define enzyme inhibitor. Contrast competitive and noncompetitive enzyme inhibition. Outline one example of a competitive enzyme inhibitor and one example of a noncompetitive enzyme inhibitor. Describe allosteric regulation of enzyme activity. Outline the mechanism and benefit of end-product inhibition. Illustrate end-product inhibition of the threonine to isoleucine metabolic pathway. State the consequences of an increase in isoleucine concentration. Explain why the rate of reaction with increasing substrate concentration is lower with a non-competitive inhibitor 1 8.1.A2 Use of databases to identify potential new anti-malarial drugs. 2.5.S1 Design of experiments to test the effect of temperature, pH, and substrate concentration on the activity of enzymes. 2.5.S2 Experimental investigation of a factor affecting enzyme activity. Experimental design - accurate, quantitative measurements in enzyme experiments require replicates to ensure reliability. 2.5.U5 Immobilized enzymes are widely used in industry. 2.5.A1 Methods of production of lactosefree milk and its advantages. 2.5.NOS compared to a competitive inhibitor. Outline the use and benefits of the bioinformatics technique of chemogenomics in development of new pharmaceutical drugs. Outline the reasons for development of new anti-malarial drugs. Explain the use of databases in identification of potential new anti-malarial drugs. Identify the manipulated, responding, and controlled variables in descriptions of experiments testing the activity of enzymes. Describe three techniques for measuring the activity of an example enzyme. Define quantitative and qualitative. Determine measurement uncertainty of a measurement tool. Explain the need for repeated measurements (multiple trials) in experimental design. Explain the need to control variables in experimental design. List industries that use commercially useful enzymes. Explain how and why industrial enzymes are often immobilized. State the source of the lactase enzyme used in food processing. State the reaction catalyzed by lactase. Outline the reasons for using lactase in food processing. METABOLISM _______________ is the chemical reactions of life; all the various processes by which you obtain energy, grow, heal, think, feel and dispose of wastes. These reactions are controlled by ________________. 2 Anabolism Catabolism Anabolism is … Catabolism is … Energy is added Energy is released Examples: Examples: Enzymes are Proteins 3 Metabolic Pathways A series of ‘steps’ from a starter molecule or ___________ towards a final end product. Each step is __________ by a different enzyme. (Catalyze means to __________________________________.) Cyclical Pathways Some metabolic pathways operate in a ____________ way. Often named after the scientists who discover them. Metabolism of Phenylalanine The metabolism of Phenylalanine is an example of a CHAIN ________________ ______________. Failure of the enzymes controlling this metabolic pathway leads to a range of ________________ _________________. 4 Protein in Diet 5 Why Enzymes? All chemical reactions require an initial energy input to get started. The initial energy input in the reaction is called the ______________ ____________. __________ are employed to __________ (speed up) chemical reactions in cells. Enzyme Structure Enzymes have a pocket called an ___________ ___________. Reactants (____________) bind to the active site. 6 Distinctive shape of active site is complementary and _____________ to the substrate. Active site amino acids bind to the substrate and distort the bonds to facilitate a reaction. Not all Enzymes are the Same Some enzymes contain only _____________. Others, called __________ ____________, require additional components to complete their catalytic properties. Enzymes will slightly shift in shape to better fit the substrate. This is called _____________ _______. Three Steps on Enzyme Catalysis How are Enzymes Named? How are enzyme-catalyzed reactions calculated? 7 Environmental Control of Enzyme Activity As proteins, the tertiary structure of an enzyme is sensitive to Each enzyme has specific environmental conditions in which its efficiency is optimized. Enzymes will __________ if the pH, temperature or [salt] is not correct. SUBSTRATE Concentration Effects Enzyme Activity Assuming the amount of enzyme is constant, an increase in substrate concentration causes a diminishing increase in the reaction rate. A maximum rate is obtained at a certain substrate concentration where all enzymes are occupied by substrate. The reaction rate cannot increase further. Draw this: ENZYME Concentration Effects Enzyme Activity An increase in enzyme concentration causes an increase in the reaction rate. Reaction rate will eventually level off as all available substrates are used up. Draw this: 8 CONTROL OF METABOLISM Remember that a given enzyme usually catalyzes a single step in a chain of metabolic reactions. The overall activity of enzymes, and therefore, metabolism, is controlled by a number of factors: 1. The rate of enzyme production and breakdown. Sometimes genes are _________ only when an enzyme product is required to catalyze reactions that may occur infrequently. Other _________ are being transcribed all the time because their enzyme products are in constants demand. 2. Enzyme interaction with the substrate or products of reaction. Substrate (starting chemical) End Product (finishing chemical) 9 3. The influence of inhibitors. Enzyme Inhibitor: Types of Inhibitors: Competitive Inhibitor Non-Competitive Inhibitor End-Production (Feedback) Inhibition Reading Enzyme Inhibition Graphs 10 We care about this because…. Enzyme inhibitors created or discovered in order to treat disease. Pesticides and herbicides are enzyme inhibitors. Chemogenomics and Anit-Malarial Drugs INDUSTRIAL APPLICATIONS OF ENZYMES Enzymes aren’t just used in scientific investigations or metabolism. Many enzymes have been used in industry to improve our lives in one way or another. Sector Role of Enzymes Example of Enzymes Detergents Textiles Food Processing 11 Pulp and Paper Immobilized Enzymes Enzymes that have been physically ____________ to a _______________. Benefits in industrial applications: - - - Used in the Production of Lactose Free Milk Reasons for using lactase in food processing: - - - CHEMOGENOMICS AND COMPUTER AIDED DRUG DESIGN WHO? WHAT? 12 WHY? Example: The use of databases to discover anti-malarial drugs. 13