Chapter 8: Energy And Enzymes - Intro To Metabolism PDF

Chapter 8: Energy and enzymes - an introduction to metabolism  Outline Energy. The laws of thermodynamics. Chemical reactions. Enzymes and the rate of a reaction. Readings: Chapter 8, p170 - p186. ...

Chapter 8: Energy and enzymes - an introduction to metabolism  Outline Energy. The laws of thermodynamics. Chemical reactions. Enzymes and the rate of a reaction. Readings: Chapter 8, p170 - p186.  Learning outcomes By the end of this lesson, you should be able to 1. distinguish between the following pairs of terms: catabolic vs. anabolic, potential energy vs. kinetic energy, endergonic vs. exergonic, inhibitors vs. activators, competitive inhibitors vs. noncompetitive (allosteric) inhibitors. 2. define energy and work. 3. explain how the potential energy of an atom or its molecule is related to the position of its electrons. 4. discuss how the two laws of thermodynamics are related to energy transformations in biological systems. 5. describe the factors that determine whether a chemical reaction would be spontaneous. 6. explain why energy coupling is necessary for cellular work. 7. describe how temperature and concentration affect the rate of a chemical reaction. 8. explain how enzymes speed up specific chemical reactions.  Introduction The living cell is a miniature chemical factory in which thousands of reactions occur. Metabolism describes all the reactions that build up and break down organic molecules. These reactions will either require or release energy. What is the major form of chemical energy used by cells?  Catabolism and anabolism Metabolism is divided into two branches: catabolism and anabolism. Catabolism is the breakdown of molecules into smaller units, producing ATP. Anabolism is the building of molecules from smaller units, requiring ATP.  Energy Energy is the capacity to cause change or to do work. What are the two major types of energy? Kinetic energy is the energy of motion including light and heat. Potential energy is stored energy. Potential energy depends on the structure of the object or its position within its surroundings, and this energy is released when there is a change in the object’s structure or position. The covalent bonds in this molecule an example of ______. A) kinetic energy B) potential energy  Potential and kinetic energy Energy can be transformed from one form to another. Here, the ball at the top of the stairs has a high amount of potential energy because of its position. As it rolls, its potential energy is converted into kinetic energy since the ball is now moving. When the ball reaches the bottom of the stairs, its remaining energy is stored as low potential energy.  ATP Cells package energy into a chemical form that is readily accessible to the cell called ATP. What does ATP stand for? What are the 3 components of ATP? The chemical energy of ATP is held in the bonds connecting the phosphate groups. Which has the most potential energy, A) ATP, B) ADP or C) AMP?  The first law of thermodynamics The first law of thermodynamics states that energy is conserved. Energy is neither created nor destroyed, it simply changes from one form to another.  The second law of thermodynamics The second law of thermodynamics states that energy transformations always result in an increase in disorder in the universe. When energy changes form, the total amount of energy remains constant. However, the energy available to do work decreases. Some of the transformed energy is lost as heat, which increases disorder (entropy) in the surroundings. Therefore, entropy increases when energy is transformed.  Chemical reactions During a chemical reaction, the atoms keep their identity but the bonds linking them change. E.g., carbon dioxide and water react to form carbonic acid.  Gibbs free energy Gibbs free energy (G) is the amount of energy in a system available to do work. The difference in Gibbs free energy (ΔG) is the difference between the Gibbs free energy of the reactants GR and the Gibbs free energy of the products GP. ΔG = GP - GR. If the products of a reaction have more Gibbs free energy than the reactants, then the ΔG is positive. If the reactants have more Gibbs free energy than the products, then the ΔG is negative. Reactions with a negative ΔG release energy and are exergonic. Reactions with a positive ΔG require energy and are endergonic. ΔG in catabolic and anabolic reactions In catabolic reactions, the products have less chemical energy than the reactants and are more disordered, yielding a negative ΔG. In anabolic reactions, the products have more chemical energy than the reactants and are less disordered, yielding a positive ΔG.  ATP hydrolysis The reaction of ATP with water is exergonic (spontaneous) and releases energy. ΔG is negative.  Energetic coupling can drive nonspontaneous reactions Reaction 1: A à B ΔG > 0 (energy is consumed) Reaction 2: B à C ΔG < 0 (energy is released) Of the two reactions shown above, which reaction do you think is spontaneous? A) reaction 1 or B) reaction 2 But if the sum of reactions 1 and 2 together have an overall negative ΔG, then the reaction formed by coupling reactions 1 and 2 is also spontaneous, despite the fact that reaction 1 has a positive ΔG.  Examples of energetic coupling In reaction (a), the hydrolysis of ATP drives the formation of the product, glucose-6-phosphate. In reaction (b), the hydrolysis of phosphoenolpyruvate drives the synthesis of ATP.  Enzymes speed up chemical reactions by lowering the activation energy (EA) Chemical reactions in cells are catalyzed by proteins called enzymes. As a new compound is forming, there briefly exists a transition state in which old bonds are breaking and new ones are forming. This transition state is unstable and therefore has a large amount of free energy. Every reactant requires an input of energy to reach the transition state. This energy is the activation energy (EA). When the activation energy is high, the reaction is slower. When the activation energy is low, the reaction is faster. Enzymes reduce EA by stabilizing the transition state.  Enzymes are highly specific 1 Enzyme available with empty active site Active site Substrate (sucrose) 2 Substrate binds to enzyme with induced fit Enzyme Glucose (sucrase) Fructose H2O 4 The enzyme releases the products and 3 Substrate is emerges converted to unchanged from products the reaction  Enzymes catalysis occurs at the active site Enzymes have a 3D structure that brings together particular amino acids to form the active site. The enzyme’s active site binds the substrate and converts it to the product. 1. The active site brings the substate into close proximity in the correct orientation. 2. The interactions between the active site and the substrate help to stabilize the transition state and lower the activation energy required for the reaction.  Enzymes catalysis occurs at the active site An enzyme’s active site is extremely small compared to the enzyme itself. The catalytic amino acids in the active site may be spaced far apart in the primary sequence of the enzyme, but when the protein is folded, they come together to form the active site. What happens to protein function if the protein becomes denatured?  Some enzymes require cofactors/coenzymes for catalysis Some enzymes require nonprotein helpers called cofactors or coenzymes, which bind to the protein and function in catalysis. – Cofactors are inorganic ions (e.g., iron, zinc, copper, etc.) or organic molecules called coenzymes (e.g., most vitamins). Enzyme inhibitors An inhibitor is a chemical that decreases the activity of an enzyme. 1. Competitive inhibitors bind to the active site of the enzyme. Competitive inhibitors compete with the the substrate for binding to the active site. 2. Noncompetitive inhibitors bind to a site different from the active site. Noncompetitive inhibitors slow down the reaction by altering the enzyme’s shape and affecting the enzyme activity.  Regulation of metabolic pathways Many chemical reactions are organized into metabolic pathways in which a molecule is altered in a series of steps, each catalyzed by a specific enzyme, to form a final product. – If a cell is producing more of that product than it needs, the product may act as an inhibitor of one of the enzymes earlier in the pathway. This is called feedback inhibition or negative feedback. What is the advantage of using a feedback inhibition system to a cell?  Example of feedback inhibition Threonine dehydratase is an example of an allosteric enzyme, an enzyme that is activated or inhibited when binding to another molecule by causing its shape to change.