Biology 2E Chapter 6 Metabolism Lecture Slides PDF

BIOLOGY 2E Chapter 6 METABOLISM Lecture PowerPoint Slides This work is licensed under a Creative Commons Attribution-NonCommercial- ShareAlike 4.0 International License. CHAPTER 6 METABOLISM 6.1 Energy and metabolism 6.2 Potential,...

BIOLOGY 2E Chapter 6 METABOLISM Lecture PowerPoint Slides This work is licensed under a Creative Commons Attribution-NonCommercial- ShareAlike 4.0 International License. CHAPTER 6 METABOLISM 6.1 Energy and metabolism 6.2 Potential, kinetic, free, and activation energy 6.3 The laws of thermodynamics 6.4 ATP: Adenosine triphosphate 6.5 Enzymes 6.1 ENERGY AND METABOLISM Learning Objectives By the end of this section, you will be able to do the following: Explain metabolic pathways and describe the two major types Discuss how chemical reactions play a role in energy transfer 6.1 ENERGY AND METABOLISM The energy that sustains most of the earth’s life forms comes from the sun. Bioenergetics is the study of energy flow through a living system Figure 6.2 METABOLISM Metabolism refers to all chemical reactions of a cell or organism. A metabolic pathway is series of biochemical reactions that converts one or more substrates into a final product. For example, energy from the sun is captured during photosynthesis to convert CO2 and H2O into glucose (C6H12O6). The energy stored in glucose is released during cellular respiration, regenerating CO2 and H2O. (We will discuss in subsequent lectures.) (credit “acorn”: modification of work by Noel Reynolds; credit “squirrel”: modification of work by Dawn Huczek)  METABOLIC PATHWAYS Two types of reactions/pathways are required to maintain the cell’s energy balance. Those that require energy and synthesize larger molecules are called anabolic. (Photosynthesis) Those that release energy and break down large molecules into smaller molecules are called catabolic. (cellular rep) EVOLUTION OF METABOLIC PATHWAYS All types of life share some of the same metabolic pathways. This commonality provides more evidence that organisms evolved from common ancestors. Over time, these pathways diverged. As organisms evolved, they developed specialized enzymes to help them adapt to their environments. ANABOLIC AND CATABOLIC EXAMPLES DISCUSSION QUESTION Is photosynthesis an anabolic or catabolic pathway? anabolic What evidence supports your answer? 6.1 ENERGY AND METABOLISM Learning Objectives You should now be able to do the following: Explain metabolic pathways and describe the two major types Discuss how chemical reactions play a role in energy transfer 6.2 POTENTIAL, KINETIC, FREE, AND ACTIVATION ENERGY Learning Objectives By the end of this section, you will be able to do the following: Define “energy” Explain the difference between kinetic and potential energy Discuss the concepts of free energy and activation energy Describe endergonic and exergonic reactions  TYPES OF ENERGY in physics a change in motion of state of matter can be defined as “work” and requires energy. Energy is the ability to do work. Work is a change in state or motion of matter Energy can be classified as kinetic or potential Objects in motion have kinetic energy Objects that have the potential to move have potential energy (credit “dam”: modification of work by "Pascal"/Flickr; credit “waterfall”: modification of work by Frank Gualtieri)  TYPES OF ENERGY Examples of potential and kinetic energy in cells: Energy of chemical/electrochemical gradients across the plasma membrane Chemical energy – Energy stored in chemical bonds (potential); energy released (kinetic)  POTENTIAL ENERGY The potential energy stored in the chemical bonds of gasoline can be transformed into kinetic energy that allows a car to race on a racetrack. (credit “car”: modification of work by Russell Trow) 6.2 FREE ENERGY To explore the bioenergetics of a system, we study the amount of energy exchanged in a metabolic reaction Gibb’s Free Energy (G) = amount of energy available to do work (aka usable energy) All chemical reactions affect G; change in G after a reaction is abbreviated as ΔG. free energy (G) is inversely related to entropy ΔG = ΔH − TΔS Where: ΔH is change in total energy of the system T is temperature in Kelvins ΔS is change in entropy (energy lost to disorder) FREE ENERGY If energy is released in a chemical reaction, then ΔG is negative. Products of these reactions will have less free energy than the substrates These reactions are classified as exergonic Exergonic reactions are spontaneous reactions because they can occur without the addition of energy. However, spontaneous reactions do not necessarily occur quickly! The hump shown in the free energy diagram is the reason. (We will discuss that soon.)  FREE ENERGY If a chemical reaction requires an input of energy, then ΔG is positive. Products of these reactions will have more free energy than the substrates. These reactions are classified as endergonic DISCUSSION QUESTION: WHICH CHEMICAL REACTION IS EXERGONIC? cellular rep is exergonic and photsynthesis is endergonic  6.2 ACTIVATION ENERGY Activation energy is the energy required for a reaction to proceed (the “hump” in the diagram). It causes reactant(s) to become contorted and unstable, which allows the bond(s) to be broken or made. This unstable state is called the transition state. Once in the transition state, the reaction occurs very quickly. Heat energy is the main source for activation energy in a cell Heat helps reactants reach their transition state  ACTIVATION ENERGY Notice on the graph that activation energy is lower if the reaction is catalyzed. We will talk more about catalysts in 6.5. Can you guess what catalysts to for reactions? Activation energy is why, for example, the rusting of iron happens slowly despite being a spontaneous, exergonic reaction. The breakdown of gasoline is another example of an exergonic reaction. A spark is required to provide sufficient heat to exceed the activation energy. Once the reaction begins, enough heat is released to drive additional reactions. 6.2 POTENTIAL, KINETIC, FREE, AND ACTIVATION ENERGY Learning Objectives You should now be able to do the following: Define “energy” Explain the difference between kinetic and potential energy Discuss the concepts of free energy and activation energy Describe endergonic and exergonic reactions 6.3 THE LAWS OF THERMODYNAMICS Learning Objectives By the end of this section, you will be able to do the following: Discuss the concept of entropy Explain the first and second laws of thermodynamics 6.3 THE LAWS OF THERMODYNAMICS Thermodynamics is the study of energy and energy transfer involving physical matter. The first law of thermodynamics states that the total amount of energy in the universe is constant: energy cannot be created or destroyed. The second law of thermodynamics states that the transfer of energy is not completely efficient. With each chemical reaction, some energy is lost in a form that is unusable, such as heat energy. The result is increased entropy (disorder). LAWS OF THERMODYNAMICS These kids convert the chemical energy from the ice cream cone, to kinetic energy of riding a bike. Some heat energy is released, too. Heat energy is also lost when plants utilize sunlight during photosynthesis. 6.3 THE LAWS OF THERMODYNAMICS Learning Objectives You should now be able to do the following: Discuss the concept of entropy Explain the first and second laws of thermodynamics 6.4 ATP: ADENOSINE TRIPHOSPHATE Learning Objectives By the end of this section, you will be able to do the following: Explain ATP's role as the cellular energy currency Describe how energy releases through ATP hydrolysis  6.4 ATP: ADENOSINE TRIPHOSPHATE What provides the energy for a cell’s endergonic reactions? Usually, the hydrolysis of ATP. ATP STRUCTURE ATP is composed of an adenosine backbone with three phosphate groups attached. Adenosine is a nucleoside consisting of the nitrogenous base adenine and a five-carbon sugar, ribose. The three phosphate groups, in order of closest to furthest from the ribose sugar, are alpha, beta, and gamma. The bonds that link the phosphate groups are high-energy bonds: When the bonds are broken, the products have lower free energy than the reactants.  ATP HYDROLYSIS ATP + H2O → ADP + Pi + free energy ΔG = -7.3 kcal/mol ATP is an unstable molecule and will hydrolyze quickly. If it is not coupled with an endergonic reaction this energy is lost as heat. If it is coupled with an endergonic reaction, much of the energy can be transferred to drive that reaction. ATP Hydrolysis is reversible THE SODIUM-POTASSIUM PUMP The sodium-potassium pump is an example of energy coupling. The energy derived from exergonic ATP hydrolysis is used by the integral protein to pump 3 sodium ions out of the cell and 2 potassium ions into the cell. 6.4 ATP: ADENOSINE TRIPHOSPHATE Learning Objectives You should now be able to do the following: Explain ATP's role as the cellular energy currency Describe how energy releases through ATP hydrolysis 6.5 ENZYMES Learning Objectives By the end of this section, you will be able to do the following: Describe the role of enzymes in metabolic pathways Explain how enzymes function as molecular catalysts Discuss enzyme regulation by various factors  6.5 ENZYMES Enzymes are protein* catalysts that speed up reactions by lowering the required activation energy. Enzymes bind with reactant molecules promoting bond- breaking and bond-forming processes. Enzymes are very specific, catalyzing a single reaction. * While the overwhelming majority of biological enzymes are proteins, some non-protein enzymes exist, including RNA enzymes (ribozymes). ENZYME-SUBSTRATE SPECIFICITY The 3D shape of the enzyme and the reactants (aka substrates) determines this specificity. Substrate molecules interact at the enzyme’s active site. Enzymes can catalyze a variety of reactions. In some cases, two substrates bond together to form a larger molecule; in others one molecule breaks down into smaller products. 3D IMAGE OF ENZYME ACTIVE SITE Credit: Thomas Shafee [CC BY 4.0 (https://creativecommons.org/licenses/by/4.0)], from Wikimedia Commons INDUCED FIT At the active site, there is a mild shift in shape that optimizes reactions. This is called induced fit. The slight changes at the active site maximizes the catalysis. Induced fit is a relatively recent discovery. It is viewed as an expansion of the previously-held “lock-and-key” model. 3D IMAGE OF INDUCED FIT By Thomas Shafee [CC BY 4.0 (https://creativecommons.org/licenses/by/4.0)], from Wikimedia Commons PROTEIN STRUCTURE REVISITED Reminder: the 3-D shape of a protein is determined by the amino acid sequence of the polypeptide. The AAs of the active site are particularly important for the enzyme’s function – allow binding with unique substrate(s) The cellular environment is also important for enzyme function: Suboptimal temperatures can denature the enzyme (loss of shape) Suboptimal pHs can reduce substrate-enzyme binding Figure 3.23. Refer back to Chapter 3 for more information.  6.5 HOW ENZYMES LOWER ACTIVATION ENERGY The enzyme can help the substrate reach its transition state in one of the following ways: position two substrates so they align perfectly for the reaction provide an optimal environment, i.e. acidic or polar, within the active site for the reaction contort/stress the substrate so it is less stable and more likely to react temporarily react with the substrate (chemically change it) making the substrate less stable and more likely to react. After a catalyzed reaction, the product is released, and the enzyme becomes available to catalyze another reaction. OVERVIEW OF ENZYME FUNCTION https://pdb101.rcsb.org/learn/videos/how-enzymes-work 6.5 ENZYME REGULATION Regulation of enzyme activity helps cells control their environment to meet their specific needs. For example, digestive cells in your stomach work harder after a meal than when you sleep. Enzymes can be regulated by Modifications to temperature and/or pH Production of molecules that inhibit or promote enzyme function Availability of coenzymes or cofactors 6.5 ENZYME INHIBITION Competitive inhibitors have a similar shape to the substrate, competing with the substrate for the active site. Noncompetitive inhibitors bind to the enzyme at a different location, causing a slower reaction rate https://en.wikipedia.org/wiki/Non-competitive_inhibition 6.5 ENZYME INHIBITION (FIGURE 6.17) Competitive inhibitors slow reaction rates but do not affect the maximal rate. Noncompetitive inhibitors slow rates and reduce the maximal rate. Maximal rate – speed of a reaction when substrate is not limited. 6.5 ENZYME REGULATION (FIGURE 6.18) Allosteric inhibitors modify the active site of the enzyme so that substrate binding is reduced or prevented. Allosteric activators modify the active site of the enzyme so that the affinity for the substrate increases. EVERY DAY CONNECTION (DRUG DISCOVERY) FIGURE 6.19 Have you ever wondered how pharmaceutical drugs are developed? Look for inhibitors to enzymes in specific pathways  ENZYME COFACTORS Some enzymes require one or more cofactors or coenzymes to function. Cofactors are inorganic ions, such as Fe++, Mg++, Zn++ DNA polymerase requires Zn++ Coenzymes are organic molecules, including ATP, NADH+, and vitamins These molecules are provided primarily from the diet. 6.5 FEEDBACK INHIBITION IN METABOLIC PATHWAYS (FIGURE 6.21) Reminder, metabolic pathways are a series of reactions catalyzed by multiple enzymes. Feedback inhibition, where the end product of the pathway inhibits an upstream step, is an important regulatory mechanism in cells. Example: ATP is an allosteric inhibitor for some enzymes involved in cellular respiration 6.5 ENZYMES Learning Objectives You should now be able to do the following: Describe the role of enzymes in metabolic pathways Explain how enzymes function as molecular catalysts Discuss enzyme regulation by various factors This PowerPoint file is copyright Rice University. All Rights Reserved. Modified by E.G. Cantonwine, Valdosta State University. Updated for Biology 2e by OpenStax.