Enzymes and Metabolism 1306 Biology for Science Majors 1 PDF

6/4/22 Learning Goals Enzymes and Metabolism 1306 Biology for Science Majors 1 Jenifer Gifford, Ph.D. [email protected] 1 1. Describe the structure of an enzyme and explain how and why it can be used to speed up a chemical reaction 2. Describe what happens to all the energy stored in chemical bond...

6/4/22 Learning Goals Enzymes and Metabolism 1306 Biology for Science Majors 1 Jenifer Gifford, Ph.D. [email protected] 1 1. Describe the structure of an enzyme and explain how and why it can be used to speed up a chemical reaction 2. Describe what happens to all the energy stored in chemical bonds in reactants during a chemical reaction 3. Use Gibbs free energy to describe a reaction as endothermic/exothermic and spontaneous/nonspontaneous 4. Explain how, pH, temperature and concentration of enzymes/substrates affect enzyme activity and reaction rates 5. Understand what a redox reaction is and be able to identify if an atom or molecule has been oxidized or reduced 6. Describe how phosphorylation can be used to drive reactions that would normally be nonspontaneous 7. Explain how feedback works in metabolic pathway 2 Enzymes work toThe help cells acquire and use energy by Nature of Science facilitating chemical reactions Enzymes work toThe help cells acquire and use energy by Nature of Science facilitating chemical reactions • Enzymes are a type of protein that is known to speed up chemical reactions. • They do this by binding a substrate or multiple substrates in a certain way that makes it easier to break or form new bonds. • Typically the making and breaking of bonds in the substrate(s) would not be able to happen efficiently without the help of an enzyme. • Activities change constantly in response to signals from cells or environment • Enzymes direct which reactions occur and when and can increase the speed at which the reactions occur • Metabolic pathways: Ordered series of chemical reactions that build up or break down molecules. These can involve multiple enzymes working together to make a final product This lecture will go deeper into how chemical reactions work, building on what you learned at the end of “The chemistry of life” lecture. Then we’ll discuss what enzymes do to make the process easier and faster. 3 4 1 6/4/22 Review: Chemical energy is transformed The Nature of Science during chemical reactions • Potential energy—energy stored in position or configuration: Energy and Chemical Reactions: Enthalpy, Entropy, and Gibbs Free Energy • Chemical energy: energy stored in chemical bonds • Kinetic energy—energy of motion: • Thermal energy is a type of kinetic energy that describes the movement of molecules • Temperature is a measurement of thermal energy • Energy can be transformed from one type to another 5 6 Enthalpy describesThe the Nature sum of all the energy in a molecule of Science Review: Potential energy in bondsofisScience highest in nonpolar bonds The Nature • Recall that energy is stored in chemical bonds and that different types of bonds have a higher potential to participate in chemical reactions. • Amount of potential energy in covalent bond reflects the position of shared electrons relative to the nuclei of the atoms. • Longer, weaker bonds with equally shared electrons have high potential energy • Shorter, stronger bonds with unequally shared electrons have low potential energy Molecules can contain many individual bonds, each with their own amount of potential energy Enthalpy (H)—total energy in a molecule: • Includes potential energy in bonds of molecule and the effect the molecule’s movement (kinetic energy) has on pressure and volume of it’s surroundings 7 8 2 6/4/22 Review: In Spontaneous entropy increases and TheReactions, Nature ofoverall Science potential energy in bonds decreases Second Law of Thermodynamics: in spontaneous reactions, entropy (S) is the amount of disorder in a system and it always increases in the products Spontaneous Reactions are chemical reactions that can occur on their own without continuous input of energy or influence. Reactions will be spontaneous if the products have lower potential energy (electrons are held more tightly) than the reactants and the product molecules are less ordered than the reactant molecules. Review: Chemical Reactions Involve Energy Transformations The Nature of Science In chemical reactions, Products formed tend to have shorter, stronger covalent bonds than reactants, which means that the overall potential energy in bonds decreases First law of thermodynamics states that energy cannot be created or destroyed, only transferred or transformed Why during explosions do we see heat, sounds, and light? 9 Total potential energy in bonds is low The difference in energy has to go somewhere. It doesn’t just disappear. 10 Chemical Reactions Involve of Energy Transformations The Nature Science Products Reactants • Difference in potential energy between the reactants and products is transformed into an equal amount of kinetic energy, often in the form of heat or light Intermediates Energy put in to break bonds Ends up being heat Products Potential Energy Reactants Potential Energy Total Energy in System 11 Total potential energy in bonds is high • This is because energy cannot be created or destroyed, only transformed into another form Chemical Reactions Involve of Energy Transformations The Nature Science Changes in enthalpy (ΔH) are primarily based on differences in potential energy from the products to the reactants Exothermic reactions: • Reactions release heat • ΔH is negative • Products have less potential energy than reactants Endothermic reactions: • Heat energy is taken up during reaction • ΔH is positive • Products have higher potential energy than reactants 12 3 6/4/22 Chemical Reactions Involve of Energy Transformations The Nature Science + LOTS OF HEAT Chemical Reactions InvolveofEnergy Transformation The Nature Science • Gibbs free energy (G) determines whether reaction is spontaneous or requires added energy to proceed • Free-energy change equation: ΔG = ΔH − TΔS: • ΔH = change in enthalpy • ΔS = change in entropy • T = temperature in degrees Kelvin • Chemical reaction spontaneous when ΔG < 0. These reactions are exergonic • Chemical reaction is nonspontaneous when ΔG > 0. The reaction requires energy input to occur and are endergonic • ΔG = 0 = reaction at equilibrium *Enzymes help this process along* 13 14 Temperature and The Concentration of the reactants affects Nature of Science Reaction Rates • Even if reaction is spontaneous, it may not happen quickly: • For most reactions to proceed: Temperature and Concentration Affect Reaction Rates • One or more chemical bonds have to break • Others have to form • Substances must collide in specific orientation to brings electrons involved near each other • Higher concentrations increase number of collisions • Higher temperature increases thermal movement and therefore increases reaction rate 16 17 4 6/4/22 The energy from one reaction can drive other nonspontaneous reactions • Energetic coupling can be used to drive nonspontaneous (endergonic) reactions. This allows chemical energy released from one reaction to drive another reaction In cells, this reaction occurs in one of two ways: 1. Through transfer of electrons in redox reactions Transferring Electrons During Redox Reactions Chemical reactions that involve electron transfer: • Oxidation: loss of an electron(s) and becomes more positive • Reduction: gain of an electron(s) and becomes more negative • OIL RIG (Oxidation is loss; Reduction is Gain)/LEO the lion says GER • Oxidation and Reduction always occur together • Represents and example of energetic coupling of two halfreactions: 2. Through transfer of phosphate group (phosphorylation) 18 • Oxidation is an exergonic process (spontaneous) • Reduction is an endergonic process (nonspontaneous) 19 Transferring Electrons During Reactions • During redox reactions, electrons may be gained or lost in two ways: • Change in number of electrons in valence shell of atom • Electrons transferred as new covalent bonds formed with other atoms: • Atom is reduced or oxidized Transferring Electrons During Reactions • Electrons can be transferred from electron donor to electron acceptor • Most electron acceptors gain potential energy as they are reduced • Electrons are usually accompanied by a proton (H+): • Reduction often “adds H’s” • Oxidation often “removes H’s” 20 22 5 6/4/22 Transferring Phosphate Groups During Reactions • Adenosine triphosphate (ATP)—energy currency for cells: • Provides fuel for most cellular activities • Ribonucleotide used for RNA synthesis Transferring Phosphate Groups During Reactions • ATP reacts with water during hydrolysis reaction: • Bond between ATP’s outermost phosphate group and its neighbor is broken • Results in ADP—highly exergonic reaction • ATP has a great deal of potential energy: • Forms bonds between three negatively charged phosphate groups • Negative charges repel each other • Cells do not lose 7.3 k cal/mol as heat like other reactions we’ve seen. Instead, of releasing the phosphate group into solution, the energy is used to attach it to other molecules in a process called phosphorylation. • The new bond formed with phosphate increases potential energy of target molecule which makes it a much better reactant for a future chemical reaction. • Therefore, Phosphorylation can couple exergonic and endergonic reactions 23 24 Transferring Phosphate Groups During Reactions From previous slide: The new bond formed with phosphate increases potential energy of target molecule which makes it a much better reactant for a future chemical reaction. Therefore, Phosphorylation can couple exergonic and endergonic reactions How Enzymes Aid Chemical Reactions 25 26 6 6/4/22 How Enzymes Work Many unassisted reactions are slow. Activation energy: • A certain amount of kinetic energy is required to strain chemical bonds in molecules to encourage them to react to form products Transition state: Intermediate point between breaking old bonds and forming new ones Free energy of transition state is high 27 How Enzymes Work Before reaction can take place, reactants need to: 1. Collide in precise orientation 2. Have enough kinetic energy to overcome activation energy barrier and achieve transition state • Enzymes are catalysts: • Bring reactants together in precise orientations • Make reactions more likely • Are specific for single type of reaction • When reactants undergo chemical reaction by binding to an enzyme, they are substrates 28 Enzymes Bring Substances Together • Substrates bind to enzyme’s active site: • Active-site binding helps substrates collide in precise orientation • Bonds break and form to generate products • Many enzymes undergo conformational change: • When substrates are bound to active site, this change is called an induced fit Enzymes Bring Substances Together • Substrates enter active site—are held in place by: • hydrogen bonding • other weak interactions with amino acid residues in active site • As interactions between substrate and enzyme increases bonds in substrate are destabilized to form transition state • Therfore, enzymes decrease activation energy required for reaction to proceed 29 30 7 6/4/22 Enzymes Bring Substances Together Enzyme catalysis has three steps: 1. Initiation—substrates precisely oriented as they bind to active site 2. Transition state facilitation—interactions between substrate and active site R-groups lower activation energy 3. Termination—reaction products are released from enzyme What Limits Catalysis? • Speed of enzyme-catalyzed reaction: 1. Increases linearly at low substrate concentrations 2. At intermediate substrate concentrations, increase in speed begins to slow 3. At high concentrations, reaction rate plateaus • All enzymes show type of “saturation kinetics:” • Active sites cannot accept substrates any faster no matter how large concentration of substrates gets • Reaction rates level off because all available enzyme molecules are being used Notice that the enzyme itself is unchanged 31 32 Do Enzymes Work Alone? • Molecules that are not part of enzyme are required for enzyme functionality: 1. Cofactors—inorganic ions, such as Zn2+, Mg2+, and Fe2+ that reversibly interact with enzymes 2. Prosthetic groups—nonamino acid atoms or molecules permanently attached to proteins 3. Coenzymes—organic molecules, such as NADH or FADH2, that interact with enzymes 33 Enzymes are optimized to work at a specific conditions Enzyme’s structure critical to its function. Their activity is sensitive to alteration of their protein shape which can be affected by temperature, pH, and interactions with other molecules. • Temperature: • Affects folding and movement of enzyme and substrates • Affects kinetic energy • pH: • Affects enzyme’s shape and reactivity • Affects charge on acidic and basic groups 34 8 6/4/22 Enzymes are optimized to work at a specific conditions Enzymes Activity is Regulated by Molecular Interactions Regulatory molecules may regulate cell’s enzymatic activity: • May change enzyme’s structure • May change ability to bind to its substrate • May either activate or inactivate the enzyme’s function • Reversible regulatory interactions work in two ways: • Competitive inhibition: • Molecule competes with the substrate for active site • Allosteric regulation: • Molecule binds at location other than active site • Causes change in enzyme shape • Can activate or deactivate enzyme 35 36 Enzymes Can Be Regulated By Phosphorylation Enzymes Work Together In Metabolic Pathways Metabolic pathways: • Series of reactions • Each catalyzed by different enzyme • Build biological molecules 37 38 9 6/4/22 Enzymes Work Together In Metabolic Pathways Enzymes Work Together In Metabolic Pathways Two Types of Metabolic Pathways: Catabolic pathways: Break down molecules for sources of energy and carbon building blocks Anabolic pathways: Use energy and carbon building blocks to synthesize molecules 39 40 Enzymes Work Together In Metabolic Pathways Enzymes Work Together In Metabolic Pathways • Feedback inhibition: • Occurs when enzyme in pathway is inhibited • Inhibition is by final product of pathway • As concentration of product becomes abundant: • It “feeds back” to stop reaction • Amount of initial substrate is not depleted • Stored or used for other reactions 41 42 10 6/4/22 TheChapter Nature Recap of Science 43 11