Enzymes and Energetics PDF

Enzymes and Energetics Biota use enzymes to facilitate chemical reactions (rxn). To react, e– within established bonds must be excited so they change their bonding patterns. Reactions need a nudge to get going. The m...

Enzymes and Energetics Biota use enzymes to facilitate chemical reactions (rxn). To react, e– within established bonds must be excited so they change their bonding patterns. Reactions need a nudge to get going. The magnitude of this nudge is termed a reaction’s activation energy (Ea). Enzymes catalyze chemical reactions by ↓ Ea making a rxn go. Enzymes lower Ea by: 1)align substrate functional groups so they can react (dehydration rxn) 2)stretch substrate straining bonds (hydrolysis rxn) 3)create microenvironments (↓ pH) Enzyme Affinities and Cycles Enzymes have affinities for specific substrates because the shape of the substrate fits into the enzyme’s active site. Consequently, one enzyme tends to only interact with one (or a few) substrate. The enzyme-substrate complex changes shape resulting in rxn catalysis. A single enzyme molecule can catalyze numerous cycles of the same rxn because it is not destroyed during the catalysis cycle. Rate of enzyme activity depends on the ratio of [substrate] to open [enzyme active sites]. Optimization and Inhibition Enzymes activity depends on other factors such as availability of rxn helpers called cofactors (e.g., ions) and/or coenzymes (e.g., NAD+). Enzyme activity is optimized to work better within environs with optimal temperature, pH, salinity. Our Pepsin hydrolyzes proteins in the stomach best at 37°C and pH=2. Enzymes are inhibited by competitive (blocks active site) and non-competitive (deforms active site by attaching elsewhere) inhibitors either irreversibly or reversibly. Activators and Inhibitors Allosteric activators stabilize active form of allosteric (4° proteins) enzymes. Allosteric inhibitors stabilize inactive form of allosteric (4° proteins) enzymes. Feedback Inhibitors Feedback inhibition occurs when products of a pathway inhibit enzymes that catalyze reactions in early portion of the pathway. Often occurs by reversible non- completive inhibition. Biochemical Pathways A biochemical pathway is a group of chemical reactions linked together in a series. The product(s) of a preceding reaction become reactant(s) of the subsequent reaction (e.g., mevalonic acid becomes melanovate-5-phosphate). Enzymes catlyze reactions in biochemical pathways. Cholesterol is made via the mevalonate pathway. Biochemical Pathways Biochemical reactions proceed at a given rate; some reactions are faster than others. The slowest reaction in a pathway is the a rate-limiting reaction of that pathway (e.g., HMG-CoA ➟ Mevalonic acid). The rate-limiting reaction is often targeted by pharmaceuticals to modify a pathway (e.g., statins competitively inhibit HMG-CoA Reductase ↓ cholesterol synthesis). Basics About Energy Energy is the capacity to do work. It can change the position, composition, and temperature of matter. Energy has two states: Potential energy is stored energy that has + capacity to do work (e.g., membrane potential). – Kinetic energy is actively doing work. Energy exists in different forms: solar, electrical, mechanical, chemical, and heat. Chemical energy is found within chemical bonds. It can transfer to other matter when bonds break. Forms of energy differ in their ability to perform work. Solar energy has a greater potential to perform work than heat (heat does not usually perform biological work). Thermodynamic Laws Thermodynamics: study of energy transfer and transformation. First Law: Energy can be transferred and transformed but it cannot be created nor destroyed. Chloroplasts transform solar energy into chemical energy (e.g., sugars) during photosynthesis. Mitochondria transform chemical energy in sugar to ATP. ATP powers biological work (e.g., active transport). Photosynthesis Respiration ATP Powers biological work No transformation is 100% efficient, so heat is produced. Thermodynamic Laws Second Law: Energy transfer during transformation increases the entropy within the universe. Entropy is a measure of disorder. Energy harnessed to do work is required to maintain order. Heat, limited in its ability to perform biological work, does little to maintain biological order. Consequently, as more ‘higher order’ forms of energy (e.g., solar) are transformed to heat, less energy in the system is available to maintain biological order (entropy ↑). Who Says Energy is Free? (Gibbs) Free energy (G) is the energy that is available to do work. ΔG is the “change in free energy.” ΔG = GFinal – GInitial GInitial –ΔG Reactions that release energy are exergonic (–ΔG)(3 – 10 = –7). Energy G Such reactions are spontaneous 10 GFinal (occur without outside energy) because the reactants are less 3 Reactants Products stable and have more free energy than the products. Chemical Rxn → GFinal Reactions that require energy are +ΔG endergonic (+ΔG)(8 – 2 = 6). Energy G Such reactions are not spontaneous GInitial 8 because the products are less stable and have more free energy 2 Reactants Products than the reactants. Chemical Rxn →  Cells Transform Energy Overall, photosynthesis is endergonic. It requires at least +686 kcal of solar energy to synthesize 1 mol of glucose. Chloroplast + + Light C6H12O6 + 6 O2 6 CO2 + 6 H2O Overall, cellular respiration is exergonic (ΔG= –686 kcal/mol glucose metabolized). Some of the free energy from glucose is used to ‘recharge’ ATP and some is ‘lost’ as heat. Mitochondrion Cellular Respiration + + C6H12O6 + ATP 6 O2 6 CO2 + 6 H2O Cytosol Mitochondrion Don’t Equilibrate to Live Many chemical rxns are reversible and continue until the rxn reaches reaction equilibrium (⇄ rxn at same rate). Reaction equilibria are not desirable in biota because at equilibrium ΔG=0; i.e., no more free energy to do work. Biota must have metabolic pathways that maintain –ΔG (left) otherwise they can’t do work and die (right). Seeking to maintain –ΔG is called the metabolic steady state. To maintain a steady state requires: 1)ingesting reactants (aka food) 2)using products of one rxn as reactants in subsequent rxns within biochemical pathways 3)excreting waste products Cells Must Pay For Work Staying alive is a lot of work: chemical work (e.g., endergonic rxn during biosynthesis), transport work (e.g., pumping ions), and mechanical work (e.g., muscle contraction), etc. Cells couple exergonic rxns such as ATP hydrolysis (ΔG about –7 kcal/mol) to pay for endergonic work processes. ATP hydrolysis may facilitate a rxn by exciting e– to form new bonds. ATP hydrolysis may also facilitate a rxn via phosphorylation (adding – ℗) of reactants, changing their shape. Cells eventually will run out of ATP as it is hydrolyzed to power work. It can be recharged during cellular respiration...