5: CHAPTER DIRECTIONS AND RATES OF BIOCHEMICAL PROCESSES
Boltzmann the man who championed the idea that atoms were real, not abstract in 19th century Most important application of ideas were in: thermodynamics the study of the relationships among different forms of energy kinetics the study of the rates of reaction 5.1 WHAT DETERMINES WHICH WAY A REACTION GOES? HOW MAY WORK BE CONVERTED TO KINETIC OR POTENTIAL ENERGY? Work movement of an object against a force Potential energy stored energy; energy yet to be used Kinetic energy energy of moving objects Construction of an ATP molecule stores potential energy can be released later as kinetic energy HOW DOES THERMODYNAMICS PREDICT THE DIRECTION OF A REACTION? First Law of Thermodynamics the total amount of energy in any process stays constant Energy can switch between kinetic and potential, but is neither created nor destroyed Second Law of Thermodynamics in any process the energy available for work decreases Unofficially: the amount of disorder in the universe is always increasing Calories amount of energy needed to raise the temperature of 1 gram of water by 1C ATP stores energy (ADP too, but not as much) Splitting ATP contracts muscles, etc., or releases heat Reactions usually run in the direction that releases heat HOW DO CHANGES IN FREE ENERGY PREDICT THE DIRECTION OF A REACTION? Free energy (G) energy in a system available for doing work Reactants molecules that react in a reaction Products molecules formed in a reaction G = G products G reactants Exergonic processes that release energy; G negative; can occur spontaneously, given time Endergonic processes that require energy input; G positive WHAT IS SOURCE OF FREE ENERGY RELEASED/CONSUMED DURING A REACTION? ATP + H2O ADP + phosphate New P-O bond in phosphate is more stable than old O-H (in water) and P-O (in ATP) Generally, free energy decreases when unstable bonds break and stable ones form High-energy bonds unstable chemical bonds that give up energy easily; represented by "~" HOW CAN ONE PROCESS PROVIDE THE ENERGY FOR ANOTHER? Coupled 2 processes are ~ when an exergonic reaction drives an endergonic reaction A ~ reaction must be exergonic overall Enzymes large molecules, usually proteins, that speed up chemical reactions They don't affect G, just speed up what would have happened anyway HOW DO CONCENTRATION (AND ENTROPY) AFFECT EQUILIBRIUM? Entropy formal measure for disorder; high value when objects are disordered Whether a reaction occurs depends not only on the energy in the individual bonds, but also on the concentrations of both chemical reactants and products Equilibrium when free energy of product B equals the free energy of reactant A (G=0) 5.2 DETERMINES WHAT THE RATE OF A CHEMICAL REACTION? HOW DOES MOLECULAR MOTION HELP EXPLAIN REACTION RATES?
When a substance absorbs heat, temperature increases, atoms move around more e.g. frogs jumping from level A to level B: --A-----^\____B__ Kinetic theory, based on random movements of atoms and molecules, helps predict the rates of chemical reactions WHAT STOPS A CHEMICAL REACTION? A chemical reaction stops when it reaches equilibrium (depends in part on temperature) WHAT STARTS A CHEMICAL REACTION? Activation energy minimum energy needed for a process to occur Lower ~ more rapidly equilibrium is reached Catalyst substance that lowers the activation energy of a reaction but isn't consumed/changed Initiation of a chemical reaction depends on the temperature of the molecules (kinetic energy) & activation energy of the reaction. In organisms, enzymes can hasten a chemical reaction by lowering the activation energy 5.3 HOW DO ENZYMES WORK? HOW DOES AN ENZYME BIND TO A REACTANT? Substrates reacting molecules that enzymes bind to Active site a groove or cleft on its surface with which it binds to the small substrate molecule Usually binds by weak noncovalent bonds Each enzyme lowers the activation energy for one reaction HOW DOES AN ENZYME LOWER ACTIVATION ENERGY OF CHEMICAL REACTION? Transition state distorted form of a substrate Enzymes lower activation energy for a reaction by aligning 2 or more substrate molecules, by straining the covalent bonds within the substrates, & even by participating directly in the reaction Similar to: take paperclip, open it, and put it around paper both hand & clip change temporarily HOW DO ENVIRONMENTAL CONDITIONS AFFECT THE RATES OF ENZYMATIC REACTIONS? Denatured an enzyme is ~ when it loses its shape and activity it then dies The rates of enzymatic reactions increase with temperature, but only up to a point. Most enzymes work in a narrow pH range 5.4 HOW DOES A CELL OR ORGANISM REGULATE ITS OWN METABOLISM? WHY DO ENZYMATIC REACTIONS OFTEN OCCUR IN SMALL STEPS? Anabolism when cells synthesize large molecules from small ones Catabolism breakdown of food molecules Any biological reactions occur in series of small steps Allows cells to carry out complex transformations, couple reactions, capture smaller denominations of energy, and generate useful intermediate products HOW DO ORGANISMS REGULATE ENZYME FUNCTION? Cells can regulate enzyme activity is through inhibitors that decrease the activity of enzymes HOW DO INHIBITORS INFLUENCE ENZYMES? Inhibitors molecules that inhibit enzymes Steric inhibitor inhibitors that work by resembling the substrate Allosteric inhibitor inhibitor that binds to an enzyme somewhere other than active site