Bio Study Guide Test 2 Thermodynamics Thermodynamics The study of energy transformation Metabolism the total chemical activity of a cell an emergent property that occurs through the molecular interactions of the cell Anabolic complex molecules are synthesized from their building blocks require energy Catabolic complex molecules are broken down and energy is released In cells chemical reactions occur as steps in metabolic pathways that interconnect an enzyme catalyzes each step Diver example shows how potential energy can be transformed into kinetic energy Climbing up steps converts KE of muscle movement to potential energy On the platform the diver has more PE Diving converts PE to KE In the water the diver has less PE First Law of Thermodynamics energy can be transferred or transformed but it cannot be created or destroyed Second Law of Thermodynamics every energy transfer or transformation increases the entropy of the universe Chemical reactions of biological systems obey the laws of thermodynamics For a chemical reaction to occur spontaneously the products of the reaction must have a lower free energy G than the reactants The energy lost to heat during the reaction increases the entropy of the system More free energy high G less stable greater work capacity Lower free energy low G more stable less work capacity Free Energy the energy in a system available to do work spontaneous reaction negative G exergonic reaction nonspontaneous reaction positive G endergonic reaction For a chemical reaction aA bB The equilibrium constant is the ratio of the concentrations of reactants and products at equilibrium cC dD C Keq c D A a B b d A physical constant unique to each chemical reaction is called the standard free energy change Standard conditions pH 7 0 25oC initial concentration of each reactant and product is 1 M G Go RT lnKeq G Greactants Gproducts A living system is not at equilibrium Because living cells acquire free energy from nutrient molecules or light G G o RT ln C D A B G begins as negative in order to be spontaneous as reaction proceeds G becomes less negative G is zero when the reaction has reached equilibrium and the reaction ceases An endergonic reaction can be driven forward when it is coupled to an exergonic reaction Enzymes often couple such reactions A cell performs 3 types of work mechanical chromosome movement ATP phosphorylates motor proteins transport active transport ATP phosphorylates transport proteins chemical endergonic reaction ATP phosphorylates key reactants In energy coupling the cell uses energy released from exergonic reactions to drive endergonic reactions ATP hydrolysis releases more chemical energy than most other organic molecules Enzymes speed up metabolic reactions by lowering energy barriers Enzyme is a catalytic protein that speeds up a reaction without being consumed by the reaction Activation energy is the energy absorbed for the bonds to begin to contort to the transition state Enzymes increase the rate of the reaction by lowering activation energy Structure of an enzyme dictates its substrate Substrates enter active site and enzyme changes shape so the active site embraces the substrates substrates held in active site by weak interactions h bonds and ionic bonds Active site and R groups of its amino acids can lower activation energy by acting as a template for substrate orientation stressing the substrate and stabilizing transition state providing a favorable microenvironment participating directly in the catalytic reaction covalent bonding Substrates converted to products products released active site is once again available Enzymes Enzyme activity is influenced by local conditions temperature and pH is specific for each protein Enzyme inhibition a substrate can bind normally to the active site of an enzyme competitive inhibitor mimics the substrate competing for the active site noncompetitive inhibitor binds to the enzyme away from the active site altering the conformation of the enzyme so its active site no longer functions Allosteric regulation of enzyme activity catalytically active catalytically inactive Cooperativity binding of one substrate molecule to active site of one subunit locks all subunits in active conformation Feedback inhibition Regulation of enzyme activity by subcellular location Classifications of enzymes Oxidoreductases Catalyzes transfer of electrons through hydride ions or H atoms Transferases Catalyzes group transfer reactions Hydrolases Catalyzes hydrolysis reactions transfer of functional groups to water Lyases Catalyzes the addition of groups to double bonds or the formation of double bonds by the removal of groups Isomerases Catalyzes the transfer of groups within molecules to yield isomeric forms Ligases Catalyzes the formation of C C C S C O and C N bonds by condensation reactions coupled to ATP cleavage dehydration synthesis The B vitamins are coenzymes organic molecules that associate with enzymes and contribute to a biochemical reaction apoenzyme protein portion of an enzyme holoenzyme entire functional enzyme including protein portion and coenzyme and or cofactor cofactors are non chemical compounds that are bound to a protein to assist in biochemical reaction Reaction coordinate diagram often trace elements ground state is the starting point for either the forward or reverse reaction To decrease the activation energy of a reaction either increase temperature or add an enzyme An enzyme affects the rate of a reaction not the equilibrium of a reaction Reaction coordinate diagram of a biochemical reaction involving an enzyme ES and EP are reaction intermediates What is the source of energy that allows the EA to decrease in the presence of an enzyme When the enzyme and substrate interact weak chemical bonds form and release free energy and the enzyme substrate complex is stabilized The free energy released from this interaction is binding energy of free energy used by the enzyme to lower the activation energy D G B which is the source Enzymes are complementary to the transition state transition state is reached when all weak interactions have formed amount of energy needed to reach transition state is offset by the energy released as weak chemical bonds form Enzyme Kinetics substrate binding specificity catalysis formation of product rate of product formations critical factors are substrate concentration enzyme concentration and product formation simplest approach to studying enzyme kinetics is by measuring