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Study Guide for Chapter 13: Bioenergetics and Biochemical Reaction types – BSC 450/5501. Solve problems using equations describing free energy, equilibrium constants and Q.Bioenergetics and ThermodynamicsBioenergetics is the quantitative study of energy transductions – change of one form of energy into anotherThe first law of the principle of energy is:o For any physical or chemical change, the total amount of energy in the universe remains constants; energy may change form but it cannot be created nor destroyedThe second law of thermodynamics:o The universe tends toward increasing disorderThermodynamic quantitiesGibbs free energy (G) – expresses the amount of energy capable of doing work during a reaction at constant temperature and pressure. When a reaction proceeds with the release of free energy, the freeenergy change, G, has a negative value and the reaction is said to be exergonic. In endergonic reactions, the system gains free energy and G is positiveEnthalpy (H) – the heat content of the reacting system. It reflects the number and kinds of chemical bonds in the reactants and products. When a chemical reaction releases heat it is said to be exothermic; the heat content of the products is less than that of the reactants and H has a negative value. Reacting systems that take up heat from their surroundings are endothermic and have a positive HEntropy (S) – is a quantitative expression for the randomness or disorder in a system. When the products of a reaction are less complex and more disordered than the reactants, the reaction is said to proceed with a gain in entropy G = H TSStandard FreeEnergy Change is Directly Related to the Equilibrium ConstantAt the equilibrium concentration of reactants and products, the rates of the forward and reverse reactions are exactly equal and no further net charge occurs in the system. Keq = [C]c[D]d / [A]a[B]bWhen a reacting system is not at equilibrium, the tendency to move toward equilibrium represents a driving force.Under standard conditions, when reactants are products are initially present at 1 M concentrations the force driving the system toward equilibrium is defined as the standard free energy change, GPhysical constants based on this biochemical standard state are called standard transformed constants, G’, also known as standard freeenergy changes G’ = RTlnK’eq – the standard freeenergy change of a chemical reaction is simply an alternative mathematical way of expressing its equilibrium constantIf K’eq of a reaction is greater than 1.0, its G’ is negative. If K’eq is less than 1.0 its G’ is positiveSmall changes in G’ respond to large changes in K’eq
Actual FreeEnergy Changes Depend on Reactant and Product Concentrations G – actual free energy change G’ – standard freeenergy changeThe standard free energy change tells us in which direction and how far a given reaction must go to reach equilibrium when the initial concentration of each component is 1.0 MThe actual free energy change is a function of reactant and product concentrations and of the temperature prevailing during the reaction G of any reaction proceeding spontaneously toward its equilibrium is always negativethe free energy change for a reaction is independent of the pathway by which the reaction occurs2. Understand the structure of ATP and where the free energy of hydrolysis comes from in chemical terms.a. Heterotrophic cells obtain free energy in a chemical form by the catabolism of nutrient molecules and they use that energy to make ATP from ADP and Pib. ATP donates some of its chemical energy to endergonic processes suchas the synthesis of metabolic intermediates and macromoleculesc. There is a large, negative, standard free energy of hydrolysis of ATP d. The hydrolytic cleavage of the terminal phosphoric acid anhydride bond in ATP sparates one of the three negatively charged phosphates and thus relieves some of the electrostatic repulsion in ATPe. The Pi released is stabilized by the formation of several resonance forms not possible in ATPf. Free energy change is -30.5 kJ/mol g. The actual free energy of hydrolysis of ATP under intracellular conditions is often called its phosphorylation potentialh.3. Explain the general chemical reasons that ATP is the energy currency of the cell.a. ATP is the chemical link between catabolism and anabolism b. The exergonic conversion of ATP to ADP and P is coupled to many endergonic reactions and processesc. Direct hydrolysis of ATP is the source of energy in some processes driven by conformational changedd. It is the transfer of phosphoryl, pyrophosphoryl or adenylyl group from ATP to a substrate that couples the energy of ATP breakdown to endergonic transformations e. ATP provides energy for synthesis of informational macromolecules, and the transport of molecules and ions across membranes against concentration gradientsf. ATP has high phosphoryl group transfer potential4. Understand and be able to explain the reasons why phosphoesters (Phosphoenolpyruvate) and thioesters (Acetyl CoA) can be used as energy currency similar to ATP.a. Phosphoenolpyruvate contains a phosphate ester bond that undergoes hydrolysis to yield the enol form of pyruvate
b. PEP has only one form (enol) and the product (pyruvate) has two possible formsc. The product is stabilized relative to the reactant d. This is the greatest contributing factor to the high standard free energyof hydrolysis of phosphoenolpyruvate G’ = 61.9 kJ/mole. Thioesters, in which a sulfur atom replaces the usualy oxygen in the ester bond, also has large, negative standard free energies of hydrolysisf. AcetylCoA is one of many thioesters important in metabolism g. The acyl group is activated by transacylation, condensation or oxidationreduction reactionsh. Thioesters have greater free energy than oxygen esters i.5. Be able to recognize the mechanisms for Aldol and Claisen condensation, isomerization, group transfer and NAD oxidation/reduction reactions. Drawing these out to follow the electrons will be helpful for full understanding of these processes.a. Aldol condensation – common route to the formation of a C-C bond b. Claisen condensation – the carbanion is stabilized by the carbonyl of anadjacent thioesterc. Group transfer reactions – acyl group transfer generally involves the addition of a nucleophile to the carbonyl carbon of an acyl group to form a tetrahedral intermediated. Oxidation/reduction – every oxidation must be accompanied by a reduction, in which an electron acceptor acquires the electrons removed by oxidation6. Describe how carbonyl groups can be used in biological reactions.a. The carbon of a carbonyl group has a partial positive charge due to theelectron withdrawing property of the carbonyl oxygen, and thus is an electrophilic carbonb. A carbonyl group can thus facilitate the formation of a carbanion on an adjoining carbon by delocalizing the carbanion’s negative chargec. A carbanion intermediate is stabilized by a carbonyl group7. Compare and contrast NAD(P)H and Flavin chemistry.a. NAD+ (oxidized) to NADH (rediced) is high in ratio, favoring hydride transfer from a substrate to NAD+ to from NADHb. NAD and NADPH are the freely diffusible coenzymes of many dehyrogenases. Both aceot two electrons and one protonc. FAD and FMN serve as tightly bound prosthetic groups of flavoproteins. They can accept either one or two electrons and one or two protons
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