Amino Acids, Proteins, and Enzymes

1Types of Chemical transformations within the cellsOrganisms Transform EnergyLaws of Thermodynamics Free EnergyEndergonic and Exergonic ReactionsBioenergetics and Thermodynamics

General Types of Chemical TransformationOxidation-ReductionReduced:Molecule/atom gains electrons.Reducing agent:Molecule/atom that donates electrons.Oxidized:Molecule/atom loses electrons.Oxidizing agent:Molecule/atom that accepts electrons.Oxidation and Reduction are always coupled reactions.4May involve the transfer of H+ rather than free electrons.Molecules that serve important roles in the transfer of hydrogen are NAD and FAD.Coenzymes that function as hydrogen carriers.Oxidation-Reduction5

Thermodynamics: Study of energy transformations.Energy: Capacity to do work.Kinetic energy: Energy in the process of doing work (energy of motion). For example:Heat (thermal energy) is kinetic energy expressed in random movement of molecules.Light energy from the sun is kinetic energy which powers photosynthesis.Organisms Transform EnergyPotential energy: Energy that matter possesses because of its location or structure (energy of position). For example:In the earth's gravitational field, an object on a hill or water behind a dam have potential energy.Chemical energy is potential energy stored in molecules because of the structural arrangement of the nuclei and electrons in its atoms.Organisms Transform EnergyFirst Law: (Conservation of energy)Energy can be transferred or transformed but neither created nor destroyed. (energy of the universe is constant).Second Law:Every energy transfer or transformation increases the disorder (entropy) of the universe.Laws of Thermodynamics1st & 2nd Laws of Thermodynamics

Energy can be transferred or transformed but neither created nor destroyed.Every energy transfer or transformation increases the disorder (entropy) of the universe.Note especially the waste heat Organisms are Energy TransducersOrganisms take in energy & transduce it to new forms (1st law)As energy transducers, organisms are less than 100% efficient (2nd law)Organisms employ this energy to:GrowProtectRepairReproduceCompete with other OrganismsIn the process, organisms generate waste chemicals & heatOrganisms create local regions of order at the expense of the total energy found in the Universe!!! We are Energy Parasites!First Law of Thermodynamics:Energy can be neither created nor destroyedTherefore, energy generated in any system is energy that has been transformed from one state to another (e.g., chemically stored energy transformed to heat)Second Law of Thermodynamics:Efficiencies of energy transformation never equal 100%Therefore, all processes lose energy, typically as heat, and are not reversible unless the system is open & the lost energy is resupplied from the environmentConversion to heat is the ultimate fate of chemical energyLaws of ThermodynamicsEntropy: Quantitative measure of disorder that is proportional to randomness (designated by the letter S).Closed system: Collection of matter under study which is isolated from its surroundings.Open system: System in which energy can be transferred between the system and its surroundings.The entropy of a system may decrease, but the entropy of the system plus its surroundings must always increase. Highly ordered living organisms do not violate the second law because they are open systems. For example, animals:Maintain highly ordered structure at the expense of increased entropy of their surroundings.Take in complex high-energy molecules as food and extract chemical energy to create and maintain order.Return to the surroundings simpler low energy molecules (CO2 and H2O) and heat.Energy can be transformed, but part of it is dissipated as heat which is largely unavailable to do work. Heat energy can perform work if there is a heat gradient resulting in heat flow from warmer to cooler.e.g. Only 25% of the chemical energy stored in the fuel tank of an automobile is transformed into the motion of the car; the remaining 75% is lost as heat which dissipates rapidly through the surroundings.Organisms live at the expense of free energy Spontaneous process = Change that can occurs without outside help.A spontaneous change can be harnessed in order to perform work.e.g. The downhill flow of water can be used to turn a turbine.When a spontaneous process occurs in a system, the stability of that system increases.Unstable system tends to change in such a way that it becomes more stable.e.g. A system of charged particles is less stable when opposite charges are apart than when they are together.A spontaneous process, when occurs, increases the disorder (entropy) of the universe.Not all of a system's energy is available to do work. The amount of energy that is available to do work is described by the concept of free energy. Free energy (G) is related to the system's total energy (H) and its entropy (S) in the following way:G = H TSwhere:G = free energy (energy available to do work)H = enthalpy or total energyT = absolute temperature in K (K= C + 273)S = entropyFree Energy: A Criterion For Spontaneous ChangeFree energy (G) = Portion of a system's energy available to do work when temperature is uniform throughout the system. It is the difference between the total energy (enthalpy) and the energy not available for doing work (TS).It is a measure of a systems instability: its tendency to change to a more stable state.Systems that are rich in energy (high energy and low entropy) are unstable, and tend to change spontaneously to a more stable state. e.g. Separated charges, and compressed springs.In any spontaneous process, the free energy of a system decreases:

Endergonic and Exergonic ReactionsEndergonic :Reactions require an input of energy to make reaction go.Products must contain more free energy than reactants.

Exergonic:Reactions convert molecules with more free energy to molecules with less.Release energy in the form of heat.Heat is measured in calories.Reactions can be classified based upon their free energy changes:20If a chemical process is exergonic, the reverse process must be endergonic. For example:Cellular respirationC6H12O6 + 6 O2 6 CO2 + 6 H2O G = 686 kcal/mol For each mole (180 g) of glucose oxidized in the exergonic process of cellular respiration 686 kcal (kilocalorie) are released (G = 686 kcal/mol )To produce a mole of glucose, the endergonic process of photosynthesis requires energy input of 686 kcal (G = or +686 kcal/mol).21Calorie (cal)= 4.184 Joule (J)Kilocalorie (kcal)= 1000 calKilojoule (kJ) = 1000 J

Cellular respirationPhotosynthesisC6H12O6 + 6 O2 6 CO2 + 6 H2O22Exergonic ReactionEndergonic ReactionChemical products have less free energy than the reactant molecules.Products store more free energy than reactants.Reaction is energetically downhillReaction is energetically uphill.Spontaneous reaction.Non-spontaneous reaction (requires energy input).G is negative.G is positive.G is the maximum amount of work the reaction can perform+G is the minimum amount of work required to drive the reaction.Metabolic Disequilibrium:Since many metabolic reactions are reversible, they have the potential to reach equilibrium:At equilibrium, G = 0, so the system can do no work.Metabolic disequilibrium is a necessity of life; a cell at equilibrium is dead.

24Reactions in closed systems eventually reach equilibrium and can do no work.A cell that has reached metabolic equilibrium has a delta G = 0 and is dead!Metabolic disequilibrium is one of the defining features of life. Cells maintain disequilibrium because they are open with a constant flow of material in and out of the cell. A cell continues to do work throughout its life.In the cell, these potentially reversible reactions are pulled forward away from equilibrium, because the products of some reactions become reactants for the next reaction in the metabolic pathway.For example, during cellular respiration a steady supply of high-energy reactants such as glucose and removal of low energy products such as CO2 and H2O, maintain the disequilibrium necessary for respiration to proceed.

A cell does three main kinds of work:Mechanical work, beating of cilia, contraction of muscle cells, and movement of chromosomesTransport work, pumping substances across membranes against the direction of spontaneous movementChemical work, driving endergonic reactions such as the synthesis of polymers from monomers.In most cases, the immediate source of energy that powers cellular work is ATP. ATP powers cellular work by coupling exergonic reactions to endergonic reactionsATP (adenosine triphosphate): Nucleotide with unstable phosphate bonds that the cell hydrolyzed for energy to drive endergonic reactions.ATP consists of :Adenine, a nitrogenous base.Ribose, a five-carbon sugar.Chain of three phosphate groups

The Structure and Hydrolysis of ATP

When the terminal phosphate bond is hydrolyzed, an inorganic phosphate group [(P)i] is removed producing ADP (adenosine diphosphate):ATP + H2O ADP + (P)iUnder standard conditions in the laboratory, this exergonic reaction releases 7.3 kcal of energy per mole of ATP hydrolyzed: G = 7.3 kcal/mol In a living cell, this reaction releases 13 kcal/mol, about 77% more than under standard conditions.28The bonds between phosphate groups can be broken by hydrolysis.Hydrolysis of the end phosphate group forms adenosine diphosphate [ATP -> ADP + Pi] and releases 7.3 kcal of energy per mole of ATP under standard conditions.In the cell delta G is about -13 kcal/mol.

Coupled Reactions: ATPCells must maintain highly organized, low-entropy state at the expense of free energy.Cells cannot use heat for energy.Energy released in exergonic reactions used to drive endergonic reactions.

Require energy released in exergonic reactions (ATP) to be directly transferred to chemical-bond energy in the products of endergonic reactions.29Formation of ATP

Formation of ATP requires the input of a large amount of energy.Energy must be conserved, the bond produced by joining Pi to ADP must contain a part of this energy.This energy released when ATP converted to ADP and Pi.ATP is the universal energy carrier of the cell.30