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by: Kari Harber Jr.


Kari Harber Jr.
GPA 3.72


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Class Notes
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This 8 page Class Notes was uploaded by Kari Harber Jr. on Thursday September 17, 2015. The Class Notes belongs to BSC 2010 at Florida State University taught by Staff in Fall. Since its upload, it has received 19 views. For similar materials see /class/205429/bsc-2010-florida-state-university in Biological Sciences at Florida State University.

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Date Created: 09/17/15
Topic 7 METABOLISM THERMODYNAMICS CHEMICAL EQUILIBRIA ENERGY COUPLING and CATALYSIS lectures 910 OBJECTIVES 1 Understand the concepts of kinetic vs potential energy 2 Understand the concepts of free energy and entropy use these concepts and thermodynamic principles to show whether a particular reaction is going be spontaneous or not 3 Be able to define equilibrium constant and how this relates to degree of spontaneity of a given reaction 4 Understand the process by which an endergonic reaction is coupled to a highly exergonic reaction and the role ofATP in biological systems 5 Understand the principle of mass action 6 Draw a free energy diagram to explain the concept of activation energy Ea and then show the impact of enzymatic catalysis on Ea 7 Understand the concepts of enzyme velocity maximal velocity Vmax and affinity as well as the factors substrate concentration pH temperature etc which impact the rate of enzyme catalyzed reactions Energy physicochemical term for the capacity to do work work moving a force over a distance units are in calorie or more commonly in Joule note force mass X acceleration There are two forms of energy 1 kinetic energy that is actively engaged in doing work 2 potential energy that is not actively engaged in doing work but has the potential to do so Energy transformation the process by which energy is converted from one form to another chemical energy into mechanical energy as would take place during muscle contraction chemical energy into covalent bonds as would take place during the biosynthesis of macromolecules Bioenergetics the study of energy conversion in biological systems Metabolism the sum total of all the chemical reactions taking place in an organism consists of a network of chemical reactions often called pathways Two general types of pathways 1 catabolic breakdown complex molecules into simpler molecules 2 anabolic form complex molecules from simpler molecules biosynthesis requires energy input Thermodynamics the study of energy transformations as applied to all physico chemical systems including biological Consider the following model chemical reaction A 9 B we ask the simple question what determines whether this reaction takes place spontaneously or not The principles of thermodynamics help us to understand this question First ofall we need to define yet anotherterm free energy as applied to molecular reactions it is the energy available to do work often denoted by the symbol G for Gibbs free energy first law of thermodynamics energy transformations do not create nor destroy energy but simply result in the interconversion from one form to the other second law of thermodynamics all energy transformations result in an increase in disorder entropy is a term which is a measure of the extent of disorder in a system Thus the second law can be restated by saying that all energy transformations result in an increase in entropy in the system Now lets apply the above two laws to defining whether a reaction is spontaneous or not AB CD Gi Gf Si Sf where G free energy at initial state G free energy at final state and AG GfGi and S entropy at initial state Sf entropy at nal state and AS Sf Si Thus when AG negative value reaction is spontaneous it is said to be exergonic spontaneous reactions lead to a decrease in free energL AS positive value reaction is spontaneous spontaneous reactions lead to an increase in entropy Exergonic reactions lead to a decrease in free energy and an increase in entropy Endergonic reactions are not spontaneous movement in this direction would lead to an increase in free energy and a decrease in entropy A good example is biosynthesis of large molecules We ll see in a few minutes how it is possible to drive endergonic reactions by coupling them with exergonic reactions Fig 65 relationship of free energy to stability work capacity and spontaneous change Fig 66 exergonic vs endergonic reactions Chemical eguilibria Suppose you mix A and B together they will react to form C and D which will accumulate C D will begin to react to form A B Eventually A B 9 C D reaction rate C D 9 A B reaction rate at this point we can say that the reaction has reached chemical equilibrium Each kind of reaction has its own unique chemical equilibria which can be de ned by the equilibrium constant Keq Keq product of concentrations of products at equilibrium product of concentrations of reactants at equilibrium in our example above Keq C X D A X B Eguilibria and spontaneity 1 reactions which have Keq gtgtgtgt 1 are highly exergonic 2 reactions which have Keq ltltltlt 1 are highly endergonic However you can make an endergonic reaction go in a nonspontaneous direction by coupling it with an exergonic reaction Energy coupling the use of an exergonic process to drive an endergonic process suppose A9 B AG Agt B positive value X9 Z AG Xgtz negative value AGnet AG AgtB AG xgt z if AGnet is negative then the A 9 B reaction will proceed Energy coupling is extremely common in biological systems By far the most common coupling reaction is the reaction which involves the hydrolysis of a compound known as ATP adenosine triphosphate ATP 9 ADP inorganic phosphate Pi fig 68 ATP is very unstable and is spontaneously hydrolyzed by water this reaction however can be coupled to another reaction as shown in fig 69 glutamine formation ATP is often referred to as the energy currency of cells it is constantly being utilized to drive endergonic processes In addition ATP is unstable If you were to add ATP to a beaker of water it would spontaneously hydrolyze so that at chemical equilibrium 9999 of the ATP would have been hydrolyzed to ADP and Pi In cells the concentration of ATP is 100 times greater than ADP Thus cells keep the ATP hydrolysis reaction far displaced from chemical equilibrium This is accomplished by a process known as cellular energy metabolism energy metabolism catabolism of organic molecules yielding ATP and other useful forms of chemical energy Fig 610 the ATP hydrolysisregeneration cycle in cells Rates of reactions For a chemical reaction like A 9 B the rate of the reaction is a function of the concentrations of reactants and products Thus the principle of chemical mass action tells us that we can increase the rate ofA 9 B by increasing A decreasing B or both However biological systems have evolved enzymes which function as catalysts to speed up chemical reactions enzyme catalytic protein catalyst an agent which accelerates a chemical reaction without being consumed Energy barriers for a reaction to proceed fig 612 reactants must absorb energy to reach a critical state at which the reaction will proceed This amount of energy is known as the activation energy Ea and is unique for each chemical reaction What an enzyme does is that it lowers the Ea by bringing the reactants very close together as well as by using the special chemistry of its amino acids to create a new chemical pathway for the reaction to take place see fig 613 The net effect is to speed up the reaction tremendously Enzyme terminology 1 substrate reactant 2 enzyme velocity the rate of the enzyme catalyzed reaction 3 substrate specificity the degree of selectivity for a substrate molecule enzymes are typically very speci c This is due to the unique structure of the active site active site region of protein where catalysis takes place Fig 615 catalytic cycle Fig 614 concept of induced fit substrate causes 3D change in enzyme 4 substrate af nity a measure of the how readily an enzyme binds a substrate molecule for catalysis Factors influencing enzyme velocity 1 Substrate concentration S as 8 increases enzyme velocity V increases however the relationship below is a rectangular hyperbola Thus velocity increases rapidly at low S s but the rate of increase decreases at higher S s and reaches a maximum and longer increases even if S is increased Under these conditions the enzyme is said to be saturated at any given point in time all enz me molecules are in the act of catal sis Vmax maximal velocity 100 iiquot 3 so 7 V 60 40 20 O 7 r r o 20 4o 60 8O su bstrate 2 affinity of enzyme for substrate substrate affinity a measure of the how readily an enzyme binds a substrate molecule for catalysis or alternatively the strength of binding ofS to the enzyme enzymes differ in terms of how readily they bind substrate molecules This in turn influences the impact of S on enzyme velocity Let s consider two enzymes that differ in terms of their affinity for substrate This would be reflected in terms of the shape of their V vs 8 curves The low affinity enzyme would have a curve shifted to the right which means that at lower S s this enzyme would have a lower V than the V for the corresponding high affinity enzyme a quantitative index for affinity high and loW affinity are imprecise qualitative terms Thus it is useful to use a more quantitative index The useful index is the Km Michaelis constant named after a 19th century physical chemist Km S that produces 50 of maximal velocity Vmax Vmax maximal velocity of the enzyme catalyzed reaction enzyme is saturated The higher the Km the lower the affinity and vice versa Affinity is important When viewed in the context that the enzyme is functioning namely inside of cells Km is an index of affinity Vmax maximal velocity i 100 80 V60 40 Km 8 that producces 50 of Vmax 20 0 20 40 60 80 substram l One typically finds that the Km for a typical enzyme falls in the range of concentrations of the substrate in the cell This means that small changes the physiological S s produce large changes in the velocity of the enzyme catalyzed reaction cellular range of S small changes in S produce large changes in V 0 20 40 60 80 S 3 temperature temperature increases cause an increase in the rates of enzyme catalyzed reactions fig 616 however at critical temperatures weak bonds start to break and activity will fall and reach zero when the protein is denatured 4 pH hydrogen ions may be participants literally substrates in enzyme catalyzed reactions further changes in pH may alter the ionization states of amino acid residues Thus it is not surprising that pH influences enzyme activity Typically enzymes show pH optima fig 616 5 low molecular weight activators and inhibitors often the activity of enzymes is regulated by low molecular weight organic and sometimes inorganic molecules These serve to change activity by altering Vmax andor Km a activators bind to some binding site other than the active site typically increase affinity observed decrease in Km b inhibitors reduce enzyme velocity Fig 617 competitive inhibitors mimic the structure of the substrate compete with the substrate for binding at the active site In effect the inhibitor raises the Km thereby reducing its apparent af nity for substrate noncompetitive inhibitors bind to some site other than the active site


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