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Thermodynamics & ATP Review thermodynamics, energetics, chemical sense, and role of ATP
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Lecture 24 Thermodynamics in Biology
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A Simple Thought Experiment
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Driving Forces for Natural Processes Enthalpy –Tendency toward lowest energy state Form stablest bonds Entropy –Tendency to maximize randomness
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Enthalpy and Bond Strength Enthalpy = ∆H = heat change at constant pressure Units –cal/mole or joule/mole 1 cal = 4.18 joule Sign –∆H is negative for a reaction that liberates heat
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Entropy and Randomness
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Entropy = S = measure of randomness –cal/deg·mole T∆S = change of randomness For increased randomness, sign is “+”
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“System” Definition
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Cells and Organisms: Open Systems Material exchange with surroundings –Fuels and nutrients in (glucose) –By-products out (CO 2 ) Energy exchange –Heat release (fermentation) –Light release (fireflies) –Light absorption (plants)
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1 st Law of Thermodynamics Energy is conserved, but transduction is allowed Transduction
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2 nd Law of Thermodynamics In all spontaneous processes, total entropy of the universe increases
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2 nd Law of Thermodynamics ∆S system + ∆S surroundings = ∆S universe > 0 A cell (system) can decrease in entropy only if a greater increase in entropy occurs in surroundings C 6 H 12 O 6 + 6O 2 6CO 2 + 6H 2 O complex simple
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Entropy: A More Rigorous Definition From statistical mechanics: –S = k lnW k = Boltzmann constant = 1.38 10 –23 J/K W = number of ways to arrange the system S = 0 at absolute zero (-273ºC)
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Gibbs Free Energy Unifies 1 st and 2 nd laws ∆G –Gibbs free energy –Useful work available in a process ∆G = ∆H – T∆S –∆H from 1 st law Kind and number of bonds –T∆S from 2 nd law Order of the system
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∆G Driving force on a reaction Work available distance from equilibrium ∆G = ∆H – T∆S –State functions Particular reaction T P Concentration (activity) of reactants and products
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Equilibrium ∆G = ∆H – T∆S = 0 So ∆H = T∆S –∆H is measurement of enthalpy –T∆S is measurement of entropy Enthalpy and entropy are exactly balanced at equilibrium
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Effects of ∆H and ∆S on ∆G Voet, Voet, and Pratt. Fundamentals of Biochemistry. 1999.
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Standard State and ∆Gº Arbitrary definition, like sea level [Reactants] and [Products] –1 M or 1 atmos (activity) T = 25ºC = 298K P = 1 atmosphere Standard free energy change = ∆Gº
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Biochemical Conventions: ∆Gº Most reactions at pH 7 in H 2 O Simplify ∆Gº and K eq by defining [H + ] = 10 –7 M [H 2 O] = unity Biochemists use ∆Gº and K eq
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Relationship of ∆G to ∆Gº ∆G is real and ∆Gº is standard For A in solution –G A = G A + RT ln[A] For reaction aA + bB cC + dD –∆G = ∆Gº + RT ln –Constant Variable (from table) º [C] c [D] d [A] a [B] b }
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Relationship Between ∆Gº and K eq ∆G = ∆Gº + RT ln At equilibrium, ∆G = 0, so –∆Gº = –RT ln –∆Gº = –RT ln K eq [C] c [D] d [A] a [B] b [C] c [D] d [A] a [B] b
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Relationship Between K eq and ∆Gº
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Will Reaction Occur Spontaneously? When: –∆G is negative, forward reaction tends to occur –∆G is positive, back reaction tends to occur –∆G is zero, system is at equilibrium ∆G = ∆Gº + RT ln [C] c [D] d [A] a [B] b
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A Caution About ∆Gº Even when a reaction has a large, negative ∆Gº, it may not occur at a measurable rate Thermodynamics –Where is the equilibrium point? Kinetics –How fast is equilibrium approached? Enzymes change rate of reactions, but do not change K eq
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∆Gº is Additive (State Function) Reaction A B B C Sum: A C Also: B A Free energy change ∆G 1 º ∆G 2 º ∆G 1 º + ∆G 2 º – ∆G 1 º
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Coupling Reactions Glucose + HPO 4 2– Glucose-6-P ATP ADP + HPO 4 2– ATP + Glucose ADP + Glucose-6-P ∆Gº kcal/mol kJ/mol +3.3 +13.8 –7.3 – 30.5 –4.0 – 16.7
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Resonance Forms of P i –– –– –– ––
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Phosphate Esters and Anhydrides
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Hydrolysis of Glucose-6-Phosphate ∆Gº = –3.3 kcal/mol = –13.8 kJ/mol
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High ∆Gº Hydrolysis Compounds ∆Gº = –14.8 kcal/mol = –61.9 kJ/mol
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High ∆Gº Hydrolysis Compounds ∆Gº = –11.8 kcal/mol = –49.3 kJ/mol
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High ∆Gº Hydrolysis Compounds ∆Gº = –10.3 kcal/mol = –43 kJ/mol
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Phosphate Anhydrides (Pyrophosphates) ∆Gº = –7.3 kcal/mol = –30.5 kJ/mol
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Thiol Esters ∆Gº = –7.5 kcal/mol = –31.4 kJ/mol
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Thiol Esters Thiol ester less resonance-stabilized
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“High-Energy” Compounds Large ∆Gº hydrolysis –Bond strain (electrostatic repulsion) in reactant ATP –Products stabilized by ionization Acyl-P –Products stabilized by isomerization PEP –Products stabilized by resonance Creatine-P
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“High-Energy” Compounds “High-energy” compound is one with a ∆Gº below –6 kcal/mol (–25 kJ/mol)
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High-Energy Compounds
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Group Transfer Potential
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Lecture 25 Chemical Sense in Metabolism
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Making and Breaking C–C Bonds Homolytic reactions Heterolytic reactions
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Making and Breaking C–C Bonds Nucleophilic substitutions
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Nucleophilic Substitution Reactions S N 1
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Carbocation
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Common Biological Nucleophiles
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S N 2 Nucleophilic Substitution –– ––
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Reactivity is S N 2 Reactions
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Leaving Group Must accommodate a pair of electrons –And sometimes a negative charge
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Major Role of Phosphorylation Converts a poor leaving group ( – OH) into a good one (P i, PP i )
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Acid Catalysis of Substitution Reactions This H is often donated by an acidic sidechain of enzyme
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Central Importance of Carbonyls 1. Can produce a carbocation 2. Can stabilize a carbanion
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Biological Carbonyls
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Aldol Condensation
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Aldolase Reaction Glycolysis and gluconeogenesis
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Claisen Condensation
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Thioesters in Biology In thioesters, the carbonyl carbon has more positive character than carbonyl carbon in oxygen ester.
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“High-Energy” Thioester Compounds
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Coenzyme A
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Fatty Acid Metabolism Uses Claisen condensation Thiolase acts in fatty acid oxidation for energy production
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Thiolase: Role of Cys-SH
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Energy Diagram for Reaction ‡ is the transition state –Pentacovalent carbon, for example
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Functional Groups on Enzymes Amino acid side chains – –Imidazole –
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Functional Groups on Enzymes Coenzymes/cofactors –Pyridoxal phosphate Metal ions and complexes – Mg 2+, Mn 2+, Co 2+, Fe 2+, Zn 2+, Cu 2+, Mo 3+
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Enzyme Inhibitors and Poisons Chelating agents –EDTA (divalent cations) –CN – (Fe 2+ ) Cofactor analogs –Warfarin Suicide substrates
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Lecture 26 ATP and Phosphoryl Group Transfers
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Phosphate Esters and Anhydrides
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Phosphoryl Group Transfers
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Phosphoryl (Not Phosphate) Transfers
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Nucleophilic Displacements
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ATP as a Phophoryl Donor 2 roles for ATP –Thermodynamic Drive unfavorable reactions –Mechanistic Offer 3 electrophilic phosphorous atoms for nucleophilic attack
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ATP as Phosphoryl Donor 3 points of nucleophilic attack
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Adenylyation: Attack on -P
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Adenylation: Attack on -P
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Pyrophosphorylation: Attack on -P
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Phosphorylation: Attack on -P
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Amino Acid Sidechains as Nucleophiles
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Enzymatic Phosphoryl Transfers Four classes –Phosphatases Water is acceptor/nucleophile –Phosphodiesterases Water is acceptor/nucleophile –Kinases Nucleophile is not water –Phosphorylases Phosphate is nucleophile
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Phosphatases: Glucose-6- Phosphatase
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Phosphatases: Glucose-6- Phosphate
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Phosphodiesterases: RNAase
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Kinases: -Phosphoryl Transfer Transfer from ATP
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Kinases: P-Enzyme Intermediates
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Kinases
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Pyruvate Kinase Makes ATP (∆Gº= –31 kJ/mol) from PEP ∆Gº= –62 kJ/mol
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Phosphoryl-Group Transfer Potential
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Significance of “High-Energy” P Compounds Drive synthesis of compounds below Phosphated compounds are more reactive –Thermodynamically –Kinetically If organism has ATP (etc…), it can do work and resist entropy Cells must get ATP
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