Thermodynamics

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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 and Randomness

• Entropy S measure of randomness
• cal/degmole
• T?S change of randomness
• For increased randomness, sign is

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System Definition
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System Definition
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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 (CO2)
• Energy exchange
• Heat release (fermentation)
• Light release (fireflies)
• Light absorption (plants)

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1st Law of Thermodynamics

• Energy is conserved, but transduction is allowed
• Transduction

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2nd Law of Thermodynamics

• In all spontaneous processes, total entropy of
  the universe increases

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2nd Law of Thermodynamics

• ?Ssystem ?Ssurroundings ?Suniverse gt 0
• A cell (system) can decrease in entropy only if a
  greater increase in entropy occurs in
  surroundings
• C6H12O6 6O2 ? 6CO2 6H2O
• complex simple

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Entropy A More Rigorous Definition

• From statistical mechanics
• S k lnW
• k Boltzmann constant 1.38?1023 J/K
• W number of ways to arrange the system
• S 0 at absolute zero (-273ºC)

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Gibbs Free Energy

• Unifies 1st and 2nd laws
• ?G
• Gibbs free energy
• Useful work available in a process
• ?G ?H T?S
• ?H from 1st law
• Kind and number of bonds
• T?S from 2nd 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 H2O
• Simplify ?Gº and Keq by defining H 107 M
• H2O 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
• GA GA RT lnA
• For reaction aA bB ? cC dD
• ?G ?Gº? RT ln
• Constant Variable
• (from table)

º?
Cc Dd

Aa Bb
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Relationship Between ?Gº? and K?eq
Cc Dd

• ?G ?Gº? RT ln
• At equilibrium, ?G 0, so
• ?Gº? RT ln
• ?Gº? RT ln K?eq

Aa Bb
Cc Dd
Aa Bb
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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

Cc Dd
Aa Bb
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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 Keq

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?Gº? is Additive (State Function)

• Reaction
• A ? B
• B ? C
• Sum A ? C
• Also B ? A

• Free energy change
• ?G1º?
• ?G2º?
• ?G1º? ?G2º?
• ?G1º?

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Coupling Reactions

• Glucose HPO42 ? Glucose-6-P
• ATP ? ADP HPO42
• 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 Pi
?
?
?
?
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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 CC Bonds

• Homolytic reactions
• Heterolytic reactions

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Making and Breaking CC Bonds

• Nucleophilic substitutions

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Nucleophilic Substitution Reactions

• SN1

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Carbocation
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Common Biological Nucleophiles
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SN2 Nucleophilic Substitution
?
?
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Reactivity is SN2 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 (Pi, PPi)

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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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Aldol Condensation
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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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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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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
• Mg2, Mn2, Co2, Fe2, Zn2, Cu2, Mo3

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Enzyme Inhibitors and Poisons

• Chelating agents
• EDTA (divalent cations)
• CN (Fe2)
• 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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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 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