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Biochemical Thermodynamics. Andy Howard Biochemistry, Fall 2009 IIT. Thermodynamics matters!. Thermodynamics tells us which reactions will go forward and which ones won’t. Thermodynamics: Basics Why we care The laws Enthalpy Thermodynamic properties Units Entropy.

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Biochemical thermodynamics l.jpg

Biochemical Thermodynamics

Andy Howard

Biochemistry, Fall 2009IIT

Biology 401: Thermodynamics

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Thermodynamics matters!

  • Thermodynamics tells us which reactions will go forward and which ones won’t.

Biology 401: Thermodynamics

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Thermodynamics: Basics

Why we care

The laws


Thermodynamic properties



Special topics in Thermodynamics

Solvation & binding to surfaces

Free energy



Coupled reactions

ATP: energy currency

Other high-energy compounds

Dependence on concentration


Biology 401: Thermodynamics

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Energy in biological systems

  • We distinguish between thermodynamics and kinetics:

  • Thermodynamics characterizes the energy associated with equilibrium conditions in reactions

  • Kinetics describes the rate at which a reaction moves toward equilibrium

Biology 401: Thermodynamics

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  • Equilibrium constant is a measure of the ratio of product concentrations to reactant concentrations at equilibrium

  • Free energy is a measure of the available energy in the products and reactants

  • They’re related by DGo = -RT ln Keq

Biology 401: Thermodynamics

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  • Horton et al put this in the middle of chapter 10;Garrett & Grisham are smart enough to put it in the beginning.

  • You can tell which I prefer!

Biology 401: Thermodynamics

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Why we care



  • Free energy is directly related to the equilibrium of a reaction

  • It doesn’t tell us how fast the system will come to equilibrium

  • Kinetics, and the way that enzymes influence kinetics, tell us about rates

  • Today we’ll focus on equilibrium energetics; we’ll call that thermodynamics

Biology 401: Thermodynamics

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… but first: iClicker quiz!

  • 1. Which of the following statements is true?

    • (a) All enzymes are proteins.

    • (b) All proteins are enzymes.

    • (c) All viruses use RNA as their transmittable genetic material.

    • (d) None of the above.

Biology 401: Thermodynamics

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iClicker quiz, continued

  • 2. Biopolymers are generally produced in reactions in which building blocks are added head to tail. Apart from the polymer, what is the most common product of these reactions?(a) Water(b) Ammonia(c) Carbon Dioxide(d) Glucose(e) None of the above. Polymerization doesn’t produce secondary products

Biology 401: Thermodynamics

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iClicker quiz, continued

  • Which type of biopolymer is sometimes branched?(a) DNA(b) Protein(c) Polysaccharide(d) RNA(e) They’re all branched.

Biology 401: Thermodynamics

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iClicker quiz, concluded

Free Energy


  • 4. The red curve represents the reaction pathway for an uncatalyzed reaction. Which one is the pathway for a catalyzed reaction?





Reaction Coordinate

Biology 401: Thermodynamics

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Laws of Thermodynamics

  • Traditionally four (0, 1, 2, 3)

  • Can be articulated in various ways

  • First law: The energy of an isolated system is constant.

  • Second law: Entropy of an isolated system increases.

Biology 401: Thermodynamics

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What do we mean by systems, closed, open, and isolated?

  • A system is the portion of the universe with which we’re concerned (e.g., an organism or a rock or an ecosystem)

  • If it doesn’t exchange energy or matter with the outside, it’s isolated.

  • If it exchanges energy but not matter, it’s closed

  • If it exchanges energy & matter, it’s open

Biology 401: Thermodynamics

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That makes sense if…

  • It makes senseprovided that we understand the words!

  • Energy. Hmm. Capacity to do work.

  • Entropy: Disorder. (Boltzmann): S = klnW

  • Isolated system: one in which energy and matter don’t enter or leave

  • An organism is not an isolated system:so S can decrease within an organism!



Biology 401: Thermodynamics

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Enthalpy, H

  • Closely related to energy:H = E + PV

  • Therefore changes in H are:H = E + PV + VP

  • Most, but not all, biochemical systems have constant V, P:H = E

  • Related to amount of heat content in a system

Kamerlingh Onnes

Biology 401: Thermodynamics

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Kinds of thermodynamic properties

  • Extensive properties:Thermodynamic properties that are directly related to the amount (e.g. mass, or # moles) of stuff present (e.g. E, H, S)

  • Intensive properties: not directly related to mass (e.g. P, T)

  • E, H, S are state variables;work, heat are not

Biology 401: Thermodynamics

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  • Energy unit: Joule (kg m2 s-2)

  • 1 kJ/mol = 103J/(6.022*1023)= 1.661*10-21 J

  • 1 cal = 4.184 J:so 1 kcal/mol = 6.948 *10-21 J

  • 1 eV = 1 e * J/Coulomb =1.602*10-19 C * 1 J/C = 1.602*10-19 J= 96.4 kJ/mol = 23.1 kcal/mol

James Prescott Joule

Biology 401: Thermodynamics

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Typical energies in biochemistry

  • Go for hydrolysis of high-energy phosphate bond in adenosine triphosphate:33kJ/mol = 7.9kcal/mol = 0.34 eV

  • Hydrogen bond: 4 kJ/mol=1 kcal/mol

  • van der Waals force: ~ 1 kJ/mol

  • See textbook for others

Biology 401: Thermodynamics

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  • Related to disorder: Boltzmann:S = k ln k=Boltzmann constant = 1.38*10-23 J K-1

  • Note that k = R / N0

  •  is the number of degrees of freedom in the system

  • Entropy in 1 mole = N0S = Rln

  • Number of degrees of freedom can be calculated for simple atoms

Biology 401: Thermodynamics

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Components of entropy

Liquid propane (as surrogate):

Biology 401: Thermodynamics

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Real biomolecules

  • Entropy is mostly translational and rotational, as above

  • Enthalpy is mostly electronic

  • Translational entropy = (3/2) R ln Mr

  • So when a molecule dimerizes, the total translational entropy decreases(there’s half as many molecules,but ln Mr only goes up by ln 2)

  • Rigidity decreases entropy

Biology 401: Thermodynamics

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Entropy in solvation: solute

  • When molecules go into solution, their entropy increases because they’re freer to move around

Biology 401: Thermodynamics

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Entropy in solvation: Solvent

  • Solvent entropy usually decreases because solvent molecules must become more ordered around solute

  • Overall effect: often slightly negative

Biology 401: Thermodynamics

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Entropy matters a lot!

  • Most biochemical reactions involve very small ( < 10 kJ/mol) changes in enthalpy

  • Driving force is often entropic

  • Increases in solute entropy often is at war with decreases in solvent entropy.

  • The winner tends to take the prize.

Biology 401: Thermodynamics

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Apolar molecules in water

  • Water molecules tend to form ordered structure surrounding apolar molecule

  • Entropy decreases because they’re so ordered

Biology 401: Thermodynamics

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Binding to surfaces

  • Happens a lot in biology, e.g.binding of small molecules to relatively immobile protein surfaces

  • Bound molecules suffer a decrease in entropy because they’re trapped

  • Solvent molecules are displaced and liberated from the protein surface

Biology 401: Thermodynamics

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Free Energy

  • Gibbs: Free Energy EquationG = H - TS

  • So if isothermal, G = H - TS

  • Gibbs showed that a reaction will be spontaneous (proceed to right) if and only if G < 0

Biology 401: Thermodynamics

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Standard free energy of formation, Gof

  • Difference between compound’s free energy & sum of free energy of the elements from which it is composed

Biology 401: Thermodynamics

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Free energy and equilibrium

  • Gibbs: Go = -RT ln Keq

  • Rewrite: Keq = exp(-Go/RT)

  • Keq is equilibrium constant;formula depends on reaction type

  • For aA + bB  cC + dD,Keq = ([C]c[D]d)/([A]a[B]b)

Biology 401: Thermodynamics

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Spontaneity and free energy

  • Thus if reaction is just spontaneous, i.e. Go = 0, then Keq = 1

  • If Go < 0, then Keq > 1: Exergonic

  • If Go > 0, then Keq < 1: Endergonic

  • You may catch me saying “exoergic” and “endoergic” from time to time:these mean the same things.

Biology 401: Thermodynamics

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Free energy as a source of work

  • Change in free energy indicates that the reaction could be used to perform useful work

  • If Go < 0, we can do work

  • If Go > 0, we need to do work to make the reaction occur

Biology 401: Thermodynamics

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What kind of work?

  • Movement (flagella, muscles)

  • Chemical work:

    • Transport molecules against concentration gradients

    • Transport ions against potential gradients

  • To drive otherwise endergonic reactions

    • by direct coupling of reactions

    • by depletion of products

Biology 401: Thermodynamics

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Coupled reactions

  • Often a single enzyme catalyzes 2 reactions, shoving them together:reaction 1, A  B: Go1 < 0 reaction 2, C D: Go2 > 0

  • Coupled reaction:A + C  B + D: GoC = Go1 + Go2

  • If GoC < 0,then reaction 1 is driving reaction 2!

Biology 401: Thermodynamics

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How else can we win?

  • Concentration of product may play a role

  • As we’ll discuss in a moment, the actual free energy depends on Go and on concentration of products and reactants

  • So if the first reaction withdraws product of reaction B away,that drives the equilibrium of reaction 2 to the right

Biology 401: Thermodynamics

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Adenosine Triphosphate

  • ATP readily available in cells

  • Derived from catabolic reactions

  • Contains two high-energy phosphate bonds that can be hydrolyzed to release energy: O O- || |(AMP)-O~P-O~P-O- | || O- O

Biology 401: Thermodynamics

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Hydrolysis of ATP

  • Hydrolysis at the rightmost high-energy bond:ATP + H2O  ADP + PiGo = -33kJ/mol

  • Hydrolysis of middle bond:ATP + H2O  AMP + PPiGo = -33kJ/mol

  • BUT PPi  2 Pi, Go = -33 kJ/mol

  • So, appropriately coupled, we get roughly twice as much!

Biology 401: Thermodynamics

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ATP as energy currency

  • Any time we wish to drive a reaction that has Go < +30 kJ/mol, we can couple it to ATP hydrolysis and come out ahead

  • If the reaction we want hasGo < +60 kJ/mol, we can couple it toATP  AMP and come out ahead

  • So ATP is a convenient source of energy — an energy currency for the cell

Biology 401: Thermodynamics

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Coin analogy

  • Think of store of ATPas a roll of quarters

  • Vendors don’t give change

  • Use one quarter for some reactions,two for others

  • Inefficient for buying $0.35 items

Biology 401: Thermodynamics

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Other high-energy compounds

  • Creatine phosphate: ~ $0.40

  • Phosphoenolpyruvate: ~ $0.35

  • So for some reactions, they’re more efficient than ATP

Biology 401: Thermodynamics

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Dependence on Concentration

  • Actual G of a reaction is related to the concentrations / activities of products and reactants:G = Go + RT ln [products]/[reactants]

  • If all products and reactants are at 1M, then the second term drops away; that’s why we describe Go as the standard free energy

Biology 401: Thermodynamics

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Is that realistic?

  • No, but it doesn’t matter;as long as we can define the concentrations, we can correct for them

  • Often we can rig it so[products]/[reactants] = 1even if all the concentrations are small

  • Typically [ATP]/[ADP] > 1 so ATP coupling helps even more than 33 kJ/mol!

Biology 401: Thermodynamics

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How does this matter?

  • Often coupled reactions involve withdrawal of a product from availability

  • If that happens,[product] / [reactant]shrinks, the second term becomes negative,and G < 0 even if Go > 0

Biology 401: Thermodynamics

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How to solve energy problems involving coupled equations

  • General principles:

    • If two equations are added, their energetics add

    • An item that appears on the left and right side of the combined equation can be cancelled

  • This is how you solve the homework problem!

Biology 401: Thermodynamics

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A bit more detail

  • Suppose we couple two equations:A + B  C + D, DGo’ = xC + F  B + G, DGo’ = y

  • The result is:A + B + C + F  B + C + D + GorA + F  D + G, DGo’ = x + y

  • … since B and C appear on both sides

Biology 401: Thermodynamics

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What do we mean by hydrolysis?

  • It simply means a reaction with water

  • Typically involves cleaving a bond:

  • U + H2O  V + Wis described as hydrolysis of Uto yield V and W

Biology 401: Thermodynamics