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Thermodynamics in
Bioenergetics

Jean-Louis Burgot
University of Rennes 1-France
Rennes, France

p,
p,
A SCIENCE PUBLISHERS BOOK
A SCIENCE PUBLISHERS BOOK
Cover credit: Cover illustration reproduced by kind courtesy of Jean-Louis Burgot

CRC Press
Taylor & Francis Group
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Version Date: 20190423

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Title: Thermodynamics in bioenergetics / Jean-Louis Burgot (University of
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Description: Boca Raton, FL : CRC Press, 2019. | “A science publishers book.”
| Includes bibliographical references and index.
Identifiers: LCCN 2019016030 | ISBN 9781138490925 (hardback)
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Preface

Undergraduate biology courses are becoming more and more dependent on mathematics, physics
and chemistry. Among the involved physical sciences, there is no need, certainly, to emphasize the
part played by thermodynamics! At its origin, thermodynamics was the branch of physics devoted
to energy and its transformations. Now, even if its goal remains the same, its realm of applying has
considerably grown up to the point that, since for several decades, this science is endowed with a
cosmogonic impact! No more!
Energy, the great concept ceaselessly involved in the handling of thermodynamics, can be
defined by any property which can be produced from work or which can be converted into work.
There are various manifestations of energy as there are different kinds of works. Among them, let us
for example mention the thermal, electrical, radiant, potential kinetic ones. It is a well known fact
that the conversion of one kind of them into another one together with the “interconversion” energy
work are of utmost importance in physics, in chemistry and also in biology. It is also known that if
work can be entirely converted into heat, the converse is only partially true, according to the second
principle of thermodynamics. In view of all these considerations, heat and work (whatever the kind
the latter is) are regarded as being two forms of energy. Hence, it is not surprising that all forms of
energy are expressed in work units.
Over the pre-past century, the question to know whether or not living cells obey the laws of physics
and chemistry was open. Its negative answer was related to the theory named in the french language
as “dogme de la force vitale”. Now, we know that physico-chemical laws hold in the biological world
and, of course, it is the case of thermodynamics laws. Therefore, we can already assert that living
cells, indeed, do possess very powerful systems for transforming energy.
Bioenergetics is the term used to denote the study of energy transformations in living organisms
in particular but not only at the cellular level. Bioenergetics is now a study which cannot get away
from biochemistry and molecular biology courses, even in the undergraduate ones. But…… there
exists a “but”! Beginner students who have chosen to study biological sciences may not be interested
in the study of physical sciences. As a result, their background in this realm may be too weak and,
therefore, they may quickly exhibit problems of understandings. This is particularly the case with
thermodynamics, even with classical thermodynamics. It is true that, at first glance, it appears to be
an abstract science. The reason, from the physical standpoint, is that it involves idealized systems
which often carry out imaginary experiments! Moreover, from the mathematical one, the symbolism
involved in its study is somewhat discouraging because of the fact that it is rather cumbersome with
the quasi-systematic presence, notably, of several partial derivatives.
However, for the development of this part of thermodynamics, only a moderate knowledge of
mathematics is an essential condition. However, from another standpoint, it is clear that the notion
of entropy which is at the heart of thermodynamics complicates its approach more. As for them,
statistical thermodynamics and non equilibrium thermodynamics are, both mathematically and
physically, more difficult to grasp than the classical one. Some results coming from non equilibrium
thermodynamics are only given in this book. It is true that the need for introducing some elements
of statistical thermodynamics in it was questionable. Nevertheless, the author has not hesitated: the
book does not contain elements of statistical thermodynamics even if its development tremendously
iv Thermodynamics in Bioenergetics

confort the theory and results of the classical one. Concerning the introduction of some elements
of non equilibrium thermodynamics, there is no doubt. It is, purely and simply, imposed by the fact
that living cells are often open systems and because of this fact, it must be known, as we shall see
it, that the notion of entropy appears to be endowed with a greater importance than that it has in
classical thermodynamics sensu stricto.
After these few words concerning thermodynamics, it is now time to give some general
considerations on the biological transformations of energy in living organisms. In this book, they are
essentially regarded at the cellular level. Actually, the bioenergetics of the cell is one of the central
elements in the study of biochemistry as are the basic molecular units intervening in the cellular
energy-transforming systems, i.e., the enzymes. The extraordinary biological complexity must firstly
be noticed. Its maintenance and its tendency to increase would imply that a kind of energy obeying
to thermodynamic principles devoted to them would be defined. Still noteworthy, living organisms
possess a very important quality. By some means, they have at their disposal some kinds of information
and they can handle them. One of them (and not the least!) is the genetic information. Beyond that,
according to the relatively new science of information, the information would actually be also a form
of energy. In any case, the information is directly related to the great function of thermodynamics:
the entropy. According to some authors, entropy is nothing but a measure of the missing information.
This book is essentially a “book of thermodynamics”. Its purpose is to provide the readers,
who essentially possess a biological background, with elementary and also with slightly more in
depth thermodynamic notions permitting to grasp some thermodynamics aspects of the bioenergetic
processes. It does not develop classical thermodynamics in its entirety. Hence, we confined ourselves
to mention the items which are directly related to bioenergetics. Nevertheless, and this is not in
contradistinction with what has just been said, we did not hesitate to start our recalls of thermodynamics
far below the presentation in amount with the exposition of the first and second laws. This is done for
the sake of continuity. In the same manner, we have somewhat emphasized the concept of entropy
which is puzzling.
The plan of the book is as follows:
– In the first chapters constituting the first part, we develop the necessary basics of thermodynamics
together with some other topics which are not obligatorily in the domain of the latter. They are
treated, however, because they are of undubitable importance for our purpose and, also, because
they are not easily understandable at the sophomore level. We can say that this part is treated
in such a way as to introduce and emphasize the notion of Gibbs energy which is the pivotal
thermodynamic concept in relation to bioenergetics, as we shall stress it.
– In the following chapters, we recall some developments concerning some points of the chemistry
in solutions because, on one hand, they are constantly present in the processes of bioenergetics
and, on the other, because they provide interesting examples of processes which are governed
by the Gibbs energy rule. The recalled phenomena are the acid-base, redox, complexation and
transports in aqueous solutions. Then, we consider rudiments of the thermodynamics of non
equilibrium because living cells are open systems. We also recall some properties of enzymes.
Of course, we also devote two whole chapters to the Gibbs rule.
– In the third part, we apply these developments to most of the transformations of bioenergetics.
Deliberately, we limit ourselves to give explanations justifying the directions of the numerous
steps occurring in the way of conversion of energy in cells. Thus, we justify the generation of
the cellular energy. The part played by the Gibbs energy in bioenergetics will appear in all its
importance in these ways of conversion of energy.
Rennes—December 2018 Jean-Louis Burgot
Acknowledgments

I thank Mr. Arsène Lancien who, as usual, has corrected my imperfect English.
To my family…..
Contents

Preface iii
Acknowledgments v
Glossary xvii

Part I: Fundamentals of Classical Thermodynamics

1. Some Recallings of Physics 3

1. An approach to a perfect gas 3
2. Elastic collisions 4
3. Kinetic theory of perfect gases—A molecular view of pressure 4
4. The kinetic theory of heat and of temperature 7
5. Temperature measurement 7
6. Work 9

2. Some Definitions of Thermodynamics 12

1. Thermodynamic systems 12
2. Thermodynamic state of a system 12
3. Extensive and intensive properties 13
4. Transformation 13
5. Thermodynamic equilibrium 13
6. Reservoir 13
7. Reversible and irreversible processes—Quasi-static processes 13
8. Isothermal process 14
9. Monothermal process 14
10. Isobaric process 14
11. Isochoric process 14
12. Adiabatic process 14
13. State functions 14

3. Equation of State 15

1. Case of a single substance—The perfect gas law 15

2. The state principle 15
3. Generalization 16
viii Thermodynamics in Bioenergetics

4. The First Law of Thermodynamics 17

1. Heat 17
2. Internal energy and global energy 17
3. The conservation of energy 18
4. The first law of thermodynamics 19
5. Some consequences of the first law 19

5. Mathematical Counterparts of First Law 21

1. Mathematical expression of the first law 21
2. Two exceptions of these statements 22
3. Mathematical handling of the state function “internal energy” 22
4. Cyclic transformations—Other form of the first law 23

6. Enthalpy and Heat Capacity 25

1. Enthalpy 25
2. Heat capacity 28

7. Heats of Reactions—Thermochemistry 31
1. Enthalpy change when only “p-V work’’ is carried out—Heat of reaction 31
2. Calorimetry 31
3. Standard states and standard reactions in chemical systems 32
4. The biological standard state 33
5. Law of constant heat summation—Hess’ law 33

8. Thermochemistry (Following)—Heats of Reactions and Bond Energies 35

1. Heats of formation 35
2. Calculations of standard enthalpies of reactions from heats of formation 36
3. Heats of combustion 36
4. Heats of hydrogenation 37
5. Heat of phase changes: Latent heats of vaporization, fusion, etc. 37
6. Heat changes of reactions in solutions 37
7. Bond energies 38
8. Other methods of calculation of heats of reactions—Thermochemical groups 40
9. Heat of reaction as a function of temperature—Kirchhoff’s rule 40

9. The First Law and the Ideal Gases 45

1. Ideal gases 45
2. Dependence of the enthalpy of an ideal gas on pressure and volume 46
3. Relationship between Cp and Cv 46
4. Thermodynamic changes in expansion processes 47

10. The Second Law of Thermodynamics 50

1. Entropy and bioenergetics 50
2. Clausius’ statement of the second law 50
 Contents ix

3. Carnot’s theorem of heat engines 51

4. Other statements of the second law 52

11. The Entropy Function 53

1. Notion of balance-sheet 53
2. Conservative and non-conservative quantities 54
3. Irreversible and reversible processes 54
4. The need of a common quantitative measure of the tendency of systems to 54
evolve in a given direction
5. The function entropy 55
6. A second, but equivalent, definition of the function entropy 56
7. The second law of thermodynamics 57
8. Some consequences of the above statement of the second law 57
9. Come back to the notion of reversibility 58

12. Calculations Involving the Function Entropy 61

1. Entropy and internal energy 61
2. General principle of the calculation of the entropy changes of systems 62
3. Entropy changes and partial derivatives involving it 69
4. Expressing the different partial derivatives—Maxwell relations 69
5. Entropy change accompanying a reversible phase transition 72

13. Further Considerations on the Meaning of Function Entropy 73

1. Carnot’s cycle 73
2. Heat is a degraded form of energy 75
3. Energies of great and weak entropies 78
4. Come back on the fact that entropy is a thermodynamic property 78
5. Calculation of entropy changes from thermal data 79
6. Questions about the meaning of the quantity entropy 79
7. Some molar entropy values—so-called absolute entropy values ST° 81
8. A brief summary of the properties of the entropy and of its implications 82
on the second law

14. Free Energy, Free Enthalpy—Helmholtz and Gibbs Energies 83

1. Monothermal transformation—Free energy and enthalpy related to the surroundings 83
2. Helmholtz energy 86
3. Gibbs energy function 88
4. Relationships between Helmholtz and Gibbs energies 91
5. Gibbs energy and phase changes 91
6. Exergonic and endergonic reactions 91

15. Open and Closed Systems—Different Expressions of the Composition of a Solution 92

1. Closed and open systems 92
2. Different expressions of the composition of a solution 93
x Thermodynamics in Bioenergetics

16. Escaping Tendency—Gibbs Energy Change Accompanying a Reaction 95

Between Perfect Gases
1. The escaping tendency 95
2. The molar Gibbs energy of a substance as a measure of the escaping tendency 96
3. Change of the molar Gibbs energy of a perfect gas with pressure 96
4. Gibbs energy change accompanying a reaction between perfect gases 97

17. Partial Molar Quantities—Chemical Potential 99

1. The need for new variables for systems of variable compositions 99
2. On the necessity to introduce the partial molar quantities when the 100
species are in solution
3. Definition of partial molar quantities 101
4. Physical meaning of the partial molar quantities 102
5. Molar quantities and partial molar quantities 103
6. Fundamental equation of the partial molar quantities 103
7. Thermodynamic relations between partial molar quantities 104
8. Experimental determination of partial molar quantities 104
9. The chemical potential 104

18. Gibbs Energy Change Accompanying a Chemical Reaction—General 107

Equilibrium Condition of a Chemical Reaction
1. Gibbs energy change in any process 107
2. Clapeyron equation—Entropy change during a phase transition 108
3. Gibbs energy of a chemical system 109
4. Gibbs-Duhem relation 110
5. Actual molar reactional Gibbs function 110

19. Activity–Ideal Solutions–Standard States 113

1. Definitions of an activity 113
2. A Physico-chemical meaning of an activity 113
3. Some properties of an activity 114
4. Standard states and activities 115
5. Ideal solutions 115
6. Ideal character of a system and interactions between the particles constituting it 116
7. Come back to the activity coefficients 117
8. Standard states and activity coefficients 118
9. Usual conventions for the definitions of the activities 119
10. Osmotic pressure 119

20. The Mass Action Law—Equilibrium Constant of a Chemical Reaction 121

1. Evolving reactions and equilibrium conditions 121
2. Obtaining the mass action law 122
 Contents xi

3. Standard reaction Gibbs energy 123

4. Consequences of the arbitrary character of the choice of the standard state 124
5. Formal equilibrium constants—Advantage of the use of activities to express 124
the mass action law
6. Differences of values between activities and concentrations 125
7. Come back on the reaction quotient and mass action law 125
8. Calculations of Gibbs energy changes accompanying a chemical reaction 126
9. The Gibbs-Helmholtz equation 126
10. Changes of K and ∆G with temperature 127

21. Gibbs Energy Function Changes: Further Comments 128

1. The Gibbs energy function 128
2. Coupled reactions 129
3. Biological standard states 130
4. Exercises 131

22. Obtention of Standard Reactional Gibbs Energies, Enthalpies and Entropies 132
1. Precise methods 132
2. Approximate methods 137

23. Ligand Binding to Macromolecules 139

1. Definitions 139
2. On the ability of biological macromolecules to interact with various small 139
and large molecules
3. Adsorption, another phenomenon for which theories of binding apply 140
4. General equilibrium expression describing the reversible binding of 140
a protein P to a ligand L
5. The simplest case of binding 141
6. Achieving experimental data 143
7. A graphical treatment of the preceding case—Scatchard’s plot 143
8. Case in which several classes of sites exist 145
9. Cooperative ligand binding—Hill’s equation 145
10. The binding of dioxygen to hemoglobin and myoglobin 146
11. Allosterism 147

24. Open Systems—Some Rudiments of Non-Equilibrium Thermodynamics 148

1. Open systems 148
2. A property of enthalpy 149
3. Energy in open systems-exergy 150
4. Useful maximum work, exergy and free enthalpy versus the ambience 150
5. Rate of the exergy decrease and rate of the entropy increase in an 151
irreversible process
6. More on open stationary systems 151
xii Thermodynamics in Bioenergetics

7. Difference between equilibrium and stationary (non equilibrium) states 152

8. An example of a stationary open system 152
9. Principles of the study of stationary systems 153
10. Linear thermodynamics of irreversible processes 154
11. Entropy production due to chemical reactions 156
12. General applications in biology 156

25. Some Generalities on the Kinetics of Chemical Reactions 157

1. Some generalities 157
2. Kinetics and equilibria 158
3. Influence of temperature on the rate of chemical reactions: energetic aspects 159

Part II: Some Aspects of Chemical Reactions in Aqueous Solutions

26. Acid-Base Reactions in Aqueous Solutions 165
1. Definitions of acids and bases and consequences 165
2. Quantitative aspects of acid-base reactions 167
3. Notion of pH 169
4. Distribution diagrams and predominance area 170
5. Buffer solutions 172
6. Macroscopic and microscopic acid-base equllibrium constants 174
7. Prevision of acid-base reactions in aqueous solutions 176

27. Redox Reactions–Redox Couples—Brief Description of an Electrochemical Cell 178

1. Redox equilibria 178
2. Oxidation numbers—A discussion 179
3. Definition of the global reaction of an electrochemical cell 180
4. Description of an electrochemical cell—The galvanic and electrolytic cells 180
5. Some other definitions found in electrochemistry 182
6. Electromotive force of a galvanic cell—Cell potential difference 182
7. Nernst’s equation 183
8. Standard reaction entropy change from the temperature coefficient of the 184
emf. of a reversible cell-Determination of the enthalpy change
9. Electrode potentials 184
10. Some standard electrode potentials 186
11. Prevision of redox reactions 188
12. Formal potentials 190

28. Other Equilibria in Solutions 191

1. Complexation equilibria 191
2. Partition equilibria between two non-miscible solvents 192
3. The concentration work 193
 Contents xiii

29. The ‘‘Natural Trick’’ for Bioenergetics to Function 195

1. Displacements of chemical equilibria by coupling reactions 195
2. Inversion of the direction of a reaction 197
3. Coupling of reactions 198

Part III: Thermodynamics of Biological Cells

30. Enzymes–Kinetics of Enzymatic Reactions 203

1. The structure of enzymes 203
2. Classification of enzymes 204
3. Some properties of enzymes 205
4. A diversion on the origin of the L configuration of the amino-acids 206
5. Catalysis 207
6. Kinetics of the catalysis by enzymes—The Michaelis-Menten equation 208
7. Reversible and irreversible inhibitors of enzymes 211
8. Regulatory enzymes—Allosterism of enzymes 211
9. Coenzymes 211

31. The Flow of Energy in the Biological World 212

1. The flow of energy in the biological world 212
2. Sunlight, the ultimate origin of the biological energy 212
3. Photosynthesis 213
4. The great stages (metabolic pathways) of the flow of biological energy 214
5. Respiration 215
6. Biological work 215
7. The flow of matter in the biological world 217
8. Transformation of energy in heterotrophic anaerobic cells—fermentation 217
9. The fate of the energy coming from the fuel: A first view on the part played by ATP 217
10. The machinery of cells 218

32. Adenosine Triphosphate, Adenosine Diphosphate, Monophosphate and 220

Derivatives NAD+: Some Physico-Chemical Properties
1. Chemical structure of adenosine triphosphoric acid and derivatives 220
2. Some physico-chemical properties of adenosine triphosphoric acid and derivatives 223
3. The reaction of hydrolysis of ATP 225
4. The reaction of hydrolysis of ATP and complexation with Mg2+ ions 227
5. Coenzymes NAD+, NADP+, NADPH 228

33. The Transfer of Chemical Energy with the Aid of ATP 230
1. Come back to the free energy of hydrolysis of ATP 230
2. Gibbs energies of hydrolysis of some phosphorylated compounds 231
3. An unfortunate qualifier 232
4. ATP provider of energy by groups transfers 232
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