BIO-Physical Chemistry

Foundations and Applications of Physical Biochemistry

Robert B. Gennis
1
Robert Gennis - University of Ill Urbana

Chapter 1: An introduction to thermodynamics- work, heat, energy
and entropy
1.1 Introduction
BOX 1.1 A word about mathematics
1.2 Potentials, Forces, Tendencies and Equilibrium
What do we mean by work?
BOX 1.2 Differential changes and integration
1.3 Equilibrium and the extremum principle of minimal energy: a ball in a
parabolic well.
BOX 1.3. A word about units
1.4 From one to many: The Principle of Maximal Multiplicity
Probabilities and Microscopic States

1.5 Entropy and the Principle of Maximal Multiplicity: Boltzmann`s Law
1.6 Thermodynamic Systems and Boundaries
1.7 Characterizing the System: State Functions
1.8 Heat
1.9 Pathway-independent functions and thermodynamic cycles.
1.10 Heat and work are not state variables
1.11 Internal Energy (U) and the First Law of Thermodynamics
1.12 Measuring U for processes in which no work is done
1.13 Enthalpy and heat at constant pressure
1.14 The caloric content of foods: reaction enthalpy of combustion
2
1.15 The heat of formation of biochemical compounds
1.16 Thermodynamic Definition of Entropy
1.18 Entropy and the Second Law of Thermodynamics
1.19 The thermodynamic limit to the efficiency of heat engines, such as the
combustion engine in a car.
1.20 The absolute temperature scale.
1.21 Summary

3
Chapter 1: An introduction to thermodynamics- work, heat, energy
and entropy
1.1 Introduction
Biological Systems are subject to the same Laws oI Nature as is inanimate matter.
Thermodynamics provides the tools necessary to solve problems dealing with energy and
work, which cover many issues oI interest to biologists and biochemists. The principles
oI thermodynamics were developed during the 19
th
century, motivated by an interest to
determine how to maximize the eIIiciency oI steam engines. In this case, the work
involved the expansion oI heated gases within a piston, deIined in terms oI changes in
pressure and volume, or PV work. The concerns oI these early scientists were Iocused on
the conversion oI heat to work. In biological systems, it is rare to be concerned with PV
work or with heat Ilow Irom hot to cold bodies. We are more concerned with the making
a breaking oI chemical bonds, moving material across membranes, electrical work,
changes in molecular conIormations, ligand binding, etc. Nevertheless, the principles oI
thermodynamics are universal and extraordinarily powerIul Ior predicting how systems
behave under deIined circumstances. Thermodynamics tells us the conditions under
which a system is at equilibrium and, Ior a system that is not at equilibrium, which
certainly applies to all living systems, thermodynamics will allow us to determine what
changes will occur spontaneously, the magnitude oI the driving Iorce, and the maximum
amount oI work that can be done by that system during the process oI moving towards
equilibrium. Understanding cellular metabolism (i.e., metabolomics or systems biology)
requires not only knowing which enzymes are present and the concentrations oI
metabolites, but also the direction and driving Iorce oI each reaction.
4
Thermodynamics provides a universal language oI energetics and work potential
to quantitatively describe the many and diverse coupled processes that take place within a
cell - metabolic reactions, protein synthesis, active transport, ligand binding, ion Iluxes
across membranes, etc. The thermodynamic description will allow us to understand
simple chemical equilibria oI isolated reactions, or more complex, coupled reactions such
as the active transport oI solutes coupled to ATP hydrolysis, or the Ilux or protons across
a membrane driving ATP synthesis. This is a long way Irom steam engines! The
universality oI the principles oI thermodynamics, makes this one oI the major intellectual
achievements in the history oI science and natural philosophy.
The goal oI this Chapter is to demonstrate why thermodynamics is both necessary
and useIul and to deIine the thermodynamic parameters enthalpy and entropy. In Chapter
2, the introduction to the Ioundations oI thermodynamics will be extended to the concepts
oI Gibbs Iree energy and the chemical potential. Following this, we will explore some
applications oI thermodynamics to solving biological problems.
BOX 1.1 A word about mathematics
. Mathematics is the language oI science, and these days that most certainly includes
biology. Many students in the biological sciences Ieel uncomIortable with mathematics,
and with calculus in particular. It is not necessary to have great skills in mathematics to
understand the material in this text. However, it is assumed that the student has had a
course in introductory calculus and is at least Iamiliar with the meaning oI derivatives
and integrals. The mathematics used in this text carries physical meaning in the context
oI the concepts being described. It is this physical meaning that is most important, not the
details oI the mathematical manipulations. The mathematics used is not simply
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disembodied, abstract equations, but they describe how nature works. Seeing what an
equation means and understanding where is comes Irom is more important (aside Irom
examinations) than memorizing the equation or simply plugging numbers into it to get an
answer. There are only a Iew mathematical tools that are needed, and these will be
introduced within this Chapter.
END BOX

1.2 Potentials, Forces, Tendencies and Equilibrium
BeIore we discuss thermodynamics, it will be useIul to examine some basic
concepts derived Irom the behavior oI mechanical systems. The concepts are analogous
to those used in thermodynamics, and the mathematical tools are essentially the same.
Since the concepts as applied to mechanics are more intuitive to most students, we will
review some basic concepts using simple mechanical systems, and then explore the
analogous concepts applied to chemical and biological systems.
What do we mean by work?
Let`s Iirst consider what we mean by work. Work in a mechanical system usually
involves moving an object in some manner against an opposing Iorce. There are diIIerent
kinds oI Iorces: gravitational, electrical, pressure, centriIugal Iorces are commonly
encountered. In each case, we can consider the object to be under the inIluence oI a Iorce
whose magnitude and direction depends on physical location. To move an object or a
particle against the Iorce requires that work be done on the particle by an applied Iorce,
increasing the potential energy oI the particle. II the particle moves under the inIluence oI
the Iorce, then the potential energy oI the particle is decreased. Hence, we can think oI a
6
Iunction describing the potential at any point in space, such as a gravitational potential or
electrical potential (Figure 1.1). The change in potential energy (dU) in a particular
direction (dx) is what deIines the Iorce on the particle in that direction, as in equation
(1.1)

( )
( )
dU x
f x
dx
= (1.1)
The natural tendency is Ior a particle to move to a position oI lowest potential energy.
The Iorce will be positive iI dU is negative, i.e., iI the potential energy decreases when
the particle is displaced. The Iorce is larger in magnitude iI there is a steep change in
potential with position.


Figure 1.1: Force is the negative of the
change in potential energy (dU) per unit
of displacement (dx) for an infinitesimal
displacement. This is the slope of the
curve describing potential energy as a
function of position. In this example we
are considering only one dimension (x).


In mechanical systems, work done on an
object quantiIies the energy to displace the
particle under the inIluence oI a Iorce.
Let`s consider the spontaneous displacement oI a particle under the inIluence oI a Iorce
such as gravity or an electric potential. II we are simply displacing the particle Irom one
place to another, the work must be equal to the diIIerence in the potential energy oI the
7
particle beIore and aIter the displacement. II we displace an object Irom position x by a
small amount (dx) to a new position x dx, then the work done is given by

( )
x dx x
w U U o
+
=

But, since ( ) (
x dx x
dU
U U dU dx
dx
+
= = ) and, since ( ) ( )
dU
f x
dx
= , we can now write
( ) w f x dx o = (1.2)
The particle moves spontaneously in the direction oI the positive Iorce to a position oI
lower potential energy. The diIIerential amount oI work done, w o , is negative because
the potential energy oI the particle is decreased iI it is displaced spontaneously by the
Iorce due to the potential Iield.
Now, we can apply an external Iorce,
app
f , to counteract the Iorce Iield and move
the object in the opposite direction. At a minimum, the applied Iorce must be slightly
greater than the Iorce due to the Iield, and in the opposite direction, or the particle won`t
be displaced. In this case, work is done by the external applied Iorce on the particle, its
potential energy increases and the sign oI the work is positive:
app
w f dx o = .
The language and concepts oI thermodynamics are analogous to the way we
describe simple mechanical systems. Thermodynamics provides us with a way to
quantiIy the work required to displace a chemical or biological system, and we speak oI a
chemical potential and a thermodynamic driving Iorce and the analogs, Ior example, oI
gravitational potential energy and gravitational Iorce. ThereIore, it is useIul to review the
concepts and terms as they apply to simple mechanical systems. Several simple examples
8
oI mechanical Iorces are listed below, in which we are considering displacements oI an
object in only one direction ('x) Ior simplicity.
a) Dropping a weight (Figure 1.2): The Iorce oI gravity (
grav
f ) is deIined as
positive in the downwards direction, and by convention the sign on the displacement is
also deIined as being positive in the downwards direction.

Figure 1.2 (from Dill and Bromberg, fig .2). The force
of gravity pulls the weight down, decreasing the
potential energy. This is defined as the ~positive
direction. An applied force is required to lift the
weight up (negative direction).



The Iorce due to gravity is deIined as

grav
f mg = (1.3)
where m is the mass and g is the gravitational constant (9.80665 ms
-2
). Consider an
object oI mass, m, that is displaced downwards by a small amount, dx (meaning 'down,
due to the Iorce oI gravity (
grav
f ). The work done is

grav
w f dx mgdx o = = (1.4)
II we drop a weight oI mass m Irom x h to x 0, the change in potential energy is
( ) (0 )
final initial
U U mgh mgh = = (1.5)
which is negative since the potential energy oI the mass is decreased. The decrease in the
potential energy is equal to the work done by gravity on the mass, which is negative
w mgh = (1.6)
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b) Maximizing useful work by dropping a weight- reversible vs irreversible
processes: To do work, we need to apply a Iorce (
app
f ) greater than the opposing Iorce oI
gravity in order to liIt an object (Figure 1.2). Let`s consider a pulley, pictured in Figure
1.3, where we start with a weight oI mass m
1
suspended on one end oI the rope at a
height oI h. The initial potential energy oI the system is equal to the . How
can the maximum amount oI work be accomplished by lowering this weight back to the
Iloor? Figure 3A illustrates that iI we simply drop the weight, with no mass on the other
end oI the rope, no useIul work is accomplished although the potential energy oI the
system has decreased to zero (assuming the rope has no mass). What happened to the
energy that we initially invested in the system by liIting the weight to height h? In
dropping the weight, the potential energy was converted to kinetic energy, and when the
weight hit the Iloor, the kinetic energy was converted to heat. No useIul work has been
accomplished. Note that once we drop the weight, it Ialls irreversibly towards its Iinal,
equilibrium position, on the Iloor. It will not go backwards.
1 initial
U m = gh
gh gh
Figure 3B illustrates the case where we attach a second weight to the other end oI
the rope, with a mass oI m
2
which is less than m
1
. We now drop the weight m
1
again.
Once again, the weight will Iall to the Iloor. At equilibrium, we end up with the weight
m
1
on the Iloor and the weight m
2
raised to a height oI h. The initial potential energy is
again , but the Iinal potential energy is
1 initial
U m =
2 final
U m = since we have liIted
the second weight to the same height, h. The Iorce that has been applied by the weight
with mass m
1
is always greater then the Iorce oI gravity on the weight with mass m
2
at
any position oI the pulley. As in the example illustrated in Figure 3A, this process is also
irreversible and will not spontaneously go backwards. The pulley has coupled the process
10
oI dropping one weight to the process oI liIting a second weight. The diIIerence between
the Iinal and initial potential energies oI the system is lost as heat. As the mass oI the
second weight being liIted gets closer and closer to m
1
, the amount oI useIul work done
on the second mass increases and the amount oI the initial potential energy that is wasted
as heat decreases.


Figure 3A:





Figure 3B




Figure 3C




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II the weight oI the second mass is equal to that oI the Iirst mass, m
1
m
2
, then when we
release the raised weight, nothing will happen. The Iorces balance each other and the
second mass will stay on the Iloor. But iI the second mass is just slightly less than the
Iirst, we can consider a hypothetical situation in which we have a very slight net Iorce
slowly causing a small displacement, dx (Figure 3C). We can consider the process oI
liIting the second mass by a series oI small displacements, reaching equilibrium aIter
each step. This hypothetical process is called a reversible process, and this process
maximizes the amount oI work that can be obtained Irom lowering the mass m
1
to the
ground.
We can calculate the work done oI the mass being liIted by this reversible
process, because under these conditions, the applied Iorce is approximately equal to the
gravitational Iorce

1 app grav
f f m g = = (1.7)
The amount oI work done Ior a small displacement is

1
( )( )
app grav
w f dx f dx m g dx m gdx
1
o = = = = (1.8)
The work done to liIt the weight is
1
w m gh = , which is numerically equal the negative
work done on the Iirst weight, being lowered to the ground, equation (1.6).
We will encounter the same concepts or reversible and irreversible processes
again when we consider how to obtain the maximum amount oI work Irom a biochemical
system or chemical reaction that is coupled to another biochemical process. The eIIicient
coupling oI biological processes is at the heart oI biological energy conversion and
bioenergetics.

12
c) Stretching a spring (Figure 1.4): We will encounter this later when we discuss
molecular vibrations.

Figure 1.4 (from Dill and Bromberg, fig 3.1)
The force of the stretched spring pulls the mass to the left, decreasing the potential
energy as the spring tends towards it equilibrium position. An applied force in the
opposite direction is required to move the mass to the right, increasing the potential
energy.

For a spring with a resting position at x 0, the Iorce oI the spring when stretched to
restore the equilibrium (resting) position, is proportional to the extent by which the spring
has been stretched (x) multiplied by a spring constant (k
S
):
S S
f k x = . Without an
applied Iorce to counter the Iorce oI the spring, the potential energy decreases as the mass
is returned to the resting position. With an slightly larger applied Iorce in the opposite
direction, stretching the spring Iurther,
app S
f k x = , work is positive on the mass. For a
small displacement, dx, the work is given by
( )
app S
w f dx k x dx o = = (1.9)
c) Expansion work (Figure 1.5): The Iorce is the pressure (P) and the
displacement the change in volume, dV.
13
Doing work against the internal pressure requires an external pressure, P
ext
, slightly larger
than the internal pressure, P, resulting in positive work on the system.

PV ext
w P dV o = (1.10)


Figure 1.5: Isothermal xpansion of gas in a piston requires that the external
pressure be lower than the internal pressure. If the external pressure is adjusted to
be just slightly less than the internal pressure for the entire process, so that
int ext
P P ~ ,
the process is called a ~reversible process.





II the external pressure is slightly less than the internal pressure (P), then the spontaneous
change will be Ior the system to expand, decreasing the energy oI the system, so that
PV
w PdV o = . II the gas behaves as an ideal gas, then the equation oI state is given by
, where n is the number oI moles oI gas, R is the gas constant, and T is the
temperature (Kelvin). II the temperature is held constant, the expansion is called
isothermal.
PV nRT =
14
d) Electrical work (Figure 1.6): The work oI moving a charge, Q, by a distance dx, in an
electrostatic potential, is given by
( )
el
w d Q o = + (1.11)
A negative charge will move spontaneously towards a more positive potential, in which
case the work done is negative since the potential energy is decreased, i.e., iI Q0 and
~0, then d+ 0
el
w o < .


Figure 1.6: The negative electric potential from the charged surface is a measure of
how much work is required to move a charge near the surface. The potential energy
decreases as a positive charge gets closer to the negative surface. Positive work is
required to move the positive charge away from the negative surface.

We will consider later the work oI moving ions across membranes or to move a charged
substrate near a charged surIace oI a protein, membrane or polynucleotide, Ior example.
The work oI moving an ion Irom the aqueous medium to the inside oI a protein or to the
inside oI a membrane is more complicated because the medium changes.
e) Moving an object in a centrifugal force field (Figure 1.7): This will be
encountered when we consider how molecules behave in a centriIuge.

2
cent
f m r e = (1.12)
(1.13)
2
( )
cent
w m r o e = dr
15
where m is the mass oI the molecule (which we need to adjust Ior buoyancy), is the
circular velocity oI the rotor (radians/sec) and r is the distance Irom the center oI the
centriIuge rotor to the location oI the molecule in the centriIuge tube. As the particle
sediments under the inIluence oI the centriIugal Iorce, its potential energy is decreased
and the work is negative.

Figure 1.7: The centrifugal force on a particle in a spinning centrifuge tube drives
the particle away from the center of rotation. As the particle is displaced, the
potential energy decreases.




BOX 1.2 Differential changes and integration

It is oIten more convenient to Iunctional relationships in diIIerential Iorm, as in
equations(1.8), (1.9) or (1.10), Ior example In asking what work is required to move a
particle which is at a particular position, x
1
, by an inIinitesimally small amount, dx, the
Iorce can be considered to be constant between positions x
1
and the new position (x
1

dx):
1 1
( ) ( ) f x f x dx ~ + . II we want to compute the amount oI work in going Irom one
16
position ,x
1
, to another position, x
2
, we can sum up the w o values Ior each step. This is
illustrated in Figure 1.8, which schematically shows the plots oI Iorce vs position Ior
liIting a weight (gravity), stretching a spring, expanding an ideal gas, and centriIugation
oI a particle. In each case, ( ) w f x dx o = , and we can break up the displacement Irom
the starting position ('1) to the Iinal position ('2) into a sequence oI small,
inIinitesimal steps (dx, dV or dr). Note that the expression Ior the work at each step is
equal to the area oI the rectangle between x and xdx (shaded in Figure 1.7). Hence,
summing up the work accomplished in each step between the deIined limits (position 1 to
position 2) is equivalent to evaluating the area under the curve deIined by I(x) vs x.

Figure 1.8: Four examples of the work done by displacing an object in the presence
of a force. In each case the process is taken in small steps, and after each step the
system re-equilibrates. In the examples of lifting an object or stretching a spring, an
external applied force is used to do work on the object (positive work). In these
examples, the applied force is just slightly larger than the force tending to restore
the system towards equilibrium. For the isothermal expansion of an ideal gas the
external pressure is adjusted to be just slightly less than the pressure within the
piston and negative work is done by the gas in the piston. For the centrifugation of a
particle, the force displaces the particle towards the bottom of the tube. Note that
work is expressed as the area underneath each curve between the initial and final
limits.

17
In each example, asides Irom gravity, the value oI the Iorce, and thereIore the work Ior
each inIinitesimal step, changes with position. The area under each curve is given by the
integral oI I(x) between the deIined limits. In these examples we can relate the integrals
to the amount oI work done.
a) liIting a weight:
2
1
2 1
( )
x
x
w mgdx mg x x = =
}
b)stretching a spring:
2
2
1
1
2 2
2 1
1 1
( )
2 2
x
x
S S S
x
x
w k xdx k x k x x ( = = =
}
2

c)isothermal expansion oI an ideal gas:
2 2
1 1
1
2
( ) ln(
V V
V V
V nRT
w PdV dV nRT
V V
= = =
} }
)
d) centriIugation oI a particle:
2
2
1
1
2 2 2 2 2
1 2
1 1
( )
2 2
r
r
r
r
w rdr r r r e e e ( = = =
}
2
h

END BOX

1.3 Equilibrium and the extremum principle of minimal energy: a ball in a
parabolic well.
Consider a ball placed in a two-dimensional well, as pictured in Figure 1.9. The
gravitational potential energy is given by
( )
pot
U h mg = (1.14)
where m is the mass oI the ball, g is the gravitational acceleration constant and h is the
height. II the well has a parabolic shape, then h x
2
and we can write
(1.15)
2
( )
pot
U x mgx =
18
We know that the ball will roll within the well until it reaches a point oI minimal
potential energy. This is an example oI an 'extremum principle.


Figure 1.9: Potential energy of a ball in a potential energy well created by a
parabolic shaped container in which the ball is under the influence of gravity.

The location oI minimal potential energy in this case is clearly the bottom oI the well,
where x
eq
0. We can obtain this by looking at Figure 1.8, and observing that at the
minimal value oI the potential energy, the slope oI the tangent to the curve is zero
(horizontal). In other words, the Iirst derivative oI U
pot
(x) with respect to x is zero.
Taking the derivative oI equation (1.15) and setting it equal to zero gives

( )
2
pot
dU x
mgx
dx
0 = = (1.16)
which is satisIied when x 0. This deIines the equilibrium position, which is where
x
eq
0.
The force on the ball is deIined as the negative oI the gradient or Iirst derivative
oI the potential energy, U
pot
(x), with respect to position (x) as in equation(1.1). The
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larger the magnitude oI the change in potential energy Ior a small displacement oI the
position (dx), means there is a larger driving Iorce towards restoring the equilibrium
position (x 0). This is pictured in Figure 1.9. Displacement to the leIt oI x
eq
results in a
Iorce that is positive, driving the ball to values oI increasing values oI x. Displacement to
positive values oI x, away Irom x
eq
results in a negative Iorce, driving the ball to the leIt.
The Iorce, by deIinition, drives the ball to decreasing values oI the potential energy until
the minimum is reached, at which point the Iorce is equal to zero.
We can also deIine the position oI equilibrium as the point where the Iorce I 0,
since the minimum oI the potential energy, equation (1.16), is identical to the condition
where the net Iorce is zero.

( ) ( )
at equilibrium, 0
pot pot
dU x dU x
force
dx dx
= = = (1.17)
The Iorce on the ball is larger as it gets Iurther Irom the equilibrium position, and the
tendency is Ior the ball to roll Irom a position oI higher potential energy to one oI lower
potential energy. The Iorce quantiIies the tendency oI the ball to roll towards its
equilibrium position, deIining both the magnitude oI the tendency and also the direction.
The equilibrium position is the conIiguration that the system tends towards
spontaneously. For a ball at the bottom oI the gravitational potential well, a displacement
oI the ball in either direction Irom its equilibrium position will result in a Iorce that will
tend to bring the ball back to the equilibrium position. Mathematically, the statement that
the equilibrium position is a minimum in potential energy (as opposed to a maximum,
where the Iorce would also be zero) means that the second derivative oI the potential has
a positive value.
20

2
2
( )
0 at
pot
eq
d U x
x x
dx
> = (1.18)
Another useIul concept we can illustrate Irom this model is the principle oI the
conservation oI energy. II we place the ball near the top oI the well, it starts with a given
amount oI potential energy ( )
pot
U h mgh = . By picking up the ball and placing it at this
position, we have done work against gravity which has been conserved as potential
energy. When we let go oI the ball, it rolls under the Iorce oI gravity, picking up kinetic
energy. At the bottom oI the well, the potential energy has been converted entirely to
kinetic energy, iI there is no loss due to Irictional Iorces. The ball would oscillate back
and Iorth Iorever were it not Ior the conversion oI some oI its kinetic energy to heat due
to Iriction encountered with the surIace oI the well in which it is rolling. The ball and
well are in thermal contact with the surroundings and the heat is lost to the environment.
Eventually, all the potential energy that we started with at the top oI the well is converted
to heat and the ball will come to rest at the equilibrium position.
This simple example contains the essence oI what we want to obtain Irom
thermodynamics. We will be deIining potentials which will tell us how energy will Ilow
in the Iorm oI work and heat, how material will move Irom one place to another, and how
chemical reactions will proceed in biological systems as they undergo changes Irom an
initial set oI conditions towards equilibrium.
It is reasonable to ask why a mechanical description is not suIIicient to describe
work done in biochemical systems. II you pick up a weight the potential energy oI the
weight is increased by a known amount, and you can calculate how much work you can
do with this weight as it is lowered back to the ground. II you hydrolyze ATP to ADP and
P
i
there is also a well-deIined bond energy Ior the hydrolysis oI the so-called 'high
21
energy bond. However, unlike the mechanical system, this inIormation is insuIIicient to
tell us how much work we can get out oI this reaction. II we have large concentrations oI
ADP and P
i
and a small concentration oI ATP, then we cannot get any work out oI the
system, whereas, iI we hydrolyze the same number oI ATP molecules in a solution with a
high concentration oI ATP and low concentrations oI ADP and P
i
, we can get work out oI
the system. There is something else going on besides what we can see by considering the
bond energies oI the molecules. Thermodynamics tells us what this additional Iactor is
and how it can be quantiIied. Thermodynamics is oI central importance in understanding
biochemical and chemical processes.
BOX 1.3 A word about units
Throughout this text, the Standard International (SI) system oI units will be used. This is
the modern version oI the metric system. There are 7 SI base units: 1) kilogram (mass);
2) meter (length); 3) second (time); 4) thermodynamic temperature (kelvin); 5) electric
current (ampere); 6) mole (substance); 7) candela (luminous intensity). All other units
Iollow Irom these. Most important Ior our purposes is the unit oI energy, the joule, named
aIter James Prescott Joule. The joule is deIined as the work expended to move an object
one meter using a Iorce oI 1 Newton. A Newton is the amount oI Iorce required to
accelerate a mass oI 1 kilogram at a rate oI one meter per second squared.

2
2
1 1
1 1
J Nm
m
J kg
s
=
=

A joule is also the amount oI energy required to move an electric charge oI 1 coulomb
through an electrical potential diIIerence oI 1 volt. II you drop this textbook to the Iloor,
the amount oI energy lost is about 1 joule.
22
Energy is still oIten reported using the unit oI the calorie (or kilocalorie). The
calorie is approximately the amount oI energy needed to raise the temperature oI 1 gram
oI water by 1
o
C (at 15
o
C).
1 calorie 4.186 joules
1 joule 0.239 cal
END BOX
1.4 From one to many: The Principle of Maximal Multiplicity
The trek Irom a mechanical system, like a spring or a ball in a well, to metabolic
reactions and active transport systems requires that we Iirst realize that in studying
biological or chemical systems we are dealing with the collective behavior oI a large
number oI molecules. A cell that is about 10m in diameter containing 1 mM ATP
contains about 1 billion molecules oI ATP. Many years oI experiment and observation
has provided us with a remarkably powerIul principle that allows us to predict the
behavior oI a large collection oI molecules. This is the Principle of Maximal
Multiplicity which, as we will see, is a statement oI the Second Law oI
Thermodynamics.
The Principle oI Maximal Multiplicity states that in any system oI many particles
that is isolated Irom its surroundings, the system will tend towards an equilibrium which
has the largest number oI equivalent microscopic states. This statement, plus the
recognition oI the equivalence oI work and heat (the First Law oI Thermodynamics) are
suIIicient to derive all oI thermodynamics, which includes a quantitative description oI
the driving Iorces that determine the behavior oI chemical and biochemical systems.
23
Probabilities and Microscopic States: To see what is meant by equivalent microscopic
states, let`s look at a simple system. In the system pictured in Figure 1.10, there are 4
particles. The energy oI each particle is quantized and can take on values oI 0, 1, 2, 3 or
4, and we will assume that the particles can exchange energy so each oI the particles
might have any oI the allowed energies (0, 1, 2, 3 or 4). Now, we will constrain the total
energy, U, to be 4 units. There are 35 distinct combinations where the total energy is
distributed among the 4 particles to yield this total (Figure 1.10). We can deIine a
variable, W, as the multiplicity oI a system. In this example, W 35. These microscopic
states can be assigned to one oI Iive distinct configurations.
i) Any one oI the Iour particles can have an c 4 while the other three c 0.
There are Iour diIIerent arrangements.
ii) Any one oI the Iour particles can have c 3, and another c 1 with the
remaining two having c 0. There are 12 distinct arrangements.
iii) Any two particles can have c 2 and the remaining two particles each have c
0. There are 6 distinct arrangements.
iv) Any two particles can have 1 and one other particle have 2. There are
12 distinct arrangements.
v) All the particles can have 1. There is only one such arrangement.

24

Figure 1.10: There are five different energy configurations and 35 equivalent
microscopic states in which a total of 4 energy units is distributed among 4
indistinguishable particles, in which each particle is allowed to have an energy of 0,
1, 2, 3 or 4 energy units. Each card represents a distinct microscopic state.

Each oI these 35 microscopic states is consistent with the macroscopic constraint on the
total energy. The Principle oI Maximal Multiplicity simply states that at equilibrium each
oI the 35 microscopic states is equally likely to be present at any instant in time. This is
common sense. We might initially add to our box one particle with c 4 and three
particles with c 0, but we are very unlikely to Iind this distribution oI energy among the
particles aIter letting them equilibrate. Equilibration implies that there is some
mechanism by which the energy can be redistributed among the particles. For molecules,
this mechanism would be by collisions. We cannot know with certainty the distribution
25
we will Iind at any instant. All we can do is compute the probabilities oI Iinding
particular microscopic states. For example, 12 oI the 35 microscopic states have one
particle with c 3, so in this set oI 12 states, the probability oI Iinding a particle with c
3 is 0.25. In the other Iour conIigurations (Figure 1.10), the probability oI Iinding a
particle with c 3 is 0.0. Hence, over all 35 microscopic states, the probability oI
Iinding a particle with c 3 is the weighted average over the three conIigurations.

3
12 1 4 12 6
(0) (0) (0) (0.25) (0) 0.086
35 35 35 35 35
p = + + + + =
Similarly, the probabilities oI Iinding a particle with energies oI 4, 2, 1 and 0 energy are
readily determined at equilibrium, using the criterion that each microscopic state is
equally probable.

1
12 1 4 12 6
(0.5) (1.0) (0) (0.25) (0) 0.28
35 35 35 35 35
p = + + + + =

2
12 1 4 12 6
(0.25) (0) (0) (0) (0.5) 0.17
35 35 35 35 35
p = + + + + =

4
12 1 4 12 6
(0) (0) (0.25) (0) (0) 0.028
35 35 35 35 35
p = + + + + =

0
12 1 4 12 6
(0.25) (0) (0.75) (0.5) (0.5) 0.43
35 35 35 35 35
p = + + + + =
In the case oI the single ball in a parabolic well, iI we have no Irictional loss oI energy,
then the total energy oI the ball (potential plus kinetic energy) remains constant and is
exactly deIined. II the energy is divided among a number oI particles, as in the current
example, the total energy is consistent with many equivalent microscopic states. With a
small number oI particles, as in this example, we can easily count the number oI
microscopic states consistent with the macroscopic constraints oI energy and particle
26
number (total energy, U 4 and number oI particles, n 4, in this example). When we
have a large number oI indistinguishable particles (or molecules), we cannot literally
count microscopic states to arrive at the value Ior the multiplicity (W), but the same
Principle oI Maximal Multiplicity applies and deIines how energy is distributed among
the particles at equilibrium.

1.5 Entropy and the Principle of Maximal Multiplicity: Boltzmann`s Law
Multiplicity is a Iundamental property oI any system, and is determined by the
way in which energy and material is dispersed. In any isolated system the energy and
material within the system will evolve spontaneously Irom any starting point to maximize
the multiplicity, W, at which point the system is in equilibrium. It was Ludwig
Boltzmann, in the later halI oI the 19
th
century, who recognized the Iundamental
importance oI multiplicity, and he deIined Entropy, S, as the Iunctional Iorm that would
be most useIul.
ln( ) S k W = (1.19)
where k is Boltzmann`s constant and has a value oI 1.380662 x 10
-23
JK
-1
. Since
maximizing W will also maximize ln(W), an isolated system at equilibrium can be
defined as having the maximum entropy. The units and value oI Boltzmann`s constant
are deIined to Iit into the Iramework oI thermodynamics as it had been previously
established. This is described in the next Section.
The deIinition oI entropy in equation (1.19) has a drawback insoIar as it involves
counting up microscopic states oI a system to get W. Clearly, this is not practical Ior most
27
problems oI interest. An alternative deIinition that is mathematically equivalent Ior a
system with a large number oI possible conIigurations is

1
ln
n
i
i
S
p p
k

=
i
(1.20)
where
i
p is the probability oI the system being in a particular conIiguration. We will not
derive this Iorm oI the equation, which can be Iound in Dill and Bromberg. For the
example in Figure 1.10, with 4 particles, the Iive possible energy distributions are
4,0,0,0}, 3,1,0,0}, 2, 1, 1, 0}, 1, 1, 1, 1} and 2, 2, 0, 0}with probabilities oI
4 12 6 1 12
0.11, 0.34, 0.17, 0.03 and 0.34
35 35 35 35 35
= = = = = , respectively. However, the
number oI conIigurations is too small Ior equation (1.20) to be valid.
Figure 1.11: The increase in entropy for a simple situation of bringing two systems
together. System A has 2 particles and 2 units of energy. Each particle can have
either 0 or 1 unit of energy. System B has only 4 particles but also has 2 units of
energy. The multiplicity of the two systems considered together ( )is the
product of the multiplicity of the two separate systems. The numerical solution to
the number of equivalent systems is given, where
, and there are 270 equivalent ways to
arrange identical particles in this manner. If the systems are brought into contact
and one energy unit is allowed to move from the small system (B) to the larger
system (A), the multiplicity increases to 480. This shows that this process would be
spontaneous since the energy flow in this direction results in increasing the entropy.
A
W W +
B
N "N Iactorial" ! (1)(2)(3)...( 1)( ) N N =

28
As an example, let`s say that we start with two separate systems, each at
equilibrium. The larger system (A) has 10 particles with a total oI 2 energy units, and we
will allow each particle to have an energy oI either 0 or 1 unit. The smaller system (B)
has only 4 particles but also an energy oI 2 units (see Figure 1.11). System A has 45
equivalent states and system B has 6 equivalent states. Hence, the two systems together
have 45(6) 270 equivlalent states. We will now bring these two systems into contact
and allow energy to exchange. Without worrying about the Iinal equilibrium state, which
would maximize the multiplicity, we will simply ask iI it is Iavorable Ior one unit oI
energy to Ilow Irom the small to the large system, pictured on the right side oI Figure
1.11. There are now 120 equivalent microscopic states Ior system A and 4 Ior system B.
The total multiplicity is now (120)(4) 480, which is higher than the initial energy
distribution. Redistribution oI energy in this simple model system can be seen to increase
the multiplicity, and, hence, this would be a spontaneous process towards equilibrium.
Energy Ilow in the opposite direction (Iorm the large system to the small system)
decreases the multiplicity and, would not occur spontaneously.
The equilibrium condition Ior an isolated system, in which no energy or matter
can enter or leave (in this example, the combination oI systems A system B is isolated
Irom the surroundings), is that entropy is maximized. It is important to emphasize that the
principle oI maximizing entropy applies to isolated systems, meaning that the energy and
material within the system is Iixed. We will soon see how to apply this principle to
biological or chemical systems where this constraint does not apply. BeIore we do this,
however, we need to introduce additional concepts in thermodynamics, out oI which will
29
come another deIinition oI entropy (Section 1.16) providing Iurther insight into the
meaning oI entropy as well as the means to measure entropy experimentally.
Our goal is to end up with a potential Iunction, analogous to potential energy in a
mechanical system, that can be used to quantiIy the driving Iorce Ior biochemical
processes and also to quantiIy how much work can be obtained Irom such processes.
1.6 Thermodynamic Systems and Boundaries
The universality oI thermodynamics can also make this subject appear very dry
and disembodied Irom Iamiliar objects oI interest, and the language is necessarily very
general. We will start by deIining a thermodynamic system. II we want to examine
what goes on within a biological cell, Ior example, we need to Iirst consider what goes
into or out oI the cell. It is useIul, thereIore, to diIIerentiate the object to be studied, a cell
in this case, Irom everything else. A thermodynamic system can be deIined as anything
you are interested to examine, separated Irom the rest oI the universe, or surroundings
by an imagined or real boundary.

Figure 1.12: A thermodynamic system is whatever you are interested in examining,
separated from the rest of the universe (the surroundings) by a real or imagined
boundary.

For example, a system could be a bacterial cell, the contents oI a Ilask, a pulley with
weights, a steel ball in a well or even yourselI or the entire earth(Figure 1.12). A
30
thermodynamic system can be isolated, closed or open, which deIines the properties oI
the boundary separating the system Irom the surroundings (Figure 1.13).
An isolated system is one in which the boundary does not allow either energy or
matter to pass through. Whatever occurs within an isolated system is not inIluenced by
the surroundings and can have no inIluence on the surroundings. A boundary which does
not allow heat to Ilow between the system and the surroundings is called an adiabatic
boundary. An example is the wall oI a thermos bottle. In one extreme, the entire
universe can be considered to be an isolated system.


Figure 1.13: Schematic illustrations of an isolated system, a closed system and an
open system. The definitions are based upon whether energy (U) and/or matter
(N
i
)can exchange between the system and the surroundings.

A closed system is one in which matter cannot cross the boundary, but energy can
exchange with the surroundings either in the Iorm oI heat or work. A Ilask with chemical
reactants conIined to a solution might be considered a closed system, since the contents
can exchange heat with the surroundings. The Ilask in Figure 1.12 is a closed system.
Energy added to the system is assigned a positive sign and energy leaving the system is
31
given a negative sign (see Figure 1.14), analogous to adding or subtracting Irom the
potential energy in mechanical systems.

Figure 1.14: The sign convention for energy exchange between a system and its
surroundings. Energy leaving the system is negative because it reduces the amount
of energy in the system. Energy added to the system is considered positive. The same
convention applies to matter exchanged between the system and surroundings.

An open system is one in which both matter and energy can cross the boundary which
separates the system Irom the surroundings. II material were able to exchange between
the Ilask pictured in Figure 1.14 and the surroundings, Ior example by evaporation and
condensation, this would be an open system. Material entering the system Irom the
outside is given a positive sign and material leaving is given a negative sign. The signs
denote the changes in the amount oI material or energy within the system.
Living organisms are open systems. Open systems can be separated Irom the
surroundings by boundary that is semipermeable, allowing certain molecules to pass
through but not others. This is a property oI biological membranes.

32

Figure 1.15: The nucleus and mitochrondrion can be considered as subsystems
of the cell, which itself can be considered to be a thermodynamic
system. In these cases the thermodynamic boundaries are equivalent
to the semipermeable membranes surrounding each system, allowing
certain molecules to pass (Ni])as well as allowing heat (q)to exchange


Any system can contain subsystems which are mechanically separated Irom each other
and which can exchange matter and/or energy. The mitochondrion can be considered to
be a subsystem within a cell, Ior example (Figure 1.15).
1.7 Characterizing the System: State Functions
Once a system has been deIined, the state oI that system is characterized by State
Functions or State Variables. The most obvious Iunctions are temperature (T), pressure
(P), volume (V) and material composition (N
i
}). The material composition and volume
are extensive functions, meaning that their magnitudes are proportional to the size oI the
33
system. In contrast, temperature and pressure are intensive functions, and do not vary in
proportion to the size oI the system (Figure 1.16).
Figure 1.16: Extensive variables are additive when considering multiple systems,
and include volume (V), the number of particles N
i
]), internal energy (U) and
entropy (S). Note that material and energy are not allowed to pass between systems.
Intensive variables do not change with the size of the system, and
include temperature (T) and pressure (P). In this case, the temperature and
pressure are the same for both systems 1 and 2.

Thermodynamics introduces two additional extensive state Iunctions that are oI
Iundamental importance: internal energy (U) and entropy (S). Internal energy is the
sum oI the kinetic and potential energies oI each oI the components oI the system.
Boltzmann`s statistical deIinition oI entropy in terms oI multiplicity or probabilities oI
equivalent microscopic states, equation (1.20), was added aIter the Iormulation oI
thermodynamics, but is Iully compatible with the initial thermodynamic deIinition oI
entropy, which we will encounter in Section 1.16. Basically, internal energy deIines how
much energy is present in the system and entropy expresses how the energy is dispersed
among the components at equilibrium.
34
The thermodynamic state oI any system is completely deIined by the values oI
the extensive Iunctions: volume, material composition, internal energy and entropy (V,
N
i
, U and S). Furthermore, iI V, N and U are Iixed, then the value oI S is determined,
assuming the system is at equilibrium. We saw this in the simple model in Figure 1.10,
in which the entropy at equilibrium is deIined given the internal energy and number oI
particles. Hence, there must be some Iunction oI V, N and U that deIines S at
equilibrium.
( , , ) S S V N U = (1.21)
Under some circumstances, the internal energy and entropy oI a system can be measured
and given numerical values. However, in most cases, the absolute values oI internal
energy (Joules) and entropy (Joules-K
-1
) are not readily evaluated, as are, Ior example
temperature or the concentrations oI components. Nevertheless, internal energy and
entropy are at the heart oI the First and Second Laws oI Thermodynamics. BeIore we get
to that, we need to discuss what we mean by heat and internal energy and then take
another look at the concept oI entropy. We will then arrive at Iormulations oI
thermodynamics that are suited to solve everyday problems oI interest to biologists and
chemists, using readily measured properties.
1.8 Heat
We all have an intuitive knowledge oI heat, which is designated as q. When a hot
object is brought in contact with a cold object, we speak oI heat Ilowing Irom the hot to
the cold object. Indeed, Ior many years, heat was considered to be a Iluid substance with
mass (Caloric Theory) and was thought to be conserved. However, heat has no mass, and
35
is neither a Iluid nor is it conserved. II you rub two sticks together, they get hot (at least iI
you are a boy scout), so work can be converted to heat.
Heat (q) is a concept that is inseparable Irom the process oI the transIer oI energy
(U). We now know that in molecular terms, the energy is transIerred in terms oI the
thermal motions oI molecules oI the hot object stimulating the increase in thermal motion
oI molecules in the cold object. Hence, the transIer oI heat Irom a hot to a cold object
results in decreasing the internal energy oI the hot object and increasing the internal
energy oI the cold object. We know Irom experience that at equilibrium the temperatures
oI each oI the two objects will be identical. Note that iI we have a large cold object and a
small hot object, energy in the Iorm oI heat will be transIerred Irom the hot to the cold
object even though, in quantitative terms the internal energy oI the cold object, because
oI its large size, may be much larger than that oI the hot object. Equilibration does not
result in an equal distribution oI internal energies between the objects in contact.
Consider the example in Figure 1.17 in which we have two subsystems within an
isolated system. The two subsystems are combined and heat is allowed to pass between
the two subsystems, but neither the distribution oI matter nor the volumes change. We
start with a situation where the object comprising System 1 is at a lower temperature but
is much larger than the object comprising System 2. When they merge, heat (q) is
transIerred Irom the smaller, hotter object to the larger, colder object. The total internal
energy (U
1
U
2
) remains constant, as do the total number oI molecules (N
1
N
2
) and the
36
Figure 1.17: Two subsystems are combined and heat is allowed to transfer between
them. At equilibrium, the entropy of the combined system, which is isolated from its
surroundings, will be maximal. Maximizing the entropy leads to the conclusion that
the temperatures of each system in thermal contact will be identical at equilibrium.
The redistribution of energy leads to the increase in entropy as the combined
systems attain a new equilibrium.

total volume (V
1
V
2
). However, the distribution of energy has been altered and, thus S
1

and S
2
change. The total entropy oI the isolated, combined systems, will increase as heat
Ilows, and will reach a maximal value at equilibrium. At equilibrium the only
consideration is the multiplicity oI microscopic states is maximal and all possible
microscopic states are equally likely.
A chemical process, such as the hydrolysis oI ATP, that releases energy in the
Iorm oI heat is an exothermic process. In an isolated system, this usually results in
increasing the temperature oI the system. In an open system, such as in a cell or test tube,
the heat is transIerred to the surroundings to maintain constant temperature at
equilibrium. Heat leaving the system is assigned a negative sign. A process in which heat
is acquired Irom the surroundings in an open system is called an endothermic process
(see Figure 1.18). II an endothermic process occurs within an isolated system, we expect
the temperature to decrease.
37

Figure 1.18: Endothermic and exothermic processes are illustrated by biochemical
reactions in a test tube. An exothermic process generates heat which, in system in
thermal isolation from the surroundings, generally results in an increase in
temperature or, in a system in thermal contact with the surroundings, transfers heat
to the surroundings. If the surroundings is very large (here pictured as a large water
bath), the heat will not have a measurable influence on the temperature and the
entire process is maintained at constant temperature (an ~isothermal process). In
an endothermic process, heat is taken up from the surroundings, if the system is in
thermal contact. If not, the temperature decreases.

Heat is measured in units oI calories or joules. A calorie (small calorie or gram-
calorie) is deIined as the amount oI heat needed to increase the temperature oI 1 gram oI
water by 1
o
C, Irom 14.5
o
C

to 15.5
o
C. This is equal to 4.184 joules in SI units.
Since biological systems are open systems, exothermic and endothermic processes
result in the transIer oI heat either to the surroundings (exothermic, q0), or take heat
Irom the surroundings (endothermic, q~0). II the surroundings are large enough to
acquire or release heat without changing temperature, then this also will also maintain the
temperature oI any system equilibrated with the surroundings at the same, constant
temperature. A process that occurs at constant temperature is called an isothermal
processes. When the surroundings are considered unperturbed by the transIer oI heat to or
Irom it, this is reIerred to as a heat ~reservoir.
38
1.9 Pathway-independent functions and thermodynamic cycles.
The state oI a system is deIined by the values oI state variables. II we deIine two
states oI a system, State 1 (T
1
, P
1
,V
1
, N
1
, U
1
and S
1
) and State 2 (T
2
, P
2
,V
2
, N
2
U
2
and S
2
),
the net change in the state variables iI we go Irom State 1 State 2, do not depend on
the mechanism oI the process, the order oI events, or the nature oI intermediate states
passed through along the way. The changes in the state variable are pathway-
independent. In the schematic in Figure 1.19, we consider that the temperature, pressure
and composition oI the system is altered to go Irom State 1 to State 2.


Figure 1.19: Two different pathways leading from
State 1 to State 2 (red and green arrows Pathway 134521 is a
thermodynamic cycle ( red arrows).




It does not matter iI we heat it beIore or aIter changing the composition or changing the
pressure, or iI we heat it last. The Iinal state remains the same and the net changes in the
state variables (e.g., S (S
2
S
1
), U (U
2
U
1
) etc) do not depend on the pathway
39
but only on the Iinal and initial state. In the special case in which our sequence oI
processes (the pathway) brings us back to the initial state oI the system, then there is no
change in the values oI the state variables, (e.g., S U 0, etc). This is called a
thermodynamic cycle, and one is included in Figure 1.18. Once we realize which
variables are state variables, the simple concept oI pathway-independence has a great
practical value in calculating the values oI thermodynamic parameters, as we will see.
1.10 Heat and work are not state variables
It is particularly important to realize which variables are state variables and which
are not state variables. The example oI obtaining work by lowering (or dropping) a
weight on a pulley (Figure 3) illustrates three diIIerent ways oI going Irom an intitial to a
Iinal state in which diIIerent amounts oI work and heat are generated in each pathway. To
emphasize this point, let`s look at another example in which we Iocus on the potential
energy oI a box Iilled with lead weights (Figure 1.20). Since there is no kinetic energy,
the total energy is equal to the potential energy in a gravitational Iield. We can deIine
State 1 as the Box on the ground Iloor oI a building and State 2 as the box on the second
Iloor. The potential energy is deIined entirely by the position oI the box and not on how it
got to this position. This is what is meant by pathway independence oI the internal
energy, which is a state Iunction.
We need to do work to move the box Irom State 1 State 2. The simplest
pathway is to simply carry the box up one Ilight oI steps and put it down. However, we
might carry the box up to the third Iloor and, realizing our mistake, and out oI Irustration
just drop it down to the second Iloor. When the box hits the Iloor it will generate heat
Irom the kinetic energy it has picked up as it Ialls. By carrying the box an extra Ilight oI
40
stairs, we are doing more work on the box, and that extra work is then lost to the
environment as heat aIter we drop the box. The potential energy oI the box is the same
by either pathway, but both work and heat depend on the pathway. Work and heat are not
state Iunctions.

Figure 1.20: Two pathways used to move a box of lead weights from the first to
second floor. Energy (U) is a state function, whereas each of the two pathways
involves a different amount of work and heat, which are not state functions.

The Iact that heat and work are not state Iunctions is signiIied by expressing diIIerential
changes in work or heat as w and q instead oI dw and dq, since their magnitude will
depend on the pathway used Ior the displacement. The diIIerential changes in state
Iunctions, such as internal energy and entropy will be designated by dU and dS, to
indicate that these are exact values and not dependent on the pathway oI the change in the
system.
Now we are in a position to discuss the First Law oI Thermodynamics.
1.11 Internal Energy (U) and the First Law of Thermodynamics
41
The First Law oI thermodynamics states that work and heat are equivalent, and
that the internal energy oI any system can be altered only by an exchange oI either work
(w) or heat (q) with the surroundings.
U q w or dU q w o o A = + = + (1.22)
When heat is transIerred, the random motion oI the molecules is stimulated, whereas the
transIer oI energy in the Iorm oI work stimulates a uniIorm movement oI the molecules
(such as moving an object).
In a transition Irom State 1 State 2, the diIIerence in internal energy

2
U U U
1
A = (1.23)
is Iixed, but any combination oI work and heat that is consistent with this value might be
used in the transition. The convention is that work or heat transIerred into the system
Irom the surroundings is deIined as positive (q, w), whereas when work or heat is
transIerred Irom the system to the surroundings, the sign is negative, (-q, -w) (Figure
1.14).
This Iirst law implies that in any isolated system the internal energy must remain
constant, since no work or heat is allowed through the system boundary. II we consider
the entire universe to be an isolated system, then the Iirst law states that the total energy
in the universe is a constant and, thereIore, energy can be neither destroyed nor created.
1.12 Measuring U for processes in which no work is done
II we simply heat a system and keep the volume constant, then there can be no PV
work ( ). In the absence oI any other kind oI work ( 0
PV
w = 0)
nonPV
w =
`
then and,
since , the change in the internal energy is simply equal to the heat transIerred
0 w=
U q w A = +
(1.24)

where the subscript indicates constant volume.
V
U q A =
42
Hence, we have a method, under limited circumstances, to measure U. II we have a
uniIorm substance, the amount oI heat necessary to raise the temperature by 1K under
conditions oI constant volume, is C
V
(units JK
-1
).

V V
q C dT o = (1.25)
ThereIore,

V
dU C dT = (1.26)
II C
V
is a constant, i.e., does not vary as the temperature oI the system is changed, then
we can determine the change in internal energy in heating the substance Irom T
1
to T
2
, by
simple integration
(1.27)
2 2
1 1
U T
V
U T
dU C dT =
} }
(1.28)
2 1 2 1
( ) (
V
U U U C T T A = = )
V
So, iI we heat a system that is held at constant volume, all the heat goes into increasing
the internal energy oI the system. However, most biological processes don`t occur at
constant volume, but rather at constant pressure.
1.13 Enthalpy and heat at constant pressure
Most oI the systems we will be studying are open to the atmosphere and,
thereIore, processes are measured at constant pressure (an external pressure, P
ext
1 bar).
II we heat a substance that is open to the atmosphere, then it is possible that there will be
a change in volume (dV) and, thereIore, some oI the energy added as heat to the system
will be used to do work against the atmospheric pressure,
PV ext
w P d o = , where the
negative sign indicates work done by the system on the environment (dV~0 Ior an
expansion). II no other work is allowed ( 0
nonPV
w o = ), then we can write
43

P ext
dU q w q P dV o o o = + = (1.29)
where the subscript indicates that the heat is delivered under conditions oI constant
pressure. This expression can be rearranged to yield

P
dU PdV q o + = (1.30)
where the 'ext subscript has been dropped Ior convenience.
Since pressure is constant, dP 0, so we can add a VdP term to equation to get
( ) (
P
q dU PdV VdP d U PV) o = + + = + (1.31)
The amount oI heat (
P
q ) released or taken up during a process, such as a biochemical
reaction, at constant pressure, can be experimentally measured using a calorimeter. For
this reason the thermodynamic expression on the right hand side oI equation (1.31) is
given a special name, enthalpy, H.
H U PV = + (1.32)
dH dU PdV VdP = + + (1.33)
It is only Ior a process where the pressure is the same in the initial and Iinal states
( ) that we can write 0 dP =
dH dU PdV = + (1.34)
Note that since U, P and V are state Iunctions, enthalpy is also a state Iunction.
The amount oI heat needed to raise the temperature oI a substance by 1K at constant
pressure is equal to C
P
, the heat capacity at constant pressure (units JK
-1
). Hence,

P P
q C dT o = (1.35)

P
dH C dT = (1.36)
44
The numerical value oI C
P
will depend on the pressure under which the measurement is
made. Under conditions where C
P
at a deIined pressure is constant and does not vary with
temperature, we can write

2 1
(
P
H C T T ) A = (1.37)
When a system is heated at constant pressure, e.g., maintained at atmospheric pressure,
some oI the heat goes to increase the internal energy and some oI the heat is used to do
work on the atmosphere iI the system expands. Enthalpy accounts Ior both oI these
consequences
More pertinent is the release or uptake oI heat during chemical or biochemical reactions
that take place at constant pressure. The change in enthalpy oI a system under these
conditions is due to the making and breaking oI chemical bonds. Since the amount oI
PV work is usually small in biochemical processes, the changes in enthalpy and internal
energy are usually about the same.
1.14 The caloric content of foods: reaction enthalpy of combustion
When one reIers to the energy content oI a Iood, this generally reIers to the
amount oI heat released upon combustion to yield CO
2
and H
2
O. For example, Ior
sucrose, the combustion reaction is
(1.38)
12 22 11 2 2 2
C H O (s) 12 O ( ) 12 CO (g) 11 H O (l) g +
where the (s), (g) and (l) reIer to the solid, gaseous and liquid state. The oxidation oI
sucrose also occurs in the human body, though Iortunately not in a simple combustion
reaction, but through a series oI many enzyme-catalyzed steps. As Iar back as 1780,
Lavoisier and LaPlace demonstrated that the heat produced by mammals is the same as
the heat generated upon the combustion oI organic substances, and that the same amount
45
oI O
2
is consumed. (Kleiber M. 1975. The Fire of Life. An Introduction to Animal
Energetics. New York: Robert E. Krieger Publishing; Holmes FL. 1985. Lavoisier and
the Chemistry of Life. Madison, WI: University oI Wisconsin Press.). Since enthalpy (H)
is state Iunction, the change in enthalpy due to the oxidation oI sucrose to CO
2
and H
2
O
will be exactly the same regardless oI the pathway between the initial and Iinal states.
Hence, the value oI H measured in a one-step combustion reaction is the same as that
resulting Irom the biological pathway, consisting oI many steps, but leading to the same
products.
For the combustion oI sucrose, the initial state can be deIined as 1 mole oI solid
sucrose plus 12 moles oI O
2
gas and 298.15K and 1 bar pressure, and the Iinal state is 12
moles oI CO
2
gas and 11 moles oI liquid water, also at 298.15K and 1 bar pressure. The
choice oI 298.15K and 1 bar pressure is usually taken as a 'standard state as a matter oI
convenience.
Each oI the reactants and products has absolute values Ior its internal energy and
enthalpy under the conditions oI the standard state, and we can denote these as
etc. where the subscript 'm indicates the value per
mole and the superscript 'o indicates the standard state (298.15K and 1 bar). We can
now deIine the reaction energy and reaction enthalpy
o o
m 12 22 11 m 12 22 11
U (C H O ,s), H (C H O ,s)
o
r m
U A
o
r m
H A Ior the reaction
describing the combustion oI sucrose.
(1.39)
0 0
2 2 12 22 11 2
0 0
2 2 12 22 11 2
12 ( , ) 11 ( , ) ( , ) 12 ( , )
12 ( , ) 11 ( , ) ( , ) 12 ( , )
o o
r m m m m m
o o
r m m m m m
U U CO g U H O l U C H O s U O g
H H CO g H H O l H C H O s H O
A = +
A = +
o
o
g
46
These are the molar reaction energy, ,and the molar reaction enthalpy,
o
r m
U A
o
r m
H A . Note
that the 'molar means per mole as the reaction as it is written, normalized to 1 mole oI a
particular reactant or product. II we divided every term by 12 to normalize the reaction to
one mole oI CO
2
, the values oI would be divided by 12. and
o
r m r m
U A A
o
H
Experimentally, the heat oI this reaction must be measured using a bomb
calorimeter (Figure 1.21), because gases are involved and it is necessary Irom a practical
viewpoint to do the reaction in a sealed vessel at constant volume.
The heat released at constant volume in the reaction container is transIerred by
equilibration to a large water bath and measured by the increase in temperature oI the
water. Since a large mass oI water is used, the temperature oI the reaction system itselI is
maintained at approximately the same temperature (298.15K).




47
Figure 1.21: Schematic of a bomb calorimeter used for measuring the heat of
combustion at constant volume. The liquid or solid sample is placed in the sample
cup and the steel bomb is filled with O
2
gas. The diathermal (heat-conducting walls)
container is placed in an inner water bath whose temperature is monitored. The
entire unit is insulated from the rest of the environment and is a isolated system.
(from Engel, Drobny and Reid, ~Phys Chem for Life Sci, page 72)


The heat generated at constant volume gives us the value oI Ior converting the
reactants to the products. Note that any changes in temperature during the reaction are
irrelevant as long as the initial and Iinal temperatures are the same.
o
r m
U A
Having obtained the value Ior , we can calculate the value Ior
o
r m
U A
o
r m
H A realizing that
( ) (
o o
r m r r m
) H U PV U PV A = A + = A + A (1.40)
The ideal gas law tells us that PV nRT = , so

(
o o
r m r m
) H U n RT A = A + A (1.41)

where n is the change in the number oI moles oI gas upon converting the reactants to
products. In this case, n 0 since every mole oI O
2
generates a mole oI CO
2
. Hence, Ior
this reaction,
o
r m r m
o
H U A = A . Under most circumstances with reactants in aqueous solution
or with liquid and solid components the volume changes are insigniIicant and the reaction
enthalpy and energy are virtually the same.
The heat oI combustion oI sucrose is -5639.7 kJmol
-1
.
The negative sign means
that heat is released to the environment upon the oxidation oI sucrose. Table 1.1 lists the
heats oI combustion Ior a series oI 'macronutrients along with several deIined
substances. The energy values oI Ioods used to analyze dietary needs are based on these
48
measurements and are rounded oII as shown in Table 1.1. Roughly, the energy
expenditure oI an individual person at rest is about 1 kilocalorie per minute, or about
1440 kcal/day, which is about the same as a 75 Watt light bulb (1 kcal/min 70 J/sec
70 W).
Table 1.1
Heat of combustion
(kcal/g)
standard nutritional
energy value
(kcal/g)
starch 4.18 4.0
sucrose 3.94 4.0
glucose 3.72 4.0
Iat 9.44 9.0
protein through
metabolism
a
4.70 4.0
protein through
combustion
a
5.6
ethanol 7.09 (5.6 kcal/ml)
lactate 3.6
palmitic acid 9.4

a
The heat released by protein by metabolism is less than that obtained by combustion
because the nitrogen-containing end products are diIIerent Ior the two processes. The
most common end product Ior mammals is urea, whereas during combustion nitrous
oxide is produced.(Irom Dietary Reference Intakes for Energy, Carbohydrate, Fiber, Fat,
Fatty Acids, Cholesterol, Protein, and Amino Acids (Macronutrients) A Report of the Panel on
Macronutrients, Subcommittees on Upper Reference Levels of Nutrients and Interpretation and
Uses of Dietary Reference Intakes, and the Standing Committee on the Scientific Evaluation of
Dietary Reference Intakes. The National Academies Press, 2005; and Biological
Thermodynamics, Donald Haynie, Cambridge University Press, 2001


1.15 The heat of formation of biochemical compounds
Equation (1.39) shows that iI the absolute value oI the molar enthalpy content
were known Ior each participant in a reaction under standard conditions, one could easily
compute the value oI
o
r m
H A without ever doing the experiment. In essence, this has been
done by experimentally determining and tabulating the molar enthalpies oI Iormation oI
49
many compounds, . The enthalpy oI Iormation is the enthalpy oI the reaction in
which the product is 1 mole oI the substance (e.g., sucrose) and the reactants are pure
elements in their most stable state oI aggregation. By convention,
o
f
H A
0
o
f
H A = Ior all
elements in the standard state (298.15K and 1 bar). Consider the combustion oI sucrose,
equation (1.39) To calculate the reaction enthalpy,
o
r m
H A we have to look up the values oI
Ior each product and reactant. These values are included in Table 1.2. Note that in
this reaction we are starting with solid sucrose, not in solution, and it is important to use
the correct value oI . Similarly with CO
o
f
H A
o
f
H A
2
and O
2
, which are both in the gaseous
state in this reaction.

1
12 22 11
( , ) - 2226.1
o
f
H C H O s kJ mol

A =

1
2
( , ) - 393.5
o
f
H CO g kJ mol

A =

1
2
( , ) 0
o
f
H O g kJ mol

A =

1
2
( , ) - 285.8
o
f
H H O l kJ mol

A =
ThereIore,
(1.42)
2 2 12 22 11 2
12 ( , ) 11 ( , ) ( , ) 12 ( , )
o o o o o
r m f f f f
H H CO g H H O l H C H O s H O A = A + A A A g
12(-393.5) 11(-285.8) - (-2226.1) - 12(0)
o
r m
H A = +

1
5639.7
o
r m
H kJ mol

A =
Figure 1.22 shows diagrammatically the relationships oI the enthalpy oI the
reaction and the enthalpies oI Iormation.
50

Figure 1.22: A thermodynamic cycle illustrating two different pathways to go from
elements in their reference states to form water and CO
2
. One path proceeds
through sucrose and O
2
and and second path is direct. Knowing the enthalpy of
formation of each compound allows one to compute the standard state reaction
enthalpy (indicated in red)

Note that the reactions Iorm a thermodynamic cycle. As long as the value oI Ior
each oI the compounds is determined using the same reIerence state, the choice oI the
reIerence state is not important and can be selected Ior convenience. The lower line in
Figure 1.22, indicating the reIerence state oI the elements used to make up all the
products and reactants, can be moved up or down without changing the diIIerence value
oI the reaction enthapy. This is why the elements can be arbitrarily assigned a value oI
zero Ior their enthalpies oI Iormation. From the thermodynamic cycle in Figure 1.22,
o
f
H A
(1.43)
(reactants) - (products) 0
(products) - (reactants)
o o o
f r m f
o o o
r m f f
H H H
or
H H H
A + A A
A A A
The values Ior are taken Irom tabulated lists, such as Table 1.2. Biochemists are
generally more interested in reactions that occur in aqueous solution. Hence, the standard
state used Ior biochemical substances is 1 M solution oI the substance in water (but
o
f
H A
51
assuming an 'ideal solution) at 298.15K and 1 bar pressure. Because element oxygen is
most stable under these conditions as a diatomic gas, O
2
(g) is the reIerence state, and
. However, Ior O 0
o
f
H A =
2
dissolved in water (1 M), . This
represents the release oI heat upon dissolving O
1
11.7 kJ mol
o
f
H

A =
2
into water

Table 1.2: Standard Heats of Formation of Selected Substances
a


a
The standard state, unless indicated otherwise is 298.15
o
C, 1 bar pressure, zero ionic
strength, and a 1 M solution which behaves as a dilute solution (an ideal solution).
Exceptions are O
2
(g), CO
2
(g) and sucrose(s), which are in the gas and solid phases, as
indicated. Note that separate entries are necessary Ior diIIerent ionization states. (Source:
Themodynamics oI Biochemical Reactions, Robert A. Alberty, Wiley-Interscience, 2003)
ionization
state

f
H
o
k1mol
-1
adenosine 0 -631.3
adenosine 5
`
diphosphate
-3 -2626.54
adenosine 5
`
diphosphate
-1 -2638.54
alanine 0 -554.8
ammonia 0 -80.29
ammonia 1 -132.51
adenosine 5
`
triphosphate
-4 -3619.21
CO
2
(g) 0 -393.5
CO
2
(aq) 0 -412.9
D-glucose 0 -1262.19
H
2
O(l) 0 -285.83
lactate -1 -686.64
O
2
(g) 0 0
O
2
(aq) 0 -11.7
pyruvate -1 -596.22
sucrose 0 -2199.87
sucrose(s) 0 -2226.1
urea 0 -317.65
52

1.16 Thermodynamic Definition of Entropy
The initial deIinition oI entropy emerged Irom the Iormalism oI classical
thermodynamics prior to Boltzmann`s Iormulation (Section 1.5), and is related to the
Iraction oI the total energy oI a system that is not available to do work. The interest in the
1800`s was to obtain the maximum eIIiciency possible Irom a steam engine, whereas we
are most interested in the work potential oI biological processes. For example, iI a certain
amount oI ATP is hydrolyzed in a cell under speciIied condition, how much work can be
obtained? This could be in terms oI moving muscles or transporting small molecules
across a membrane. In either case, we need to consider the pathway that is most eIIicient
and least wasteIul. This is how the concept oI entropy was Iirst established.
Let`s consider the transition oI a system Irom State 1 State 2 in which the
internal energy oI the system is decreased by U by the transIer oI heat to the
surroundings and by doing work on the surroundings. Since work and heat are not state
Iunctions, diIIerent pathways leading Irom State 1 to State 2 can utilize diIIerent
combinations oI values Ior the work and heat which are constrained to add up to the total
change in internal energy (Figure 1.23), i.e. Ior all pathways U w q A = + .

53



Figure 1.23: Illustration of several different pathways going from State 1 to State 2.
The change in internal energy is constant, but the amount of heat removed from the
system and amount of work done by the system in going from State 1 to State 2 can
be very different.


An example oI this Ior a mechanical system is illustrated in Figure 3. We will assume
that there is a pathway that maximizes the amount oI work we can get out oI the system
and wastes the minimum amount oI the internal energy removed Irom the system that is
lost as heat (Figure 1.23). Since work done on the surrounding and heat transIerred to
the surroundings is negative, we will discuss the optimal values in terms oI the absolute
values, designated by the straight brackets,
max min
and w q . ReIerence to Figure 1.23
makes it clear what is meant by maximal and minimal values. The pathway that yields
the maximal amount oI work done by the system is an idealized pathway, one in which
the process in is taken in small steps, each oI which is shiIts the equilibrium by a small
amount and is reversible. This was illustrated Ior the case oI liIting a weight using a
pulley, shown in Figure 3, but the concept oI a reversible process, yielding the maximal
useIul work, applies generally. The work obtained Irom such a pathway is called
54
reversible work, w
rev
, and the maximum work that can be done by the system on the
surroundings in going between speciIied initial and Iinal states is
rev
w
.
The same
reversible process that maximizes the work ouput must also minimize the amount oI
wasted heat (see Figure 1.23). The heat lost to the system in a reversible process is q
rev
,
and
rev
q is the minimal amount oI wasted heat possible Ior any process going Irom State
1 to State 2. In the case oI the mechanical pulley system in Figure 3, the reversible
process wasted none oI the potential energy as heat, but this is not usually the case, as we
will see in what Iollows.
II the energy oI the system is decreased, as in Figure 1.23, then and
rev rev
w q

report the minimal wasted heat and maximum work output possible The work and heat
are both negative since they each decrease the energy oI the system. On the other hand, iI
the energy oI the system increases, then the values oI and
rev rev
w q report the minimal
amount oI work needed to take the system to the higher internal energy in a reversible
pathway, which is associated with the maximal amount oI heat transIerred into the system
to accomplish the transition. The reversible process between any two states deIines a
special pathway insoIar as the values oI w
rev
and q
rev
are uniquely deIined by the initial
and Iinal states oI the system. Hence, both w
rev
and q
rev
can also be considered to be state
Iunctions because they are deIined by the states themselves.
In the 1850`s, RudolI Clausius recognized the useIulness oI deIining a new state
Iunction which he called entropy, S, where

rev
sys
sys
dq
dS
T
= (1.44)
55
Equation (1.44) says that Ior a small change oI state oI a system, the entropy change,
sys
dS , is deIined as the reversible heat required Ior the transition, dq
rev
, divided by the
temperature oI the system at the instant oI the heat transIer,T
sys
. Entropy is measured in
'entropy units or e.u., measured in joules per kelvin (JK
-1
). Since both T
sys
and dq
rev
are
state Iunctions, it Iollows that dS
sys
is also a state Iunction, and is absolutely deIined by
the initial and Iinal states oI the system. It is convenient to consider inIinitesimal changes
oI state (diIIerential Iormat) so that the temperature (T
sys
) can be considered to be
constant.
Since , we can substitute Irom the deIinition oI entropy in
max min
dU dw dq = +
(1.44) to get

max sys
dw dU TdS = (1.45)
The entropy change oI the system is related to that portion oI the internal energy which is
unavailable to do work. The product
sys
TdS has units oI energy (joules).
II the initial and Iinal states have diIIerent temperatures (T
1
and T
2
), then we can
integrate to Iind determine the value oI
sys
S A . This is the equivalent oI adding up the
changes in dS
sys
Ior a series oI small steps between the two endpoints, as pictured in
Figure 1.8.

2
1
State
rev
sys
sys State
dq
S
T
A =
}
(1.46)

Note that the reversible addition oI heat to a system at low temperature changes the
entropy by a larger amount than iI we add the same amount oI heat reversibly to a system
at higher temperature.
56
It also Iollows Irom the deIinition oI entropy in (1.44) that in any other pathway
other than the idealized 'reversible pathway,

irrev
sys
sys
dq
dS
T
> (1.47)
where the signs oI both dS
sys
and dq
irrev
are negative in Figure 1.23 but dS
sys
is a smaller
negative number.
OI course, all this is just a matter oI deIinitions and is not particularly useIul
without some way oI relating
sys
S A to measurable properties oI the system. It was the
genius oI Boltzmann to connect this thermodynamic deIinition oI entropy to the concept
oI multiplicity, deIined in equation (1.19). Indeed, one can start with Boltzmann`s
equation (1.19) and mathematically derive the thermodynamic deIinition oI entropy (we
will not do this), though this equivalence is certainly not evident on Iirst observation. The
microscopic deIinition oI entropy readily explains why the reversible addition oI heat to a
system at low temperature changes the entropy to a larger extent than the addition oI the
same amount oI heat added reversibly to the same system at high temperature. The
increase in multiplicity will be relatively small iI one adds heat, thus increasing the
internal energy, at high temperatures, because the energy is already dispersed over
molecules at many energy levels (see Figure 1.10, Ior example). At low temperatures,
Iewer energy levels will be occupied at the start, and the addition oI heat will have a
proportionately larger eIIect.

1.18 Entropy and the Second Law of Thermodynamics
The microscopic deIinition oI entropy (Boltzmann`s equation) and the Principle
oI Multiplicity (Section 1.5) state that any spontaneous process in an isolated system will
57
tend towards the maximal value oI entropy, meaning that the total entropy must increase
during any spontaneous process. This is known as the Second Law of Thermodynamics.
The statistical or microscopic deIinition is the easiest way to get a physical Ieeling Ior the
meaning oI entropy, whereas the thermodynamic deIinition provides a method to actually
measure entropy.
It is important to emphasize that the Second Law reIers to the total entropy. Take
as an example, a glass oI hot water sitting in a room, where the room is the surroundings
and the glass is the system oI interest (Figure 1.24).

Figure 1.24: A glass of hot water (the system) in a cool room (the surroundings).
Heat is spontaneously transferred from the hot water to the cool air in the room.
The entropy of the glass of water decreases, but the total entropy of the isolated
system consisting of the glass of water plus the room increases.

The water will cool spontaneously by transIerring energy in the Iorm oI heat to the air in
the room. The room is large enough so that its temperature does not change. The Second
Law applies to an isolated system, i.e. no exchange oI energy or matter with the
surroundings. The total system in this example must be deIined as the glass oI water plus
the surroundings. Together, the glass and room make up an isolated system.
Qualitatively, we know that the entropy oI the water in the glass will decrease in this
spontaneous process, since heat is being removed Irom the water. This is not in violation
oI the Second Law because the entire system is consists oI both the room plus the glass oI
58
water. The Second Law states that the total entropy change must be greater than zero Ior
any spontaneous change in the total system. During the process oI the water in the glass
cooling to an equilibrium temperature, the total entropy change will consist oI the sum oI
the entropy change in the glass oI water (which we will reIer to as the system) and the
surroundings, i.e., the room. The Second Law states that this total entropy change must
be greater than zero.
0
total sys surr
S S S A = A + A > (1.48)
In this particular example, there is no work involved, only heat transIer:
Ior the glass oI water; w
sys
0, so U
sys
q
sys

and Ior the surroundings; w
surr
0, so U
surr
q
surr
-q
sys
The decrease in the internal energy oI the glass oI water must be equal to the increase in
the internal energy oI the surroundings. Since the internal energy is a state Iunction and
no work is involved, the heat transIer by any pathway will be the same, whether the
pathway is reversible or irreversible. We can now write expressions Ior the entropy
change.
For the glass oI water:

sys
rev
sys
sys sys
dq
dq
dS
T T
= =

2
1
state
sys
sys
sys state
dq
S
T
A =
}

We need to use the diIIerential expression and then integrate to get the total entropy
change because the temperature oI the water is changing as heat is removed, i.e., T
sys
is
not a constant.
For the surroundings, where the temperature is constant (T
surr
):
59

2
1
sys
rev surr
surr
surr surr surr
state
sys sys
surr
surr surr state
dq
dq dq
dS
T T T
dq q
S
T T
= = =
A = =
}

By our sign convention, heat Ilowing out oI the system is negative, thereIore, the entropy
change in the glass oI water is negative and the entropy change in the surroundings is
positive.

0
0
0
sys
sys
surr
dq
S
S
<
A <
A >
(1.49)
Furthermore, during the entire process, until the very end, the temperature oI the water in
the glass is higher than the temperature in the surroundings,
sys
surr
sys surr
dq
dq
T T
<
since
sys surr
T T > , where the brackets dq indicate the absolute value.
Hence,
surr sys
S S A > A , Irom which it Iollows that
(1.50)
total sys surr
S S S 0 A = A + A >
Heat will Ilow spontaneously Irom the hot to the cold object, and not in the reverse
direction, since that would result in a decrease in the total entropy oI the system and
would violate the Second Law.
The equilibrium position is also deIined by the Second Law since heat Ilow will
cease when the temperature oI the water in the glass and in the surroundings are identical.
Note also that the absolute internal energy oI the room is much larger than that oI the
glass oI water. Yet, energy Ilows Irom the glass oI water to the room. The driving Iorce is
60
to maximize entropy, which corresponds to equalizing the temperatures, and it is not to
equalize the energy content.
Let`s now look at another example, which will demonstrate the diIIerences
between reversible and irreversible pathways. We start with a gas in a chamber with an
initial pressure oI 2 bar, temperature, T and volume oI V
1
. Three pathways are shown in
Figure 1.25 to go to a Iinal state in which the gas has expanded into a volume that is
twice the original volume and at the same temperature. Assuming Ior simplicity we have
an ideal gas, then we know that the Iinal pressure must be halI oI the initial pressure,
since and the Iinal volume is double the initial volume. PV nRT =
The Iirst pathway shown on the leIt oI Figure 1.25 is to open holes up in the
barrier between the right and leIt chambers. The gas will re-equilibrate by diIIusing into
the Iull volume. No heat is allowed to exchange with the environment and no work is
done. This is an irreversible process, which is easily imagined iI you consider whether it
will go backwards Irom the Iinal to initial state. This clearly will not happen
spontaneously. Since the temperature is the same in the Iinal and initial states, there is no
change in the internal energy (U 0).

61
Figure 1.25: Three processes for expanding a gas from an initial volume in one
chamber to double the volume at the same temperature. Process A (left) allows the
gas to diffuse from left to right until equilibration. Process B (center) allows the gas
to push a piston against no external pressure. Process C (right) is a reversible
process where the expanding gas does work and heat transfers from the
surroundings to maintain constant temperature. The change in entropy of the
system must be the same for all three processes, but only the first two irreversible
processes are spontaneous and proceed with a net increase of entropy of the
universe (system plus surroundings).

The second pathway in the center oI Figure 1.25 is also irreversible. In this case,
the gas is allowed to expand, but by pushing the barrier between the chambers to its
limiting position. However, the external pressure, which determines the amount oI work
accomplished is zero (P
ext
0), so no work is done. No heat is allowed to exchange with
the chamber, and the Iinal state is identical to that obtained in the Iirst pathway.
The third pathway between the initial and Iinal states is a reversible pathway in
which the gas expansion does work against an external pressure. Furthermore, to
maintain the temperature, we must allow heat to enter the system Irom the
surroundings.To make this reversible, the external pressure needs to be adjusted
continuously so that it is just slightly less than the internal pressure Iorcing the piston out.
In this way, each small step is at equilibrium throughout the process. The amount oI work
done is determined by integration.

2 2
1 1
2
1
ln ln 2
V V
rev
V V
V dV
w PdV RT RT RT
V V
= = = =
} }
(1.51)
where the Iinal volume is twice the initial volume. The Iinal state is exactly the same is in
the two irreversible pathways, and since U 0 (no change in internal energy)
ln 2
rev rev
q U w RT = A = + (1.52)
62
We can use the reversible pathway to determine the change in entropy oI the
system, i.e., the gas in the chamber.
ln 2
rev
sys
q
S R
T
A = = (1.53)
Since entropy is a state Iunction, the change oI entropy oI the system must be the same
also Ior the irreversible processes. For the irreversible processes in this example, there is
no change in entropy oI the surroundings since there is no interaction between the system
and environment. Hence,

0 Ior the irreversible processes, and
S ln 2 0 ln 2
0
surr
total sys surr
total
S
S S RT RT
S
A =
A = A + A = + =
A >
This is consistent with the Second Law, since the spontaneous, irreversible
processes occur with a net increase oI the entropy. The reversible process, being always
at equilibrium, will not occur spontaneously. In this case, the entropy change oI the
surroundings can be easily calculated Irom the amount oI reversible heat removed Irom
the surroundings, which is just the negative oI the amount oI heat transIerred into the
system.
ln 2
rev
surr
q
S
T
A = = R (1.54)
For the reversible process, the net change in entropy is zero, taking into account both the
system and the surroundings.
(1.55) ( ln 2 ln 2) 0
total sys surr
S S S R R A = A + A = =
63
1.19 The thermodynamic limit to the efficiency of heat engines, such as the
combustion engine in a car.
The thermodynamic concept oI entropy arose Irom the need to determine the
maximum eIIiciency oI engines which convert heat to work. Both steam engines as well
as the modern gasoline combustion engines are examples oI heat engines. It is useIul to
see how the simple application sets a limiting eIIiciency Ior heat engines, although such
limitations do not apply to biological systems.

Figure 1.26: Schematic of the thermodynamics of a heat engine, such as the
combustion engine in a car. Following the combustion of gasoline and oxygen in the
piston cylinder, some of the heat from the hot gases (T
hot
) is converted to useful
work and the remainder is lost to the surroundings (T
cold
). The requirement that the
total entropy must increase limits the efficiency since the only way to increase the
total entropy is to transfer heat to the surroundings.

In a combustion engine, gasoline and oxygen are combined and a combustion
reaction generates a large amount oI heat. Heat is removed Irom a hot object, in this case
corresponding to the gases inside a piston and converted to work, e.g., rotating the
crankshaIt oI an automobile engine. Some heat is exhausted to the surroundings.
64
The mechanism oI how the work is generated, e.g., expanding gases increasing the
pressure within the piston, is not relevant Ior this problem. Figure 1.26 is a schematic oI
a heat engine Irom a thermodynamic perspective. Consider one cycle oI the engine. We
have a hot object at temperature T
hot
, the gases in the piston, Irom which an amount oI
heat is removed, and a cold object, the surroundings on which work is done and
which also receives exhaust heat . Since
hot
q
cold
q
hot cold
w q q = (where since it is
leaving the system), we can deIine the eIIiciency oI the heat engine as the Iraction oI the
energy removed Irom the engine which is converted to work.
0
hot
dq <
1
cold
hot hot
q w
q q
c = = (1.56)
The change in entropy oI the total system, is the sum oI the entropy change in the engine
(hot) and the surroundings (cold). II we assume the exchange oI heat does not alter the
temperatures, Ior simplicity, then

hot cold
total sys surr
hot cold
q q
S S S
T T
A = A + A = + (1.57)

Let`s see what happens iI all oI the energy taken Irom the engine as heat (q
hot
) is
converted to work. Then and, consequently, and 0
hot cold
q w q = =
hot
total
hot
q
S
T
A = . However,
since (energy is removed Irom the system), it Iollows that 0
hot
q < 0
total
S A < . It is
impossible to convert all the heat removed Irom the engine in the Iorm oI work since this
would violate the Second Law oI Thermodynamics.
65
In order to convert heat to work, we need to take some oI the heat Irom the hot system
and transIer it to the surroundings. It is the increase in entropy in the 'cold reservoir or
surroundings which drives the system Iorward spontaneously.
The criterion Ior a spontaneous process is that 0
cold hot
total
cold hot
q q
S
T T
A = > , Irom which we
can conclude that
cold cold
hot hot
q T
q T
> . ThereIore, Irom equation (1.56)
1
cold
hot
T
T
c s (1.58)
There is a thermodynamic limit to the eIIiciency Ior any engine that converts heat to
work, whether it is a steam engine or a gasoline combustion engine, and this limit
depends on the operating temperature oI the engine and the temperature oI the
surroundings. At a high operating temperature, the eIIiciency is greater. For a typical
gasoline combustion engine in a car, 380 K and T 300 K
hot cold
T ~ ~ , giving a limiting
eIIiciency 0.21
hot
w
q
c = ~ . Nearly 80 oI the energy is wasted as heat lost to the
environment.
Is this relevant Ior biological systems? Not really. We don`t need to worry about
this ineIIiciency oI converting heat to work Ior biological systems. In principle, there is
no thermodynamic limit to the eIIiciency oI converting one type oI work into another.
There will be practical limitations, oI course, but generally, biological systems can attain
a high degree oI eIIiciency in interconverting various kinds oI work.
The important aspect to note Irom the examples oI the heat engine and the cooling
oI a hot glass oI water is that the Second Law does not prevent a process in which there is
a spontaneous decrease in entropy in part oI a system, as long as the entire process results
66
in a net decrease in entropy. Biological systems are open systems, so any biological
process occurs in contact with the surroundings. What we will do in the next Chapter is
see how we can reIormulate the thermodynamic expressions in terms oI measurable
properties oI the system oI interest and not worry about the surroundings, other than to
speciIy that temperature and pressure.
1.20 The absolute temperature scale.
Up to now we have reIerred to temperature without deIining which scale to use.
The most Iundamental scale is the Absolute or Kelvin scale, which conceptually comes
Irom thermodynamics. The zero point on this scale is the temperature at which the work
done by a system occurs with 100 eIIiciency and none is wasted. From equation (1.45)
we know that, by this deIinition, at absolute zero (T 0)

max
dw dU = (1.59)
We can also see this in the expression Ior the eIIiciency oI a heat engine, equation (1.58).
II the value oI T
cold
0, then the eIIiciency c 1, and the engine is 100 eIIicient in
taking heat and converting it to work. This is another deIinition oI the zero point oI the
absolute or Kelvin temperature scale.
From a molecular perspective, at absolute zero the entropy content is zero,
meaning that our material is a perIect crystal with only one microscopic state possible
that is consistent with the properties.
(1.60) ln ln(1) 0 at T 0 Kelvin S k W k = = =
We can also see this in the expression Ior the eIIiciency oI a heat engine, equation (1.58).
II the value oI T
cold
0, then the eIIiciency c 1, and the engine is 100 eIIicient in
67
taking heat and converting it to work. This is another deIinition oI the zero point oI the
absolute or Kelvin temperature scale.
From a molecular perspective, at absolute zero the entropy content is zero,
meaning that our material is a perIect crystal with only one microscopic state possible
that is consistent with the properties.
(1.61) ln ln(1) 0 at T 0 Kelvin S k W k = = =
Experimentally, absolute zero is at T
Celsius
-273.15. The Kelvin scale must be used in all
thermodynamic calculations. The scale is the same as that deIined by Celsius, but shiIted
so that the zero point is absolute zero. The unit used is deIined as the Kelvin (K).
( ) 273.15
Celsius
T K T = (1.62)
1.21 Summary
We have deIined the Principle oI Multiplicity, which states that the dispersal oI
energy and matter in any isolated system will spontaneously tend towards a state in which
the number oI equivalent microscopic states is maximal. This is expressed quantitatively
by the Boltzmann deIinition oI the entropy Iunction. The equilibrium condition Ior any
isolated system is, thus, that entropy is at its maximum value.
The practical application oI the principle oI maximizing entropy is provided by
the Iormal structure oI thermodynamics, which shows how entropy can be measured and
quantiIied by measuring the amount oI heat transIerred into or out oI a system under
speciIied conditions.

68