LECTURE NOTES

in biophysics for medical students

2018-2019

Chapter I. BIOTHERMODYNAMICS
Boris Tenchov, Rumiana Koynova

1. Basic concepts of thermodynamics. First law of thermodynamics

Subject and basic concepts of thermodynamics. First law of thermodynamics. Internal energy,
heat and work.
2. Entropy and second law of thermodynamics. Тhermodynamic potentials
Second law of thermodynamics. Thermodynamic probability and Boltzmann formula about
entropy. Entropy as a measure of disorder. Thermodynamic potentials – definitions and
properties.
3. Basics of non-equilibrium thermodynamics
Free energy and entropy of closed and open systems. Steady states and thermodynamic
equilibrium. Linear nonequilibrium thermodynamics – Onsager relations between fluxes and
driving forces.
4. Thermodynamics of living systems
Living organisms as open thermodynamic systems. Basic applications of thermodynamics to living
systems. Thermodynamic restrictions on life processes. Limits of the thermodynamic approach.
5. Bioenergetics
Energy sources and transformations in living systems. Chemiosmotic mechanism.
Electrochemical gradient. Proton pump and ATP-synthase. Efficiency of the energy transfer from
glucose to ATP. Bioenergetics and evolution.
6. Thermodynamics of biopolymers
Temperature stability and denaturation of proteins. Conformational unfolding transition
"globule-coil". Protein misfolding. Denaturation and hybridization of nucleic acids. Thermal
injuries.

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1. BASIC CONCEPTS OF THERMODYNAMICS. FIRST LAW OF THERMODYNAMICS
Subject and basic concepts of thermodynamics. First law of thermodynamics. Internal energy,
heat, work.

WHAT IS THERMODYNAMICS?

Thermodynamics is a branch of physics that studies the effects of temperature and the processes of
energy transformation in macroscopic bodies.

Macroscopic bodies, also called thermodynamic systems, are bodies consisting of very large
number of particles (atoms, molecules).
Virtually all objects and substances we encounter in everyday life (e.g., solids, liquids, gases
and light) are macroscopic bodies, which must obey the laws of thermodynamics.
Thermodynamics is a discipline with an exceptionally wide range of applications in
engineering (technical thermodynamics), in chemistry (chemical thermodynamics), and in biology
and medicine (biothermodynamics).
The distinction between macroscopic and microscopic bodies is based on their sizes. A system is
microscopic if it is roughly of atomic dimensions and only contains a small number of atoms or
small molecules (typically below 100). A system is macroscopic, if it is visible with simple eye.
Although there is no precise boundary between microscopic and macroscopic bodies, in the
typical case a macroscopic body contains enormous number of atoms and molecules that may
be represented using the Avogadro’s number NA = 6.022x1023. NA is the number of particles
(atoms, molecules) in 1 mol of a given substance.

EXAMPLES OF ENERGY TRANSFORMATIONS. APPLICATIONS IN EVERYDAY LIFE.

Fuel energy conversion into mechanical work

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Conversion of sunlight and nuclear energy into electricity

Electric motors convert electrical energy into mechanical work. They have numerous
applications

Use of electric energy for cooling and heating

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BASIC CONCEPTS OF THERMODYNAMICS
• Thermodynamic system
• Thermodynamic parameters of a system, or state variables, like volume V, pressure p,
temperature T, that determine the thermodynamic state of a system. There are two kinds of
state variables: extensive, which depend on the size of the system size and increase with
increasing the system size, e.g., volume V, and intensive, which do not depend on the system
size, e.g., temperature T
• Thermodynamic equilibrium
• Temperature T
• Energy Е (internal energy U, heat Q, work W, etc.)
• Entropy S

THERMODYNAMIC SYSTEM
A thermodynamic system is a macroscopic region of finite volume, defined by real or
imaginary boundaries or walls. All space outside the thermodynamic system is known as the
surroundings, or environment, or reservoir.

Thermodynamic system.
A thermodynamic system is characterized by a set of parameters such as volume, pressure,
temperature, concentration, etc. that fully define the state of the system.

TYPES OF THERMODYNAMIC SYSTEMS

Thermodynamic systems are distinguished by the type of exchange between the system and its
environment. Three basic types of thermodynamic systems are the isolated, closed and open
systems.

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Isolated system - no exchange of energy E and matter m (∆E = 0, ∆m = 0)
Closed system - exchange of energy but no exchange of matter (∆E ≠ 0, ∆m = 0)
Open system - exchange of both energy and matter (∆E ≠ 0, ∆m ≠ 0)
The energy E may be in the form of work W or heat Q
Isolated and closed systems are idealizations only valid for short enough times.
Examples: thermos bottle is an isolated system; Earth is a closed system; living organisms are
open systems.

THERMODYNAMIC STATE
The thermodynamic state of a system is fully defined by the values of a suitable set of
experimentally measurable properties of the system known as state variables, or thermodynamic
parameters.
Examples of state variables: volume V, pressure P, temperature T, internal energy U,
enthalpy H, entropy S.

THERMODYNAMIC EQUILIBRIUM
A thermodynamic system is said to be in thermodynamic equilibrium if its parameters do not
change with time and if it is isolated, i.e., there are no macroscopic flows of energy or matter
into or out of the system created by external sources.
Equilibrium states are stable and can exist for indefinitely long times. Such states may be
moved to another state only by external forces from other systems.
Open and closed systems, due to the exchange of energy and/or matter with their
environment, cannot reach a state of thermodynamic equilibrium.
Isolated systems in thermodynamic equilibrium have maximum thermodynamic probability Ω
and maximum entropy S and (Ω = max, S = max).

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In the process of reaching thermodynamic equilibrium heat is transferred from the warmer
object to the cooler object. At thermodynamic equilibrium, T1 = T2 and the heat transfer is zero.

Two systems in equilibrium with a third system are in equilibrium with each other (zeroth law of
thermodynamics). This property provides an operational definition of temperature and serves
as the basis of thermometry (science and methods of temperature measurement).
If systems 1 и 2 are in equilibrium with system 3, then systems 1 и 2 are in equilibrium with each
other as well, although there is no direct contact between them.

TEMPERATURE
Temperature is a most important quantity in thermodynamics. Temperature is an intensive
state variable used to measure the warmth (or coldness) of a body (a thermodynamic system).
A temperature scale typically used in everyday life is in degrees Celsius [oC]. It is defined by
two points – melting of ice at 0 oC and boiling of water at 100 oC, measured at atmospheric
pressure of 1 atm (at sea level).
Thermodynamic temperature, also called absolute temperature, is such that the zero
temperature is the absolute zero at -273.15 oC. It is measured in degrees Kelvin [K], which are
equal to the Celsius degrees.

1K = 1°C T(K) = T(°C)+273.15

ABSOLUTE TEMPERATURE
Reference points of the absolute temperature scale are:

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1) Absolute zero. This is the temperature thought to be the lowest possible temperature, at
which substances possess no thermal energy (all thermal motions of atoms and molecules have
come to a stop), and equal to exactly -273.15 oC and 0 degrees Kelvin.
2) Triple point of water is at a temperature of ≈0.01°C or 273.16 K, and pressure 4.58 mm Hg, at
which all three states of water (liquid, vapour and ice) can coexist in equilibrium.
These two points define the absolute (or thermodynamic) temperature scale.
The SI unit for the absolute temperature is degree Kelvin named after Lord Kelvin (William
Thompson, 1824-1907). It is defined as 1/273.16 of the temperature of triple point of water.

TYPES OF ENERGY – INTERNAL ENERGY U, HEAT Q AND WORK W

Internal energy U is the energy contained by a thermodynamic system. It is equal to the sum of
the energies of all particles in the system, including their kinetic energy, potential energy,
interatomic and intraatomic energy, and so on. Internal energy may be changed in two ways:
1) By heat transfer
2) By doing work on or by the system
Internal energy is an extensive state variable. It only depends on the state that the
thermodynamic system is in, and not on what path the system took to get there.

Heat Q is the amount of energy absorbed or released by the system in a heat transfer process,
e.g., by means of heat conductance, radiation, or convection.
Heat Q is not a state variable – it characterizes the process of heat transfer by which that state is
being reached.

Transfer of heat Q between two bodies which are in contact with each other and have different
temperatures.
Heat Q is the amount of energy transferred from one system to another because of the
temperature difference between the two systems.
Heat capacity C is the amount of thermal energy that must be added to a system to raise its
temperature by 1 degree.

C is an important characteristic of the materials. It depends on the temperature and its values
are specific for each material. Some important examples are given in the Appendix.
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______________________________________________________________________________
APPENDIX
SPECIFIC HEAT CAPACITIES OF SOME MATERIALS.
1) The specific heat capacity of water is 4.186 Joules/(gram.K) = 1 calorie/(gram.K). Water has the
second highest specific heat capacity next to liquid ammonia. That is why water is frequently
used and plays important role in processes of temperature regulation. The high specific heat of
water tends to stabilize ocean temperatures, creating a favorable environment for marine life.
Because of its high specific heat, water that covers about 70% of the surface of Earth is able to
abosrb a lot of heat without a significant rise of its temperature. Thus, it keeps temperature
fluctuations on land and in water as well as seasonal temperature variations within limits that
permit life.
2) At a temperature of 300 K (~27 oC) and pressure of 1 bar, the specific heat capacity of air is
1.007 kJoules/(kg.K). Main components of air which are practically the same throughout the
globe are nitrogen (about 78 volume %) and oxygen (about 21 vol %). Along with them air
contains about 1 vol % of argon and about 0.04 vol % of carbon dioxide. The air of such a
composition is named dry. Its molecular mass is considered to be M = 28.96 g/mol. Air also
contains a variable amount of water vapor, on average around 1% at sea level, and 0.4% over the
entire atmosphere.
3) Table. Specific heats C of metals and other materials.

Substance C Molar C
J/gram K J/mol K
Aluminum 0.9 24.3
Bismuth 0.123 25.7
Copper 0.386 24.5
Brass 0.38 ...
Gold 0.126 25.6
Lead 0.128 26.4
Silver 0.233 24.9
Tungsten 0.134 24.8
Zinc 0.387 25.2
Mercury 0.14 28.3
Alcohol(ethyl) 2.4 111
Water 4.186 75.2
Ice (-10°C) 2.05 36.9
Granite 0.79 ...
Glass 0.84 ..

______________________________________________________________________________

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Thermodynamic work W is the amount of energy transferred to a system as a result of forces
acting upon the system, causing displacement of the system or parts of it.
An example of thermodynamic work is the pressure-volume work. For a reversible process in a
closed system it is described by the relation:

∆W = P(V1 − V2 ) = P∆V
or, in differential form: dW = PdV
The relation about the pressure-volume work is easily derived from the
standard relation mechanical work W = force F x distance r:

W = Fr = PSr, where P is pressure and S is area to which the pressure P is applied

In differential form:

δW = Fdr = (PS)dr = P(Sdr) = PdV

Thus we obtain
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δW = PdV and the overall work W is obtained by integrating W = ∫1 𝑃𝑃𝑃𝑃𝑃𝑃

LAWS OF THERMODYNAMICS
Basic Laws:
• First Law: The total energy of an isolated system is conserved.
• Second Law: The total entropy of an isolated system never decreases; all processes tend
to increase the entropy over time
Auxiliary laws:
• Zeroth Law: if two systems are in thermal equilibrium with a third system, then they must
be in equilibrium with each other.
• Third Law: The total entropy of a perfect crystal at zero absolute temperature (0 degrees
Kelvin) is zero.
FIRST LAW OF THERMODYNAMICS
The law of energy conservation states:
Energy in nature may neither be created, nor destroyed. It only passes from one form to another,
or from one body to another, so that the sums of all the energies in the system (kinetic,
potential, heat, etc.) is a constant. When applied to a thermodynamic system, the law of energy
conservation is called First Law of thermodynamics:
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A thermodynamic system can only change its internal energy as a result of performing work or by
way of heat exchange with the environment (provided there is no exchange of matter with the
environment).
The first law of thermodynamics is expressed by the equation:

dU = δQ – δW
dU is the change in internal energy of the system
dQ is the amount of heat added to the system
dW is the work performed by the system (therefore the "minus" sign)
The first law of thermodynamics states that energy can neither be created, nor destroyed, but it
can be transferred across the system boundaries by means of processes involving heat transfer
dQ or work done dW.
The heat dQ and work dW transferred across system boundaries depend not only on the system
state, but also on the process of heat exchange or doing work, respectively. For this reason dQ
and dW are not state variables, or state functions. However, their difference dU termed internal
energy does not depend on the specific path between different states and it is a function of the
system state only.
A thermodynamic system can be driven from state 1 into state 2 along
different pathways with different values of dQ and dW but the change of
internal energy dU will always be the same

dU = dQred - dWred = dQblue - dWblue

dQ and dW are not state variables. They depend on the pathway that
the system moves from state 1 to state 2 and characterize the processes
of heat exchange and doing work along the pathway. They are "transfer"
variables.

First Law of Thermodynamics in Isolated Systems

dU = δQ – δW
In an isolated system dQ = dW = 0, therefore, according to the first law, also dU = 0. It is thus
clear that the internal energy U of an isolated system is constant:
U = const

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2. ENTROPY AND SECOND LAW OF THERMODYNAMICS. ТHERMODYNAMIC POTENTIALS
Second law of thermodynamics. Thermodynamic probability and Boltzmann formula about
entropy. Entropy as a measure of disorder. Thermodynamic potentials – definitions and
properties.

SECOND LAW OF THERMODYNAMICS

The entropy S of an isolated system never decreases, it can only increase or remain constant in
the state of thermodynamic equilibrium. All processes tend to increase the entropy over time
(∆S ≥ 0). At equilibrium S = max.
What is entropy? Entropy is a very important quantity, which is central to thermodynamics.
There are two definitions of entropy:
1. Microscopic definition based on the concept of thermodynamic probability Ω
(Boltzmann 1875).
2. Macroscopic definition (Clausius 1865)
Thermodynamic probability Ω is the number of microstates which result in the same macrostate
of the system. It is a measure of the system disorder (randomness).
Microstate is defined by the spatial coordinates and velocities of all the atoms that make up the
system.
Macrostate (also called thermodynamic state) is uniquely defined by the thermodynamic
parameters which describe the system, such as T, p, V, c, U
The same macrostate is realized by a gigantic number of different microstates

THE BOLTZMANN DEFINITION OF ENTROPY

According to the concept developed by Boltzmann around 1875, the

entropy S of a system is equal to the natarual logarithm of the
thermodynamic probability Ω, multiplied by a constant k

S = k ln Ω
S - entropy
k - Boltzmann constant (1.38x10-23 J.K-1)
Ω - thermodynamic probability is the number of microstates of equal

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energy that result in the same state of the thermodynamic system (macrostate) defined by the
same thermodynamic parameters.
The Boltzmann formula provides the statistical explanation why entropy increases in isolated
systems (second law of thermodynamics). Isolated systems move spontaneously from states of
lower probability to states of higher probability, i.e., Ω → max and S → max. At equilibrium, Ω
= max, respectively, S = max.

Example. Macrostate and microstates for a system of 6 particles distributed in 2 groups/2

boxes

Particles are distinguishable microscopically, but not distinguishable from macroscopic

viewpoint. Their possible arrangements (microstates) are Ω = 6!/n!(6-n)! and the most probable
state of this system is the last state in the figure with highest Ω = 20.

ENTROPY AND DISORDER

Disorder and entropy are closely related.

Let’s consider gas expansion. If we open the small box, the gas will spontaneously expand and
will occupy the big box. Why the gas will not spontaneously get back into the small box?

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Greater entropy means higher disorder.

Standard molar entropy So of water H2O in its three different phases, J/(mol.K):
ice 44.3, liquid 69.9, vapor 188.7.

ENTROPY
Entropy S is an extensive state variable associated with the second law of thermodynamics.
Entropy is a thermodynamic parameter which determines the direction of the thermodynamic
processes and shows how close a system has come to equilibrium. In fact, it is the only physical
quantity in classical physics that is associated with a particular direction of time (time arrow).
For an equilibrium state with given internal energy, the entropy S is greater than that of any
other non-equilibrium state with the same energy (S = max).
There are two definitions of entropy S giving identical results:
1) Microscopic definition based on statistical mechanics definition, developed by Ludwig
Boltzmann in 1875.
2) Macroscopic definition based on classical thermodynamics, developed by Rudolf
Clausius in the 1850s.
According to the macroscopic (thermodynamic) definition, the entropy change dS in reversible
processes is defined as the ratio of the heat exchange dQ to the absolute temperature T

dS = δQ/T → δQ = TdS
For irreversible processes, the above equality is replaced by the following inequality

dS > δQ/T
Here dS = dSex + dSint where dSex denotes the entropy exchange between the system and its
environment, and the second term dSint denotes the internal entropy production For reversible
processes dSint = 0, while for irreversible processes dSint > 0, according to the second law of
thermodynamics

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SECOND LAW OF THERMODYNAMICS
The second law of thermodynamics states that the entropy of an isolated system can only
increase until the system reaches its equilibrium state. In equilibrium, the entropy of isolated
systems is at maximum and constant (S = max).
There are various alternative formulations of the second law:
- Heat cannot spontaneously move from a cold to a warm body. It always moves in the
opposite direction – from warm to cold bodies.
- All irreversible processes in isolated systems result in entropy increase (∆S ≥ 0).

ΔS = ΔS(sys) + ΔS(sur) ≥ 0

CONVERSION OF HEAT INTO WORK

A most important outcome of the second law is that heat cannot be fully converted into work
thus setting a theoretical limit on the efficiency of heat engines that cannot be exceeded by any
design.
A heat engine is a system that performs conversion of heat to mechanical energy which can then
be used to do mechanical work.
Derivation of Carnot’s formula about the efficiency coefficient η:

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The theoretically most efficient heat engine was proposed by Sadi Carnot in 1824. It is based on
the Carnot cycle and its maximum efficiency is given by the relation

η = W/QH = 1 – TC/TH Carnot’s formula about η

Numerical example:

For TH = 373.15K = 100°C

and TC = 273.15K = 0°C
η = 0.27 = 27%

THIRD LAW OF THERMODYNAMICS

The third law of thermodynamics (Nernst theorem) provides an absolute reference point for
entropy. The third law states:

The entropy of a perfect crystal at 0 K is zero

More precisely, the third law states that the entropy of all perfect crystals at absolute 0 is the
same, so we might as well call it zero. In other words, systems have no thermal energy at 0 K.
The Third law makes the following sense from molecular point of view and the Boltzmann's
formula for entropy:

S = k ln Ω
A perfect crystal at 0 K has only one possible arrangement of atoms, i.e., there is only possible
microstate at 0 K.

For Ω = 1, ln Ω = 0
Therefore the entropy S = 0 at T = 0 K

THERMODYNAMIC POTENTIALS
According to the first law of thermodynamics, the internal energy in differential form dU is given by:
= d Q − dW
dU (First law)

where the heat transfer is d Q = TdS and the thermodynamic work is d W = PdV

We thus obtain the following relation about the internal energy U of the system in differential form:

dU = TdS – pdV
This equation defines the internal energy U as a function of the independent variables S and V.
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U = U(S,V)
U is a thermodynamic potential that describes the state of the system at constant S and V. The
problem with it is that the pair of independent variables S and V is rather inconvenient because
entropy is hard to measure or control. We want to have functions representing the state of the
systems with independent variables that are easier to control, such as T and V, or T and p.
The thermodynamic potentials are functions used to represent the thermodynamic state of a
system. Four most common thermodynamic potentials are:
U(S,V) = F + TS – internal energy

H(S,p) = U + pV – enthalpy (heat content of a body)

F(T,V) = U – TS – Helmholtz’s free energy

G(T,p) = U+pV-TS = H –TS – Gibbs free energy

Each of the thermodynamic potentials is a function of two independent state variables from the
following four: p, V, T, S (only one variable from the pairs p, V and T, S). Note that F(T,V) and
G(T,p) are functions of pairs of variables that are easy to measure (T,V and T,p, respectively).
That explains their wide use in thermodynamic descriptions of various systems.

"FREE" AND "BOUND" ENERGIES

THERMODYNAMIC POTENTIALS

Thermodynamic potentials: internal energy U, enthalpy H, Helmholtz’s free energy F and Gibbs’
free energy G

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For irreversible processes:

dU < TdS – pdV, if dS = dV = 0, then dU < 0

dH < TdS + Vdp, if dS = dp = 0, then dH < 0

dF < – SdT – pdV, if dT = dV = 0, then dF < 0

dG < – SdT + Vdp, if dT = dp = 0, then dG < 0

In irreversible processes, the thermodynamic potentials decrease (when their independent

variables stay constant).

EQUILIBRIUM CRITERIA
All processes in nature taking place spontaneously lead to a decrease of the thermodynamic
potentials (when their independent variables stay constant) and to increase of the entropy. The
processes continue until a state of thermodynamic equilibrium is reached. In the latter state, the
thermodynamic potentials reach their minimum values, and the entropy is maximal.
During a process: U,H,F,G ↓ , while S ↑
At equilibrium: U,H,F,G = min, S = max

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 _______________________________________________________________________________

APPENDIX.
HISTORY OF THERMODYNAMICS
Thermodynamics has its origins in the 18th century in the studies of engines, in particular, steam
engines. Most of the progress in the development of thermodynamics has been achieved in 19th century.
• Sadi Carnot developed a theory (Carnot cycle) to describe the efficiency of heat engines
(1822-1824)
• The term thermodynamics was introduced by Lord Kelvin in 1849
• Rudolf Clausius introduced the term entropy in 1860
• Ludwig Boltzmann developed a statistical description of entropy in 1875
• J. Willard Gibbs (1839-1903) made big contributions to the development of statistical
thermodynamics

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GIBBS FREE ENERGY

G(p,T) = H – TS = U + pV – TS

The Gibbs free energy G(p,T) is a most important and widely used
thermodynamic potentials for the characterization of thermodynamic
systems

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3. BASICS OF NON-EQUILIBRIUM THERMODYNAMICS
Free energy and entropy of closed and open systems. Steady states and thermodynamic
equilibrium. Linear non-equilibrium thermodynamics – Onsager relations between driving forces
and fluxes.

Applying thermodynamic considerations to open biological systems requires an extension

towards explanations of irreversible processes, i.e., towards non-equilibrium thermodynamics.
This extension is made in two steps: Firstly, only small deviations away from the equilibrium are
considered. In this case, linear relations between forces and rates can be assumed. In contrast to
these linear approaches, the thermodynamics of nonlinear processes is applied to systems far
from equilibrium. In this case, so-called dissipative structures appear, which are stationary states
with completely new qualities. It seems important to emphasize that although the far-from-
equilibrium condition of an organism represents an absolute precondition of life, nevertheless
there exist many subsystems, which can be properly calculated using equilibrium
thermodynamics, or thermodynamics of linear approaches. This means that biophysics must
encompass the whole scale of thermodynamic approaches.

EQUILIBRIUM AND NON-EQUILIBRIUM THERMODYNAMICS

The distinction between equilibrium and non-equilibrium thermodynamics is based on whether

the thermodynamic systems studied are in a state of thermal equilibrium or not.

Equilibrium thermodynamics deals with systems that are in a state of thermal equilibrium. It is
engaged with studies of reversible processes, in which the systems undergo transitions from one
equilibrium state to another.

Non-equilibrium thermodynamics deals with systems that are not in a state of thermal
equilibrium. It is engaged with studies on time-dependent, finite-rate irreversible processes
between the different states.

Many systems found in nature, most notably, the living systems are not in a state of
thermodynamic equilibrium.

REVERSIBLE AND IRREVERSIBLE PROCESSES

A reversible process is a process in which the system and environment can be restored to
exactly the same initial states that they were in before the process occurred, if we go backward
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along the path of the process. The necessary condition for a reversible process is therefore the
quasi-static requirement. Note that it is quite easy to restore a system to its original state; the
hard part is to have its environment restored to its original state at the same time. For example,
in the example of an ideal gas expanding into vacuum to twice its original volume, we can easily
push it back with a piston and restore its temperature and pressure by removing some heat from
the gas. The problem is that we cannot do it without changing something in its surroundings,
such as dumping some heat there.

Examples of irreversible processes:

1) Heat transfer

2) Gas expansion

These processes are spontaneous.

Example of a reversible process:

Gas expansion

Reversible process is a process that proceeds along a pathway of equilibrium states only. It can
proceed backwards (in the opposite direction) along the same sequence of equilibrium states in
reversed order, so that the exchange between system and environment has same values with

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opposite sign. In a reversible process, the system undergoes transitions at infinitely small rate
from one equilibrium state to another. In principle, the reversible processes are infinitely slow.

Reversible processes do not really exist but they are a very useful idealization that allows to
describe thermodynamic systems in a much more simple way by using the equilibrium
thermodynamics.

Irreversible processes are processes that do not fulfill the above criteria. They proceed along
pathways of irreversible states and they cannot be reverted in order to proceed in the opposite
direction. All spontaneous processes are irreversible and virtually all real processes in nature are
irreversible.

REVERSIBLE AND IRREVERSIBLE PROCESSES IN THE DIFFERENT THERMODYNAMIC SYSTEMS

The isolated systems in state of thermodynamic equilibrium are described by equilibrium

thermodynamics.
There are two types of processes of energy and matter transfer across the boundaries of closed
and open systems – reversible and irreversible processes.
Systems displaying reversible processes are described by equilibrium thermodynamics and
systems with irreversible processes are described by non-equilibrium thermodynamics.

THERMODYNAMICS OF SYSTEMS WITH VARIABLE NUMBER OF PARTICLES

If the number of particles and/or composition of the system changes during a process, then two
independent variables are not sufficient to describe the state of the system. Chemical reactions
or exchange of matter with surroundings can lead to changes in the amount of the species
comprising the system (number of particles of the different species, N1, N2,…, Nk).

The internal energy U, as well as all the other thermodynamic potentials enthalpy H, Helmholtz
free energy F and Gibbs free energy G are extensive variables. They depend on the system size.

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G (T , p ) G (T , p, N1 , N 2 ...N k )
In open systems, besides parameters such as p, V , T, S, they will also depend on the particle
numbers N1, N2,…, Nk.

in closed systems in open systems

INTERNAL ENERGY OF OPEN AND CLOSED SYSTEMS

For a closed system, the first law of thermodynamics states:

dU = δQ – δW

In an isolated system dQ = dW = 0, therefore, according to the first law dU = 0. It is thus clear

that the internal energy U of an isolated system is constant:

U = const.

For open systems, which exchange both energy and matter with the environment, the first law
takes the form:

dU = δQ – δW + δUm

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Here dUm = dUin - dUout accounts the contribution to the energy of the system due to
substance flows in and out of the system.

In closed systems:

dU = δQ – δW = TdS – pdV

In open systems:

dU = δQ – δW + δEm = TdS – pdV + µdN

µ is chemical potential (energy per 1 particle). At dS=dV=0

µ = dU/dN

For a system with k species, U is a function of S, V and Ni, i=1,…k:

GIBBS FREE ENERGY

G(p,T) = U +pV – TS

Because it is in pressure p and temperature T variables, which are constant in many processes
(for example, in living systems), the Gibbs free energy G(p,T) is a convenient and likely the most
frequently used thermodynamic potential for characterization of thermodynamic systems.

In differential form

dG(p,T) = dU + pdV +Vdp – TdS - SdT

substituting here the expression for dU, we obtain

This is the basic equation of chemical thermodynamics for systems with variable particle number,
containing k components with Ni particles of component i.

In the same way, formulas for the chemical potentials in the respective variables can be obtained
for the other thermodynamic potentials F(T,V), H(S,p), U(S,V).

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For the last two potentials, these formulas have limited application due to the need to keep
entropy constant (S=const) that can be only achieved in perfectly isolated systems.
k
dG = − SdT + Vdp + ∑ µi dN i
i =1

Here, the chemical potential of component i is given by

∂G
µi = ( ) T , p , N j ≠i
∂N i

For open systems with variable particle number, the chemical potential µi shows how much the
energy of the systems changes upon a change of the number of particles of type i.

At constant pressure p and temperature T , i.e., dT = dp = 0, the expression for dG reduces to

k
dG = ∑ µi dN i = µ1dN1 + µ 2 dN 2 + ...
i =1

In equilibrium, the free energy G is minimum, G = min, i.e., dG = 0 and the sum of the chemical
potentials µi, multiplied by the particle numbers Ni for the respective components, is also equal
to zero (at constant pressure p and temperature T).

dG = µ1dN1 + µ 2 dN 2 + ... = 0

CHEMICAL POTENTIAL

Expression for the chemical potential

µi = µi0 + kT ln(Ni/N) = µi0 + kT ln ci

Here µi0 is the standard chemical potential that depends on the nature of the respective
material; k is Boltzmann's constant; T is absolute temperature; Ni and N are particle
concentrations.

Expression for the electrochemical potential

For systems with charged particles in electric field, their electrical energy zϕ also needs to be
taken into account

µi = µi0 + kT ln ci + zϕ

25
Here z is the particle (ion) charge; ϕ is electric potential

ENTROPY OF OPEN AND CLOSED SYSTEMS

In reversible processes, the entropy change is defined as

dS = δQ/T

It follows directly from the entropy definition that the sign of entropy change dS in reversible
processes may be either positive or negative, depending on whether these systems are being
heated (dQ > 0) or cooled (dQ < 0). If dQ > 0, entropy will increase (dS > 0) , if dQ < 0, entropy
will decrease (dS < 0).

The equation of entropy balance plays central role in the thermodynamics of open and closed
systems:

dS = dSint + dSex

This equation reflects the circumstance that the entropy of a system may change with time due
to two processes – internal and external. The internal process is the entropy production dSint
resulting from irreversible processes in the system, and the external is the entropy exchange
between system and environment dSex . According to the second law, dSint >0, while dSex may
have either positive or negative sign. This means that the entropy of a non-equilibrium system
may increase or decrease depending on its interactions with the surrounding medium.

ENTROPY OF SYSTEMS IN STEADY STATE

By definition, thermodynamic systems in steady state have constant entropy S = const.

dS = dSint + dSex = 0

dSint = -dSex

According to the second law, the production of entropy inside the system is always a positive
quantity, dSint > 0. Consequently, the exchange of entropy with the environment is always with
negative sign dSex = - dSint < 0.

We reach the following conclusion:

The entropy produced by a thermodynamic system in steady state is entirely transferred to the
surrounding medium.
26
Using time derivatives, the entropy change of а system in steady state with S = const may be
represented as

This equation shows that the rate of entropy production σ = dSint/dt > 0 in steady state, resulting
from an irreversible dissipative process taking place in the system, is exactly equal to the rate of
entropy outflow from the system to its surroundings dSex/dt < 0.

STEADY STATES IN NON-EQUILIBRIUM SYSTEMS

Definition:

A non-equilibrium thermodynamic system is said to be in steady (stationary) state, when the

quantities describing the state of this system do not change with time (U = const, S = const, p =
const, V = const, etc.)

The steady state is maintained by energy and/or matter fluxes between the system and its
environment.

COMPARISON OF EQUILIBRIUM AND STEADY STATES

Distinctions between equilibrium and steady states

27
HEAT TRANSFER IN STEADY STATE

The heat transfer ∆Q from the warmer object to the cooler object is proportional to the
temperature difference ∆T = T1 – T2 and their relation is desribed with a linear dependence:

ΔQ = cΔT

Here ∆T is the driving force and ∆Q is the flux. At ∆T = const ≠ 0 the system is in steady state.
At thermodynamic equilibrium, T1 = T2 and the heat transfer ∆Q becomes equal to zero.

LINEAR NON-EQUILIBRIUM THERMODYNAMICS. DRIVING FORCES AND FLUXES (FLOWS)

Тhе steady states of many thermodynamic processes can be described by an approach called
linear non-equilibrium thermodynamics. In the framework of this approach, the relations
between driving forces and fluxes are linear.

Examples:

Fick's diffusion law JD = -D(dc/dx)

Ohm's electrical conduction law JE = -σ(dϕ/dx)

Heat conductivity (Fourrier's law) JT = -k(dT/dx)

The general linear relation is 𝑱𝑱 = 𝑳𝑳𝑳𝑳, where 𝑱𝑱 is the flux, 𝑿𝑿 is the driving force, 𝑳𝑳 is a
phenomenological coefficient.

Onsager phenomenological relations

In irreversible processes, there are two types of quantities characterizing the process – driving
forces and fluxes. For the process of thermal conductivity such quantities are heat flux Q and the
temperature gradient ∆Т causing the flux. In the case of electrical conductivity, the electrical

28
current I is proportional to the potential difference (voltage) ∆ϕ (Ohm's law). Fick's law is a
linear relation between the flow of the diffusing material and the concentration gradient ∆c.

The gradients ∆Т, ∆ϕ and ∆c that cause the fluxes are known as driving forces and are denoted
as X, The fluxes (flows) are usually designated with the symbol J. In the examples given, the laws
of these irreversible processes reduce to proportionality between flux and the relevant driving
force:

J = L.X

In non-equilibrium systems with several interacting processes, each flux depends not only on its
own driving force but also on the driving forces of the other conjugated processes. This cross-
dependence is given by the Onsager equations (1931).
n
J i = Li1 X 1 + Li 2 X 2 + ... = ∑ Lik X k where i = 1, 2, 3, …, n
k =1

The fluxes Ji are linear functions of the forces Xk; Lik are phenomenological coefficients.

Example: Onsager equations for coupling between processes of heat flow and diffusion.

The coefficients L12 и L21 are called coupling or cross coefficients. They account for the possible
cross-influence between the two processes of heat transfer and diffusion.

For steady states close to equilibrium L12 = L21

Soret effect (thermodiffusion) dc dT

J D = −D + DT
dx dx

For non-equilibrium states that are close to the state of thermodynamic equilibrium, the cross-
coefficients form a symmetrical matrix

Lik = Lki

This equation is called the Onsager reciprocal relation.

The rate of entropy production in a system is called dissipative function.

29
It can be proven that σ is equal to the sum of the JiXi multiples. This function characterizes the
rate of free energy dissipation in the irreversible processes taking place in the system.

Prigogine's theorem

According to Prigogine's theorem, the dissipative function, i.e., the rate of entropy production in
the steady state of a non-equilibrium thermodynamic system at fixed values of the driving forces
is positive and of minimum value:

In other words, the rate of free energy dissipation in steady state is at minimum. The validity of
this theorem is limited to to steady states close to the equilibrium state.

30
4. THERMODYNAMICS OF LIVING SYSTEMS
Living organisms as open thermodynamic systems. Basic applications of thermodynamics to living
systems. Thermodynamic restrictions on life processes. Limits of the thermodynamic approach.

VALIDITY OF THERMODYNAMICS IN LIVING SYSTEMS

The long-standing question about the validity of thermodynamic laws in living systems has been the
subject of numerous discussions in the past.

According to the contemporary views, the laws of thermodynamics are certainly valid but not sufficient to
explain all the properties of the living systems.

There are no special thermodynamic laws specific for living systems.

LIVING SYSTEMS AS OPEN THERMODYNAMIC SYSTEMS

By contrast with isolated thermodynamic systems, which are in a thermodynamic equilibrium state with
maximum entropy (S = max), the living systems are open thermodynamic systems.

They exchange both energy and matter with their surroundings. As in any other open system, the entropy
ΔS that living systems exchange with the surrounding medium may either be positive or negative
depending on the direction of energy and heat exchange between the living organism and the
surrounding medium.

∆Q
∆Sex = If ΔQ > 0, entropy will increase ΔSex > 0; If ΔQ < 0, entropy will decrease ΔSex < 0
T

As open non-equilibrium thermodynamic systems, the living systems generally obey the laws of non-
equilibrium thermodynamics and in cases where their state is close to equilibrium, they also obey the
laws of equilibrium thermodynamics.
• If left alone (in isolation), systems, including the living systems, tend to proceed toward disorder,
in the same way as any other isolated thermodynamic systems. This is an entropy increase effect
directly resulting from the second law of thermodynamics.

31
 • Higher degree of order in the living systems can only be achieved with expense of energy coming
from the environment.
• Living organisms must use energy from external sources (the Sun and other sources) to
counteract the entropy increase, create low-entropy conditions and maintain their functions and
a more ordered state.
An important characteristic of the living systems from the viewpoint of thermodynamics is that all
processes in them (chemical reactions, transport of substances, transcription of genetic information,
sensory processes, signalization, cellular division, energy transformation and many other) proceed at
virtually constant temperature T = const.
This means that the living organisms are not heat engines that are in contact with a hot and a cold
reservoir, but they work rather as chemical machines, which use rich in energy chemical compounds to
support their state and life functions.

Typically, the processes In living organisms take place in condensed media (liquids and solids).These
media have low compressibility and reside at constant pressure and temperature, therefore

dT ≈ 0, dV ≈ 0, dp ≈ 0

Under these conditions, the free energies of Helmholtz F(T,V) and Gibbs G(T,p) are approximately equal
and, respectively, equally applicable for solving of biological problems.

dF ≈ dG

The thermodynamic potentials F and G have numerous applications to living systems (conversion and
utilization of energy, energetics of biochemical reactions, stability and denaturation of biological
macromolecules, phase transitions in biological membranes, etc.)

STEADY STATE OF LIVING ORGANISMS

A large number of internal, self-regulating processes taking place in living organisms support these
organisms in states which essentially are steady states from thermodynamic point of view. All parameters
in steady state are constant (T = const, p = const, V = const, S = const, etc.).

An alternative term that is frequently used for description of such states is homeostasis. It referes to the
ability of the systems, both open and closed, to regulate their internal state in a way as to support the
living organism in stable, not changing with time state (Claude Bernard, 1865).

Example: An astronaut in a space shuttle, which is well isolated and exchanges no

energy and matter with the outside cosmic space. The second law states

32
dS = dS1 + dS2 > 0

where dS1 and dS2 are the changes in the entropy of the astronaut (1) and the shuttle (2).

The astronaut is in steady state where S = const and dS1 = 0

dS1 = dS1int +dS1ext =0

As long as dS1int > 0, then dS1ext < 0

The change of the shuttle entropy is:

dS2 = dS2int + dS2ext

Here dS2int = 0 and dS2ext = - dS1ext > 0

It follows that the entropy dS2 of the shuttle increases

dS2 > 0

Conclusion

Living organisms only support their steady state at the expense of an increase of the entropy of the
surrounding medium.

APPLICATIONS OF THERMODYNAMICS TO LIVING SYSTEMS

Thermodynamics has several extremely important applications for description of the processes taking
place in living systems:

1. Processes of energy transformation and energetics of biochemical reactions (bioenergetics).

2. Transport processes of substances (membrane transport).

3. Electrical potentials (membrane potentials).

4. Thermodynamics of biopolymers (proteins, nucleic acids).

5. Thermodynamics and phase transformations in biomembranes.

THERMODYNAMIC RESTRICTIONS ON THE PROCESSES IN LIVING SYSTEMS

∆S = ∆Sint ernal + ∆Sexchange Equation of entropy balance

33
 1. The second law of thermodynamics requires the entropy production during any non-equilibrium
processes taking place in living systems to always be a positive quantity ∆Sinternal > 0.

2. . In order to prevent disordering and to be able to maintain their functional state, living organisms
need energy inflow from the surrounding medium. The energy inflow should be big enough, as to ensure
that the processes running in the system result in an entropy outflow, which will compensate the entropy
produced by the system, ∆Sexchange ∼ - ∆Sinternal.

3. In that case the overall entropy of the living organism will stay approximately constant

∆S = ∆Sint ernal + ∆Sexchange  0 ⇒ S  const

The living organisms are heterogeneous, non-equilibrium open systems capable of self-organization, self-
regulation and reproduction. They come into being and grow in irreversible processes of individual and
evolutionary development as a result of consumption of free energy from the surrounding medium. Their
death and decay are accompanied by the establishment of thermodynamic equilibrium in the system and
the surrounding medium.

While the laws of thermodynamics cannot be broken in the processes taking place in living systems, these
laws only explain particular features in the functioning of the living systems, but they cannot predict and
explain phenomena such as the origin and development of life on Earth in its entirety.

PROCESSES IN LIVING SYSTEMS NOT RELATED TO THERMODYNAMICS

1. Origin of life and evolution of living systems

2. Individual development of the living organisms (development according to a program recorded in

the inherited genetic information)

3. Reproduction of living organisms

The listed above processes, which are specific of the living organisms, do not violate the laws of
thermodynamics (same as they do not violate any other laws of physics), but these laws are not sufficient
to predict and explain these processes.

Well known scientists believe that the appearance of life and highly organized living organisms on Earth is
an event of extremely low probability from the point of view of the laws of statistical physics and
thermodynamics.

Nobel Prize laureate (1977) Ilya Prigogine has noted:

"The probability that at ordinary temperatures a macroscopic number of molecules is assembled to give
rise to the highly ordered structures and to the coordinated functions characterizing living organisms is

34
vanishingly small. The idea of spontaneous genesis of life in its present form is therefore highly
improbable, even on the scale of billions of years during which prebiotic evolution occurred."

Formation of proteins and nucleic acids

It is widely agreed that both proteins and nucleic acids are essential, indispensable components of every
living cell and living organism today. Both types of biopolymers are much more information rich than the
monomers from which they form. Yet they are only produced by living cells. No processes are known in
nature that can lead to their abiotic formation in non-living nature and to the coupling of DNA synthesis
with the protein synthesis (transcription of genetic information). This is one of the still unsolved mysteries
in the studiеs of the origin of life on Earth.

Living systems as dissipative structures

The dissipative systems are open thermodynamic systems typified by processes, which are running, as a
rule, well away from the state of thermal equilibrium and which are supported by the exchange of energy
and matter with their environment. In these respects, they resemble living systems.

Ordered structures may arise in dissipative systems from completely chaotic initial states and this has
given rise to the hope that the dissipative systems may serve as a model for spontaneous formation of
biological systems.

Whether this hope is justified remains to be shown by future studies. The present level of research in this
field gives no grounds for conclusions in this respect.

35
5. BIOENERGETICS
Energy sources and transformations in living systems. Chemiosmotic mechanism.
Electrochemical gradient. Proton pump and ATP-synthase. Efficiency of the energy transfer from
glucose to ATP. Bioenergetics and evolution.

ENERGY TRANSFORMATIONS IN LIVING SYSTEMS

Bioenergetics is concerned with the processes of energy transformation in living systems, as well as with
the energetics of biochemical reactions (formation and breaking of chemical bonds in the biological
molecules).

If left alone (in isolation), living systems will proceed toward disorder and randomness similarly to any
other isolated thermodynamic systems. Their progress from order to disorder, tantamount to entropy
increase, directly follows from the second law of thermodynamics.

The living systems maintain a higher degree of order and counteract the tendency to disordering by
means of consumption and utilization of energy from the surrounding medium. Energy must be used to
support the higher degree of order and the functioning of the living organisms.

Living organisms need inflow of energy to maintain their structure and functions

ENERGY SOURCE OF LIVING SYSTEMS

Living organisms use energy from the Sun to support life processes and maintain their ordered functional
state.

On annual basis, approximately 5.7 x 1024 joules of solar energy are irradiated to the Earth. Part of this
energy is reflected back into space and the total solar energy absorbed by Earth's atmosphere, oceans

36
and land masses is estimated to be approximately 3.85 x 1024 joules per year. This energy gives rise to
various processes on Earth such as atmosphere circulation and ocean currents. In addition, the inflow of
Sun energy creates suitable conditions for maintenance of life in the biosphere.

Sun radiation is the major energy source of living systems

Photosynthesis captures approximately 3 x 1021 joules of solar energy per year. This energy is used for
biomass production and to support the functioning of the living organisms. This energy is about 1/1000
(0.1 %) of the total Sun energy absorbed by the Earth.

For comparison, the electrical energy produced by humans is ~3 x 1020 joules per year, representing only
~10% of the energy converted during photosynthesis. The energy coming from the Sun is more than 10
000 times greater than the electrical power generation by people. In other words, the energy coming
from the Sun in one hour is more than the energy produced by mankind in one year.

The Earth biosphere absorbs energy from a high-temperature source (TSun = ~5800 K) and dissipates part
of that energy into the surrounding medium, which resides at much lower temperature Tм = ~300 K (the
temperature of Universe is TU = ~3 K).

The energy of the Sun is utilized by the plants in a process termed photosynthesis. In the latter process,
the chlorophyll molecules absorb photons in the red part of the visible spectrum with wavelengths λ=680
nm and λ=700 nm for Photosystems I и II, respectively, corresponding to photon energy of ≈ 2.8x10-19 J.
At least 48 photons are needed for the synthesis of 1 molecule of glucose from carbon dioxide СО2 and
water Н2О, while the necessary for that energy is ≈ 48x10-19 J. This estimate shows that the
photosynthesis efficiency is about 35%.

Plants absorb light from the Sun and transform the light energy in a process called photosynthesis into
chemical energy stored in various organic compounds (sugars). It is later used via feeding by the animals
and transformed into other forms of energy such as mechanical work and heat.

37
Тhe synthesis of organic compounds in plants requires absorption of carbon dioxide СО2 (source of
carbon) and water Н2О (source of hydrogen) and results in release of oxygen О2 into the atmosphere.
Тhe synthesis of 1 molecule of glucose consumes 6 molecules of СО2, 6 molecules of Н2О and produces 6
molecules of О2.

ENERGY TRANSFORMATIONS IN LIVING SYSTEMS

Energy pathway
Sun light Plants (chloroplasts) Animals (mitochondria)
PLANTS
Sun light → Electron transport chain (thylakoid membranes) → Proton gradient (H+ pump) → Synthesis of
energy-rich compounds (ATP, sugars, fats, etc.) → Metabolism
ANIMALS
Food (chemical energy) → Oxidation → Electron transport chain (mitochondria) → Proton gradient (H+
pump) → Synthesis of energy-rich compounds (ATP, sugars, fats, etc.) → Metabolism

ENERGY TRANSFORMATIONS
Light energy → Electron energy → Proton gradient energy → Chemical energy (ATP, sugars, fats, etc.) →
Metabolism, mechanical work, heat, electrical work, transport, light → Dissipation of heat

38
Adenosine triphosphate (АТP) mw 507.16. А. Chemical structure; B. Molecular model

ATP is a universal chemical energy transporter used by both plants and animals

ATP hydrolysis: ATP + H2O → ADP + Pi ΔG = -30.5 kJ/mol

100-200 g of ATP recycled ~500 times daily (in humans)

ENERGY TRANSFORMATIONS IN LIVING SYSTEMS

An important characteristic of the living organisms from the viewpoint of thermodynamics is that all
processes in them (chemical reactions, transport of substances, transcription of genetic information,
sensory processes, signalization, cellular division, energy transformation and many other) proceed at
virtually constant temperature T = const.
This means that the individual living organisms are not heat engines that are in contact with a hot and a
cold reservoir, but they rather work as chemical machines, which use rich in energy chemical compounds
to support their state and life functions.
Rich in energy compounds, utilized by the living organisms, are the carbohydrates (glucose, sucrose,
starch, glycogen, various other polysaccharides) and the fats (fatty acids, triglycerides and various other
lipids). The energy released during their oxidation is used to synthesize ATP (adenosine triphosphate).

39
CARBOHYDRATE AND FAT METABOLISM
Carbohydrates (glucose, sucrose, starch, various polysaccharides) and fats (fatty acids, triglycerides and
various other lipids) are two large groups of energy-rich organic compounds that play essential role in the
energetics of the living organisms.
Their synthesis is an endergonic (energy absorbing) reaction and their oxidation is an exergonic (energy
releasing) reaction.
Oxidation of one gram of carbohydrate yields about 16 kJ of energy, while the oxidation of one gram of
fats yields approximately 38 kJ of energy.
Carbohydrates and fats are used as an energy depot in the living organisms and their oxidation is a major
source of energy in all metabolical reactions.
In a typical bioenergetic reaction chain, plants synthesize carbohydrates from carbon dioxide and water
by photosynthesis and store the absorbed energy internally, often in the form of starch. Plants are then
consumed by animals and used as fuel in the cellular metabolism.
А most important carbohydrate is glucose, a monosaccharide that is metabolized by nearly all known
organisms. Energy obtained from oxidation of glucose is usually stored temporarily within cells in the
form of ATP.

SYNTHESIS AND OXIDATION OF GLUCOSE

Similarly to other carbohydrates, the synthesis and oxidation of glucose are important reactions in the
energetics of living organisms. Glucose is a highly caloric compound (∆Go = 2870 kJ/mol, or ~16 kJ/g)
Glucose synthesis is an endergonic reaction that absorbs energy to proceed, ∆G > 0. It builds up supplies
of chemical energy contained in the newly synthesized monosaccharide.
Glucose oxidation is an exergonic reaction that releases energy, ∆G < 0, which is used for ATP synthesis
and subsequently in various metabolical processes (muscle work, active transport, electrical potentials,
maintainance of body temperature and others).
The monosaccharide glucose (molecular formula is C6H12O6) is produced by the following overall reaction
hν
6CO2 + 6 H 2O → C6 H12O6 + 6O2

Under standard conditions of 25 oC and one atmosphere pressure, the free energy change of this reaction
is ∆Go = +2870 kJ/mol. To make this non-spontaneous process go, 2870 kJ/mol of energy must be
supplied from elsewhere, typically from light absorbed by the photosynthetic apparatus of plants. The

40
synthesis of glucose may be taken as typical of the production of carbohydrates, as well as other organic
compounds, in plants.
The exergonic reaction of glucose oxidationresults in formation of water, carbon dioxide and release of
energy, used by the living organisms for various purposes:
C6 H12O6 + 6O2 → 6CO2 + 6 H 2O + ∆G0

where ∆G0 = -2870 кJ/mol

Part of the released energy is used for ATP synthesis and another part just dissipates as heat.

If living organisms were heat engines, their efficiency coefficient η of energy transformation in a heat
cycle would have been less than 1%. Indeed, according to the Carnot's theorem η = 1 – Tc/Th, and for
Th – Tc < 1K we obtain η < 0.3%.

C6 H12O6 + 6O2 + 38 ADP ⇒ 38 ATP + 6CO2 + 6 H 2O

The oxidation of 1 molecule glucose results in the synthesis of ~38 ATP molecules. The synthesis of ATP is
endergonic reaction that requires +30.54 kJ/mol, or +1160.5 kJ for 38 mols of ATP. Glucose oxidation is
exergonic reaction that releases energy ∆G0 = -2870 кJ/mol. The efficiency of energy transfer from
glucose to ATP is then 1160.5/2870, or ~40% under standard conditions (25 oC and 1 atmosphere). Under
actual biological conditions, the latter coefficient might be slightly different.

Most of this energy transfer is mediated by the reactions of the Krebs cycle. In primitive organisms that
can only use glycolysis, most of the energy contained in glucose is not available to them and is actually
lost (efficiency coefficient ~2-3%).

Conclusion: The energetic efficiency of the higher organisms is significantly higher than that of more
primitive organisms.

TRANSMEMBRANE PROTON GRADIENT

Cells of eukaryotic organisms contain organelles (mitochondria in animals and chloroplasts in plants) that
are highly specialized energetic "factories" for energy transformation and ATP synthesis. By means of
photosynthesis, chloroplasts transform the light energy of the Sun into chemical energy, while
mitochondria process the chemical energy of animal food.
These organells share a common chemiosmotic mechanism of operation whereby the energy released in
exergonic chemical reactions, e.g., oxidation of carbohydrates and fats, is accumulated as a
transmembrane proton gradient and later used in the endergonic reaction of ATP synthesis. The protons
are moved across the biomembranes by proton pumps. The latter are transmembrane proteins that can

41
actively transport protons across the thylakoid membrane in plants and the inner mitochondrial
membrane in animals.

1. The energy obtained by photosynthesis or from food is used to run the proton pump, a
transmembrane protein which pumps protons (hydrogen H+ ions) across the membrane.
2. The latter process results in the formation of a proton gradient that accumulates the energy, released in
the preceding exergonic reactions, as a difference in the proton electrochemical potentials, ∆µ = µout - µin
3. Protons diffuse back through the ATP-synthase channel whereby their energy is used for ATP synthesis.

Chemiosmotic mechanism
Proposed in 1961 by the British biochemist Peter Mitchell, later awarded with Nobel prize for this
discovery (1978).
Energy released in exergonic reactions is utilized for active transport (pumping) of protons over the
membranes, creating transmembrane proton gradient whose energy is used in the endergonic reaction of
ATP synthesis.
Proton pumping across the membrane and ATP synthesis are carried out by specialized membrane
proteins – proton pump (H+ pump) and ATP-synthase.
exergonic reactions→ proton gradient → ATP synthesis
- No direct connection between exergonic and endergonic chemical reactions
High proton electrochemical gradient Δµ = µout - µin
cout
∆µi kT ln
= + z (ϕout − ϕin )
cin
- The proton gradient creates transmembrane electric potential of 150-200 mV (15-20 kJ/mol) and
transmembrane pH difference of 2.5 – 3.5 pH units (14-20 kJ/mol). The total Δµ of a proton of ∼30-40
kJ/mol is sufficient for the synthesis of 1 molecule ATP (30.5 kJ/mol).
Analogy with hydro-electric power stations.
Is the proton gradient really necessary?
Why nature did not select a direct conjugation of the energy releasing exergonic reactions with the
endergonic reaction of ATP synthesis?

42
Exergonic reactions release energy that does not exactly match the energy necessary to make 1 ATP
molecule. For example, the reaction of CO2 with H2 to produce methane releases enough energy to make
1.5 ATP molecules. Because it is not possible to make 1.5 ATP molecules, the spare energy in a
stoichiometric chemical reaction for ATP synthesis will be lost. Such losses are averted by the
chemiosmotic mechanism because of the intermediary formation and energy accumulation in the proton
gradient.
In the energy transformation chain, the proton gradient intervenes between the exergonic and
endergonic reactions so that all the energy released in the exergonic reactions is transformed into proton
gradient energy.
Structure of the proton pump

The structure of complex I, the largest protein complex involved in respiration in bacteria and
mitochondria, as revealed by X-ray crystallography

The structure (a) suggests the piston mechanism shown (b), whereby shunting the piston drives protons
across the membrane through three separate channels. Efremov, R. G., Baradaran, R., & Sazanov, L. The
architecture of respiratory complex I. Nature 465, 441 (2010) (Web of Science: 400 citations as of
31.03.2019)

BIOENERGETICS AND EVOLUTION

It is clear from the available data about the energy transfer from glucose oxidation to ATP synthesis that
higher organisms have significantly higher efficiency of energy utilization than more primitive organisms
(40% in higher organisms vs. 2-3 % in primitive organisms).

These estimates show that the evolutionary transition from more primitive to higher organisms has also
been accompanied by improvements in their energy transformation mechanisms. Contemporary studies
provide grounds for the concept that a big step in this direction has been realized with the transition
procaryotes → eucaryotes that is believed to have taken place about 2 billion years ago.

43
It is presently believed that eukaryotes have emerged from prokaryotes about 2 billion years ago in a
process called endosymbiosis.

ENDOSYMBIOSIS

Eukaryotes contain highly efficient energy "factories" – mitochondria in animals and chloroplasts in
plants. Consequently, eukaryotes have much more energy at their disposal than prokaryotes.

Eukaryotes have much more energy at their disposal than prokaryotes

What this energy is used for?

1. Bigger cell sizes

2. Much bigger genome

44
 3. Origination of multicellular organisms

In the present time, Earth biosphere is almost entirely occupied by multicellular eukaryotic organisms.
The transition to these more complicated life forms has been made possible by the abrupt increase of the
energy transformation efficiency of the organisms due to the appearance of the intracellular energy
"factories" – mitochondria and chloroplasts as a likely result of endosymbiosis between prokaryotic cells.

45
6. THERMODYNAMICS OF BIOPOLYMERS
Temperature stability and denaturation of proteins. Conformational transition "helix-coil".
Protein misfolding. Denaturation and hybridization of nucleic acids. Thermal injuries of biological
systems.

PROTEIN STABILITY AND DENATURATION

LEVELS OF PROTEIN STRUCTURE
1. PRIMARY STRUCTURE
- the linear sequence of amino acids connected by peptide bonds.
2. SECONDARY STRUCTURE
- areas of folding into α-helices and β-sheets, which are stabilized by hydrogen bonding.
3. TERTIARY STRUCTURE
- the three-dimensional structure of a protein, which results from a large number of non-
covalent interactions and occasional disulfide bridges between amino acids.
4. QUATERNARY STRUCTURE
- non-covalent interactions that bind multiple polypeptides into a single larger protein.

Stabilization by means of hydrogen bonds and disulfide bridges

Tertiary structure of a mouse major urinary protein

By Emw - Own work, CC BY-SA 3.0,

https://commons.wikimedia.org/w/index.php?curid=10617285

46
Beta-Hydroxysteroid Dehydrogenase

PROTEIN STABILITY AND DENATURATION

Native tertiary and quaternary protein structures are typically stable under physiological
conditions but may be disrupted by sufficiently large deviations of parameters such as pH,
temperature, ionic composition away from the physiological conditions. This process is called
protein denaturation.
Protein denaturation involves disruption of both the secondary and tertiary structures.
Denaturation reactions are typically not strong enough to break the peptide bonds and the
primary structure (the sequence of amino acids) remains the same after denaturation. In some
cases, the native protein structure may be restored (renaturation).

Temperature denaturation

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globule → coil transition of lysozyme
Td is temperature and ∆Н enthalpy of the transition (area under the peak).

Chemical denaturation

Urea denaturation
globule – coil transition

Protein denaturation is often not reversible and the native state cannot be restored.

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REVERSIBLE AND IRREVERSIBLE DENATURATION

A major cause leading to irreversibility of denaturation is the formation of aggregates from the
denatured protein molecules, so that the restoration of their original native structure is
practically impossible.

Energetics of protein denaturation and aggregation

PROTEIN MISFOLDING

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Molecular origin of various diseases is associated with protein misfolding into non-functional
structures.

Transition from native into fibrillar amyloid

conformation of the proteins, accompanied by free
energy decrease ∆G<0.

Molecular origin of various diseases is associated

with protein misfolding into non-functional
structures.

Molecular origin of various diseases is associated with protein misfolding into non-functional
structures. Currently, there are over 50 human protein misfolding diseases.

Molecular Mechanisms of Protein Misfolding Diseases

Protein misfolding diseases are defined as disorders of protein metabolism, acquired or

inherited, in which normally stable proteins adopt non-native conformations that display a
tendency to aggregate and to form fibrillar deposits in the intra- or extracellular spaces. Because
these fibrillar amyloid deposits are highly stable, they gradually accumulate, ultimately resulting
in organ dysfunction, failure and death.

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Energy diagram of protein stability and misfolding into non-functional structures

Protein misfolding diseases, also known as proteopathies or proteinopathies refer to a class of

diseases in which certain proteins fail to fold into their native conformation and lose their normal
function. Presently, over 50 such diseases are known, and at least 20 of them are
neurodegenerative disorders.

Risk factors that promote protein misfolding include destabilizing changes in the primary amino
acid sequence of the protein, post-translational modifications (such as hyperphosphorylation),
changes in temperature or pH, an increase in production of a protein, or a decrease in its
clearance. Advancing age is a strong risk factor, as is traumatic brain injury.

“Seeding” of proteinopathies. Some proteins can be induced to misfold and aggregate by

exposure to the same (or similar) protein that has folded into a disease-causing conformation.
This process is called “seeding”. The best known form of such induced proteopathy is prion
disease, which can be transmitted by exposure of a host organism to a prion protein in disease-
causing conformation.

A number of other proteinopathies can be induced by a similar mechanism, including a variety of

amyloidoses, tauopathy, synucleinopathy, the aggregation of superoxide dismutase-1 (SOD1),
polyglutamine, and other.

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Examples of proteinopathies

Chaperones control the folding of newly synthesized proteins and prevent protein misfolding

COLD DENATURATION OF PROTEINS

Proteins may lose their native conformation and denature not only at high temperatures but
also at low temperatures

Cold denaturation is a reversible process and upon reheating to the physiological range proteins
restore their native conformation and functional state.

This unusual phenomenon is related to the explaination to the loss of protein enzymatic activity
at low temperatures (~ 0 – 10 оС).

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A likely (but not the only possible) explanation of the cold denaturation is based on the
circumstance that low temperatures facilitate the unfavorable contacts of the protein non-polar
groups with water creating in this way conditions for unfolding of the protein native structure
upon cooling.

NUCLEIC ACID DENATURATION

At high temperatures, the hydrogen bonds between the two strands are broken and the double
strand separates into two single strands. This process is called DNA denaturation.

Upon subsequent cooling (annealing), the nucleic acid strands realign and bind back
(hybridization).

The separation-hybridization heating-cooling cycle of FNA has been used to develop the
polymerase chain reaction (PCR) method, which is presently widely used in molecular biology to
make multiple copies of a specific DNA segment.

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The melting temperature Tm depends on the DNA length. Shorter chains melt at lower
temperature
MECHANISM OF THERMAL INJURY OF CELLS AND TISSUES
Numerous studies suggest that the mechanism of hyperthermic thermal injury in cells and tissues
is related to the macromolecular conformational transitions in proteins and DNA.
Proteins denature predominantly between 40–80°C. DNA and RNA are also targets of thermal
injury but they are typically damaged at and above 85–90°C.
Thus, protein denaturation appears to be the critical event in cell killing induced by
hyperthermia.
Estimates show that denaturation of about 5-6 % of the cellular proteins is sufficient to cause cell
death.

STERILIZATION AND PASTEURIZATION

Sterilization and pasteurization by heat are widely used methods based on the processes of
thermal injury of microorganisms and biomolecules by elevated temperatures.
Sterilization is any process that kills or deactivates all forms of life and biological agents such as
fungi, bacteria, viruses, prions, spore forms, unicellular eukaryots such as plasmodium, etc.,
which are biological pathogens. Sterilization has numerous applications in medicine.
Methods of sterilization:
1. Heating and incubation at high temperature (~ 120 oC)
2. Radiation (ionizing, non-ionizing)

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 3. Chemical sterilization (ozone, nitrogen dioxide, ethylene oxide)
4. Mechanical sterilization (filtration)
Pasteurization is heat-treatment process that destroys pathogenic microorganisms in certain
foods and beverages.
Invented by Louis Pasteur during the nineteenth century (1864), although known much earlier in
China, Japan and also in Europe. Pasteur discovered that heating beer and wine was enough to
kill most of the bacteria that caused spoilage, preventing these beverages from turning sour.
Eliminating pathogenic microbes and lowering microbial numbers prolonged the quality of the
beverage.
Today, the process of pasteurization is used widely in the dairy and food industries for microbial
control and preservation of the food consumed.
TEMPERATURE TREATMENTS

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