Essential of Thermodynamics

1. Essentials of thermodynamics
Concept of entropy, enthalpy
and Gibb’s free energy
Miss Yusra

2. Introduction to Biophysics and Thermodynamics
• Biophysics as the interdisciplinary field that applies principles
of physics to study biological systems.
• Highlight that thermodynamics provides a powerful framework
to understand the energy transformations and physical
processes within living organisms.
• This exploration is not only intellectually fascinating but also
has profound implications for advancements in medical
research, drug development, and technologies that impact
healthcare.

3. Thermodynamics
• Thermodynamics provides a crucial theoretical framework for
biophysics, offering insights into the energetics of biological
processes.
• By applying thermodynamic principles, we can explain how
energy is transformed and utilized in living organisms.
• It helps us understand the spontaneity of biochemical
reactions and sheds light on crucial processes like protein
folding, ligand binding, and membrane transport.

4. Introduction
• Thermodynamics is a Greek word which means flow of
heat/energy in physical, chemical and biological reactions.
“Thermodynamics is a branch of science which deals with study
of different forms of energy and their interconversions”
• It deals with energy changes in physical and chemical
processes.

6. Laws of Thermodynamics in
Biophysics

7. Laws of Thermodynamics in Biophysics
• Zeroth Law: The concept of thermal equilibrium is crucial in
understanding temperature regulation within living organisms. Cells
and organisms maintain thermal equilibrium to function optimally.
• The zeroth law states that if two systems are each in thermal
equilibrium with a third system, then they are in thermal equilibrium
with each other.
• In biophysics, this law is fundamental for understanding temperature
regulation and thermal equilibrium within biological systems.
• For instance, it helps in understanding how organisms maintain
homeostasis by regulating their internal temperature in response to
external changes.

9. Example:
Three containers (A, B, C) with different temperatures.
• To determine the temperature of container C using the Zeroth Law of Thermodynamics, we
need to compare its temperature with the temperatures of containers A and B.
• The Zeroth Law states that if two systems are in thermal equilibrium with a third system,
then they are in thermal equilibrium with each other.
• Let's denote the temperatures of containers A, B, and C as TA​, TB​, and TC​ respectively.
• First, we need to establish thermal equilibrium between two containers. Let's say we do this
between containers A and C.
• If container A and container C are in thermal equilibrium, then TA​=TC​. Similarly, if container
B and container C are in thermal equilibrium, then TB​=TC​.
• So, by comparing the temperatures of containers A and B with container C, we can
determine the temperature of container C. Once we have the temperatures of A and B, we
can compare them and find the temperature of C.

12. Example
• Lets consider a common example which we use in our day-to-
day life i.e., thermometer having mercury in a tube.
• As the temperature is increased this mercury expands since the
area of the tube is constant.
• Due to this expansion, the height of the mercury label shows
the changes in temperature and basically helps us to measure
it.

13. First law of Thermodynamics

14. First Law of thermodynamics is also known as Law
of Conservation of energy.
• This states that
“ Energy can be neither created nor destroyed. However, energy
can flow from on place to another. The total energy of an
isolated system does not change”.

15. • First Law (Law of Energy Conservation): The conservation of energy is
evident in cellular processes, where the energy obtained from
nutrients is transformed into various forms to support cellular
activities.
• The first law states that energy cannot be created or destroyed in an
isolated system; it can only be transformed from one form to another.
• In biophysics, this law is crucial for understanding energy flow within
biological systems.
• For example, it explains how organisms acquire, transform, and utilize
energy from their surroundings for various physiological processes
such as metabolism, muscle contraction, and nerve signaling.

16. • Mathematically, the First Law of Thermodynamics can be
expressed as:
ΔU=Q−W
Where:
ΔU represents the change in internal energy of the system.
Q represents the heat added to the system.
W represents the work done by the system.
• This equation essentially says that any change in the internal
energy of a system is equal to the heat added to the system
minus the work done by the system.
• It's a statement of energy conservation in thermodynamic
processes.

17. First law of Thermodynamics in Biological systems
• All biological organisms require energy to survive.
• Cells, for example, perform a number of important processes. These
processes require energy.
• In photosynthesis, the energy is supplied by the sun. light energy is
absorbed by cells in plant leaves and converted to chemical energy.
• The chemical energy is stored in the form of glucose, which is used to
form complex carbohydrates necessary to build plant mass.
• The energy stored in glucose can be released through cellular
respiration.
• This process allows plant and animal organisms to access the energy
stored in carbohydrates, lipids and other macromolecules through the
production of ATP.
• This energy is needed to perform cell functions such as DNA replication,
mitosis, meiosis, cell movement, endocytosis, exocytosis and apoptosis.

18. Second law of Thermodynamics

19. • Second Law: Biological systems exhibit an increase in entropy
over time, reflecting the tendency toward disorder. However,
within cells, specific structures and processes are highly
organized despite the overall increase in entropy.
• The second law states that in any spontaneous process, the total
entropy of a closed system (isolated from its surroundings) tends
to increase over time.
• This law is crucial in understanding processes like protein folding,
molecular diffusion, and cellular respiration.
• It helps in predicting the direction of spontaneous processes and
provides insights into the efficiency of biological systems.

20. • Concept of Entropy: In biophysics, entropy (S) can be understood as a
measure of disorder or randomness within biological systems.
Biological systems tend to evolve towards states of higher entropy,
which corresponds to greater disorder or randomness.
• Entropy Change: Consider the change in entropy (ΔS) associated with
a particular biological process. The Second Law of Thermodynamics
states that for any spontaneous process, the total entropy of the
system and its surroundings must increase or remain constant.
• ΔS total​ ≥ 0
• This inequality implies that the entropy of the system (ΔS system​) can
decrease as long as the entropy of the surroundings (ΔS surroundings​)
increases by a greater amount, maintaining a positive overall change
in total entropy.

22. Second law of Thermodynamics in Biological
systems
• As with other biological processes, the transfer of energy is not
100% efficient.
• In photosynthesis, for example, not all of the light energy is
absorbed by the plant. Some energy is reflected and some is lost as
heat. The loss of energy to the surrounding environment results in
an increase of disorder or entropy.
• Unlike plants and photosynthetic organisms (plants, algae, and
some bacteria), animals can not generate energy directly from the
sunlight. They must consume plants or other animal for energy.
• The higher up an organisms is on the food chain, the less available
energy it receives from its food source.

23. • Much of this energy is lost during metabolic
processes performed by the producers and
primary consumers that are eaten.
• Therefore, much less energy is available for
organisms at higher trophic levels.
(Trophic levels are groups that help ecologists
understand the specific role of all living things in
the ecosystem).
• The lower the available energy, the less
number of organisms can be supported.

24. Third law of Thermodynamics

25. • Third Law:
• This law states that the entropy of a
perfect crystal approaches zero as
the temperature approaches
absolute zero.
• While not as directly applicable in
biophysics as the other laws, it has
implications for understanding the
behavior of biological molecules at
low temperatures, such as in
cryobiology studies or the stability of
biomolecules in extreme
environments.

26. • “The temperature of a system approaches absolute zero, its
entropy becomes constant, or the change in entropy is zero”.
• The third law of thermodynamics predicts the properties of a
system and the behaviour of entropy in a unique environment
known as absolute temperature.
• The entropy of a bounded or isolated system becomes
constant as its temperature approaches absolute temperature
(absolute zero).

27. Third law of Thermodynamics in Biological systems
• Living systems require constant energy input to maintain their
highly ordered state. Cells, for example, are highly ordered and
have low entropy.
• In the process of maintaining this order, some energy is lost to
the surroundings or transformed. So while cells are ordered,
the processes performed to maintain that order result in an
increase in entropy in the cell’s / organism’s surroundings.
• The transfer of energy causes entropy in the universe to
increase.

28. Biological Thermodynamics
The study of internal biochemical dynamics as:
ATP hydrolysis, protein stability, DNA binding, membrane
diffusion, enzyme kinetics and other such essential energy
controlled pathways.

29. Applications in Biophysics
• Thermodynamics principles are used to study protein folding,
DNA stability, and enzyme kinetics, which are essential for
understanding cellular processes.
• Energy transfer and conversion mechanisms within cells, such
as ATP synthesis and photosynthesis, are governed by
thermodynamic principles.
• Thermodynamics is also applied in biophysical modeling, drug
design, and understanding the thermodynamics of membrane
transport processes.

30. Thermodynamic Principles
•Thermodynamic principles play a fundamental role in
understanding the behavior of biological systems at the
molecular level.
•One of the key thermodynamic principles applied in
biophysics is the second law of thermodynamics, which
states that in any spontaneous process, the total entropy of
a closed system (isolated from its surroundings) tends to
increase over time.

31. • This principle is particularly relevant in understanding processes such as
protein folding, molecular recognition, and membrane transport in
biological systems.
For example:
• Protein Folding: Proteins are essential molecules in living organisms, and
their function is intricately linked to their three-dimensional structure. The
process of protein folding is governed by thermodynamic principles, where
the protein seeks its most stable conformation, typically characterized by
the lowest Gibbs free energy. Thermodynamics of protein folding helps
elucidate how proteins achieve their native structures and how these
structures may be perturbed under different conditions.

32. • Molecular Recognition: Biological processes often involve molecular
interactions, such as ligand*-receptor binding or enzyme-substrate
interactions.
• Thermodynamics governs the affinity and specificity of these
interactions.
• The binding affinity between molecules is often quantified by the
equilibrium constant, which is related to the change in Gibbs free energy
upon binding.
• Thermodynamic principles help predict and analyze the thermodynamic
driving forces behind molecular recognition events.
• * an ion or molecule which donates a pair of electrons to the central metal atom or ion to form a coordination complex.

33. • Membrane Transport: Biological membranes play a crucial role in
compartmentalization and transport of molecules across cellular
boundaries.
• The processes of passive and active transport across membranes are
governed by thermodynamic principles.
• For instance, the diffusion of molecules down their concentration gradient
(passive transport) follows the principles of entropy and energy
minimization.
• In contrast, active transport processes, such as ion pumps, utilize energy to
transport molecules against their concentration gradients, with
thermodynamics providing insights into the energetic costs and efficiency
of such processes.

34. Enthalpy and Gibbs Free Energy

35. The concept of Enthalpy and Entropy
Introduction:
• In physics, thermodynamics is the study of the effect of heat, energy and
work on the system.
• The term enthalpy was introduced by a Dutch scientist, Heike Kamerlingh
Onnes in 1990.
• The word enthalpy means total heat content.
• Enthalpy tells us how much heat is added or removed from the system.
• The term entropy was introduced by the scientist Rudolf Clausius in 1859.
• This idea comes from the concept that heat always flows from hot to cold
regions.
• Entropy is the measure of disorderness of the system.

36. Enthalpy and Gibbs Free Energy in Biochemical
Reactions:
• Enthalpy as the heat content of a system and its significance in biological reactions.
• Enthalpy (H): The total heat content of a system. In biological reactions, changes in enthalpy provide
insights into the heat absorbed or released.
• Gibbs Free Energy (ΔG): Represents the energy available to do work in a system at constant
temperature and pressure.
• ΔG is a crucial parameter in understanding the spontaneity of biochemical reactions.
• If ΔG is negative, a reaction is spontaneous.
• Gibbs free energy (G) is defined as the maximum amount of work that can be extracted from a
system at constant temperature and pressure.
Mathematically, it is expressed as:
G=H−TS
Where:
• H is the enthalpy (total heat content) of the system.
• T is the temperature in Kelvin.
• S is the entropy (disorder) of the system.

37. • ΔG in Biochemical Reactions: The Gibbs free energy change
(ΔG) determines the spontaneity of biochemical reactions.
• In cellular respiration, for example, the negative ΔG of ATP
hydrolysis provides the energy required for cellular work.

38. Enthalpy
• It is defined as;
“the sum of internal energy of a system and the product of its pressure and
volume”.
• It is denoted by symbol H
• Units used to express- joule
• It deals with the heat contained in any system. Thereby, it changes when
heat enters or leaves the system.
H=U+PV
• H- enthalpy, U- internal energy, P- pressure, V- volume
• Change in enthalpy
ΔH=ΔU+PΔV

39. • When enthalpy change more than zero, energy enters into the
system and the reaction is endothermic.
• When the energy is lost from a system the enthalpy change is
less than zero and the reaction is exothermic.
• The sign of ΔH is negative or positive depends upon the heat is
evolved or absorbed,
When the heat is evolved ΔH –ve
When the heat is absorbed ΔH +ve
• Changed in enthalpy measured calorimetrically.
• As q represents the heat absorbed from the surroundings
medium or heat given up to the medium
• ΔH=q

41. Enthalpy (H)
• Enthalpy represents the total heat content of a system at constant pressure. It includes the
internal energy of the system plus the product of pressure and volume.
• In biological systems, enthalpy changes are crucial for understanding processes such as
protein folding, DNA denaturation, and enzyme catalysis.
• Protein Folding: Enthalpy changes play a significant role in protein folding, where the
formation of hydrogen bonds, van der Waals interactions, and hydrophobic interactions
contribute to changes in enthalpy. Understanding these changes helps in predicting protein
stability and folding kinetics.
• DNA Denaturation: Enthalpy changes are involved in the process of DNA denaturation,
where the double-stranded DNA molecule is converted into single strands due to disruption
of hydrogen bonds. The enthalpy change associated with this process provides insights into
the stability of DNA structures.
• Enzyme Catalysis: Enthalpy changes occur during enzyme-substrate binding and catalysis.
The binding of substrates to enzymes involves enthalpy changes due to the formation of
enzyme-substrate complexes. The enthalpy change associated with catalytic reactions
provides information about the energetics of the reaction and the stability of the transition
state.

43. Standard enthalpy change
• It is the measure of energy released/consumed when one mole of
substance is created under standardized conditions from its pure
elements.
• Symbol ΔH °f
Characteristics of enthalpy
• Enthalpy is an extensive property (depends upon the amount of
substance)
• It is a state function (depends upon the state variables)
• It is a useful and important thermodynamic function
• When a system undergoes physical and chemical change, its enthalpy
also changes
• ΔH=H final – H initial

44. Importance of enthalpy
• Measuring the change in enthalpy allows us to determine
whether the reaction exothermic or endothermic.
• Enthalpy change occurs during a change in the state of matter.
• Change in enthalpy is used to measure heat flow in
calorimetrically.

45. Relationship between ΔH and ΔU
• ΔH and ΔU related by the equation
ΔH = ΔU + PΔV
• For reactions between solids and liquids, ΔV is very small
ΔH = ΔU
• For the reactions involving gases
ΔH = ΔU + PΔV
ΔH = ΔU + P (V2-V1)
ΔH = ΔU + PV2 - PV1)

46. Entropy (ΔS)
• It is quantity introduced to denote the orderliness of a system.
• It is measure of the degree of disorder any system.
• It is designated by the symbol S.
• The SI unit for entropy is joules/kelvin
• In the ice crystals – entropy is minimum.
• In a liquid state – entropy increases.
Change in entropy
• Calculated only for a reversible process.
• It is defined as the ratio of the amount of heat taken up to the absolute
temperature at which the heat absorbed.
• Entropy change (ΔS) = heat absorbed in a reversible process
temperature in Kelvin

47. Total entropy of an isolated system
• It can never decrease
• It must increase in irreversible process
• It remains constant in reversible process
• All physical process occur with an increase in entropy when changes in
both the system and its surroundings increases.
Entropy changes in a closed system
• In a closed system the exchange of energy is possible but not matter,
with the surroundings.
• So, far a closed system as the process moves towards equilibrium, the
entropy of the system plus the surroundings increases.
Free energy
• As the system moves toward equilibrium in a spontaneous process it
loses energy and that can be used to perform work.

48. Entropy at molecular level
• For a given substance, the entropy of the liquid state is greater
than the entropy of the solid.
• Entropy increases when a substance broken up into multiple
parts.
• Entropy increases when a temperature increases.
• Entropy generally increases in reactions in which the total
number of product molecules is greater than the number of
reactant molecules.

49. Difference between enthalpy and entropy
Enthalpy Entropy
Enthalpy is a kind of energy. Entropy is a property.
It is the sum of the internal energy and the
flow of energy
It is the measurement of the randomness
of molecules.
It is denoted by the symbol H It is denoted by the symbol S
It was termed by a scientist named Heike
Kamerlingh Onnes.
It was termed by a scientist named Rudolf
Clausius.
Its unit is Jmol
-1
Its unit is JK
-1
It is applicable to related standard
conditions.
It does not have any limits or conditions.
The system favours minimum
enthalpy<./td>
The system favors maximum entropy.

50. Free energy
• Gibbs realized that for a reaction, a certain amount of energy
goes to an increase in entropy of a system and certain amount
goes to a heat exchange for a reaction.
• Gibbs free energy (G) is a state variable, measured in KJ/mol.

51. • The sign of ΔG indicates the spontaneity of the reaction:
i. A negative ΔG indicates that the reaction is spontaneous and will
proceed without the addition of energy.
ii. A positive ΔG indicates that the reaction is non-spontaneous and will
not proceed without the addition of energy.
• Exergonic reaction: A chemical reaction where the change in the
standard change in free energy is positive, and energy is absorbed.
• Endergonic reaction: A chemical reaction that is available after
accounting for entropy.
• In other words, Gibbs free energy is useable energy or energy that is
available to do work.
• For all spontaneous reaction ΔG is always negative.

53. Spontaneity of forward and reverse reactions
• If a reaction is endergonic in one direction (e.g., converting
products to reactants), then it must be exergonic in the other,
and vice versa. As an example, let’s consider the synthesis and
breakdown of the small molecule adenosine triphosphate
(ATP), which is the "energy currency" of the cell.
• ATP is made from adenosine diphosphate (ADP) and
phosphate (Pi) according to the following equation:

54. • This is an endergonic reaction, with ∆G =+7.3 kcal/mol under
standard conditions (meaning 1M concentrations of all
reactants and products,1atm pressure, 25˚C, and pH of 7.0).
• In the cells of your body, the energy needed to make ATP is
provided by the breakdown of fuel molecules, such as glucose,
or by other reactions that are energy-releasing (exergonic).

55. • The reverse process, the hydrolysis (water-mediated breakdown)
of ATP, is identical but with the reaction flipped backwards:
• ATP+H20 ADP + Pi
• This is an exergonic reaction, and its ∆G is identical in magnitude
and opposite in sign to that of the ATP synthesis reaction (∆G = -7.3
kcal/mol under standard conditions).
• This relationship of same magnitude and opposite signs will always
apply to the forward and backward reactions of a reversible
process.

56. • Spontaneity of Reactions:
• ΔG < 0 (Negative ΔG): A negative ΔG indicates that a reaction is
exergonic and releases free energy.
• In biological systems, exergonic reactions are often associated
with processes that release energy, such as the breakdown of
nutrients like glucose during cellular respiration.
• ΔG > 0 (Positive ΔG): A positive ΔG signifies an endergonic
reaction, requiring an input of energy.
• Examples in biology include the synthesis of complex molecules
like proteins and nucleic acids, which absorb energy to form
higher-energy products.

57. ΔG=ΔH–TΔS
There are three cases
• ΔG < 0 - the reaction proceeds as written
• ΔG = 0 - the reaction is at equilibrium
• ΔG > 0 - the reaction runs in reverse
• In biological systems, the standard Gibbs free energy change (ΔG°) is
often used to predict the direction of a reaction under standard
conditions (pH 7.0, 25°C, and 1 atm pressure).
• A negative ΔG° indicates that a reaction is energetically favorable, while
a positive ΔG° indicates that a reaction is energetically unfavorable.
• However, cellular conditions often deviate from these standard
conditions, so the actual ΔG values inside cells may differ from the
standard values

58. • For most biological systems, the temperature, T, is a
constant for a given reaction.
• Since ΔG°’ is also a constant for a given reaction, the ΔG is
changed almost exclusively as the ratio of {Products}/
{Reactants} changes.
• This is why people say that a negative ΔG°’ indicates an
energetically favorable reaction, whereas a positive ΔG°’
corresponds to an unfavorable one.

59. • Intuitively, this makes sense and is consistent with Le Chatelier's principle – a system
responds to stress by acting to alleviate the stress. If we examine the ΔG for a reaction
in a closed system, we see that it will always move to a value of zero (equilibrium), no
matter whether it starts with a positive or negative value.
• Another type of free energy available to cells is that generated by electrical potential.
For example, mitochondria and chloroplasts partly use Coulombic energy (based on
charge) from a proton gradient across their membranes to provide the necessary energy
for the synthesis of ATP.
• Similar energies drive the transmission of nerve signals (differential distribution of
sodium and potassium) and the movement of some molecules in secondary active
transport processes across membranes (e.g., H+ differential driving the movement of
lactose). From the Gibbs free energy change equation,
ΔG=ΔH–TΔS
• it should be noted that an increase in entropy will help contribute to a decrease in ΔG.
This happens, for example when a large molecule is being broken into smaller pieces or
when the rearrangement of a molecule increases the disorder of molecules around it.
The latter situation arises in the hydrophobic effect, which helps drive the folding of
proteins.

60. References
• https://www.khanacademy.org/science/biology/energy-and-
enzymes/free-energy-tutorial/a/gibbs-free-energy
• https://www.biologydiscussion.com/plant-physiology-2/how-
enthalpy-entropy-and-gibbs-free-energy-are-
interrelated/23768