14 - en - Thermodynamics & Macroergic Bonds3

BIOENERGETICS
Prof. Zhelev
Fundamentals of
Bioenergetics.
The Energy of Human Body.
Subject Matter of Bioenergetics
All oxidative and reductive (redox)

processes in human body
1. These are the processes which yield
energy for our body.
2. These are the processes that starts
many pathologies.
The human body as a mechanical machine
Energy is what makes mechanisms to move and what is characteristic of both
The human body as a mechanical machine
Hydrocarbons + О2  СО2 + H2O + Е

Two engines – one principle of energy production
– oxidation of an organic substrate
Chemical
energy

Two engines – one principle of energy production
– oxidation of an organic substrate
Chemical
energy
Carbohydrates + О2  СО2 + H2O + Е

Why these two totally different engines use one
and same chemical process to obtain energy?
Because on the planet Earth, we have in abundance

and very available, two things:
1)Huge amount of Hydrocarbons and
Carbohydrates
2)Oxygen – wherever we need (in the air and in

water pools)
Energy sources on the planet Earth
Energy conversion in the human body –
two aspects: metabolism and thermodynamics
 Forms of energy: Light energy; Electrical; Mechanical;
Chemical; Heat ...
 The human body receive and utilize chemical energy
 Chemical energy in the human body is used for:
 Biosynthesis of specific substances – transformation of
chemical energy in another type chemical energy.
 Active transport of substances – type of chemical energy
 Maintenance of the structure and organization of membranes and
cellular organelles – another type of chemical energy
 Preservation and transmission of the genetic information –
chemical energy
 Maintaining of body temperature – Heat
 Generation of action potential and transmission of nerve impulse
(nerve excitation) – Electrochemical Е
 Muscle contraction – Mechanical Е
Receiving energy in metabolic aspect
1. Only few metabolic pathways of oxidation

(combustion) of few very specific energy
substrates.
2. From the energy produced by substrates
oxidation, cells synthesize an universal energy
unit – the substance АТP – convenient for
proteins to use.
3. Proteins use molecule ATP as energy source, if
and when they have need of energy to do their
job. ATP or similar to it substances we call
macroergic compounds.
Subject Matter of Bioenergetics
Energy conversion in the human body –
metabolism
In thermodynamic aspect:
All these processes occur entirely under

the laws of thermodynamics – the
science that define the basic concepts
and laws, under which:
1) energy conversion occur from one to
another form;
2) energy is transferred from one system to
another.
Thermodynamics of
Biochemical Systems
It helps as to understand:
1) Why and when chemical reactions can produce energy.
Where it comes from?
2) Which of biochemical processes will happen spontaneously, and which
of them needs energy to be possible?
Basic thermodynamic concepts
Objects of thermodynamics
The first law of thermodynamics states:

In each process of physical or chemical change, the total energy of an isolated system
is conserved (remains constant), and the total energy of a “closed system +
surroundings” is also conserved.
In other words, energy can not be earned (born, appear) and can not be wasted (dye,
disappear), it only could be converted from one to another form and transferred from
one to another system!
The energy that contains in a system we can denote with E and we call it Тotal
Internal energy of the system (example: Hydrocarbons + О2 in closed system).
For a closed system that exchange heat or mechanical energy with the
environment, internal energy is changed (reorganized) after the process
(Hydrocarbons + О2 → СО2 + Н2О) and E = E2 – E1 represents exchanged
energy between the system and the environment (example: released heat).
Еnthalpy – definition
Еnthalpy – definition
The total energy of a system we call also enthalpy – H. It can be divided into tree
components: H = E + PV + w
where: Е – internal energy – characteristic of the substance as such
P – pressure; V – volume; PV – potential mechanical work, or potential
mechanical energy
w – other potential energies – electric, magnetic, et.c.
w – we do not take into account, because the laws of thermodynamics are derived for closed systems,
that do not share with the environment any other type of energy except heat, or mechanical energy. The
other components are not produced also in biochemical reactions
If we conduct biochemical reaction in closed systems, the initial energy state of the
system is: H1 = E1 + P1V1 (Hydrocarbons + О2). When the process is carried out
(Hydrocarbons + О2 → СО2 + Н2О), the final energy state of the system is: H2 = E2
+ P2V2
For a closed system, in which the given process is performed, and which
exchanges heat and mechanical energy with the environment at constant
pressure – H = E + PV
where : H – change in the enthalpy of the system
Е – is produced energy by the reaction in form of heat;
P – pressure; V – volume change; PV – performed mechanical work
Еnthalpy – definition and significance
What is the significance of the enthalpy concept?
1) Each chemical process takes place with release or absorption of heat.
If Н < 0 – exothermic process – release (production) of heat
If Н > 0 – endothermic process – absorption of heat
The sign of the value is negative, when the internal energy of the system
after the process (H2) is less, and the difference is released as heat.
H1 = 66 H2 = 61 kJ/mol
H = – 5 kJ/mol
The sign of the value is positive, when the internal energy of the system
after the process (H2) is more, and the difference is absorbed as heat.
H2 = 66 H1 = 61 kJ/mol
H = 5 kJ/mol
2) The enthalpy concept allows to determine the energy (enthalpy) of the chemical bond –
energy needed for the cleavage of these bond.
Energy of the covalent bond
Еnthalpy – significance
We can consider that: When we conduct a given process, chemical
bonds between atoms of the reactants decompose and energy (heat)
is released. After that new chemical bonds between the atoms of the
products are created and energy (heat) is absorbed.
Н is may be due to the
rearrangement of the
chemical bonds!

calorimeter 4 equations with four unknowns –

solvable task

Еnthalpy – shortcoming
The value of H which we have for a given reaction, allows to find the energy of covalent bonds,
measuring the enthalpy of irreversible processes.
When we have a irreversible process with release of large amounts of heat H << –100 kJ/mol
the process always proceeds spontaneously only in the direction in which heat is released.
But in many chemical and biochemical reactions that rule is not valid. The value of the H in
most reactions is small and the sign of H (positive or negative) does not allow to determine
whether a reaction will occur spontaneously in the direction which we have written.
When the processes are reversible, when the absolute value of H is small, is even possible,
that processes will proceed spontaneously with absorbing heat from the environment.
This discrepancy is due to the fact that chemical
processes take place with the release or
absorption of heat, which not only comes
from the rearrangement
of the covalent bonds,
but also from additional
release or absorption of
heat, due to some other
phenomenon – ENTROPY.

Entropy – definition and significance
This is because each substance is characterized
by:
Phenomenon, termed entropy – the quantity of
heat which the substance is absorbed from the
environment, if the temperature rises from
absolute zero (−273.15° on the Celsius scale) to the
temperature in which it exist currently;
Heat capacity of a substance – the amount of
heat, which 1 mole of it can absorb, while its
temperature rises by one degree.
And the absolute entropy of a substance at a

certain temperature is:
Different materials (substances) have different heat

capacities and hence different levels of entropy.
When we convert one substance into another, the system has a new level of entropy. The
difference is covered by spontaneous release or absorption of heat to/from the environment.
Gibbs free energy – definition and significance
Gibbs free energy G (energy which can perform work) may be defined as:
part of the total enthalpy of the system, adjusted with the product of T
and S (TS) – which is the thermal energy stored in the system (or material)
from the environment. And the change of the free energy (G) is equal to the
total change of the energy (Н) minus the energy that goes to the
increase of entropy (the chaos) (ТS).
G = H – TS G = H – TS aA + bB cC + dD
If G has a negative value (G<0), the process proceed spontaneously in
the direction written. If G has a positive value (G>0) , the reaction or the
process proceed spontaneously in the reverse direction.
The product TS is heat which is taken from, or given to the environment as a
result of the differences in entropies between initial and final state of the system.
G and Н are measured in J/mol or kcal/mol
If  G < 0 – exergonic, favourable, spontaneous, without need of energy
If  G > 0 – endergonic, unfavourable, impossible without applying additional E
If  Н <0 – exothermic
If  Н >0 – endothermic
Entropy – definition as probability
Definition of entropy S and change of entropy S, as the degree of disorder
Entropy (S) is a magnitude, that characterizes the degree of the disorder in a
system. In fact, the more kinetic energy have the molecules of a substance, the
greater is the chaos (disorder) in the system. The probability that a system will
go towards chaos is greater.
OR: Second law of thermodynamics states:
The processes are carried out spontaneously from more ordered (low
probability) state toward less ordered (high probability) state – towards the
achievement of maximum disorder.
Entropy – definition as probability
Definition of entropy S and change of entropy S, as the degree of disorder
Entropy (S) is a magnitude, that characterizes the degree of the disorder in a
system. In fact, the more kinetic energy have the molecules of a substance, the
greater is the chaos (disorder) in the system. The probability that a system will
go towards chaos is greater.
OR: Second law of thermodynamics states:
The processes are carried out spontaneously from more ordered (low
probability) state toward less ordered (high probability) state – towards the
achievement of maximum disorder.
For example, as a result of dissociation of a molecule on several components,

we get smaller and more fast-moving molecules – chaos grows, but the
likelihood that they will meet together at one point, in the same time, and will be
reordered into the more complex and orderly molecule, is much smaller.
Important: Working with a probabilities has a small weakness – does not take
into account the essential detail – that less ordered (high probability) state is
linked to spontaneous absorption of heat from the environment by the
smaller and chaotically moving molecules.
Entropy and the reversible processes
Biochemical reactions are carried out in a system of several substances.
Each of the substances, taken separately has its own intrinsic value of entropy. But for a mixture
of substances, the entropy of the system is neither the sum nor the average of the entropy of
all substances of which it consists. It is third thing (different) which depends on the intermolecu-
lar interactions between the new molecules, old molecules, and between them and the solvent.
More and stronger temporary intermolecular interactions decrease entropy in the system, while
fewer and weaker intermolecular interactions enhances entropy.
As a consequence, in reversible process, the equilibrium can occur in the middle of the
process, because right there, intermolecular interaction between all components is minimal in
force and entropy is on maximum.
aA + bB cC + dD
20% 80%
Calculating the Gibbs free energy
aA + bB cC + dD
In reversible biochemical process G is independent of the flow path of the chemical
process, but depends only on the initial and final state of the system (the
concentrations of reactants (S) and received (P) substances)
Under standard conditions (concentrations of S and P = 1 М, pH 7, to=25oC) - G is
called the standard free energy change G0
G0 is constant for a specific substance and depends entirely and only on the
equilibrium constant K’eq of the process and characterize it.
In equilibrium – a condition in which free energy is not released and not absorbed –
the system can not perform work. That is to say, in equilibrium  G = 0.
In equilibrium we can experimentally determined the value of К’eq.
Calculating the Gibbs free energy
The Important Effect of Concentration on
Net Change of the free energy
Real change of free energy, however, G might be (and usually is) other than the
standard free energy change G0, because the concentrations from which reaction
starts, are different from standard concentration. Moreover, living systems maintain
constant concentrations of each substance, removing it from the cell or by eliminate
it in another reaction. On the other hand, the cells may take substances from the
environment, or can synthesize them.
АТP + H2O АDP + Ph G0 = –30,5 kJ/mol
Under physiological conditions in the cell, the concentrations are as follows:

АТP – 2.25 mM, АDP – 0.25 mM, Ph – 1.65 mM, H2O is assumed to be 1.0
[АDP] [Ph]
G = G0 + RT ln ––––––––––––––
[АТP] [H2O]
G = (-30.5 kJ/mol) + (8.314 J/mol K) x (298 K) x ln[(0.25 x 10-3)(1,65 x 10-3)/2.25 x 10-3 =–52 kJ/mol
●
R = 8.314 J/mol K – the universal gas constant

●
Summary of key concepts and laws of
thermodynamics
Objects of thermodynamics
First law of thermodynamics: Energy can not be earned (born, appear) and
can not be wasted (dye, disappear), it only could be converted from one to
another form and transferred from one to another system!
Second law of thermodynamics: All processes (physical or chemical) seek
to proceed in the direction leading to a maximum disorder (chaos).
The variable, that characterizes the degree of disorderliness in a system –
entropy (S). The system is in equilibrium and it is most stable when S of
the system as a whole, has a maximum value.
Processes proceed spontaneously in the direction written, if the change of
free energy G < 0
Organisms as open thermodynamic systems
The laws of thermodynamics are drawn for closed systems, but living organisms
are open systems.
In living systems, reactions rarely reach equilibrium state, due to the extraction
of the products in subsequent processes.
50% aA + bB cC + dD 50%
are open systems.
20% aA + bB cC + dD 80%
are open systems.
50% aA + bB cC + dD 50%
If the rate at which substrates are supplied to the system, reaches the speed of the
process and speed of excretion of the products is same – we have a situation, where
concentrations are equal, however the process occurs continuously – seemingly
equilibrium = steady state = dynamic equilibrium.
At steady state, the process occur continuously, and can continuously release free
energy – the system can continuously work. But to reach this steady state, the
system continuously spend energy for import and export of the reaction components.
Living cells constantly perform work. They require energy for maintaining their
highly organized structures, synthesizing cellular components, generating electric
currents, and many other processes.
are open systems.
30% aA + bB cC + dD 70%
are open systems.
10% aA + bB cC + dD 90%
Coupling of endergonic with exergonic
processes
Living cells can rule biochemical reactions with expense of energy.
This energy may come from other reactions with release of G.
G = H – TS – Heat or Work
Some reactions in the human body are performed with the release
of G (negative G – exergonic processes). On the other hand, it is
necessary to perform many reactions which are thermodynamically
unfavorable (positive G – endergonic processes).
Cells can use released G from exergonic processes to perform
work (to conduct thermodynamically unfavorable processes) thru
Coupling of endergonic with exergonic processes.
How released free energy in exergonic processes turns into
work to drive endergonic processes?
How protein molecules use released free energy in exergonic
processes, to drive endergonic processes (to do their job)?
Coupling of endergonic with exergonic processes
 Through mutual metabolite – the product of the endergonic reaction is drawn
into the next – exergonic one
G0 = +2,9
fumarate G0 = -15,4
malate G0 = -12,5 aspartate

 Through compound, which is an intermediate carrier of hydrogen atoms
(electrons, or reducing equivalents): cofactors of dehydrogenases (NADH,
NADPH, FADH2)
Carrier
Carrier-H2
 Through simultaneous decomposition (hydrolysis) of one molecule High-

Energy Compound (Macroergic Compound).
Glucose + P Glucose-6-phosphate + H2O
G10 = +13,8 kJ/mol
АТP + H2O АDP + P G20 = –30,5 kJ/mol
G0 = + 13,8 –30,5 = –16,7 kJ/mol

Coupling of endergonic with exergonic processes
Previous chemical reaction represents transfer of a high-energy containing
phosphate moiety to another molecule. It is easy to understand, that
part of the energy released goes to the connection of the same
phosphate moiety with glucose molecule in same enzyme.
But many protein molecules (or enzymes) use the energy released from
ATP, to catalyze energetically unfavorable chemical reactions,
even if these two reactions have nothing to do with each other.
What is the molecular mechanism of this type of coupling ?

Principles of operation of protein molecules:
The energy from one part of the protein molecule is transferred to another
through conformational change after hydrolysis of molecule ATP –
The energy from one part of the protein molecule is transferred to another
through conformational change after hydrolysis of molecule ATP –
In enzymes, specific conformational changes occur in the catalytic subunit, at the time
of the straight and/or the reverse reaction. Conformational changes are a signal to the
other subunit of the enzyme. It degrades ATP when the enzyme is in conformation A +
BC. The breakdown of ATP releases free energy, and changes the conformation of the
catalytic subunit, which loses affinity to A + BC at the time of the reverse reaction. So
the energy of ATP goes for, preferred loss of the enzyme affinity, to the substrates A +
BC. If there is not coupled breakdown of ATP, enzyme will lose affinity with preference
of products AB + C, which have bigger entropy.
A+BC
AB+C
A+BC
AB+C
Operation of the supramolecular complexes and
cellular structures
http://csls-text.c.u-tokyo.ac.jp/flash/0342_2.html
Macroergic (high-energy) compounds – importance
What is achieved by ATP, and other similar
macroergic compounds?
 By conjugating reactions of receiving and
degradation of ATP, intermediate macroergic
compound serves as a bargaining chip of the
chemical energy.
 Intermediate macroergic compound serves as a
reservoir of chemical energy.
Release of Biosynthesis,
energy in Electrical and
oxidative and Macroergic osmotic work,
catabolic compounds mechanical
(exergonic) work.
processes
This form two opposite types, but interrelated metabolic processes:

1) Processes that deliver energy – they are oxidizing, catabolic and exergonic – eg. glycolysis,
β-oxidation of fatty acids, oxidation in the respiratory chain.
2) Processes that require energy – they are reducing, anabolic and endergonic – eg.
biosynthesis, muscle contraction, nerve excitation, osmotic work, cell division and others.
Macroergic (high-energy) compounds – definition, types
Macroergic compounds are those, in whose hydrolysis (when they hydrolyzed) the
change of the standard free energy G0 is greater than 30 kJ/mol.
The covalent
High-energy compound Macroergic bond Role in metabolism bonds, that are
Phosphoenolpyruvate hydrolyzed and
Enol-phosphate Metabolite of glycolysis release such
bond and gluconeogenesis
energy, we call
1,3-bisphosphoglycerate “macroergic
Acyl-phosphate Metabolite of glycolysis bonds”. We mark
bond and gluconeogenesis them with a wavy
line ~. It is not
Creatine phosphate about the energy
Guanidine- Standby macroergic of the bond itself,
P phosphate bond compound in muscles but the energy of
its hydrolysis.
Acyl-CoA and acetyl-CoA Metabolites of High-Energy
Thioester bond Biomolecules
H3C–CO~S–CoA β-oxidation
Nucleoside diphosphates and

Nucleoside triphosphates – i.e.
Pyrophosphate bond Energy for many
ATP AMP + PP processes
ATP ADP + P
High-energy compounds – central role of ATP
Phosphoenolpyruvate
1,3-bisphosphoglycerate
ADP Glycerol-3-phosphate
Succinyl-CoA Glucose-6-phosphate
P
Oxidation of NAD.H and P
FADH2 in the respiratory chain Fructose-1,6-bisphosphate
ATP
Phosphocreatine
Other phosphorylations,
Creatine activations and other
endergonic processes
Reasons for the central role of ATP:

1) Has the smallest value of G0 than other macroergic compounds, and mediate
between them and normoergic compounds which needs activation. Also has
sufficient energy for the other endergonic processes.
2) АТP do not give spontaneously phosphate group to water molecule and is
kinetically stable, because of the high activation energy of the reaction (200-400
kJ/mol).
Phosphoenolpyruvate
1,3-bisphosphoglycerate
ADP Glycerol-3-phosphate
Succinyl-CoA Glucose-6-phosphate
P
Oxidation of NAD.H and P
FADH2 in the respiratory chain Fructose-1,6-bisphosphate
ATP
Phosphocreatine
Other phosphorylations,
Creatine activations and other
endergonic processes
G = –51.9 kJ/mol
Energy for ATP hydrolysis
G0 = –30,5 kJ/mol
G0 = –43,0 kJ/mol

Creatine-phosphate shuttle
Thank you

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BIOENERGETICS

All oxidative and reductive (redox)

Hydrocarbons + О2  СО2 + H2O + Е

Hydrocarbons + О2  СО2 + H2O + Е

Carbohydrates + О2  СО2 + H2O + Е

Because on the planet Earth, we have in abundance

2)Oxygen – wherever we need (in the air and in

1. Only few metabolic pathways of oxidation

All these processes occur entirely under

The first law of thermodynamics states:

Hydrocarbons + О2  СО2 + H2O + Е

calorimeter 4 equations with four unknowns –

Hydrocarbons + О2  СО2 + H2O + Е

Hydrocarbons + О2  СО2 + H2O + Е

And the absolute entropy of a substance at a

Different materials (substances) have different heat

For example, as a result of dissociation of a molecule on several components,

АТP + H2O АDP + Ph G0 = –30,5 kJ/mol

Under physiological conditions in the cell, the concentrations are as follows:

R = 8.314 J/mol K – the universal gas constant

malate G0 = -12,5 aspartate

 Through simultaneous decomposition (hydrolysis) of one molecule High-

G0 = + 13,8 –30,5 = –16,7 kJ/mol

What is the molecular mechanism of this type of coupling ?

This form two opposite types, but interrelated metabolic processes:

Nucleoside diphosphates and

Reasons for the central role of ATP:

G0 = –43,0 kJ/mol

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