Thermodynamics in Biochemistry
Thermodynamics in Biochemistry
1. If two thermodynamics systems are each in thermal equilibrium with a third, then they are
in thermal equilibrium with each other.
2. When two systems are put in contact with each other, there will be a net exchange of
energy between them unless or until they are in thermal equilibrium. That is the state of
having equal temperature.
The first law of thermodynamics, also known as Law of Conservation of Energy, states
that energy can neither be created nor destroyed, energy can only be transferred or changed from
one form to another.
1. In any process in an isolated system, the total energy remains the same.
2. For a thermodynamics cycle the net heat supplied to the system equals the net work done
by the system.
Where,
E= Internal energy.
T= Temperature
S= Entropy
P= Pressure
V= Volume
This is a statement of conservation of energy. The change in internal energy (dE) equals to
the heat energy that flows in (Tds).
2ND LAWS OF THERMODYNAMICS:
The second law of thermodynamics says that the entropy of any isolated system always
increases. Isolated systems spontaneously evolve towards thermal equilibrium—the state of
maximum entropy of the system. More simply put the entropy of the universe (the ultimate
isolated system) only increases and never decreases.
The entropy of an isolated system consisting of 2 regions of state, isolated from one
another, each in thermodynamics equilibrium in itself but not in equilibrium with one another.
When the isolation that separates the two regions is broken, so that the two regions become able
to increase overtime. Approach a maximum value when the jointly communication system
reaches thermodynamics equilibrium.
The first law is conversed with the conservation of energy within a ‘system’ where a
system is defined as a body (For e.g. – A cell or organism) and its surroundings.
The law applies to all levels of organisation in the living world, it applies to organism
cells, organelles and to the individual chemical reactions that characterise metabolic. In practice it
is difficult to measure the energy may escape into the environment surrounding the cell during the
measurement.
Similarly energy may be acquired by the cell, its environment for e.g. A photosynthesised
absorbed energy from its environment in the form of light.
For e.g.- Some of the cells potential energy can be converted into electrical or thermal
energy but the cell cannot create or destroy energy. When a cell breaks down a polysaccharide to
ultimately from CO2 and H2O. Some of the potential energy present in the carbohydrate is
conserved as the potential energy by phosphorylating ADP forming ATP.
The ATP produced represents a new energy source. However, not all of the energy of the
original carbohydrate is conserve as potential energy, some of its become thermal energy and it’s
transferred to the surrounding as heat. It is important to recognise that none of the energy is
destroyed. This energy is needed to perform cell function such as DNA replication, mitosis, cell
movement, exocytosis etc.
From a biological point of view the 1st law of thermodynamics indicated that at any given
moment a cell posses a specific quantity of energy. These energy takes several forms, it includes.-
A. POTENTIAL ENERGY:
The energy of the bonds that link the energy of the atoms in a molecule or the
pressure volume, relationship within the cell as a whole or within membrane enclosed
intracellular components.
B. ELECTRICAL ENERGY:
E.g. The distribution of different amounts of electrical charge across cellular
membrane.
C. THERMAL ENERGY:
E.g. The temperature dependent constant and random motion of molecules and
atoms. According to the first law these forms of energy maybe inter-converted
2. APPLICATION OF SECOND LAW OF THERMODYNAMICS:
As with other biological processes, the transfer of energy is not 100 % efficient. In
photosynthesis, 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 other photosynthetic organisms, animals cannot generate
energy directly from the sunlight. They must consume plants or other animal organisms for
energy. The higher up an organism is on the food chain, the less available energy it receives from
its food sources. 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 in higher trophic levels. The lower the available energy, the less number of organisms
can be supported. This is why there are more producers than consumers in an ecosystem.
Living systems require constant energy input to maintain their highly ordered state. For
example, cells 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 or organism's
surroundings. The transfer of energy causes entropy in the universe to increase.
ATP AND OTHER HIGHER PHOSPHATE AS ENERGY CARRIER:
The chemical or potential energy of food stuff is locked in the covalent bonds, between the
atom of a molecule. For e.g.- during the hydrolysis of typical chemical bonds, about 3000
calories per mol are liberated. In a molecule of Glucose (180 gm) between the various atoms of
C, H and O. There are about 6,86,000 calories of potential energy that can be liberated by
complete combustion as in the following reaction-
Within the living cell this enormous amount of energy is not released suddenly. It is made
available in a step wise and a controlled manner, requiring a great number of enzymes that finally
converted the fuel into CO2 and H2O.
The liberation energy may be used by the cell-
1. To synthesis new molecules (i.e. Proteins, Carbohydrates and lipids) by means of
endergonic reactions, which can then used to replace others or for the normal growth and
metabolism of the cell.
2. To perform mechanical work such as cell division, cell movement or muscle contraction.
3. To carry out active transport against an osmotic or ionic radiant.
4. To maintain membrane potentials, as in nerve.
5. To perform cell secretion.
6. To produce radiant energy.
Only in the reaction to produce new bio-molecules. The energy provided by nutrient is
transformed into chemical bond energy. In all the other types of reactions, chemical energy is
transformed into other form of energy.
The common link in all these transformation is the compound ATP. ATP is found in all
cells. It’s most significant chemical characteristics is that it has 2 terminal bonds with a potential
energy much higher than that of all the other chemical bonds. ATP is composed of the purine
based adenine a ribose molecule and 3 molecules of phosphoric acid, adenine + ribose forms
the nucleoside adenosine.
ATP and the closely related molecule ADP are the most important compounds in energy
transformation. If phosphate is represented by P the simplified form of ATP and its
transformation into ADP or ATP as follows:-
Note that the release of any one of the two terminal phosphates of ATP yields about 7300
Cal per mol. Instead of the 3000 cal from common chemical bonds. The high energy phosphate
bond enables the cell to accumulate a great quantity of energy in a very small space and keep it
ready for use. Whenever it is needed.
Other nucleotide having high energy bonds such as Cytosine triphosphate (CTP).
Uridine triphosphate (UTP) and Guanosine triphosphate (GTP) are involved in biosynthetic
reaction. The energy source for these nucleotide triphsphate derives ultimately from ATP.
pH dependent plants pigments that can be used as pH indicators, occurs in many plants,
including- Hibiscus, red cabbage and red wine. The juice of citrus mainly because it contains
citric acid. Other carboxylic acids occurs in many living system. For e.g.- lactic acid is produced
by muscle activity. The state of protonation of phosphate derivatives such as ATP, is pH
dependent. The following of the oxygen transport enzyme haemoglobin is affected by pH.
pH IN LIVING SYSTEM:
The pH of different cellular compartments, body fluids and organs is usually lightly
regulated in a process called acid-base homeostasis is acidosis, which means an acid overload in
the body generally defined by falling below, 7.35. Alkalosis is the opposite condition with blood
pH being excessively high, usually the body maintains, the pH of blood close to 7.40. This value
is often referred to as physiological pH in biology and medicine enzyme and other proteins have
an optimum range and can become inactivated or denatured outside the range pH ranges in
different system of living body are listed below-
Acids pH
Gastric Acid 1.5-3.5
Lysosomes 4.5
Human Skin 4.7
Urine 6
Cytosol 7.2
Blood (natural pH) 7.35-7.45
Cerebro spinal fluids 7.5
Mitochondrial matrix 7.5
Pancreas secretions 8.1
CONCEPT OF pH:
pH is a measure of Hydrogen ion concentration, a measure of the acidity or alkalinity of a
solution. The pH scale usually ranges from 0-14. Aqueous solutions at 25°C with a pH less than
7 are acidic, while those with a pH greater than 7 are basic or alkaline. A pH level of 7.0 at
25°C is defined as “neutral” because the concentration of H3O+ equals the concentration of OH-
in pure water. Very strong bases might have a pH greater than 14.
Hydrochloric Acid 0
Lemon Juice 2
Vinegar 2.2
Wine 4
Pure Water 7
Lye 13
Sodium Hydroxide 14
pH has only meaning in an aqueous solution (in water). Many chemicals, including liquids
do not have pH values. If there is no water, there is no pH for e.g. there is pH value for vegetable
oil, gasoline or pure alcohol.
ACIDS:
If a solution has a higher concentration of hydornium ions than pure water. It has a pH
lower than 7. A solution with a pH lower than 7 is called an acids. As the hydronium ion
concentration increases the pH value decreases. Therefore, the more acidic a solution is the lower
it’s pH value is.
Or
An acid is a chemical species that donates protons or hydrogen ions and or accepts
electrons. Most acids contains a hydrogen atom bounded that can release (dissociate) to yield a
cation and anions in water. The higher the concentration of hydrogen ions produced by an acid
the higher its acidity and the lower the pH of the solutions.
WEAK ACIDS:
A weak acid is an acid that partially dissociates into its ions in an aqueous solution or
water. In contrast a strong acid fully dissociates into its ions in water. The conjugate base of a
weak acid is weak base, while the conjugate acids of weak base is weak acid. At the same
concentration, weak acids have a higher pH value than strong acids.
Weak acids are much more common than strong acids. They are found in daily life in
vinegar (acetic acid) and lemon juice (citric acid) another examples of weak acids are as
follows-
STRONG ACIDS:
Most plants tends to do best in the pH range of approximately 6-7, which is the
range over which the most nutrients are available. However some plants prefers more
acidic or basic conditions, such as blueberries (4-6 pH) or hyacinth (6.5-7.5 pH).
When soil pH is outside of the desired range, the pH can be altered by adding
(sulfur) or basic (lime) materials to the soil. To correct the pH of acidic soil by liming, an
exchangeable acidity analysis must be conducted so that the required amount of lime can
be calculated.
2. WATER TREATMENT:
Swimming pool typically have pH values in the range of 7.2-7.8. if the pH is too
high, the effectiveness of the chorine disinfectant becomes to low, making the pool
becomes susceptible to algal growth and preventing it from effectively killing viruses and
bacteria. If the pH is too low, the water becomes irritating to the eyes and nose and it may
corrode plaster or metal surfaces.
4. FOOD INDUSTRY:
In the food industry, pH is measured to test for quality to control microbial activity
to control the taste and other properties to prolong the shelf life of food. In milk pH is
tested to check for impurities or infection. The pH is also affected by the souring of milk
and maturation of cream, and the pH determines whether cheese will be soft or hard. The
ph of cream also determines whether butter will be sour or sweet. For production of yogurt,
the pH of cultured milk is kept low to maintain a desirable environment for appropriate
microbial activity.
IMPORTANCE OF pH IN EVERYDAY LIFE:
1. The living body works normally within a pH range of 7-7.8. When pH of river water goes
below 5.6 due to acid rain, aquatic life feels a difficulty in their survival.
2. Every type of plants requires a specific pH range for healthy growth. Therefore, the nature
of soil is known first by testing its pH and then a particular crop is grown in it. It is also
suitable for selecting the fertilizer for a particular crop by knowing the pH of the soil.
3. HCl present in the stomach helps in the digestion of food. When acidity increases in the
stomach, pain, irritation and indigestion is caused. To correct the disturbed pH range,
“milk of magnesia” is used as a medicine. Which is also called antacid as it reduces the
effect of acid (or acidity).
4. Tooth enamel is made up of calcium phosphate and is the hardest substance in the body.
If the pH inside the mouth decreases than 5.5, the decay of tooth enamel begins. This
happens when the bacteria present in the mouth work on the left over food particles and
produce acid. To prevent tooth decay toothpastes (basic) are used which neutralise the
excess of acid.
5. When insects like honeybee, ant bite; they leave an acid in the skin, that causes pain and
irritation. If a mild base like baking soda is applied on the affected area it gives relief.
6. Stinging hair of neetle leaves injects methanoic acid in the skin, which causes pain. It is
cured by rubbing the affected area with the leaves of dock plant, found in the same
locality where the neetle plant is found.
1. Carboxylic acids are very important biologically. The drug aspirin is a carboxylic acid and
some people are sensitive to its acidity. The non-aspirin pain reliever “ibuprofen” is also a
carboxylic acid.
2. Carboxylic acids that have very long chains of carbon attached to them are called “fatty
acids”. As their name suggests they are important in the formation of fat in the body.
3. Many carboxylic acids are present in the foods and drinks we ingested, like malic acids
(apples), tartaric acid (tamarind, grapes) oxalic acids (spinach, tomato) and lactic acids
(sour milk).
A base is a chemical species that donates electrons, accepts protons or releases hydroxide
-
(OH ) ions in aqueous solution. Bases display certain characteristic features that can be used to
help identify them. They tend to be slippery to “touch” (soap) can taste bitter, react with acid to
form salts and catalyze certain reaction.
TYPES OF BASES:
Bases may be categorized accordingly to their degree of dissociation in water and
reactivity.
1. Strong Base:
A strong base completely dissociates into its ions in water or is a compound that
can remove a proton (H+) from a very weak acid. Examples of strong bases include
sodium hydroxide (NaOH) and potassium hydroxide (KOH).
2. Weak Base:
A weak base incompletely dissociated in water. It is a aqueous solution includes
both the weak base and its conjugate acid.
PROPERTIES OF BASE:
The removal of hydrogen from carbon and hydrogenation represents a major class of
chemical process, called oxidation-reduction or Redox-Reaction.
Or
The reactions in which oxidation and reduction reactions occur simultaneously are called
Redox-Reactions. The redox reactions are electron transfer reactions.
For example, consider the following reaction.
Zn + Cu2+ Zn2+ + Cu
Zn atom loses two electrons. Hence it is oxidised to Zn (II) ions.
Every redox reaction consists of two half-reactions one being an oxidation, the other a
reduction. In the course of a redox reaction, the reducing agents become oxidised and the
oxidising become reduced. In the case of dehydrogenation for e.g.- removal of a H atom from a
hydrogen donor substance represents the oxidising half reaction. The reducing half reaction then
takes place when the removed H is attached to another substance, a hydrogen acceptor these
reactions are always coupled. One can occur only if the other occurs as well.
In most of the cases, redox reactions involve the transfer of electrons from the reducing
agent to the oxidising agents. In some redox reactions, a proton tags along with the electron on its
transfer and the transfer then involves the transfer of a H- atom.
REDOX - POTENTIAL:
The tendency for release and acceptance of electrons is called, the redox potential. It is
the ratio of the reduced form of the atom to the oxidised form. The redox potential is an electro-
chemical concept which is expressed mathematically as the value Eȼ0.
The redox potential of many biological important redox couples are known. For example,
the redox potential of the NAD+: NADH couple is – 0.32 volt. Whereas that of the pyruvate:
lactate couple is-0.19 volt.
0 +1
REDUCTION:
Reduction is the gain of electrons. It may also occur through shifts of electrons closer to
atomic. Reduction makes an atoms more electronegative and thus lowers its oxidation state.
Reduction: Requires energy.
0 -1
Waters has several unique properties that make it vital not only for human beingds, but for
all living organisms to survive.
Some of the important properties of water is discussed below-
1. Water is liquid at room temperature, which provides a marine environment for organisms
to live in and also provides a liquid environment inside the cell, which holds significant
importance as metabolic reactions that are key to life take place in solution.
2. Water molecules are dipolar, i.e. they have positively and negatively charged region. The
charges of these areas attract polar and ionic substances that are dissolved in it and the
water molecules from a layer around each charged ion, keeping the substance in solution.
As water can dissolves much more substances then common solvents, therefore it is
known as “Universal solvent”.
3. Water has the highest surface tension (of 72.8) any known liquid. That is why water can
easily rises to high levels in narrow capillary tubes as in Xylem.
4. Water being transparent and colourless, it transmits sunlight, enabling aquatic plants to
photosynthesis and also provide us visibility since our eyes are coated in water.
5. Animal with external fertilization such as amphibians require water for completing their
fertilization.
BUFFERS:
An acid-base balancing or control reaction by which the pH of a solution is protected
from major change when acid or base are added to it. The protection is afforded by the presence
in the solution of a weak acid and related salt (for example- acetic acid. and sodium acetate)
which maintains the equilibrium by means of ion transfer and neutralization.
The same effect can he obtained by use of a blend of two acid salts- Phosphates,
carbonates, and ammonium salts are common buffering agents. The ability to prevent large
changes in pH is an important property of most intact biological organisms.
The cytoplasmic fluid which contains dissolved proteins, Organic substances and
inorganic salts resist excessive changes in pH. The blood plasma is a highly effective buffer
solution almost ideally designed to keep the range of pH of the blood between 7.2 to 7.3.
In animals, a complex and vital buffer system is found in the circulating blood. The
components of their system are CO2-, HCO3-, Na2HPO4 the oxygenated and mono-oxygenated
forms of haemoglobin, and the plasma proteins. Many commercial products are approximately
buffered to retain their original strength.
Buffer solutions are the solutions in water that mark the combination of acids and bases.
They help in a neutralization reaction to a certain extent. Acidic buffer solutions are those that
have strong acids and weak bases as their components. They are used for neutralizing alkaline
solutions. Alkaline or basic buffer solutions are those that have strong alkalis and weak acids in
the mixture. They are used for neutralizing acidic aqueous solutions.
Blood itself tends to be a buffer solution by keeping its pH value constant. Buffer
solutions help in the adjustment of the nature of blood. They play a major role in the anatomy of
every human being. If the alkaline nature of blood increases, buffer solutions tend to bring down
the pH value of blood. The reverse happens if blood becomes acidic, i.e. acidic nature increases
the pH value of blood.
ROLE OF BUFFERS IN HUMAN BODY:
Reactions inside the human body take place in the blood plasma. These reactions might be
fail to happen if the pH changes. For complete reaction to take place the pH of the blood should
remain constant. Biochemical reactions are quite sensitive to the nature of blood. The reaction
inverts by changes in the pH of blood. However, these buffers generally prevent such mishap.
These changes is also affect the biological activity of a human being.
If the pH value of blood remains in either alkaline or acidic form then it could prove
harmful to a human being. It may even lead to death. This may prevent the working of some
organs also. This serves to be the best example as to why buffer solutions are important for the
body. Buffer solutions prevent the body from permanent damage.
When carbon dioxide dissolves in blood. It decreases the pH value, thereby increasing the
acidic content of blood. In this case, alkaline buffers come into play. They tend to mix with the
plasma of blood and then neutralize its value. The same happens in the plasma when the alkaline
value of blood increases. In this case, acidic buffers in the blood plasma play their role. If the
alkalinity or the acidity of blood proteins for a longer period, the body gets into a hazardous state,
which is left unaddressed, can prove fatal.
Without buffer solutions, our body may undergo a lot of changes. The enzyme action is
regulated by blood. Therefore, the change of pH value also affects the enzymes indirectly.
Enzyme actions require low energy involvement. Changes in the temperature of the body can
affect enzyme action to a wider range.
The three major buffer systems of our body are carbonic acid bicarbonate buffer
system, phosphate buffer system and protein buffer system.
The body’s chemical buffer system consists of three individual buffers out of which the
carbonic acid bicarbonate buffer is the most important.
CABONIC ACID BICARBONATE BUFFER:
CO2 + H2O H2CO3 HCO3- + H2CO3 (Weak acid) HCO3- (Conjugate base)
As with any buffer system the pH is balanced by the presence of both a weak acid (for
e.g.- H2CO3) and its conjugate base (for e.g.- HCO3-) so that any excess acid or base introduced
to the system is neutralized.
Failure of this system to function properly results in acid-base imbalance, such as Acidosis
(pH<7.35) and Alkalosis (pH>7.45) in the blood.
Protein buffer system help to maintain acidity in and around the cells. Haemoglobin makes
an excellent buffer by binding to small amounts of acids in the blood. Before they can alter the
pH of the blood. Other proteins containing amino acid histidine are also good at bufferings.
The main purpose of all the buffers is to maintain proper pH within the body system so
that all biochemical process can take place.