CHAPTER Biochemical
1 Perspective to Medicine
CHAPTER AT A GLANCE
The reader will be able to answer questions on
the following topics:
1. History of biochemistry
2. Biomolecules and metabolism
3. Ionic bonds
4. Hydrogen bonding
5. Hydrophobic interactions
6. Principles of thermodynamics
7. Donnan membrane equilibrium
Biochemistry is the language of biology. The tools
for research in all the branches of medical science
are based on principles of biochemistry. The study
of biochemistry is essential to understand basic
functions of the body. This will give information
regarding the functioning of cells at the molecular
level. How the food that we eat is digested, absor-
bed, and used to make ingredients of the body?
How does the body derive energy for the normal
day to day work? How are the various metabolic
processes interrelated? What is the function of
genes? What is the molecular basis for immuno-
logical resistance against invading organisms?
Answer for such basic questions can only be derived
by a systematic study of medical biochemistry.
Modern day medical practice is highly dependent
on the laboratory analysis of body fluids, especially
the blood. The disease manifestations are reflected
in the composition of blood and other tissues.
Hence, the demarcation of abnormal from normal
constituents of the body is another aim of the study
of clinical biochemistry.
The word chemistry is derived from the Greek word "chemi"
(the black land), the ancient name of Egypt. Indian medical
science, even from ancient times, had identified the
metabolic and genetic basis of diseases. Charaka, the great
master of Indian Medicine, in his treatise (circa 400 BC)
observed that madhumeha (diabetes mellitus) is produced
by the alterations in the metabolism of carbohydrates and fats;
the statement still holds good.
Biochemistry has developed as an offshoot of organic
chemistry, and this branch was often referred as "physiological
chemistry". The term "Biochemistry" was coined by Neuberg
in 1903 from Greek words, bios (= life) and chymos (= juice).
One of the earliest treatises in biochemistry was the "Book of
Organic Chemistry and its Applications to Physiology and
Pathology", published in 1842 by Justus von Liebig (1803-
73), who introduced the concept of metabolism. The "Textbook
of Physiological Chemistry" was published in 1877 by Felix
Hoppe-Seyler (1825-95), who was professor of physiological
chemistry at Strausbourge University, France. Some of the
milestones in the development of science of biochemistry are
given in Table 1.1.
The practice of medicine is both an art and a science.
The word "doctor" is derived from the Latin root, "docere",
which means "to teach". Knowledge devoid of ethical back-
ground may sometimes be disastrous! Hippocrates (460 BC
to 377 BC), the father of modern medicine articulated "the
Oath". About one century earlier, Sushrutha (500 BC), the
great Indian surgeon, enunciated a code of conduct to the
medical practitioners, which is still valid. He proclaims: "You
must speak only truth; care for the good of all living beings;
devote yourself to the healing of the sick even if your life be
lost by your work; be simply clothed and drink no intoxicant;
always seek to grow in knowledge; in face of God, you can
take upon yourself these vows."
Biochemistry is perhaps the most rapidly developing
subject in medicine. No wonder, the major share of Nobel
prizes in medicine has gone to research workers engaged
in biochemistry. Thanks to the advent of DNA-recombination
technology, genes can now be transferred from one person
to another, so that many of the genetically determined
diseases are now amenable to gene therapy. Many genes,
(e.g. human insulin gene) have already been transferred
to microorganisms for large scale production of human
proteins. Advances in genomics like RNA interference for
silencing of genes and creation of transgenic animals by
gene targeting of embryonic stem cells are opening up new
vistas in therapy of diseases like cancer and AIDS. It is
hoped that in future, physician will be able to treat the
patient, understanding his genetic basis, so that very
efficient "designer medicine" could cure the diseases. The
large amount of data, especially with regard to single
2 Textbook of Biochemistry; Section A: Chemical Basis of Life

Table 1.1. Milestones in history of biochemistry

Scientists Year Landmark discoveries
Rouell 1773 Isolated urea from urine
Lavoisier 1785 Oxidation of food stuffs
Wohler 1828 Synthesis of urea
Berzelius 1835 Enzyme catalysis theory
Louis Pasteur 1860 Fermentation process
Edward Buchner 1897 Extracted enzymes
Fiske & Subbarow 1926 Isolated ATP from muscle
Lohmann 1932 Creatine phosphate
Hans Krebs 1937 Citric acid cycle
Avery & Macleod 1944 DNA is genetic material
Lehninger 1950 TCA cycle in mitochondria
Watson & Crick 1953 Structure of DNA
Nirenberg 1961 Genetic code in mRNA
Holley 1963 Sequenced gene for tRNA
linked to each other to form macromolecules of the
Khorana 1965 Synthesized the gene
cell, e.g. glucose to glycogen, amino acids to
Paul Berg 1972 Recombinant DNA technology
proteins, etc. Major complex biomolecules are
Kary Mullis 1985 Polymerase chain reaction Proteins, Polysaccharides, Lipids and Nucleic acids.
1990 Human genome project started The macromolecules associate with each other by
2003 Human gene mapping completed noncovalent forces to form supramolecular
systems, e.g. ribosomes, lipoproteins.
nucleotide polymorphisms (SNPs) that are available, could Finally, at the highest level of organisation in the
be harnessed by "Bioinformatics". Computers are already hierarchy of cell structure, various supramolecular
helping in drug designing process. Studies on oncogenes complexes are further assembled into cell organelle.
have identified molecular mechanisms of control of normal
In prokaryotes (e.g. bacteria; Greek word "pro" =
and abnormal cells. Medical practice is now taking more
and more help from the field of biochemistry. With the help before; karyon = nucleus), these macromolecules
of human genome project (HGP) the sequences of the whole are seen in a homogeneous matrix; but in eukaryotic
human genes are now available; it has already made great cells (e.g. higher organisms; Greek word "eu" = true),
impact on medicine and related health sciences. the cytoplasm contains various subcellular
organelles. Comparison of prokaryotes and
BIOMOLECULES
eukaryotes are shown in Table 1.2.
More than 99% of the human body is composed of 6
elements, i.e. oxygen, carbon, hydrogen, nitrogen,
STUDY OF METABOLIC PROCESSES
calcium and phosphorus. Human body is composed
Our food contains carbohydrates, fats and proteins
of about 60% water, 15% proteins, 15% lipids, 2%
as principal ingredients. These macromolecules are
carbohydrates and 8% minerals. Molecular
structures in organisms are built from 30 small Table 1.2. Bacterial and mammalian cells
precursors, sometimes called the alphabet of
Prokaryotic cell Eukaryotic cell
biochemistry. These are 20 amino acids, 2
purines, 3 pyrimidines, sugars (glucose and ribose), Size Small Large; 1000 to 10,000 times
palmitate, glycerol and choline. Cell wall Rigid Membrane of lipid bilayer
In living organisms the biomolecules are Nucleus Not defined Well defined
ordered into a hierarchy of increasing molecular Organelles Nil Several; including mito-
complexity. These biomolecules are covalently chondria and lysosomes
 Chapter 1; Biochemical Perspective to Medicine
Fig. 1.1. Covalent bond Fig. 1.2. Ionic bond
to be first broken down to small units; carbohydrates
to monosaccharides and proteins to amino acids.
This process is taking place in the gastrointestinal
tract and is called digestion or primary metabolism.
After absorption, the small molecules are further
broken down and oxidised to carbon dioxide. In this
process, NADH or FADH2 are generated. This is
named as secondary or intermediary metabolism.
Finally, these reducing equivalents enter the electron
transport chain in the mitochondria, where they are
oxidised to water; in this process energy is trapped
as ATP. This is termed tertiary metabolism.
Metabolism is the sum of all chemical changes of a
compound inside the body, which includes synthesis
(anabolism) and breakdown (catabolism). (Greek
word, kata = down; ballein = change).
STABILIZING FORCES IN MOLECULES
1. Covalent Bonds
Molecules are formed by sharing of electrons
between atoms (Fig. 1.1).
2. Ionic Bonds or Electrostatic Bonds
Ionic bonds result from the electrostatic attraction
between two ionized groups of opposite
charges (Fig. 1.2). They are formed by transfer of
one or more electrons from the outermost orbit of
an electropositive atom to the outermost orbit of an
electronegative atom. This transfer results in the
formation of a ‘cation’ and an ‘anion’, which get
consequently bound by an ionic bond. Common
examples of such compounds include NaCl, KBr
and NaF.
With regard to protein chemistry, positive
charges are produced by epsilon amino group of
lysine, guanidium group of arginine and imidazolium
3
Fig. 1.3. Ionic bonds used in protein interactions
group of histidine. Negative charges are provided
by beta and gamma carboxyl groups of aspartic acid
and glutamic acid (Fig. 1.3).
3. Hydrogen Bonds
These are formed by sharing of a hydrogen
between two electron donors. Hydrogen bonds
result from electrostatic attraction between an
electro-negative atom and a hydrogen atom that is
bonded covalently to a second electronegative
atom. Normally, a hydrogen atom forms a covalent
bond with only one other atom. However, a
hydrogen atom covalently bonded to a donor atom,
may form an additional weak association, the
hydrogen bond with an acceptor atom. In biological
systems, both donors and acceptors are usually
nitrogen or oxygen atoms, especially those atoms
in amino (NH2) and hydroxyl (OH) groups.
With regard to protein chemistry, hydrogen
releasing groups are -NH (imidazole, indole,
peptide); -OH (serine, threonine) and -NH2 (arginine
lysine). Hydrogen accepting groups are COO –,
(aspartic, glutamic) C=O (peptide); and S–S
(disulphide). The DNA structure is maintained by
hydrogen bonding between the purine and
pyrimidine residues.
Fig. 1.4. Hydrophobic interaction
4 Textbook of Biochemistry; Section A: Chemical Basis of Life
4. Hydrophobic Interactions
Non-polar groups have a tendency to associate with
each other in an aqueous environment; this is
referred to as hydrophobic interaction. These are
formed by interactions between nonpolar
hydrophobic side chains by eliminating water
molecules. The force that causes hydrophobic
molecules or nonpolar portions of molecules to
aggregate together rather than to dissolve in water
is called the ‘hydrophobic bond’ (Fig. 1.4). This
serves to hold lipophilic side chains of amino acids
together. Thus, nonpolar molecules will have
minimum exposure to water molecules.
5. Van Der Waals Forces
These are very weak forces of attraction between
all atoms, due to oscillating dipoles, described
by the Dutch physicist Johannes van der Waals
(1837-1923). He was awarded Nobel prize in 1910.
These are short range attractive forces between
chemical groups in contact. Van der Waals
interactions occur in all types of molecules, both
polar and nonpolar. The energy of the van der
Waals interaction is about 1 kcal/mol and are
unaffected by changes in pH. This force will
drastically reduce, when the distance between
atoms is increased. Although very weak, van der
Waals forces collectively contribute maximum
towards the stability of protein structure, especially
in preserving the nonpolar interior structure of
proteins.
WATER: THE UNIVERSAL SOLVENT
Water constitutes about 70 to 80 percent of the
weight of most cells. The hydrogen atom in one
water molecule is attracted to a pair of electrons in
the outer shell of an oxygen atom in an adjacent
molecule. The structure of liquid water contains
hydrogen-bonded networks (Fig. 1.5).
The crystal structure of ice depicts a tetrahedral
arrangement of water molecules. Four others bound
by hydrogen bonds surround each oxygen atom.
On melting, the molecules get much closer and this
results in the increase in density of water. Hence,
liquid water is denser than solid ice. This also
explains why ice floats on water.
Water molecules are in rapid motion, constantly
making and breaking hydrogen bonds with adjacent
molecules. As the temperature of water increases
Fig. 1.5: Water molecules hydrogen bonded
toward 100°C, the kinetic energy of its molecules
becomes greater than the energy of the hydrogen
bonds connecting them, and the gaseous form of
water appears. A few gifted properties of water
make it the most preferred medium for all cellular
reactions and interactions.
a. Water is a polar molecule. Molecules with polar
bonds that can easily form hydrogen bonds with
water can dissolve in water and are termed
“hydrophilic”.
b. It has immense hydrogen bonding capacity both
with other molecules and also the adjacent water
molecules. This contributes to cohesiveness of
water.
c. Water favors hydrophobic interactions and provides
a basis for metabolism of insoluble substances.
Water expands when it is cooled from 4oC to
o
0 C, while normally liquids are expected to contract
due to cooling. As water is heated from 0oC to
4 oC, the hydrogen bonds begin to break. This
results in a decrease in volume or in other words,
increase in density. Hence, water attains high
density at 4oC. However, above 4oC the effect of
temperature predominates.
PRINCIPLES OF THERMODYNAMICS
Thermodynamics is concerned with the flow of heat
and it deals with the relationship between heat and
work. Bioenergetics, or biochemical thermo-
dynamics, is the study of the energy changes
accompanying biochemical reactions. Biological
systems use chemical energy to power living
processes.
1. First Law of Thermodynamics
The total energy of a system, including its
surroundings, remains constant.
 Chapter 1; Biochemical Perspective to Medicine
Or, ∆E = Q – W, where Q is the heat absorbed by
the system and W is the work done. This is also
called the law of conservation of energy. If heat
is transformed into work, there is proportionality
between the work obtained and the heat dissipated.
A system is an object or a quantity of matter, chosen
for observation. All other parts of the universe,
outside the boundary of the system, are called the
surroundings.
2. Second Law of Thermodynamics
The total entropy of a system must increase if a
process is to occur spontaneously. A reaction
occurs spontaneously if ∆E is negative, or if the
entropy of the system increases. Entropy (S) is a
measure of the degree of randomness or disorder
of a system. Entropy becomes maximum in a
system as it approaches true equilibrium. Enthalpy
is the heat content of a system and entropy is that
fraction of enthalpy which is not available to do
useful work.
A closed system approaches a state of
equilibrium. Any system can spontaneously
proceed from a state of low probability (ordered
state) to a state of high probability (disordered
state). The entropy of a system may decrease
with an increase in that of the surroundings. The
second law may be expressed in simple terms
as Q = T x ∆S, where Q is the heat absorbed, T
is the absolute temperature and ∆S is the change
in entropy.
3. Gibb's Free Energy Concept
The term free energy is used to get an equation
combining the first and second laws of
thermodynamics. Thus, ∆G = ∆H – T∆S , where
∆G is the change in free energy, ∆H is the change
in enthalpy or heat content of the system and ∆S is
the change in entropy. The term free energy
denotes a portion of the total energy change in
a system that is available for doing work.
For most biochemical reactions, it is seen that
∆H is nearly equal to ∆E. So, ∆G = ∆E – T∆S. Hence,
∆G or free energy of a system depends on the
change in internal energy and change in entropy of
a system.
4. Standard Free Energy Change
It is the free energy change under standard
conditions. It is designated as ∆G0. The standard
5
conditions are defined for biochemical reactions
at a pH of 7 and 1 M concentration, and differen-
tiated by a priming sign ∆G0. It is directly related
to the equilibrium constant. Actual free energy
changes depend on reactant and product.
Most of the reversible metabolic reactions are
near equilibrium reactions and therefore their ∆G
is nearly zero. The net rate of near equilibrium
reactions are effectively regulated by the relative
concentration of substrates and products. The
metabolic reactions that function far from
equilibrium are irreversible. The velocity of these
reactions are altered by changes in enzyme
activity. A highly exergonic reaction is irreversible
and goes to completion. Such a reaction that is
part of a metabolic pathway, confers direction to
the pathway and makes the entire pathway
irreversible.
Three Types of Reactions
A. A reaction can occur spontaneously when ∆G is
negative. Then the reaction is exergonic. If ∆G
is of great magnitude, the reaction goes to
completion and is essentially irreversible.
B. When ∆G is zero, the system is at equilibrium.
C. For reactions where the ∆G is positive, an input
of energy is required to drive the reaction. The
reaction is termed as endergonic.and those with
a negative ∆G as exergonic. (Examples given
below). Similarly a reaction may be
exothermic (∆H is negative), isothermic (∆H is
zero) or endothermic (∆H is positive).
Energetically unfavorable reaction may be driven
forward by coupling it with a favorable reaction.
Glucose + Pi → Glucose-6-phosphate (reaction1)
ATP + H2O → ADP + Pi (reaction 2)
Glucose+ATP→Glucose-6-phosphate+ADP (3)
Reaction 1 cannot proceed spontaneously.
But the 2nd reaction is coupled in the body, so
that the reaction becomes possible. For the first
reaction, ∆G0 is +13.8 kJ/mole; for the second
reaction, ∆G0 is –30.5 kJ/mole. When the two
reactions are coupled in the reaction 3, the ∆G 0
becomes –16.7 kJ/mole, and hence the reaction
becomes possible. Details on ATP and other
high-energy phosphate bonds are described in
Chapter 19.
Reactions of catabolic pathways (degradation
or oxidation of fuel molecules) are usually exergonic,
6 Textbook of Biochemistry; Section A: Chemical Basis of Life
Figs 1.6A and B. Donnan membrane equilibrium
whereas anabolic pathways (synthetic reactions or
building up of compounds) are endergonic.
Metabolism constitutes anabolic and catabolic
processes that are well co-ordinated.
DONNAN MEMBRANE EQUILIBRIUM
When two solutions are separated by a membrane
permeable to both water and small ions, but when
one of the compartments contains impermeable
ions like proteins, distribution of permeable ions
occurs according to the calculations of Donnan.
In Fig. 1.6, the left compartment contains NaR,
which will dissociate into Na+ and R¯ . Then Na+
can diffuse freely, but R¯ having high molecular
weight cannot diffuse. The right compartment
contains NaCl, which dissociates into Na+ and Cl¯.
Both ions can diffuse freely.
Thus, if a salt of NaR is placed in one side of a
membrane, at equilibrium
Na+ x R¯ x H+ x OH¯ = Na+ x OH¯ x H+
To convey the meaning of the mathematical
values, a hypothetical quantity of each of the ion is
also incorporated in brackets. Initially 5 molecules
of NaR are added to the left compartment and 10
molecules of NaCl in the right compartment and
both of them are ionized (Fig. 1.6A). When
equilibrium is reached, the distributions of ions are
shown in Figure 1.6B. According to Donnan's
equilibrium, the products of diffusible electrolytes
in both the compartments will be equal, so that
[Na+] L x [Cl¯ ] L = [Na+] Rx [Cl¯ ] R
If we substitute the actual numbers of ions, the
formula becomes
9 x 4 in left = 6 x 6 in right
Donnan's equation also states that the electrical
neutrality in each compartment should be
maintained. In other words the number of cations
should be equal to the number of anions, such that
In left : Na+ = R¯+ Cl¯; substituting: 9 = 5 + 4
In right : Na+ = Cl¯; substituting: 6 = 6
The equation should also satisfy that the number
of sodium ions before and after the equilibrium are
the same; in our example, initial Na+ in the two
compartments together is 5 + 10 = 15; after
equilibrium also, the value is 9 + 6 = 15. In the case
of chloride ions, initial value is 10 and final value is
also 4 + 6 = 10.
In summary, Donnan's equations satisfy the
following results:
1. The products of diffusible electrolytes in both
compartments are equal.
2. The electrical neutrality of each compartment is
maintained.
3. The total number of a particular type of ions
before and after the equilibrium is the same.
4. As a result, when there is non-diffusible anion
on one side of a membrane, the diffusible
cations are more, and diffusible anions are less,
on that side.
Clinical Applications of the Equation
1. The total concentration of solutes in plasma
will be more than that of a solution of same ionic
strength containing only diffusible ions; this
provides the net osmotic gradient (see under
Albumin, in Chapter 28).
2. The lower pH values within tissue cells than
in the surrounding fluids are partly due to the
concentrations of negative protein ions within the
cells being higher than in surrounding fluids.
3. The pH within red cells is lower than that of
the surrounding plasma is due, in part, to the
very high concentration of negative non-diffusible
hemoglobin ions. This will cause unequal
distribution of H+ ions with a higher concentration
within the cell.
4. The chloride shift in erythrocytes as well as
higher concentration of chloride in CSF are also
due to Donnan's effect (Chapter 22).