Biochemistry Chapter 1

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CHAPTER Biochemical

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

Fig. 1.3. Ionic bonds used in protein interactions

Fig. 1.1. Covalent bond Fig. 1.2. Ionic bond group of histidine. Negative charges are provided
by beta and gamma carboxyl groups of aspartic acid
to be first broken down to small units; carbohydrates and glutamic acid (Fig. 1.3).
to monosaccharides and proteins to amino acids.
3. Hydrogen Bonds
This process is taking place in the gastrointestinal
These are formed by sharing of a hydrogen
tract and is called digestion or primary metabolism.
between two electron donors. Hydrogen bonds
After absorption, the small molecules are further
result from electrostatic attraction between an
broken down and oxidised to carbon dioxide. In this electro-negative atom and a hydrogen atom that is
process, NADH or FADH2 are generated. This is bonded covalently to a second electronegative
named as secondary or intermediary metabolism. atom. Normally, a hydrogen atom forms a covalent
Finally, these reducing equivalents enter the electron bond with only one other atom. However, a
transport chain in the mitochondria, where they are hydrogen atom covalently bonded to a donor atom,
oxidised to water; in this process energy is trapped may form an additional weak association, the
as ATP. This is termed tertiary metabolism. hydrogen bond with an acceptor atom. In biological
Metabolism is the sum of all chemical changes of a systems, both donors and acceptors are usually
compound inside the body, which includes synthesis nitrogen or oxygen atoms, especially those atoms
(anabolism) and breakdown (catabolism). (Greek in amino (NH2) and hydroxyl (OH) groups.
word, kata = down; ballein = change). With regard to protein chemistry, hydrogen
releasing groups are -NH (imidazole, indole,
STABILIZING FORCES IN MOLECULES peptide); -OH (serine, threonine) and -NH2 (arginine
1. Covalent Bonds lysine). Hydrogen accepting groups are COO –,
Molecules are formed by sharing of electrons (aspartic, glutamic) C=O (peptide); and S–S
between atoms (Fig. 1.1). (disulphide). The DNA structure is maintained by
hydrogen bonding between the purine and
2. Ionic Bonds or Electrostatic Bonds pyrimidine residues.
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 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. Fig. 1.5: Water molecules hydrogen bonded

toward 100°C, the kinetic energy of its molecules


5. Van Der Waals Forces
becomes greater than the energy of the hydrogen
These are very weak forces of attraction between bonds connecting them, and the gaseous form of
all atoms, due to oscillating dipoles, described water appears. A few gifted properties of water
by the Dutch physicist Johannes van der Waals make it the most preferred medium for all cellular
(1837-1923). He was awarded Nobel prize in 1910. reactions and interactions.
These are short range attractive forces between a. Water is a polar molecule. Molecules with polar
chemical groups in contact. Van der Waals bonds that can easily form hydrogen bonds with
interactions occur in all types of molecules, both water can dissolve in water and are termed
polar and nonpolar. The energy of the van der “hydrophilic”.
Waals interaction is about 1 kcal/mol and are b. It has immense hydrogen bonding capacity both
unaffected by changes in pH. This force will with other molecules and also the adjacent water
drastically reduce, when the distance between molecules. This contributes to cohesiveness of
atoms is increased. Although very weak, van der water.
Waals forces collectively contribute maximum c. Water favors hydrophobic interactions and provides
towards the stability of protein structure, especially a basis for metabolism of insoluble substances.
in preserving the nonpolar interior structure of Water expands when it is cooled from 4oC to
o
0 C, while normally liquids are expected to contract
proteins.
due to cooling. As water is heated from 0oC to
WATER: THE UNIVERSAL SOLVENT 4 oC, the hydrogen bonds begin to break. This
results in a decrease in volume or in other words,
Water constitutes about 70 to 80 percent of the
increase in density. Hence, water attains high
weight of most cells. The hydrogen atom in one
density at 4oC. However, above 4oC the effect of
water molecule is attracted to a pair of electrons in
temperature predominates.
the outer shell of an oxygen atom in an adjacent
molecule. The structure of liquid water contains PRINCIPLES OF THERMODYNAMICS
hydrogen-bonded networks (Fig. 1.5). Thermodynamics is concerned with the flow of heat
The crystal structure of ice depicts a tetrahedral and it deals with the relationship between heat and
arrangement of water molecules. Four others bound work. Bioenergetics, or biochemical thermo-
by hydrogen bonds surround each oxygen atom. dynamics, is the study of the energy changes
On melting, the molecules get much closer and this accompanying biochemical reactions. Biological
results in the increase in density of water. Hence, systems use chemical energy to power living
liquid water is denser than solid ice. This also processes.
explains why ice floats on water.
Water molecules are in rapid motion, constantly 1. First Law of Thermodynamics
making and breaking hydrogen bonds with adjacent The total energy of a system, including its
molecules. As the temperature of water increases surroundings, remains constant.
Chapter 1; Biochemical Perspective to Medicine 5

Or, ∆E = Q – W, where Q is the heat absorbed by conditions are defined for biochemical reactions
the system and W is the work done. This is also at a pH of 7 and 1 M concentration, and differen-
called the law of conservation of energy. If heat tiated by a priming sign ∆G0. It is directly related
is transformed into work, there is proportionality to the equilibrium constant. Actual free energy
between the work obtained and the heat dissipated. changes depend on reactant and product.
A system is an object or a quantity of matter, chosen Most of the reversible metabolic reactions are
for observation. All other parts of the universe, near equilibrium reactions and therefore their ∆G
outside the boundary of the system, are called the is nearly zero. The net rate of near equilibrium
surroundings. reactions are effectively regulated by the relative
concentration of substrates and products. The
2. Second Law of Thermodynamics metabolic reactions that function far from
The total entropy of a system must increase if a equilibrium are irreversible. The velocity of these
process is to occur spontaneously. A reaction reactions are altered by changes in enzyme
occurs spontaneously if ∆E is negative, or if the activity. A highly exergonic reaction is irreversible
entropy of the system increases. Entropy (S) is a and goes to completion. Such a reaction that is
measure of the degree of randomness or disorder part of a metabolic pathway, confers direction to
of a system. Entropy becomes maximum in a the pathway and makes the entire pathway
system as it approaches true equilibrium. Enthalpy irreversible.
is the heat content of a system and entropy is that
fraction of enthalpy which is not available to do Three Types of Reactions
useful work. A. A reaction can occur spontaneously when ∆G is
A closed system approaches a state of negative. Then the reaction is exergonic. If ∆G
equilibrium. Any system can spontaneously is of great magnitude, the reaction goes to
proceed from a state of low probability (ordered completion and is essentially irreversible.
state) to a state of high probability (disordered B. When ∆G is zero, the system is at equilibrium.
state). The entropy of a system may decrease C. For reactions where the ∆G is positive, an input
with an increase in that of the surroundings. The of energy is required to drive the reaction. The
second law may be expressed in simple terms reaction is termed as endergonic.and those with
as Q = T x ∆S, where Q is the heat absorbed, T a negative ∆G as exergonic. (Examples given
is the absolute temperature and ∆S is the change below). Similarly a reaction may be
in entropy. exothermic (∆H is negative), isothermic (∆H is
zero) or endothermic (∆H is positive).
3. Gibb's Free Energy Concept Energetically unfavorable reaction may be driven
The term free energy is used to get an equation forward by coupling it with a favorable reaction.
combining the first and second laws of Glucose + Pi → Glucose-6-phosphate (reaction1)
thermodynamics. Thus, ∆G = ∆H – T∆S , where ATP + H2O → ADP + Pi (reaction 2)
∆G is the change in free energy, ∆H is the change Glucose+ATP→Glucose-6-phosphate+ADP (3)
in enthalpy or heat content of the system and ∆S is
the change in entropy. The term free energy Reaction 1 cannot proceed spontaneously.
denotes a portion of the total energy change in But the 2nd reaction is coupled in the body, so
a system that is available for doing work. that the reaction becomes possible. For the first
For most biochemical reactions, it is seen that reaction, ∆G0 is +13.8 kJ/mole; for the second
∆H is nearly equal to ∆E. So, ∆G = ∆E – T∆S. Hence, reaction, ∆G0 is –30.5 kJ/mole. When the two
∆G or free energy of a system depends on the reactions are coupled in the reaction 3, the ∆G 0
change in internal energy and change in entropy of becomes –16.7 kJ/mole, and hence the reaction
a system. becomes possible. Details on ATP and other
high-energy phosphate bonds are described in
4. Standard Free Energy Change Chapter 19.
It is the free energy change under standard Reactions of catabolic pathways (degradation
conditions. It is designated as ∆G0. The standard or oxidation of fuel molecules) are usually exergonic,
6 Textbook of Biochemistry; Section A: Chemical Basis of Life

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
Figs 1.6A and B. Donnan membrane equilibrium The equation should also satisfy that the number
of sodium ions before and after the equilibrium are
whereas anabolic pathways (synthetic reactions or the same; in our example, initial Na+ in the two
building up of compounds) are endergonic. compartments together is 5 + 10 = 15; after
Metabolism constitutes anabolic and catabolic equilibrium also, the value is 9 + 6 = 15. In the case
processes that are well co-ordinated. of chloride ions, initial value is 10 and final value is
also 4 + 6 = 10.
DONNAN MEMBRANE EQUILIBRIUM In summary, Donnan's equations satisfy the
When two solutions are separated by a membrane following results:
permeable to both water and small ions, but when 1. The products of diffusible electrolytes in both
one of the compartments contains impermeable compartments are equal.
ions like proteins, distribution of permeable ions 2. The electrical neutrality of each compartment is
occurs according to the calculations of Donnan. maintained.
In Fig. 1.6, the left compartment contains NaR, 3. The total number of a particular type of ions
which will dissociate into Na+ and R¯ . Then Na+ before and after the equilibrium is the same.
can diffuse freely, but R¯ having high molecular 4. As a result, when there is non-diffusible anion
weight cannot diffuse. The right compartment on one side of a membrane, the diffusible
cations are more, and diffusible anions are less,
contains NaCl, which dissociates into Na+ and Cl¯.
on that side.
Both ions can diffuse freely.
Thus, if a salt of NaR is placed in one side of a Clinical Applications of the Equation
membrane, at equilibrium 1. The total concentration of solutes in plasma
Na+ x R¯ x H+ x OH¯ = Na+ x OH¯ x H+ will be more than that of a solution of same ionic
To convey the meaning of the mathematical strength containing only diffusible ions; this
provides the net osmotic gradient (see under
values, a hypothetical quantity of each of the ion is
Albumin, in Chapter 28).
also incorporated in brackets. Initially 5 molecules
2. The lower pH values within tissue cells than
of NaR are added to the left compartment and 10
in the surrounding fluids are partly due to the
molecules of NaCl in the right compartment and
concentrations of negative protein ions within the
both of them are ionized (Fig. 1.6A). When cells being higher than in surrounding fluids.
equilibrium is reached, the distributions of ions are 3. The pH within red cells is lower than that of
shown in Figure 1.6B. According to Donnan's the surrounding plasma is due, in part, to the
equilibrium, the products of diffusible electrolytes very high concentration of negative non-diffusible
in both the compartments will be equal, so that hemoglobin ions. This will cause unequal
[Na+] L x [Cl¯ ] L = [Na+] Rx [Cl¯ ] R distribution of H+ ions with a higher concentration
within the cell.
If we substitute the actual numbers of ions, the
4. The chloride shift in erythrocytes as well as
formula becomes
higher concentration of chloride in CSF are also
9 x 4 in left = 6 x 6 in right due to Donnan's effect (Chapter 22).

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