BBT 302: Molecules of Life

Mrs. Mary David,

Asst. Professor,
SBB, DYPU
 Unit I: Introduction to Biochemistry

Axioms of living matter,

Importance and general
properties of organic
molecules and functional
groups
 Water

Water is the most important constituent of our body accounting for as much as
70% of our bodies. No living organism can survive without water.
The primary reason for water being so essential for life is because it is a good
solvent; it influences the structure and functioning of various macromolecules. It
also is a good reactant playing a role in several important metabolic reactions.
Water has the general formula H2O. Structurally the oxygen atom is at the
centre of a tetrahedron. The four corners of the tetrahedron are occupied by four
sp3 hybridized orbitals of O2. Two of the orbitals have a lone pair of electrons,
while two have single electrons. These orbitals bond with the s orbitals of H2. The
105o angle between the H2 differ from the ideal tetrahedral angle of 109.5o

3 Water
 Hydrogen bonds in water

Water is a strong dipole with its electrical charges

distributed asymmetrically about its structure. The
strongly electronegative oxygen atom pulls electrons
away from the hydrogen nuclei, leaving them with a
partial positive charge, while its two unshared electron
pairs constitute a region of local negative charge.
The hydrogen atom with its partial positive charge
can interact with an oxygen atom with partial negative
charge to form a hydrogen bond. Thus water
molecules are self associated to form ordered arrays,
each water molecule being associated with 3.5 other
water molecules. The hydrogen bonds though weak
require about 4.5 K cals / mole of energy for its
rupture.
The physical properties of water viz. its cohesive
behaviour, high viscosity, surface tension, expansion
upon heating, resistance to change in temperature
and boiling point of water is due to its hydrogen
bonds.

4 Water
 Properties of water due to hydrogen bonding

• Cohesion is responsible for the

transport of the water column in
plants. Cohesion among water
molecules plays a key role in the
transport of water against gravity
in plants. Adhesion between
different molecules also occurs
due to hydrogen bonding of
water. Thus cohesion between
water molecules and adhesion
between water molecules and
walls of plant conducting vessels
facilitates the capillary rise of
water in plant conducting vessels
even upto 100 metres as in the
giant redwood trees.

Water 5
 Properties of water due to hydrogen bonding

• Surface tension, a measure of

the force necessary to stretch or
break the surface of a liquid, is
related to cohesion. Water has a
greater surface tension than most
other liquids because hydrogen
bonds among surface water
molecules resist stretching or
breaking the surface. Water
behaves as if covered by an
invisible film. Some animals can
stand, walk or run on water
without breaking the surface.

Water 6
 Water moderates Temperatures on Earth

• Water stabilizes air temperatures by absorbing heat from warmer air and
releasing heat to cooler air. Water can absorb or release relatively large
amounts of heat with only a slight change in its own temperature. Three
fourths of the earth is covered by water. It serves as a large heat sink
responsible for prevention of temperature fluctuations that are outside the
range suitable for life. It also provides a stable marine environment.

• Cooling of a surface occurs when the liquid evaporates. Mammals sweat

when their body temperature is high. As the sweat evaporates it creates a
cooling effect lowering the body temperature of the organism

Water 7
 Anomalous behaviour of water when cooled
• Water contracts until
40C.and is most dense at
40C. It then expands from
40C to 00C. This is because
water molecules get locked
into a crystalline lattice with
each molecule bonded to a
maximum four partners. As
ice starts to melt some of
the hydrogen bonds break
and some water molecules
can come closer together
than when they are in a
crystalline lattice. As water
molecules in the liquid state
are closer together they are
more dense than the ice
state. Thus ice is 10% less
dense than water at 40C. So
water in liquid state which
is more dense would sink to
the bottom of a lake. Water 8
 Anomalous behaviour of water when cooled

• The peculiar behaviour of water thus prevents ice from freezing from the
bottom up. Thus ice forms only on the surface. This allows aquatic
organisms to survive even in winter.
• The ice at the surface of a water body serves as an insulating layer. It also
makes transitions between seasons less abrupt.

Water 9
 Water is a good solvent.

• Hydrogen bonding enables water to dissolve many organic biomolecules

participating in H2 bonding. The O2 atom of carbonyl groups of aldehydes,
ketones (carbohydrates), amino acids and amides (proteins) can interact
with hydrogen of water whereas the hydrogen atom of –OH groups (sugars)
amino groups (amino acids) and amido groups (proteins) can interact with
the electronegative oxygen atom of water.

• Water has a high dielectric constant of 78.5. It greatly decreases the force
of attraction between charged and polar groups in molecules. Thus due to
its strong dipolar character and high dielectric constant, it can dissolve
charged entities such as salts.

Water 10
 Water influences the structure of various macromolecules

• Biomolecules are held together

by covalent and non covalent
bonds (weaker but still
significant). Most biomolecules
are amphipathic having charged
polar groups and hydrophobic
regions. These biomolecules fold
or orient themselves so as to
exclude water. Proteins fold in
such a way that those amino
acids that have hydrophobic R
groups lie towards the interior
whereas amino acids with
hydrophilic polar side chains are
towards the exterior and in
contact with water.

Water 11
 Water influences the structure of various macromolecules

• The lipid bilayer occurs such

that the charged head
(phosphate) groups of the
phospholipids lie in contact
with water while the
hydrophobic fatty acyl side
chains lie together
excluding water. Thus
energetically favourable
interactions occur between
biomolecules and water and
unfavourable contact
between water and
hydrophobic groups is
avoided

Water 12
 Water influences the structure of various macromolecules
• The double helix of the DNA is also
oriented so that the hydrophobic
nitrogen bases of each polynucleotide
strand are oriented towards the
interior of the double helix whereas
the hydrophilic sugar phosphate
backbone is towards the outside. The
DNA is stabilized by a number of
bonds. The individual strands of the
DNA molecule are held together by
covalent phosphodiester bonds. The
two strands are held together by weak
hydrogen bonds between the bases of
the two strands. Van der Waal’s
interactions occur between the
stacked purine and pyrimidine bases.
The charged sugar phosphate
backbone may be extended to
minimize unfavourable electrostatic
interactions.
• Thus water influences the structure
and functioning of various
macromolecules.
Water 13
 Water is also a good reactant

• Water is not just a good solvent in which chemical reactions take place but it
is a direct participant in many biochemical reactions.

• Hydrolytic reactions: These occur due to nucleophilic attack by the lone

pair of electrons in the sp3 hybridized orbitals of H2O. These attack
glycosidic/ peptide/ phosphodiester bonds of carbohydrates, proteins and
nucleic acids to release their monomers. They are exergonic reactions
accompanied by the release of energy.

• Condensation reactions: Formation of cellular polymers from their

monomers occurs by elimination of a molecule of H2O. This is an
endergonic reaction accompanied by the breakdown of ATP.

Water 14
 Water is also a good reactant

• Oxidation reduction reactions: Green plants and algae use the energy of
sunlight to split water in the process of photosynthesis.
light
2H2O + 2A O2 + 2AH2
• Here water serves as an electron donor in the oxidation reduction reaction.
• In the process of respiration, glucose is oxidised to yield H2O and CO2

C6H12O6 + O2 CO2 + H2O

Thus water is an important participant in the most important life supporting

reactions in living organisms.

Water 15
 References

• Harper’s Illustrated Biochemistry

• Fundamentals of Biochemistry by J L Jain
• Biochemistry by Matthews, van Holde

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Thank You