Molecules of Living Systems (Part-4)

WATER AND LIFE

Water is the most abundant substance in living

systems, making up 70% or more of the weight of
most organisms.

The first living organisms on Earth arose in an

aqueous environment, and the course of evolution
has been shaped by the properties of the aqueous
medium in which life began.
WATER SHOWS UNUSUAL PROPERTIES DUE TO
INTERMOLECULAR HYDROGEN BONDING

Water has a higher melting point, boiling point, and heat of

vaporization than most other common solvents.

These unusual properties are a consequence of attractions

between adjacent water molecules that give liquid water
great internal cohesion.

This is due to hydrogen bonding between neighboring water

molecules which results from the electronic structure of
water molecule.
WATER SHOWS UNUSUAL PROPERTIES DUE TO
INTERMOLECULAR HYDROGEN BONDING

sp3
hybridized
oxygen
atom

In liquid water each molecule forms hydrogen bonds with

an average of 3.4 other molecules.
HYDROGEN BONDED WATER MOLECULES FORM
“FLICKERING CLUSTERS” IN LIQUID PHASE
Hydrogen bonds are relatively weak. At room temperature,
the thermal energy of an aqueous solution (the kinetic
energy of motion of the individual atoms and molecules,
depends on temperature) is of the same order of magnitude
as that required to break hydrogen bonds.

1 – 20 ps
WATER MOLECULE CAN FORM EXTENDED HYDROGEN-
BONDED NETWORK WITH MACROMOLECULES

The centrally-placed water molecule makes strong hydrogen bonds to

residues in three separated parts of the ribonuclease molecule holding
them together. This water molecule plays critical role in structure and
function and its binding site are conserved across the entire family of
microbial ribonucleases.
COMMON HYDROGEN BONDS IN BIOLOGICAL SYSTEMS

The hydrogen acceptor is usually oxygen or nitrogen;

the hydrogen donor is another electronegative atom.

Water forms hydrogen bonds with polar solutes.

This is a major factor that drives the solubility of
such molecules in aqueous environment.
SOME BIOLOGICALLY IMPORTANT HYDROGEN BONDS
FORMED BETWEEN BIOMOLECULES
HYDROGEN BONDS ARE HIGHLY DIRECTIONAL

The attraction between the partial electric

charges is greatest when the three atoms
involved in the bond (in this case O, H, and O) lie
in a straight line.
DIRECTIONALITY OF HYDROGEN BONDS GOVERNS
MACROMOLECULAR GEOMETRY
This property of
hydrogen bonds
guides very
precise three-
dimensional
structures on
protein and
nucleic acid
molecules, which
have many
intramolecular
hydrogen bonds.
WATER INTERACTS WITH POLAR SOLUTES THAT FAVORS
THEIR SOLUBILITY
Water is a polar solvent.
It readily dissolves most biomolecules, which are generally
charged or polar compounds; compounds that dissolve easily
in water are hydrophilic (Greek, “water-loving”).

In contrast, nonpolar solvents such as chloroform and

benzene are poor solvents for polar biomolecules but easily
dissolve those that are hydrophobic—nonpolar molecules
such as lipids and waxes.

Amphipathic molecules have both polar and nonpolar parts.

SOME BIOMOLECULES WITH VARYING POLARITY
MANY BIOLOGICALLY IMPORTANT GASES ARE NONPOLAR
AND HENCE POORLY SOLUBLE IN WATER
The nonpolar nature of these gases (e.g., N2, O2, CO2) and
the decrease in entropy when they enter solution combine
to make them very poorly soluble in water.
Some organisms have water-soluble “carrier proteins”
(hemoglobin and myoglobin, for example) that facilitate the
transport of O2.
Carbon dioxide forms carbonic acid (H2CO3) in aqueous
solution and is transported as the HCO3- (bicarbonate) ion,
either free — bicarbonate is very soluble in water (~100 g/L
at 25 °C)—or bound to hemoglobin.
Three other gases, NH3, NO, and H2S, also have biological
roles in some organisms; these gases are polar, dissolve
readily in water, and ionize in aqueous solution.
THE REGULAR STRUCTURE OF WATER IS UNFAVORABLY
DISRUPTED UPON ADDITION OF NONPOLAR MOLECULES
Water molecules in the immediate vicinity of a nonpolar
solute are constrained in their possible orientations as they
form a highly ordered cage-like shell around each solute
molecule:

This ordering of water

molecules reduces
entropy. The magnitude of
the entropy decrease is
proportional to the surface
area of the hydrophobic
solute enclosed within the
cage of water molecules.
HYDROPHOBIC INTERACTIONS ENTROPICALLY DRIVE
AMPHIPATHIC MOLECULES TO CLUSTER
HYDROPHOBIC CLUSTERING LEADS TO ACHIEVEMENT OF
SPECIAL STRUCTURES OF PROFOUND BIOLOGICAL
IMPORTANCE
LIPID BILAYER

TRANSMEMBRANE PROTEIN

Assembly of lipids
and proteins in
cellular membranes.
LIPID BILAYER

TRANSMEMBRANE PROTEIN
HYDROPHOBIC CLUSTERING LEADS TO ACHIEVEMENT OF
SPECIAL STRUCTURES OF PROFOUND BIOLOGICAL
IMPORTANCE

Hydrophobic
interactions
between
nonpolar
amino acids
also stabilize
the three-
dimensional
structures of
proteins.
INTERACTIONS BETWEEN POLAR SOLUTES IN WATER IS ALSO
FAVORED BY THE ENTROPY FACTOR

and van der Waals interaction

van der Waals INTERACTION IS A WEAK INTERACTIONS
BETWEEN ANY ATOMS, GROUPS OR MOLECULES

When two uncharged atoms

are brought very close
together, their surrounding
electron clouds influence each
other. Random variations in
the positions of the electrons
around one nucleus may create
a transient electric dipole,
which induces a transient,
opposite electric dipole in the
nearby atom. The two dipoles
weakly attract each other,
bringing the two atoms closer.
van der Waals INTERACTION IS A WEAK INTERACTIONS
BETWEEN ANY ATOMS, GROUPS OR MOLECULES
As the two nuclei draw
closer together, their
electron clouds begin to
repel each other. At the
point where the net
attraction is maximal,
the nuclei are said to be
in van der Waals contact.
Each atom has a
characteristic van der
Waals radius, a measure
of how close that atom
will allow another to
approach (of the range
0.1 – 0.2 nm for
biologically relevant
atoms, such as H, O, N,
C, S, P, I).
THE HIGH DIELECTRIC CONSTANT OF WATER MAKES IT AN
EFFECTIVE SCREENER FOR ELECTROSTATIC INTERACTIONS
IN DISSOLVED MOLECULES
The strength, or force (F), of ionic interactions in a solution depends on
the magnitude of the charges (Q), the distance between the charged
groups (r), and the dielectric constant (ε, which is dimensionless) of the
solvent in which the interactions occur:
For water at 25 °C, ε is 78.5, and for the very
nonpolar solvent benzene, ε is 4.6. Thus, ionic
interactions between dissolved ions are much
stronger in less polar environments. E.g., strong
attractive interactions occur between oppositely
charged amino acids when they occupy core region
of a folded protein.
The inverse dependence on r2 is such that ionic attractions or
repulsions operate only over short distances — in the range of 10 to
40 nm (depending on the electrolyte concentration) when the
solvent is water.