BASIC CHEMISTRY OF A CELL

Water
Importance of water
The properties of water are due mostly its small size, its polarity and to hydrogen bonding between its
molecules.
Water is formed when two hydrogen atoms combine with an oxygen atom by sharing electrons. The
result is a stable molecule, which is relatively unreactive but which has some unique properties. The shape of
the water molecule is triangular (wide V) rather than linear; the angle between the nuclei of the atoms is
approximately 105o. In both the oxygen-hydrogen bonds the oxygen nucleus draws electrons away from the
hydrogen nucleus. Thus there is a net negative charge on the oxygen atom and a net positive charge on the
hydrogen atom. A molecule that carries an unequal distribution of electrical charge is called a polar molecule.
Water molecules have weak attraction for each other, called hydrogen bonds. The positively charged
hydrogen atoms of one molecule are attracted to the negatively charged oxygen atoms of nearby water
molecules, leading to the formation of smaller clusters of water molecules. The hydrogen-oxygen attraction that
holds water molecules together is known as hydrogen bonding. Although individually weak, their collective
effect is responsible for many of the unusual physical properties.
(The anomalous properties of water arise from attractions between these polar molecules. The attraction
is electrical; slightly positive hydrogen of one molecule is attracted to the slightly negative oxygen of a nearby
molecule. The two molecules are thus held together by a hydrogen bond. Each water molecule can form
hydrogen bonds to a maximum of four neighbours)
Biological significance of water
Solvent properties
Water is an excellent solvent for polar substances. These include ionic substances like salts, which
contain charged particles (ions), and some non-ionic substances like sugar that contain polar groups (-OH). On
contact with water, the ions and the polar groups are surrounded by water molecules which separate
(dissociates) the ions or molecules from each other. This is what happens when a substance dissolves in water.
When ionic substances dissolve in water, each ion is surrounded by a shell of water, and is therefore called a
hydrated ion.
Once a substance is in solution its molecules or ions can move about freely, thus making it more
chemically reactive than if it were solid. Thus the majority of the cells chemical reaction takes place in aqueous
solutions. By contrasts, non-polar molecules, such as lipids, are repelled by water and usually group together in
its presence, that is non-polar molecules are hydrophobic (water-hating).
Waters solvent properties also mean that it acts as a transport medium, as in the blood, lymphatic and
excretory systems, and the alimentary canal and in xylem and phloem.
High heat capacity
The heat capacity of water is the amount of heat requires to raise the temperature of 1 kg of water by 1
o
C. Water has a high heat capacity. The specific capacity of water is 4184 J kg-1 K-1. This means that a large
increase in heat energy results in a relatively small rise in temperature. This is because much of the energy is
used in breaking the hydrogen bonds overcoming the stickiness which restrict the movement of the molecules.
Temperature changes within water are minimised as a result of its high heat capacity. Biochemical
processes therefore operate over a smaller temperature range, proceeding at more constant rates and are less
likely to be inhibited by extreme of temperature. Water also provides a very constant external environment for
many cells and organisms.
High heat of vaporisation
Latent heat of vaporisation is a measure of the heat energy required to vaporise a liquid, that is to
overcome the attractive forces between its molecules so that they can escape as gas. A relatively large amount of
energy (2.26 MJ kg-1 K-1) is needed to vaporise water (make it evaporate or boil away into gas). This is due to
the hydrogen bonding. As a result, water has an unusually high boiling point for such a small molecule.
The energy transferred to water molecules to allow them to vaporise results in a loss of energy from
their surroundings, that is cooling takes place, this is made use of in the sweating and panting of mammals, the
opening of the mouth of some reptiles, such as crocodiles, in sunshine, and may be important in cooling
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Chromatography
Chromatography is a technique used to separate and identify unknown mixtures of closely related
substances. Chromatography is carried out on a stationary medium, or phase: paper (paper chromatography), for
example, or a thin film of dried solid (thin layer chromatography). A solvent travels through the stationary phase
by capillarity, through a spot containing a mixture of the unknown substances. Components of the spot are
carried along with the solvent, but some are held back to varying extents by interaction with the stationary
phase, and so a separation is effected. Identification of the separated spots is possible by running parallel
chromatograms loaded with known substances thought to be present in the unknown mixture. The solvent front
on the chromatogram is marked at the end of the run, and the Rf values of the spots calculated:
Distance moved by the solute spot
Rf = -------------------------------------Distance moved by the solvent front
Rf values depend on the solvent used.
Chromatography
Chromatography is a technique used for separating of mixtures into their components. The technique
depends upon the differential movement of each component through a stationary medium under the influence of
a moving solvent. For example, the green pigment in plants, when dissolved in a suitable solvent and allowed to
pass through a stationary medium such as powdered chalk, separates into a number of different coloured
pigments.
There are three basic types of chromatography, depending on the nature of the stationary medium, paper
chromatography, adsorption column chromatography and thin-layer chromatography.
The movement of the solute relative to the solvent front on a chromatographic system is constant for that
solute. This can be expresses in the term Rf as shown below:
Distance moves by solute
Rf = -------------------------------------Distance moves by solvent front
Electrophoresis
Electrophoresis is modified form of chromatography used to separate charged molecules. An electric
current is applied across a chromatographic medium such that one end has a positive charge and the other a
negative charge. Individual molecules in the mixture move outwards through the medium towards the ends
depending on their relative masses and charges. Electrophoresis is commonly used in the isolation and
identification of proteins and amino acids, where the technique is improved further by adjusting the pH of the
medium.
Two factors affect the speed with which charged molecules towards an electrode:
1. The amount of charge- the greater the charge the faster the molecules moves.
2. The size of the molecule-smaller molecules moves faster than larger ones with the same charge.
Electrophoresis is a technique for separating molecules such as proteins or nucleic acid fragments on the basis
of their net charge and mass. Commonly, gel electrophoresis is used, in which the stationary phase is
polyacrylamide gel (PAG), and separation occurs when an electrical current is applied across the gel. The
method requires only a tiny quantity of a mixture; for example, 10 g is often sufficient.
Protein separation by electrophoresis
Proteins are first treated with a detergent known as SDS. This detergent unwinds the protein molecule
and attaches itself to the peptide bonds of the polypeptide chain, exposing negatively charged groups of SDS.
The resulting negative charge on the denatured protein is proportional to the number of peptide bonds.
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SDS-treated protein molecules all move towards the anode, but in passing through PAG the sieving
effect brings about separation on the basis of their size: small molecules pass relatively quickly towards the
anode whereas larger ones take longer.