Water

Water is arguably the most important biochemical of all. Without water life would not exist on this
planet. It is important for two reasons. First it is a major component of cells, typically forming between
70% and 95% of the mass of the cell. Human is about 60% water, jellyfish is about 98% water. Second, it
provides an environment for those organisms that live in water. Three-quarters of the planet is covered
in water.

The water molecule is formed from two hydrogen atoms and one oxygen atom. The bonding angle
between these atoms is 104.5˚. This causes water to have dipolar properties which means it has both
positive and negative sides. The dipolar property allows the formation of hydrogen bond between
adjacent molecules. Along with this, there is a weak intermolecular force of electrostatic between the
molecules which known as Van der Waals force. These two types of bond cause the water molecules to
act as larger units rather than the individual molecules. It explains the reason why such small molecules
are able to stay in the liquid form at normal earth temperatures.

The hydrogen bonding of water molecules makes the molecules more difficult to separate and
affects the physical properties of water. For example the energy needed to break the hydrogen bonds
makes it more difficult to convert water from liquid to gas than to convert similar compounds which lack
hydrogen bonds such as hydrogen sulfide (H2S), which is gas at normal air temperature.

As the essential molecule for the continuity of life, water has some unique characteristics. Some of
them are:

1. Water act as an excellent solvent

2. Water act as transport medium of molecules
3. Water has high specific heat capacity
4. Water has high latent heat of vaporization
5. Water has less density in solid form compared to its liquid form
6. Water has high surface tension and cohesion
7. Water takes part as a reagent in some chemical reactions inside cells
Water as a solvent
Water is capable of dissolving more substances than any other liquid. It is water chemical
composition and physical properties that make it such an excellent solvent. Water molecules have a
polar arrangement of oxygen and hydrogen atoms. The hydrogen sides have positive charge while the
oxygen side has negative charge. This allows the water molecule to become attracted to different types
of ion (charged molecule) and other polar molecule such as sugars, salts, and glycerol. This attraction
therefore makes the ions separated from each other and collects around the water. This is what
happens when a chemical dissolves in water. Once a chemical is in solution, it is free to move about and
react with other chemicals. Most processes in living organisms take place in solution in this way. By
contrast, non-polar molecules such as lipids are insoluble in water and, if surrounded by water, tend to
be pushed together by the water, since the water molecules are attracted to each other.
Based on the bonding properties with the water there are two types of molecules; hydrophilic and
hydrophobic molecule. Hydrophilic (Greek; hydros : water, philia: friendship) molecule is the molecules
with a special affinity for water those it spreads across, maximizing contact with water (For example :
salts, sugar). Hydrophobic (Greek; hydros : water, phobia : afraid, hate) molecule is the molecules that
naturally repel water, causing the droplets to form (example : lipid).
Water are fundamental component of blood plasma, tissue fluid, and lymph and are used to
dissolve a wide range of substances such as red blood cells that carry oxygen, platelets, as well as
minerals which can be easily transported and made available to the cells. Metabolic waste products such
as ammonia and urea are removed from the body in a water solution. This is because ammonia and urea
are toxic when undiluted and by diluting them, they can be recycled easily in the nitrogen cycle. Most
digestive juices have salts and enzymes in solution. Tears consist mostly of water; these are used for
cleaning the surface of the eye to avoid infections.
In plant when needed the result of photosynthesis which is stored as starch is converted into
water-soluble form of sugar (glucose). The glucose then will spread throughout the plant organs by
means of water through phloem vessels. The nutrition from the soil needed for photosynthesis is also
dissolves in water and transported from roots to leaves inside the xylem vessel.
The cytosol inside the cell is also composed mainly of water this is important in enabling the
exchange of molecule (food, waste materials, etc) to and from the cell.

Water as transport medium of molecules

Water is a very important transport medium for living organisms because of its solvent properties
and because it remains liquid over a large range of temperatures. Water is the transport medium in the
blood, in the lymphatic, excretory and digestive system of animal and in the vascular tissues of plants.
Water has high specific heat capacity
The heat capacity of a substance is the amount of heat required to raise its temperature by a given
amount. The specific heat capacity of water is the amount of heat energy required to raise the
temperature of 1 kg of water by 1˚C.
Water has a relatively high heat capacity. In order for the temperature of liquid to be raised, the
molecules must gain energy and consequently move about more rapidly. The hydrogen bond that tend
to make water molecules stick to each other make it more difficult for the molecules to move about
freely; the bonds must be broken to allow free movement. This explains why more energy is needed to
raise the temperature of water rather than would be the case if there were no hydrogen bonds.
Hydrogen bonding in effect, allows water to store more energy than would otherwise be possible for
given temperature raise.
The high heat capacity of water has important biological implications because it makes water
more resistant to changes in temperature. This means that the temperature within cell s and within the
bodies of organisms (which have high proportions of water) tends to be more constant than that of the
air around them. Biochemical reactions therefore operate at relatively constant rates and less likely to
be adversely affected by extremes of temperature. It also means that large bodies of water such as lakes
and oceans are slow to change. As a result they provide more stable habitats for aquatic organism.

Water has high latent heat of vaporization

The latent heat of vaporization is a measure of the heat energy needed to vaporize a liquid (cause
it to evaporate), changing it from liquid to gas. In the case of water, it involves the change from liquid
water to water vapor.
Water has relatively high latent heat of vaporization. This is a consequence of its high heat
capacity. The fact that water molecules tend to stick to each other by hydrogen bonds means that
relatively large amounts of energy are needed for vaporization to occur, because hydrogen bonds have
to be broken before molecules can escape as a gas. The energy transferred to water molecules during
vaporization results in a loss of energy in surrounding environment and therefore causes the
environment to cool down. This is biologically important because it means that living organisms can use
evaporation as cooling mechanism. A large amount of heat energy can be lost for relatively little loss of
water, reducing the risk of dehydration. It can also be important in cooling leaves during transpiration.
The condition is also the same when liquid water changing into solid ice. This time water should
loss a large amount of energy. These prevent water from freezing easily and provide advantages for the
aquatic organisms.
Water has less density in solid form compared to its liquid
form
Water is n unusual chemical because its solid form, ice is less dense then its liquid form. Below 4˚C
the density of water starts to decrease. Ice therefore floats on liquid water and insulates the water
under it. This reduces the tendency for large bodies of water to freeze completely, and increases the
chances of life surviving in cold conditions.
Changes in the density of water with temperature cause currents, higher temperature of water
will be moving downwards while colder water will move upwards. This will help to maintain the
circulation of nutrients in the ocean.

Water has high surface tension and cohesion

Cohesion is the attraction between molecules of the same type. Water molecules have very high
cohesion which means they tend to stick to each other. This explains why water can move in long
unbroken columns through the vascular tissue in plants, and as important property in cells. High
cohesion also results in high surface tension at the surface of water. This allows certain small organisms,
such as pond skater, to exploit the surface of water as its habitat allowing them to settle on or to skate
over its surface.

Water takes part as a reagent in some chemical reactions

inside cells
During photosynthesis energy from sunlight is used to separate hydrogen from the oxygen in
water molecules. The hydrogen is then effectively used as a fuel to provide the energy needs of the
plant for example by making glucose, an energy rich molecule. The waste oxygen from photosynthesis is
the source of oxygen in the atmosphere which is needed by aerobic organisms for respiration. Water is
also essential for all hydrolysis reactions. Hydrolysis is the mechanism by which large molecules are
broken down to smaller molecules, as in digestion.
THE BUILDING BLOCKS OF LIFE
The four most common elements in living organisms in order of abundance are hydrogen, carbon,
oxygen, and nitrogen. They account for more than 99% of the atoms found in all living things. Carbon is
particularly important because carbon atoms can join together to form long chains or ring structures.
They can be thought as the basic skeletons of organic molecules to which groups of atoms are attached.
Organic molecules always contain carbon and hydrogen.
In studying the building blocks of life we will learn some terms like macromolecules, monomers,
and polymers. Macromolecule is a large biological molecule such as a protein, polysaccharide, or nucleic
acid. A monomer is a relatively simple molecule which is used as a basic building block for the synthesis
of polymer. Many monomers are joined together to form polymer usually by the condensation
reactions. Most common examples of monomer are monosaccharide, amino acids, and nucleotides. A
polymer is a giant molecule made from many similar repeating subunits called monomer which joined
together in a chain. Examples of biological polymers are polysaccharides, protein, and nucleic acids. The
nucleic acids will combine with each other forming the most important part of cells which carry the
inheritance code called the DNA (Deoxyribose Nucleic acid) and also RNA (Ribose Nucleic Acid).
Although composed of smaller subunit, lipid is not considered as polymer because they don’t have
long chain of monomers and extremely diverse in structure. Lipid composed of fatty acids that attached
to glycerol.
Natural examples of polymers are cellulose and rubber. There are many examples of industrially
produced polymers such as polyester, polythene, PVC (polyvinyl chloride), and nylon. All these are made
up of carbon-based monomers and contain thousands of carbon atoms joined end to end.

Carbohydrate
All carbohydrates contain the element carbon, hydrogen, and oxygen. The ‘hydrate’ part of the
name comes from the fact that hydrogen and oxygen atoms are present in the ratio of 2:1, as they are in
water (hydrate refers to water). The general formula of carbohydrate can be written as Cx(H2O)y.
Carbohydrates are divided into three main groups, monosaccharides, disaccharides, and
polysaccharides. The word ‘saccharide’ refers to a sugar or sweet substance.

A. Monosaccharides
Monosaccharides are sugars. Sugars dissolve easily in water to form sweet tasting solutions.
Monosaccharides have the general formula (CH2O)n. and consist of a single sugar molecule (mono =
one). According to the number of carbon atom present in each molecule, are trioses (3C), pentose
(5C), and hexoses (6C). The names of all sugars end with –ose.

Types of sugar according to number of Carbon Common examples

Glyceraldehydes
Triose(3C)
Dihydroxyacetone
Ribose
Pentose (5C)
Deoxyribose
Glucose
Hexose (6C)
Fructose
 Galactose

Molecular and structural formulae of monosccharides

The molecular formula of a monosaccharides can be written as Cx(H2O)y. For example hexose’s
molecular formula is C6H12O6. It is also useful to show the arrangements of the atoms, which can be
done using a diagram known as the structural formulae.

(Attach the structural formula of glucose; show the hydroxyl and carboxyl group)

Ring structures
One important aspect of the structure of pentoses and hexoses is that the chain is long
enough to close up on itself and form a more stable ring structure. When glucose forms a ring,
carbon atom number 1 joins to the oxygen in carboxyl group attached to the carbon atom number
5. The ring therefore contains oxygen, and carbon atom number 6 is not part of the ring.
In the glucose molecule there are two important group which are the hydroxyl group (-OH)
and aldehyde group (-COH). The position of the hydroxyl group attached to the first carbon
determines whether the glucose is in α or β form. The form of glucose where it is below the ring is
known as α-glucose and the form where it is above the ring is β-glucose. The same molecule can
switch between these two forms. Alpha and beta glucose are each other’s isomer. An isomer is the
molecule which has the same number of atoms of each element but has different arrangement of
the atoms. The extra variety provided by the different arrangement of the hydroxyl group has
important biological consequences as we could see in the structures of starch, glycogen, and
cellulose.

Roles of monosaccharides in living organisms

Monosaccharides have two major functions. First, they are commonly used as a source of
energy in respiration due to large number of carbon-hydrogen bonds. These bonds can be broken to
release a lot of energy which is transferred to help make ATP (adenosine triphosphate) from ADP
(adenosine diphosphate) and phosphate. The most important monosaccharide in the energy
metabolism is glucose.
Second, monosaccharides are important as building blocks for larger molecules. For example,
glucose is used to make the polysaccharides starch, glycogen, and cellulose. Ribose (s pentose sugar)
is the key molecule forming RNA (ribonucleic acid) while deoxyribose (a pentose sugar) is important
in the formation of DNA (deoxyribonucleic acid).

B. Disaccharides
Disaccharides formed by two monosaccharides joining together. The three most common
disaccharides are maltose, sucrose, and lactose. Sucrose is the transport sugar in plant and
commonly bought sugar in store. Lactose is the sugar found in milk and is therefore an important
constituent of the diet of young mammal.
 Types of disaccharides Forming unit
Maltose Glucose + glucose (making α-glycosidic bond)
Sucrose Glucose + fructose
Lactose Glucose + galactose
Cellobiose Glucose + glucose (making β-gycosidic bond)

The joining of two monosaccharides takes place by a process known as condensation. For each
condensation reaction, two hydroxyl (-OH) groups line up alongside each other. One combines with
hydrogen atom from the other to form a water molecule. This allows an oxygen bridge to form
between the two molecules, holding them together and forming a disaccharide. The bridge is called
a glycosidic bond.

Theoretically, any two hydroxyl group can line up and since monosaccharide has many
hydroxyl groups there are large numbers of possible disaccharides. The shape of enzyme controlling
the reaction determines which hydroxyl groups come alongside with each other. Only few of
disaccharides are common in nature.
The reverse reaction of condensation is hydrolysis. Hydrolysis is chemical decomposition in
which a compound is split into another compound (simpler compound) by reacting with water. This
takes place during the digestion of disaccharides and polysaccharides when they are broken into
monosaccharide.

Reducing sugar
The reducing sugar is a group of sugars that can carry out reduction reaction which in the process
they are oxidized. The reducing sugar characterized by the open chain of aldehyde group which
tends to oxidize forming carboxylic acid.

Types of sugar Example of reducing sugar

Monosaccharide All types of monosaccharides (glucose,
fructose, galactose, mannose, etc)
Disaccharide Maltose, Lactose

The reducing sugar gives positive result in Benedict, Fehling, and Tollen’s test.

Common test for reducing

Control Positive
sugar
Benedict’s test Blue Reddish orange
Fehling test Dark blue Red
Tollens test Clear Silver mirror

C. Polysaccharide
Polysaccharides are polymers whose subunit (monomers) are monosaccharides. They are
made by joining many monosaccharides molecule by condensation reaction. Each monosaccharide
comes together by making glycosidic bond among them. The final molecule may be several
thousand monosaccharide units long, forming macromolecule. The most important polysaccharides
are starch, glycogen, and cellulose, all of which polymers of glucose. Polysaccharides are not sugar
therefore they are not sweet.
Since glucose is the main source of energy for cells, it is important for living organisms to store
it in the appropriate form. If glucose accumulates in cells, it would dissolve and make the content of
the cell too concentrated which would affect its osmotic properties. In addition glucose is also a very
reactive molecule and would interfere with the cell chemistry. This problem is avoided by converting
glucose by condensation reaction into polysaccharide which is convenient, compact, inert
(unreactive), and insoluble molecule. The storage polysaccharide form is starch in plants and
glycogen in animals. Glucose can be made available again quickly by an enzyme-controlled reaction.

Starch and Glycogen

Starch is a mixture of two substances – amylose and amylopectin. Amylose is made by
condensations between α-glucose molecules. In this way, a long, unbranching chain of several
thousand 1,4 linked (1,4 linked means they are linked between carbon atoms 1 and 4 of successive
glucose unit) glucose molecules is built up. The chains are curved and coil up into helical structures
like springs, making the final molecule more compact. Amylopectin is also made of many 1.4 linked
α-glucose molecules, but the chains are shorter than in amylase, and branch out to the sides. The
branches are formed by 1,6 linkages.
Mixtures of amylose and amylopectin molecules build up into relatively large starch grains, which
are commonly found in chloroplasts and in storage organs such ad potato tubers and seeds of cereal
and legumes. However starch is never found in animal cells. Instead, a substance with molecules
very like those of amylopectin used as storage of carbohydrate. This is called glycogen. Glycogen,
like amylopectin is made of chains of 1,4 linked α-glucose with 1,6 linkages forming branches.
Glycogen molecules tend to be even more branched than amylopectin molecules. Glycogen
molecules clump together to form granules which are visible in liver cells and muscle cells where
they form an energy reserve.

Cellulose
Cellulose is the most abundant organic molecule on the planet, due to its presence in plant cell walls
and its slow rate of breakdown in nature. Unlike starch and glycogen it is a strong molecule.
However, the only difference between cellulose, starch, and glycogen is that cellulose is a polymer
of β-glucose, not α-glucose.
In the ring structure of β-glucose the –OH group attached to the first carbon facing upwards thus in
order to make glycosidic bond the second glucose should rotate 180˚. This arrangement of β-glucose
molecule results in a strong molecule because the hydrogen atoms of –OH groups are weakly
attracted to oxygen atoms in the same cellulose molecule.