Biological Molecules and Metabolic Pathways
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Water is an essential molecule to humans, it makes up around 65% of the body, 75% of the brain
and 70% of the surface of the earth. The structure of a water molecule is two hydrogen atoms
bonded to one oxygen atom, through polar covalent bonding, as seen in Figure 1.
FIGURE 1
As oxygen as 6 electrons in its outer shell, it needs to gain two electrons to become stable. Hydrogen
has only one electron in its outer shell and must gain one electron to complete its outer shell. One
electron from each hydrogen atom and two electrons from the oxygen atom are shared, shown as
covalent bonding, allowing each atom to become stable.
These electrons are not shared equally between the atoms, as oxygen has a higher electronegativity
than hydrogen. Electronegativity is the tendency of an atom to attract a bonding pair of electrons;
since oxygen has the higher electronegativity of the two elements, it attracts the shared pair of
electrons (which are negatively charged) more strongly than the hydrogen atoms, making it slightly
negatively charged. As they attract the electrons less strongly than oxygen, the hydrogen atoms are
slightly positively charged. This difference in charge is what defines the water molecule as a polar
molecule, and the bonds as polar covalent bonds. It is also responsible for many of the molecule’s
unique properties.
Water molecules are bonded to each other through hydrogen bonding – a type of dipole-dipole
bond that can form between hydrogen and nitrogen, fluorine or, in water, oxygen. The lone pair of
electrons in oxygen are attracted to the slight positive charge in the hydrogen atoms of nearby water
molecules – each can make 4 bonds with other water molecules. Individually, these bonds are weak
but together are the strongest type of intermolecular bonds, making water molecules very good at
sticking to each other. (1)
Due to the polarity of water, it can interact with charges in the environment – this can be seen when
a rod is charged with a cloth, bringing free electrons to the surface, and holding it next to flowing
water. The stream of water will bend towards the charged rod as the positively charged hydrogen
atoms attract the negative electrons. This polarity also causes adhesion – water sticking to other
substances due to interactions between their charges. This property allows capillary action, water
travelling up small tubes. Plants have small tubes called xylem which transport water up the plant,
using capillary action allowed by adhesion.
As well as sticking to other surfaces, water also sticks strongly to itself, allowing the formation of
droplets f. Cohesion is a property of water caused by the strong hydrogen bonds between water
molecules. This property can be seen by adding drops of water onto a penny, until it overflows.
When many drops have been added, a dome shape forms over the penny which looks like it should
overflow. Due to cohesion, the water remains on the penny until there is too much water added.
Surface tension is another unique property of water, demonstrated by placing a needle onto a cup of
water on top of a piece of tissue. When the tissue is pushed down into the water, the needle stays
floating on top of the water. This is because of water’s tendency to shrink into the minimum possible
surface area – the needle is not strong heavy enough to break through the tension caused by
hydrogen bonds between water molecules, which are strongest at the surface of the water.
, The density of water is very unique compared to other substances. Most substances are denser in
their solid form than in their liquid form, while water is denser as a liquid than when it is solid. To
prove this, an ice cube is placed in a beaker of water, where it floats rather than sinking. This is
because of the way that hydrogen atoms adjust to hold negatively charged atoms apart, preventing
it from becoming denser; they do this by forming hexagonal lattice structures.
If an empty plastic bottle is held over an open flame, the bottle will melt quickly. Interestingly, the
bottle will take much longer to melt if it is full of water. This is because water has a much higher
specific heat capacity (the amount of energy needed to increase the temperature of 1kg of a
substance by 1°) than air, so the full bottle does not heat up as quickly as the empty one. The same
principal applies to the temperature of the oceans. Vast volumes of water are exposed to the
weather every day, and yet the temperature rarely changes from day to day due to the high specific
heat capacity of water.
Carbohydrates are another important biological molecule, made up of polyhydroxy compounds that
also contain an aldehyde or ketone functional group, they contain carbon, hydrogen and oxygen
atoms. The simplest type of sugars are monosaccharides, consisting of a single polyhydroxy aldehyde
or ketone unit, seen in figure 2 below. The general formula for monosaccharides is (CH2O)n, with n
being usually 3-7. The properties of these monomers are solubility in water, sweet taste and forming
crystals. They are classified according to the number of carbons – for example, glucose contains 6
carbons, so it is classified as a hexose monosaccharide. Its structure includes multiple H or OH
groups, which provide opportunities for hydrogen bonding with water, making it soluble in water.
These molecules have two possible forms – D (dextro) or L (levo), which are mirror images of each
other, seen in figure 2 below, D sugars such as D-Erythrose are most common. They can also be
either an aldose or ketose sugar, depending on whether they have an aldehyde or ketone group
attached. They are both reducing sugars and therefore give positive results when tested with
Benedict’s reagent. Reducing sugars are capable of acting as a reducing agent because of the free
aldehyde or ketone functional groups – all monosaccharides are reducing sugars.
FIGURE 2
Simple monosaccharides can undergo condensation reactions to form more complex di-, tri-, oligio-
and polysaccharides. Disaccharides are formed when two monosaccharide units bond together,
forming a glycosidic bond. When the condensation reaction involves a hydroxyl oxygen atom on
carbon-4 on one sugar and the α-anomeric form of carbon-1 on another, 1,4 glycosidic bonds are
formed. The 1,4 glycosidic bond is formed between the carbon-1 of one monosaccharide and
carbon-4 of the other monosaccharide. These bonds can be known as alpha glycosidic bonds, when
the OH on the carbon-1 is below the glucose ring, or beta glycosidic bonds, when the OH is above
the glucose ring. The mechanism for this reaction is shown in figure 3 below.
FIGURE 3
Monosaccharides can join in chains, too, known as oligosaccharides. These are short chains of 3-10
monosaccharide units joined by glycosidic bonds. Disaccharides are the most abundant type of
oligosaccharides. Stachyose is an oligosaccharide found in breast milk, vegetables and some beans,
and is used as a bulk sweetener. When a carbohydrate has more than 20 monosaccharide units, it is
considered a polysaccharide. These can have hundreds or thousands of units and may contain
multiple sugars. One example of a polysaccharide is starch, a polymer of glucose which is made up of
