THE MOLECULAR AND BIOCHEMICAL

BASIS OF AN ORGANISM

Chemical context of life

• Types of bonding
• Water, Carbon- Structure and Function
 CHEMISTRY OF LIFE
• All matter is composed of simple units called atoms
• Atom consists of a charged nucleus made of protons and neutrons surrounded by
electrons
• Same kind of atoms combine to form elements
• Six elements that occur in nature are: Carbon, Hydrogen, Nitrogen, Phosphorous,
Sulphur
• Two or more elements combine to form compound.
 TYPES OF CHEMICAL BONDING

Atoms always try to have a full outer shell of electrons - in order to achieve this they
will bond with other atoms/

The different types of bonds are

• Ionic Bonding
• Covalent Bonding
• Non-Covalent bonding
 IONIC BONDS
• Ionic bonding occurs between a metal and a non-metal
• The metal has a nearly empty outer shell and so loses electrons to form a
positively charged cation
• The non-metal has a nearly full outer shell and so gains electrons to form a
negatively charged anion
• The resulting charge of these two ions creates a strong electrostatic attraction
between them - an ionic bond
 COVALENT BONDS
• Covalent bonding occurs between two non-metals
• Because both atoms have a large number of electrons in their outer shell, it is not
feasible to lose or gain so many and so they share
• The number of covalent bonds able to be formed reflects the number of missing
electrons from the outer shell (e.g. carbon needs four electrons and so can form four
covalent bonds)
• Because there is no ionic charge, covalent molecules are not as strongly attracted to each
other as ionic molecules (covalent bonds are weaker)
 NON-COVALENT BONDS
Hydrogen Bonds:
•The covalent sharing of electrons between atoms may not always be equal and will depend on:
•The number of protons in an atom (more protons equals a greater attraction for electrons)
•The number of electron shells in an atom (electrons at a further distance from the nucleus are less attracted to
nucleus)
•Atoms that have a stronger affinity for electrons are said to have a higher electronegativity
•Covalently shared electrons will orbit closer to atoms with a higher electronegativity, resulting in a slight charge
difference
•Polar associations between an H atom of one molecule and an F, O or N atom of another molecule are
called hydrogen bonds
 NON-COVALENT BONDS

• Van der Waals forces

• Hydrophobic interactions
 CARBON
Carbon’s central role

• The more we explore our planet, the greater the diversity of life we encounter, from
microorganisms that can survive inside volcanoes to fish thousands of miles below sea level.

• The wide range of biodiversity on Earth relies largely on four major building blocks:
hydrogen, oxygen, carbon and nitrogen.

• All living things contain carbon in some form.

• Carbon is the primary component of macromolecules, including proteins, lipids, nucleic
acids, and carbohydrates.
• Carbon’s molecular structure allows it to bond in many different ways and with many
different elements.
• The carbon cycle shows how carbon moves through the living and non-living parts of the
environment
 CHEMICAL STRUCTURE OF CARBON
Many scientists describe life as we know it as
‘carbon-based’. Fundamentally, without carbon,
life on Earth would not be possible.
Carbon is a relatively small atom: its nucleus
contains six neutrons and six protons. It has a
full inner shell (two electrons) and four electrons
in its outer shell. Having four electrons means it
can form many different types of bonds.
• Having four electrons in its outer shell means carbon can form
many different of bonds.
• Carbon also forms covalent bonds with several other atoms,
such as hydrogen, oxygen, nitrogen, and sometimes sulfur
and phosphorus.
• Carbon readily forms single, double or triple bonds, chains,
branched chains and even rings. It can bond with itself, as
well, to form strong substances like diamond and graphite.
• This versatility and ability to form many bonds enables
carbon to form the many different shapes adopted by the
complex organic compounds that make up the bodies of
animals and plants.
 CARBON IN BIOMOLECULES
• Living things use carbon in a vast number of molecules in their bodies.
• Carbohydrates, lipids, proteins and nucleic acids all contain carbon. This means that we find carbon in everything
from cell membranes to hormones to DNA.
• Carbon’s versatility means that it is the basis of many of the complex organic compounds vital to life, such as the glucose
ring (along with a single oxygen molecule), and the backbone of the polypeptide chains that form the different proteins in
the bodies of living things.
 THE CARBON CYCLE
Living things get almost all of the carbon they need from carbon dioxide, found in the
Earth’s atmosphere or dissolved in water.. On Earth, carbon is continually recycled between
the atmosphere, plants and animals. This system is called the carbon cycle. The cycle
involves several key processes:

Photosynthesis: Plants are known as carbon sinks because they absorb carbon dioxide from
the atmosphere and ‘fix’ or hold onto carbon in the form of glucose within their tissues.

Respiration: Plants are then eaten by consumers. When this happens, the carbon, now in the
form of carbohydrates, moves from plants to animals. These carbohydrates are used by the
consumers during respiration, in which glucose and oxygen are converted into carbon
dioxide, water and energy.

Decomposition and combustion: The processes of combustion (burning fossil fuels) and
decomposition (breaking down dead organic matter) also release locked-up carbon dioxide
back into the atmosphere.

Meanwhile, another major pathway takes place in the sea. Marine organisms use carbonates
to make their shells. These organisms die and their shells fall to the sea floor, eventually
forming limestone rocks. During volcanic eruptions and natural weathering, carbon dioxide
is released back into the atmosphere.
 WATER AND LIVING ORGANISMS

Water has a number of roles in living organisms:

• Solvent
• Temperature buffer
• Metabolite
• Living environment
 STRUCTURE OF WATER MOLECULE

• Water is a molecular compound, with molecular formula H2O. The

atoms in a water molecule are held together by strong covalent bonds.
These are very difficult to break.
•
The dot-and-cross diagram for a water molecule shows there are
two bonding pairs of electrons and two non-bonding pairs of
electrons.

• The four pairs repel one another, forming a tetrahedral pattern.

• The two electrons in each oxygen-hydrogen bond are not shared equally.
They are more strongly attracted to the oxygen atom.

• A hydrogen bond forms between a non-bonding pair of electrons on the

oxygen atom of one water molecule and the hydrogen atom ('positive
end') of another water molecule.
 WATER AS SOLVENT
• Most compounds with ionic bonding, e.g. metal salts, dissolve in
water. The oxygen atoms of water molecules are attracted to cations
(ions with a positive charge) and water molecules surround it. These
water molecules attract more water molecules and hydrogen-bonds
form between them. The result is a cluster of water molecules around
the ion. We say the ion is hydrated.

• Similarly anions (ions with a negative charge) become surrounded by

clusters of water molecules. This time it is the positive ends of the
water molecule, the hydrogen atoms, that are attracted to the anion.

• Of the important biological molecules only the non-polar lipids (fats

and oils) and large polymers (e.g. polysaccharides, large proteins and
DNA) do not dissolve in water.

• The water acts as a solvent for chemical reactions and also helps
transport dissolved compounds into and out of cells.
WATER FOR STRUCTURAL STABILITY OF MOLECULES
• The role of water in the stabilization of the 3D structure of nucleic acids is important because of the presence of
negatively charged phosphate groups. Phosphate-phosphate electrostatic repulsion is diminished in water.

• Water molecules are an integral part of all folded proteins. Some of them contribute to the structure and stability of
proteins by bridging, via hydrogen bonding, different functional groups present in the protein
 TEMPERATURE BUFFER
Cells host a huge range of chemical reactions. Many of these are
catalysed by enzymes. Enzyme activity is sensitive to temperature and
reactions only occur in a narrow range of temperatures. Water helps to
buffer temperature changes because of its relatively high specific heat
capacity

METABOLITE
Chemical reactions take place in cells. Collectively these reactions
together are called metabolism. The chemicals involved are called
metabolites. Water is a metabolite in many reactions, either as a
reactant or as a product of reaction. For example, it's involved
in photosynthesis, digestion and aerobic respiration.

LIVING ENVIRONMENT
Many organisms, such as fish, live in water and cannot survive out of it.
They have adapted to living in it.