CHEMICAL BASIS OF LIFE

CHEMICAL BASIS OF LIFE

• What is an atom?
An atom is the smallest indivisible units of
matter; each type of atom is also called a
chemical element. An atom is made up of
protons, electrons and neutrons. These
three subatomic particles characterize the
chemical properties of an atom.
Protons, Neutrons and Electrons

• The protons are positively charged, while

the electrons are negatively charged. Both
the protons and neutrons are confined to
a very small volume at the center of an
atom called the atomic nucleus. On the
other hand, electrons are negatively
charged and they can be found revolving
around the nucleus.
Protons, Neutrons and Electrons

• The Electron:
– The portion of the atom outside the nucleus
contains the electrons
– Each electron carries a charge of -1
– In normal neutral atom, the number of
electrons around the nucleus is exactly the
same on the number of protons in the
nucleus.
Protons, Neutrons and Electrons
- The + charge of protons and the – charge of
electrons cancel each other, making the
atom neutral.
- Electrons are not in fixed position outside
the nucleus.
- The distance of an electron from the nucleus
is a function of its energy. The higher the
energy, the greater its probable distance
from the nucleus.
 Protons, Neutrons and Electrons
- The volume within which an electron can be
found 90% of the time is known as the orbital of
the electron
- The energy level whose orbital is nearest the
nucleus is referred to as the K shell, which
contains only 2 electrons
- The next is L,M,N etc.
- Although the 3rd and successive levels can
accommodate more than 8, they are in stable
configuration when they contain only 8.
Atomic number

• This is one characteristic that distinguish one

chemical element from another. An atomic
number is the specific number of protons found
in that chemical element. For example hydrogen
has one proton, thus its atomic number is one.
Looking at the periodic table, one can also be
able to deduct the atomic number; elements in
the periodic table are usually numbered
according to their atomic numbers.
Cont..
Hydrogen (H) has an atomic number of one;
lithium (Li) has an atomic number of three and
so on.
• What is a molecule?
A molecule is made up of two or more atoms. A
good example is water, a molecule of water
contains two hydrogen atoms and one oxygen
atom, thus water can be represented as H2O.
Fill in the missing data
Element Atomic # Mass # No. of No. of No. of
protons neutrons Electrons

Carbon 6 12 6

Aluminum 13 14 13

Uranium 238 92

Chlorine 17 18 17

Argon 18 40

Nickel 59 28 28

Zinc 65 30 30
 Important Chemical Bonds

• The atoms of most element possess the

property of binding to other atoms too
form complex aggregates.
• When two or more atoms are bound
together the force of attraction that holds
them together is called chemical bond
Chemical Bonds

• Types of Chemical Bonds:

a. Ionic Bond
- formed by transfer of electrons
- atoms tend to form complete outer
shells by reacting with other atoms
Example of an Ionic Bond
What is an Ion?
• An atom is characterized as an ion when it
loses or gains one or more electrons. For
example, when a sodium atom (Na),
which has 11 electrons, loses one
electron, it becomes a sodium ion with a
net positive charge; it still has 11 protons,
but the loss of one electron leaves it
without only 10 electrons remaining.
• On the other hand a chlorine atom which has 17
electrons can gain an electron and become a
chloride ion with a net negative charge. This
chloride ion now has 18 electrons and 17 protons.
Ions that have a net positive charge are called
cations, while those that have a net negative
charge are called anions.
• A sodium ion with its positive charge and a
chlorine ion with its negative charge tend to
attract each other, since opposite charges attract,
Held together by the attraction called Electrostatic
Attraction
Classes of Ionic Compound
• 1. Acid – can be characterized simply as a
substance that increases the concentration
of hydrogen ions (H+) in water.
• 2. Base – a substance that decreases the
concentration of hydroxyl ions, OH-
– The degree of acidity or basicity (usually
called alkalinity) of a solution is commonly
measured in terms of value known as pH.
- On the pH scale, which ranges from 0 on the
basic end to 14 to alkaline end, a solution is
neutral if its pH is exactly 7.
- Substances with pH of less than 7 are acidic
( that is it contains a higher concentration of H+
than the OH- ions)
- the lower the pH the more acidic the substance.
- Substances with a pH higher than 7 are basic
(alkaline), that is it contains a higher
concentration of OH- ions than H+ ions.
- the Higher the pH the more basic or alkaline the
substance.
• Living matter is extraordinarily sensitive to
pH, functioning best when conditions are
nearly neutral.
• Most of the interior material of living cells
has a pH of about 6.8
• The blood plasma and other fluids that bathe
the cells in our own bodies have a pH of 7.2
- 7.3
• Special mechanism aid in stabilizing these
fluids, so that cells will not be subject to
appreciable fluctuation in pH.
• Among these mechanisms are certain
substances known as buffers, which have
the capacity to bond to H+ ions, thereby
removing them from solution whenever
their concentration begin to rise and
conversely to release H+ ions into solution
whenever their concentration begin to fall.
• Buffers help minimize fluctuations in pH,
since many of the biochemical reactions
normally occurring in living organism
either release or use up H+ ions.
• B. Covalent bond
- the joining of atoms by mutually sharing
one or more electron
- not all compounds are formed by actual
transfer of electrons from one atom to
another
- A compound may be formed by some
atoms sharing common electrons.
Water is a notable example of a molecule
formed by the sharing of electrons.

Oxygen atom needs two electrons to complete the L shell and the hydrogen
atoms needs one electron to complete the K shell. The electron from each
of the two hydrogen atom and the two electrons from the oxygen atoms are
shared, by the L shell and K shell respectively, thus forming a molecule of
water.
B. Double Bond – two electrons are shared.

Example:
H H
C C
H H
• C. Triple Bond – three electrons are
shared.

• Example:

H C C H
CLASSES OF ORGANIC MOLECULES

• What are organic molecules?

These are molecules that have their basic
skeleton made of carbons atoms,
hydrogen, oxygen and sometimes nitrogen
atoms. Generally organic molecules in the
body can be classified into one of four
groups: carbohydrates, lipids, proteins and
nucleic acid.
Carbohydrates

• Carbohydrates are the abundant of the

four main organic molecules. They fill
numerous roles in living things, such as
the storage and transport of energy
(starch, glycogen) and structural
components (cellulose in plants, chitin in
animals). Most carbohydrates taste sweet,
and the carbohydrates include the
substances known as sugars.
Cont..

• The simplest sugars are known as

monosaccharides, a good example of a
monosaccharide is glucose. Glucose is the
major monosaccharide found in the blood,
when two monosaccharide are linked
together they form a disaccharides. An
example of a disaccharide is table sugar
also known as sucrose.
Cont…

• When many monosaccharide are linked

together they form a molecule known as a
polysaccharide. An example of a
polysaccharide is glycogen. Glycogen is
found in animal cells and it serves as
primary short term energy storage in
animal cells. It is made primarily by the
liver and the muscles.
Lipids

• Lipids are fat-soluble, naturally occurring

molecules; unlike carbohydrates lipids are
insoluble in water. The main biological functions
of lipids include energy storage, acting as
structural components of cell membranes, and
participating as important signaling molecules.
Lipids can be divided into four subclasses
namely: fatty acids, triglycerides, phospholipids,
and steroids.
Proteins

• Proteins are large organic compounds

made up of amino acids (amino acids are
organic molecules that are made of
carbon, nitrogen and hydrogen atoms).
These amino acids are arranged in a linear
chain and joined together by peptide
bonds between the carboxyl and amino
groups of adjacent amino acid residues.
Example illustrating the formation
of a peptide bond
Cont…

• Peptide bonds are formed between the

amino and carboxyl group. These bonds
can be broken by hydrolysis to yield
individual amino acids. The figure on the
previous slide illustrates the hydrolysis of
a protein.
 PROTEIN STRUCTURE
Proteins are characterized of three types of
structures namely: primary, secondary, tertiary
and quaternary structure.
• Primary Protein Structure
The primary structure of a protein refers to
the number and sequence of amino acids in the
protein. The primary structure of a protein is
very important in the identification of a protein.
Diagram showing the primary
structure of a protein
Cont..

• Secondary Protein Structure

The secondary protein structure is the
specific geometric shape caused by
intramolecular and intermolecular
hydrogen bonding of amide groups. The
most common secondary structures of
proteins are the alpha helices and beta
sheet.
Diagram showing the secondary
structure of a protein
Cont…

• Tertiary Protein Structure

The third type of structure found in
proteins is called tertiary protein structure.
The tertiary structure is the final specific
geometric shape that a protein assumes.
This final shape is determined by a variety
of bonding interactions between the "side
chains" on the amino acids.
 These bonding interactions may be
stronger than the hydrogen bonds between
amide groups holding the helical structure.
As a result, bonding interactions between
"side chains" may cause a number of folds,
bends, and loops in the protein chain.
Different fragments of the same chain may
become bonded together.
• The figure on the next slide, shows the
difference between primary, secondary and
tertiary protein structures:
Different protein structures
Quaternary Protein Structure

• The quaternary protein structure involves

the clustering of several individual peptide
or protein chains into a final specific
shape. A variety of bonding interactions
including hydrogen bonding, salt bridges,
and disulfide bonds hold the various
chains into a particular geometry.
Figure showing quaternary protein
structure
Nucleic Acids

• These organic molecules are responsible

for the storage, expression, and
transmission of genetic information. It is
the expression of genetic information that
determines whether a cell is a muscle cell
or a nerve cell. There are basically two
classes of nucleic acids, deoxyribonucleic
acid (DNA) and ribonucleic acid (RNA).