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ECE 593-728
Chapter Two
• 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 neutrons 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.
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.
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
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.
• 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 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.
• 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.
• 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 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 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
• 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
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
• 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
Diagram showing the secondary
structure of a protein
• 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
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).