The Chemical Basis of

Life
SARAH JANE M. BALANA
DEPARTMENT OF BIOLOGY COLLEGE OF SCIENCE
POLYTECHNIC UNIVERSITY OF THE PHILIPPINES

Nature of Molecules
Atom basic structural unit of matter.
Atomic nucleus (nucleus)

Protons positively charged subatomic particles

Neutrons uncharged subatomic particles

Electrons negatively charged subatomic particles that orbit the atomic nucleus.

An atom has an equal number of electrons and protons and is therefore

electrically neutral.
~92 types occur naturally, each forming the structural unit of a different
element.

Structure of Atoms

Model of a helium atom

Nature of Molecules
Element substance that can neither be broken down
nor converted to other substances by ordinary chemical
means.
Characteristics and chemical properties are determined by the
atomic number - # of protons in the nucleus and the
configuration of its subatomic particles (distribution of
electrons).
Example: Hydrogen atom has one proton in its nucleus,
therefore its atomic number is 1.

Isotopes atoms of the same element but with

different number of neutrons.
Examples: Carbon-12, Carbon-13, and Carbon-14 are three
isotopes of the element carbon with mass numbers 12, 13, and
14 respectively.

Nature of Molecules
Among the three subatomic particles, only electrons are
involved in the chemical activity of atoms.
Electrons vary in the amount of energy they possess the
farther an electron is from the positively charged nucleus, the
greater its energy.
Electrons move around the nucleus only at certain energy
levels, called electron shells.
Depending on an elements atomic number, an atom may have one,
two, or more electron shells surrounding the nucleus.

It is the number of electrons in the outermost shell (valence

shell) that determines the chemical properties of an atom.
Atoms whose outer shells are not full (have unpaired electrons) tend to
interact with other atomsthat is, to participate in chemical reactions.
Atoms which have full outer electron shells are chemically inert
(unreactive).

Electron shells in atoms

Chemical bonds
When two atoms with incomplete outer shells react, each
atom will share, donate, or receive electrons, so that both
partners end up with completed outer shells. These
interactions usually result in atoms staying close together,
held by attractions known as chemical bonds.
Two or more atoms held together by covalent bonds form
a molecule.
Common types of bonds in biological molecules:
Covalent bond
Polar bond
Non-polar bond
Ionic bond
Hydrogen bond

Covalent bond
Strongest kind of bond
Sharing of electrons (equal or unequal)
Non-polar covalent bond equal sharing of electrons
Example: H2 gas, O2 gas
Polar covalent bond unequal sharing of electrons
Example: H2O

Non-polar covalent bonding between H atoms

Polar covalent bonding between H and O atoms.

Ionic bond
Attractions between ions of opposite charge.
Electrons are transferred, creating positive and negative
ions that attract one another.
Example: NaCl (table salt)

Hydrogen bond
Weakest kind of bond
The slightly positive charged on a hydrogen atom involved
in a polar covalent bond attracts the slightly negative
charge on an oxygen or nitrogen atom involved in a polar
covalent bond.
Example: Hydrogen bond between two H2O molecules.

Hydrogen bonding between water (H2O) molecules

Biological Molecules
Any molecule produced by living organisms.
Carbohydrates
Lipids
Proteins
Nucleic acids

Carbohydrates
Class of molecule composing of 1 carbon atom, 2 hydrogen
atoms, and 1 oxygen atom (CH 2O)
Simplest form (building blocks / monomers) are the
monosaccharides.
Can be in the form of disaccharide, oligosaccharide,
polysaccharide.
Joined by glycosidic bonds covalent linkage formed between
monosaccharides by a dehydration reaction.
Commonly isomers - most of their forms have the same
molecular formula but are different in molecular structure (i.e.
glucose and fructose)
Can be classified according to:
Location of carbonyl group: Aldose (aldehyde sugar) or ketose (ketone sugar)
Size of carbon skeleton (typically 3-7 carbons long): Trioses, pentoses, hexoses

Structure and Classification of some monosaccharides

Carbohydrates
Monosaccharides
G: monos = single, sacchar = sugar
Generally have molecular formulas that are multiples of
the unit CH2O
Most common monosaccharide is glucose (C6H12O6)
Serves as major fuel for cellular work and raw material for
the synthesis of other types of small organic molecules.
Act
as
monomers
to
form
disaccharides
or
polysaccharides.
Examples: glucose, fructose, galactose

Carbohydrates
Disaccharides
Consist of 2 monosaccharides linked together by glycosidic
bond
Examples:
Maltose (malt sugar) = glucose + glucose
Sucrose (table sugar) = glucose + fructose
Lactose = glucose + galactose

Carbohydrates
Polysaccharides
Macromolecules, polymers with a few hundred to a few
thousand monosaccharides joined by glycosidic linkages
Serves as storage and building material for structures that
protect the cell or the whole organisms.
Storage polysaccharides:
Starch stored within plastids of plants and
Glycogen stored in liver and muscle cells.

Structural polysaccharides:
Cellulose major component of plant cell wall
Chitin major component fungal cell wall and exoskeleton in
arthropods

Architecture and function are determined by its sugar

monomers and by the positions of its glycosidic linkages.

cell wall

cytoplas
m

Starch grains or amyloplast (pointed

by the red arrows) within potato cells.

Cellulose in plant cells

Grasshopper is molting.
Exoskeleton is made up of
chitin.

Lipids
Group of hydrophobic molecules
Varies in form and function: waxes, pigments, fats,
phospholipids, and steroids.
Monomers are fatty acids varies in length and the
location of double bonds
Saturated fatty acid
Unsaturated fatty acid

Molecules are joined together by ester bonds

A fatty acid has a long carbon

skeleton, usually 16 or 18
carbon atoms in length. The
carbon at one end of the fatty
add is part of a carboxyl group
(the functional group that gives
these molecules the name fatty
acid). Attached to the carboxyl
group is a long hydrocarbon
chain. The relatively nonpolar CH bonds in the hydrocarbon
chains of fatty acids are the
reason fats are hydrophobic.

Saturated fatty acids

No double bonds between carbons atoms.
Tends to be solid at room temperature
Ex.: animal fats, lard, butter
Unsaturated fatty acids
Has one or more double bonds, resulting to the formation of a
kink in its hydrocarbon chain.
Liquid at room temperature.
Ex.: Oils (plant and fish fats)

Lipids
Fats
Consist of glycerol and fatty acids.
Glycerol is an alcohol with three carbons, each bearing a hydroxyl
group.
Functions for energy storage and insulation.

Phospholipids
Composed of two fatty acid chains (hydrophobic) attached to glycerol and a
phosphate group (hydrophilic).
Amphipathic (dual nature)
Major component of the cell membrane

Steroids
Characterized by a carbon skeleton consisting of four fused rings
Ex.: Cholesterol synthesized in the liver (vertebrates) and is a common
component of animal cell membranes and the precursor from which other
steroids are synthesized

Structure of Phospholipids
Consisting of two hydrophobic
fatty acid tails attached to
glycerol. The third hydroxyl
group of glycerol is joined to a
phosphate group, which has a
negative
electrical
charge.
Additional
small
molecules
(choline), which are usually
charged or polar, can be linked
to the phosphate group to form
a variety of phospholipids.

When phospholipids are

added to water, they selfassemble into doublelayered aggregates
(bilayer)that shield their
hydrophobic portions from
water.

Structure of Steroids
Carbon skeleton consisting of four fused rings. They may vary
in the chemical groups attached to this ensemble of rings.

Proteins
Monomers are amino acids joined together by a peptide
bond.
Consists of one or more polypeptides, each folded and
coiled into a specific three-dimensional structure.
Its structure determines its function.
Its depends on its ability to recognize and bind to some
other molecule.

Amino acids are consisting of an amino group, a

carboxylic group, a hydrogen atom, and a variable
group (R-group - differs with each amino acids)
attached to a central carbon atom.

The physical and chemical

properties of the side chain
(R-group)
determine
the
unique characteristics of a
particular amino acid and its
function.
Example:
Hydrophobic = amino acids
with nonpolar side chains
Hydrophilic = amino acids
with polar side chains
Acidic = amino acids with
side
chains
that
are
generally negative in charge
(presence of a carboxyl
group)
Basic = amino acids which
have amino groups in their
side
chains
that
are
generally positive in charge.

Nucleic acids
Polymers composed of nucleotides joined by
phosphodiester bonds.
Nucleotide component:
Five-carbon sugar ring (ribose / deoxyribose)
Phosphate group
Nitrogenous base (pyrimidine / purine)

Nucleotide

Types of nucleic acids

Deoxyribonucleic
acid (DNA)

Ribonucleic acid
(RNA)

Structure

double helix

single helix

Sugar
componen
t

deoxyribose

ribose

Nitrogeno
us bases

adenine, guanine,
cytosine, thymine

adenine, guanine,
cytosine, uracil

Function

carries the genetic

information

protein synthesis

DNA Structure
1. The molecule is composed of two
chains of nucleotides.
2. The two chains spiral around each
other to form a pair of righthanded helices*.
3. The two chains comprising one
double helix run in opposite
directions; that is, they are
antiparallel**.
*In a right-handed helix, an observer looking down the central
axis of the molecule would see that each strand follows a
clockwise path, as it moves away from the observer.
** Thus, if one chain is aligned in the 5 3 direction, its
partner must be aligned in the 3 5 direction.

DNA Structure
4. The sugarphosphatesugar
phosphatebackbone
of
each
strand is located on the outside of
the molecule with the two sets of
bases projecting toward the center.
5. The bases occupy planes that are
approximately perpendicular to the
long axis of the molecule. Together,
the helical turns and planar base
pairs
cause
the
molecule
to
resemble a spiral staircase.

DNA Structure
6. The two strands are held together
by hydrogen bonds between each
base of one strand and an
associated base on the other strand.
7. The distance from the phosphorus
atom of the backbone to the center
of the axis is 1 nm, thus, the width
of the double helix is 2 nm.
8. A pyrimidine in one chain is
always paired with a purine in
the other chain. This arrangement
produces a molecule that is 2 nm
wide along its entire length.

DNA Structure
9. The spaces between adjacent
turns of the helix form two
grooves of different widtha wider
major groove and a more narrow
minor groovethat spiral around
the outer surface of the double
helix.
10. The double helix makes one
complete
turn
every
10
residues / 3.4 nm.
11. The two chains of the double
helix are complementary to one
another.

Functions of the DNA

1. Storage of genetic information. As genetic material, DNA
must contain a stored record of instructions that determine all
the inheritable characteristics that an organism exhibits. In
molecular terms, DNA must contain the information for the
specific order of amino acids in all the proteins that are
synthesized by an organism.
2. Replication and inheritance. DNA must contain the
information for synthesis of new DNA strands (replication).
DNA replication allows genetic instructions to be transmitted
from one cell to its daughter cells and from one individual to
its offspring.
3. Expression of the genetic message. DNA is more than a
storage center; it is also a director of cellular activity.
Consequently, the information encoded in DNA has to be
expressed in some form that can take part in events that are
taking place within the cell. More specifically, the information
in DNA must be used to direct the order by which specific
amino acids are incorporated into a polypeptide chain.