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Concepts in Biology by C.C.Divina 19
This module discusses the basic
concepts of Chemistry vital in the
understanding of biological principles. It
features the important compounds in
living systems like water, carbohydrates,
lipids, proteins and nucleic acids. It also
has a short discussion on the work of
enzymes.
Concepts in Biology by C.C.Divina 20
Chemistry of Life
Chemical compounds make up living
things and they have specific functions
that contribute to the overall
performance of life activities. Within
a living system, these compounds
react with each other following the
principles of chemistry and physics.
Because Biology is a multi-science
discipline, it is helpful in
understanding the biological concepts
if you also understand the basic
principles of chemistry and. physics.
REVIEW OF BASIC CHEMISTRY
PRINCIPLES
The following are basic concepts in
Chemistry worth looking into to
facilitate your understanding of
Biology .
� Matters occupy space and have
weight.
� Elements are substances that cannot be broken into its simpler
component by ordinary means and
they are the simplest form of
matter. Most of these elements are
found in nature while others are
synthesized in the laboratory.
Concepts in Biology by C.C.Divina 21
Each element is characterized by
its atomic name and represented
most often by the first letter of
its name. Examples of elements and
their symbols are Hydrogen (H),
Carbon ©, Nitrogen (N), Oxygen (O)
and Chlorine) The list of elements
and their symbols are found in the
Periodic Table.
� The smallest amount of an element
is the atom. It is composed of
three sub-atomic particles, - the
protons, neutrons and electrons.
The positively charged protons and
the neutral neutrons are found the
central nucleus of the atom and
the negatively charged electron
roam around the nucleus in the
different energy levels called
shells or orbitals.
� The atomic number of an element is determined by the number of
protons in the nucleus, that
atomic weight is equivalent to the
number of protons and neutrons.
Each of proton and neutron
particle weighs approximately 1
dalton while the election has
negligible weight. In some atoms
of the same element, additional
neutrons are found thereby
increasing the atomic weight.
� Atoms with the same atomic number
but different atomic weights are
called isotopes. Isotopes of
Concepts in Biology by C.C.Divina 22
hydrogen are simple hydrogen (1H1),
deuterium (1H2) and tritium (1H
3).
The hydrogen atom
� Atoms are electrically neutral
because the number of protons in
the nucleus is equal to that of
the negatively charged electrons
in the orbital. The number of
electron in the outermost energy
shell determines largely the
physical and chemical properties
as well as the behavior of the
atoms. The valence of the atoms
determines the tendency to
combine with the other atoms in
a reaction to complete the
electrons in the outermost shell
and thus making the atom stable.
Concepts in Biology by C.C.Divina 23
� The forces of attraction between
the reacting atoms are called
chemical bonds. The differences
in the electron activity n the
outermost shell orbital leads to
the formation f different kinds
of chemical bonding and examples
of which are the electrovalent
or ionic bonding and the
covalent bonding.
� In ionic or electrovalent
bonding, there is the process of
transfer of electrons from one
atom to another. This transfer
of electrons makes the atoms
stable by completing the
electrons in the outermost
energy shell, this particular
bonding forms ionic compound
which readily disassociate into
charged particles called ions in
aqueous solutions. An example of
this compound is table salt or
NaCl, which easily ionizes into
Na+ and Cl- ions.
Concepts in Biology by C.C.Divina 24
� In covalent bonding, there is
the sharing of electron between
atoms, the shared electrons are
rearranged so that neither atom
loses or gains electrons. Carbon
with four electrons at its
outermost shell conveniently
forms covalent bonding with
other atoms, like hydrogen,
oxygen and nitrogen.
� When atoms in covalent bonding
do not share electrons equally,
the molecule produce behaves
like it has a positive and
negative end. This bonding is
known as polar covalent bonding
and produce a molecule called
dipoles, Water molecule (HOH)
is a dipole wherein, hydrogen
and oxygen share unequally the
electrons, so that the oxygen
end is slightly negative while
the hydrogen poles are slightly
positive.
� In chemical compounds, atoms
combine chemically in definite
proportions. Compounds are
classified into inorganic and
organic compounds. Inorganic
compounds do not usually contain
carbon but when present it is
not linked to hydrogen and
oxygen.
Concepts in Biology by C.C.Divina 25
� Organic compounds have carbons
attracted to the hydrogen and
oxygen and are found a part of
product of living things. The
chemical properties of compounds
are affected u the kinds of
atoms involved the bonds formed
and the spatial arrangement of
the atoms.
� When molecules of various
compounds come in contract, they
may form chemical bonds and
undergo chemical reaction. The
major types of reactions are
synthesis, decomposition and
displacement and rearrangement.
In synthesis, molecules combine
to form a complex one. An
example of this reaction is the
formation of carbohydrates from
simple sugars. The complex
material may be decomposed to
its simpler component by
decompositions as in th4
breakdown of proteins into its
amino acid components thee is an
exchange of molecules in
displacement reaction and change
in the position of atom in the
molecule if the rearrangement
reaction.
� The rate of chemical reactions
is influence by factors like (1)
the nature of the reactant (2)
concentration of the reactants
Concepts in Biology by C.C.Divina 26
(30 size of the reacting
molecule (4) temperature and (5)
presence of catalysts.
� Compounds vary in their
capability to react; some are
more reactive than the others do
some are inert. Faster moving
molecules have greater chance of
reacting because of collision.
Temperature increases kinetic
energy of the reacting molecules
thereby increasing the rate of
reaction catalyst increase the
rate of chemical reactions by
lowering the activation energy
of the reactions.
� Solutions may be acidic, basic
or neutral based on the presence
of hydrogen and hydroxyl ions or
other similar radical groups.
Acidity and alkalinity of the
solution is determined buy its
pH. Solutions with pH 7 is
neutral and those with lower pH
than 7 is acidic and those with
higher are basic. Buffers are
chemical systems that protect
solutions from changing to acid
or basic because of their
ability to neutralize the acid
or base introduced in the
system.
Concepts in Biology by C.C.Divina 27
Chemical Basis of Life
A living organism is chemically
composed of organic and inorganic
compounds. The organic compounds in the
organism are carbohydrates, protein
lipids and nucleic acids are organic
macromolecules. The inorganic
components of the organism are water,
salts and other minerals.
The protoplasm of the plant or
animal cell contains 75 to85% water, 10
to 12 % protein, 2 –3 % lipid and 1%
carbohydrate, 1% other inorganic
materials. The amount of water vary
from one cell to the other but water is
the most common molecule in proteins
are the most prevalent organic compound
in the cell.
Questions to Answer
1. Draw the atom of hydrogen, carbon and
oxygen showing the protons, neutrons
and electrons in the orbitals or energy
shells.
2. Give the factors that may hasten
chemical reactions. Cite a practical
example to show how each factor may
affect chemical reactions.
3. What is the difference between an ionic
compound from a covalent compound
Concepts in Biology by C.C.Divina 28
Water
Water is a solvent necessary for
life; it has a unique set of physical
and chemical characteristics that are
vital to the structure and functions of
cells as well the organisms. It is a
molecule composed of two atoms of
hydrogen and a molecule of oxygen
bonded covalently The electrons are
unequally shared wherein more are found
along the area of oxygen thereby
creating a negative pole and leaving
the hydrogen as positive pole. This
polar covalent bond of the water
molecule makes it most adapted to
performing its functions in living
systems.
Water is a dipole so that its
molecules tend to bond with each other
and form a lattice-like structure. The
bonds existing between these molecules
are hydrogen bonds. Each negative
oxygen pole is attracted to two or more
hydrogen ends of the other water
molecules thus forming a tetrahedron.
Because water is a polar covalent
compound it is highly cohesive and
adhesive, it has high specific heat and
heat of vaporization, strong tensile
strength and surface tension. All these
properties contribute to the role it
performs in living systems
Concepts in Biology by C.C.Divina 29
Water is good thermoregulator. It
prevents sudden extreme temperature
changes because it has high melting and
boiling points, high heat of fusion and
vaporization, high specific heat and
high surface tension. It means that a
lot of energy is required to bring an
increase in the temperature of the
water molecule. This large amount of
energy is needed to break down the
hydrogen bonds that are found between
water molecules. (See figure above of
water molecules and the hydrogen bonds
between them).
Water is an excellent solvent. It
serves as a natural solvent for
minerals and other important biological
compounds in the body. It is in a
liquid state at physiological
temperature,that it serves as a
dispersion medium of the colloid system
of the protoplasm. Its kinetic and
A. Water molecule showing the polar covalent
bonding
B. Water molecules showing the hydrogen bonds
between molecules
Concepts in Biology by C.C.Divina 30
Review Questions
1. Describe the molecular structure e of water. Relate its structure
with its properties.
2. Why is it better to say water is an “excellent solvent”
rather than it is a “universal solvent”? What do you think
will happen if everything is soluble in water?
3. Enumerate the different functions of water in living
systems and explain how water molecules are adapted in
performing these functions .Is it possible for the different life activities to proceed without water? Why or why not?
unique solubility properties both
result from the strong cohesive
characteristic of the water molecules.
Water does not readily
disassociate into ions so that the pH
of the cell or any living system is
maintained. Likewise water is used as a
transport system for the important
substances.
Water is very vital to living
things. The loss of water in living
system may mean death to the organisms.
It is although worth remembering that
water is not a source of energy in
living system.
The Organic Compounds
The organic macromolecules in
living systems are classified as
Concepts in Biology by C.C.Divina 31
carbohydrates, proteins, lipids and
nucleic acids. The basic framework of
the organic compounds is the skeleton
of carbon atoms, which may appear in
chains, rings, networks, or
combinations of these forms. These
compounds are very diverse and
versatile, existing in vitally
unlimited number and possessing varied
properties. This diversity is due to
the valence of carbon, which is 4; thus
allowing it to form four bonds with
hydrogen, oxygen, and nitrogen or even
another carbon. It can form single,
double and triple bonds.
The combinations of the weak and
strong bonds in organic molecules
account for their stability and
flexibility. The stability of the
organic compounds is shown by their
sluggish reactions with another with
water molecules or molecular oxygen,
its stability is due to the presence of
weaker bonds like hydrogen bond, ionic
bond and van der Waals bond. These
bonds allow the rearrangement of
molecular atoms.
Carbohydrates
Carbohydrates are organic
compounds made up of atoms of carbon,
hydrogen and oxygen, wherein there
exists a distinct ratio of 2 hydrogen
atoms to 1 oxygen atom. The general
Concepts in Biology by C.C.Divina 32
formula for carbohydrates is Cx(H2O)y, hydrates of carbons.
The simplest form of carbohydrates
are the simple sugars called
monosaccharides. Monosaccarese with
three carbons are called trioses, those
with five carbons like ribose and
deoxyribose are pentoses and those with
six carbons like glucose (blood sugar
or dextrose), fructose (fruit sugar)
and galactose are hexoses. These three
hexoses are isomers with the same
chemical formula of C6H12 O6.
Molecules of monoscaccharedes
react to form dissaccharides with the
removal of water molecule. This process
is called dehydration synthesis or
condensation (See figure below). The
bond formed between the two
monosaccharides is called glycosidic
bond. Examples of dissacharides are
maltose (glucose + glucose), sucrose or
table sugar (glucose + fructose ) and
lactose or milk sugar (glucose +
galactose).
Carbohydrates composed of many
monosacchareds are called
polysaccharides. Common examples of
these polymers of monosaccharedes are
starch, the storage form of
carbohydrates in plants, glycogen, the
storage form of carbohydrates in
animals and cellulose, the major
component of fibers and walls of plant
cell walls.
Concepts in Biology by C.C.Divina 33
Some common examples of
carbohydrates in plants and animals
Carbohydrates play important roles
in the physiology of cell. They serve
as structural component of certain
organelles and are basically the source
of usable and reserved energy. Glucose
is the immediate substrate for cellular
respiration.
Concepts in Biology by C.C.Divina 34
Lipids
Lipids are made up of carbon,
hydrogen and oxygen, howerver, there is
much less oxygen compared to carbon and
hydrogen. They are a large groups of
macromoleuces with common
characteristic of being soluble in non-
polar organic solvents, like alcohol
and ether but insoluble in water.
Lipids are stored in the cell
chiefly in the form of fat which cells
can synthesize from sugars. A fat
molecule consists of three fatty acid
molecules joined to one glycerol
molecule by condensation of dehydration
synthesis. The nature of the fat is
determined by the length of carbon
chain in the fatty acids and by whether
the acids are saturated or unsaturated.
Unsaturated fatty acids have
double bonds while the saturated fats
Review Questions
1. How would you know if the compound is a
carbohydrate given only it formula?
2. What do carbohydrates do in living systems?
3. Give other names of the following.
a. dextrose b. fruit sugar c. milk sugar
4. Identify the polysaccharides described
a. storage form of carbohydrates in plants
b. storage form of carbohydrates in animals
c. major component of fibers and plant cell wall
d. disaccharide from condensation of two
glucose.
Concepts in Biology by C.C.Divina 35
contain single bonds. Unsaturated fatty
acids common in plants than animals.
Examples of unsaturated fatty acids are
olive oil, peanut oil and corn oil and
saturated fatty acids common animals
are butter and lard.
Lipids are storage form of energy
that maybe hydrolyzed to give off heat
in times of body needs. Also parts of
the organism is made up of fats.
Examples of lipids containing three
fatty acids attached to a glycerol
molecule are true fate like
triglycerides found as stored fats in
adipose tissues in animals and oils in
plants. Phospholipids which are
component of cell membrane have a
phosphate group and two fatty acids
attached to glycerol. Example of this
is phophatidylcholine, common component
of membranes. Waxes are also lipids
with fatty acids and alcohol, examples
of which are the bee wax and the ear
Formation of fats through dehydration synthesis
Concepts in Biology by C.C.Divina 36
wax. Lipid without fatty acids are the
steroids. Examples of steroids are
cholesterol and sex hormones
testosterone, estrogen and
progesterone.
Proteins
Proteins are organic compounds
containing nitrogen aside from carbon,
hydrogen and oxygen. Phosphorus and
sulfur may also be present as
structural atoms. They are
macromolecules and are chains of
monomer compounds called amino acids.
Amino acids contain basic amino
group (-NH2) and acidic carboxyl group
(-COOH) but differ in their side
chains. See the figure below to show
some fo the amino acids. The presence
of both acidic and basic groups in the
amino acid molecules make them act as
buffers that maintain the pH of living
systems. Examples of amino acids are
lysine, glycine and glutamic acid.
Review Questions
1. Describe lipids and compare with carbohydrates.
2. Differentiate saturated from unsturated fats; fats from
sterols; glyceride from phospholipid.
3. Enumerate some examples of lipid compounds,
where they are found and what do they do?
Concepts in Biology by C.C.Divina 37
Two amino acids unite through the
amino group of one molecule and the
carboxyl group of the other through
dehydration synthesis. The bond formed
between these two amino acids is the
peptide bond and the molecule produced
is a dipeptide. A chain of three of
more acids is polypeptide. Long chains
of polypeptides are proteins which are
folded forming a three dimensions
configuration.
There are only a few known amino
acids, yet there are very many
different kinds of proteins formed from
them. This is possible because the
sequential arrangement of the amino
acids of the protein chain determines
the type of protin compound formed.
Using analogy, the Filipino alphabet
has 28 letters only and yet can form
thousands of words.
Concepts in Biology by C.C.Divina 38
Proteins are bonded by strong and
weak bonds. Thus, changes in
temperature, pH and other factors in
the environment easily denature protein
patterns. Denaturation is the loss of
the natural properties because of the
alteration of the structure of the
three dimensional protein molecule. A
good example to demonstrate
denaturation is the exposure of the egg
while or ova labumin to extreme change
in temperature, where a transparent,
sticky and almost colorless fluid is
altered to an opaque, white solid
state.
Proteins are the most abundant
organic material in living systems.
They are capable of storing energy in
the body which are released during the
body need. They are the basic
structural component of living things
Concepts in Biology by C.C.Divina 39
and thy act as enzymes and hormones.
Examples of the structural protein are
keratin and hemoglobin, contractile
proteins are myosin and actin of the
muscles; enzymes are amylase and
lipase.
Review Questions
1. Explain the following statements
a. Proteins are highly specific.
b. Proteins easily denature.
2. Where do you find the following protein
compounds
a. hemoglobin,
b. keratin
c. myosin
d. albumin
Concepts in Biology by C.C.Divina 40
Nucleic Acids
Nucleic acids are complex
molecules, larger than most proteins
and contain carbon, hydrogen, oxygen,
nitrogen and phosphorus which are
organized into compounds called
nucleotides. Nucleotides are made up of
three compounds, the nitrogenous base,
the pentose sugar and the phosphate
group.
There are two general
classification of nitrogenous bases –
the purines and pyrimidines. The
purines are the adenine and guanine and
the pyrimidines are the cytosine,
uracil and thymine. Adenine pairs with
uracil and thymine and guanine pairs
with cytosine. Nitrogeneous bases are
linked to the pentose sugar of the
nucleotide just like the phosphate
group.
The pentose sugars found in the
nucleotides are either ribose or
deoxyribose. These sugars determine
whether the nucleotide is a
ribonucleotide or deoxyribonucleotide.
Nucleotides function primarily as
structural components of nucleic acids.
Some of them are energy carriers in the
cells and examples of these are the
adenosine triphosphate (ATP) and
adenosine diphosphate (ADP) ATP is the
Concepts in Biology by C.C.Divina 41
immediate source of energy in living
systems. ATP is readily broken down
into ADP and PO4 and in the process
releasing energy.
Chains of nucleotides form nucleic
acids. The pentose sugar of one nucleic
acid binds with the phosphate of
another. This bonding between the
phosphate and pentose sugar in
nucleoties in the form of sugar-
phosphate backbone of the nucleic
acids. Nucleic acids are the chemical
components for the chromosomes that
Nitrogenous bases Nucleotides
Concepts in Biology by C.C.Divina 42
carry the information of life, the
nucleolus and ribosomes that synthesize
proteins in the cell.
Deoxyribose nucleic acid (DNA) is
a double helix structure with the
pentose deoxyribose and the bases
adenine, guanine, cytosine and thymine.
It is found in the nucleus of the cell,
specifically in the chromosomes, in the
mitochondria and chloroplasts. It is
used as a template in protein
synthesis.
Ribose nucleic acid (RNA) is a
single strand compound that has pentose
sugar ribose and the bases adenine,
guanine, uracil and cytosine. There
are three kinds of RNA, the linear
messenger RNA, the clover shaped
transfer RNA (tRNA) and the spherical
ribosomal RNA (rRNA). RNA is involved
in the process of protein synthesis and
is found in the nucleolus, ribosomes
and cytoplasm
Concepts in Biology by C.C.Divina 43
Differences of DNA and RNA
Criteria DNA RNA
Pentose
sugar
Deoxyribose Ribose
Nitrogenous
bases
Adenine –
Thymine
Guanine-
Cytosine
Adenine,
Uracil
Guanine
Cytosine
Shape Double helix Single
strand
Locations Nucleus,
Chloroplast
Mitochondrio
n
Nucleus,
Cytoplasm
Ribosomes
Review Questions
1. Draw a diagram of a nucleotide, DNA and RNA
using different shapes as symbols for the pentose
sugar, phosphate and nitrogenous bases
2. What are the functions of DNA and RNA.
Concepts in Biology by C.C.Divina 44
Summary table of major organic
compounds, their examples and functions CLASSES EXAMPLES FUNCTIONS
CARBOHYDRATES
MONOSACCHARIDE
glucose
energy source
DISACCHARIDE sucrose food component
POLYSACCHARIDE glycogen energy storage
LIPIDS
FATY ACID oleic acid energy source
TRIGLYCERIDE body fat energy storage
STEROL cholesterol steroid hormone
PHOSPHOLIPID lecithin membrane
structure
PROTEINS
CONTRACTILE myosin muscle
contraction
GAS CARRIER hemoglobin carry oxygen
CONNECTIVE collage cohesiveness
ENZME trypsin catalyst
NUCLEIC ACIDS
NUCLEOTIDE ATP energy carrier
DNA DNA information
storage,
protein
synthesis
RNA MRNA protein
synthesis
ENZYMES
Metabolism in living systems is
characterized by the myriad of
simultaneously occurring reactions.
Nearly all of these chemical reactions
Concepts in Biology by C.C.Divina 45
are catalyzed by proteins called
enzymes. Enzymes are called organic
catalysts. If enzymes were absent in
living systems, chemical reactions
would occur at very slow rate that life
activities could not be achieved.
Enzymes integrate reactions and provide
order in the metabolism without which
life would not be possible.
Enzymes hasten chemical reactions
by lowering the activation energy. This
means that the like possibility of
reacting materials to encounter and
react with each other is increased. The
association of enzymes and substrate
takes place in the active site of the
enzyme molecules. These active sites
are varied in configuration making
enzymes highly specific that particular
reactions and reactants require
specific enzymes. The theory explaining
this specificity is known as the Lock
and Key Theory. This states that
enzymes will react with substrates at
specific active sites and will only
react with particular substrates. The
reaction of the enzyme and substrate
results in the formation of the enzyme-
substrate complex which breaks and
releasing the product and the unaltered
enzymes. These organic catalysts are
not consumed in the reaction but are
reused in the next like reactions.
Enzyme activity is influence by
the temperature, pH, concentration of
Concepts in Biology by C.C.Divina 46
substrates and enzymes. As the
temperature increases, the rate of
enzyme activity also increases because
of the increase in the kinetic energy
of the reacting molecule. However, this
trend is observed up to a certain
temperature after which the trend is
reversed because of the proteinaceous
enzymes are slowly denatured. The
effect o pH is similar where the
different enzymes have varying optimum
pH of the activity. To cite an example,
digestive enzymes in the stomach
function best at very acidic pH which
other enzymes would be denatured.
Increased in the concentration of
enzyme or substrate result in the
increase enzyme activity.
Since enzymes denature, loss of
configuration of their active sites
means loss of their capabilities of
catalyzing reactions. This is one of
the reasons why a stable environment of
physiological equilibrium (homeostasis)
is important in living systems.
Concepts in Biology by C.C.Divina 47
Questions to Answer
1. What do enzymes do?
2. Explain the mechanism of action of enzymes?
3. Enumerate the factors that affect the
enzymatic activity and their effects?
What happens to enzyme activity if there is
homeostasis in the living system is not maintained?