1.1.

Atoms and electronic structure

What is atom?
Plants, animals, chair, air, water, your books are all
made up of atoms. Atoms are the tiniest thing that
cannot be further broken both mechanically and
chemically.

What is atom made up of? Figure 1.1.1. Atomic structure of helium atom with
two protons, two neutrons and two electrons.
An atom is made of negatively charged electrons that
are traveling round the central nucleus which is
made up of positively charged protons and neutral
neutrons. So a normal atom is relatively neutral that
is it has no charge.

Electronic structure
An atom has shells or rings for the electrons to travel.
An atom may have more than one shell but some
atoms only have one shell. Each shell again has sub-
shells. The most interior shell or K shell has s-sub Figure 1.1.2. Atomic structure of carbon atom
shell. The next shell, M shell has s and p sub shells. with six protons, six neutrons and six electrons.
Electrons are not resting but are in constant motion.
The path which electrons travel is called a shell. By
understanding this, we can know the electronic
structure of an atom.
There are two electrons in s-sub shell and six in p-
sub shell. Hence, 2 in K and 8 in M. We write this as
2.8 (two dot eight). This shows the maximum amount
of electrons carried in the first two shells, K and M.
For example, if the atom has only one electron, then
its electronic structure would be 1 since it only has
Figure 1.1.3. Atomic structures of neon atom
one shell. If the atom has five electrons, its electronic and oxygen atom
structure would be 2.3 because first shell can carry
only 2 electrons which left with 3 and they are in the
second shell.

Valency
Valency of carbon is 4 because there are four
electrons in outermost shell that are unpaired and
deviate from 2.8 form. If the number of electrons in
outermost shell is beyond 5, subtract it from 8
because the outermost shell can have 8 electrons as
Figure 1.1.4. Atomic structure of hydrogen atom
maximum.
Valency tells us the combining power of an atom
with other atoms. High valency means that atom is
unstable and can willingly combine with other
atoms. Valency of zero means that atom does not
combine or react.
Carbon has valency of 4. This also tells us that it
needs 4 more electrons to fulfill its outermost shell to
exist with 8 electrons. This is stable. This is called
Octet Rule. Hydrogen has valency of 1 with only
one electron. A compound methane has one carbon
bonded to four hydrogen fulfilling the Octet. For,
hydrogen, it is stable with two electrons rule called
Duplet Rule. [State the valencies of atoms in Figure
1.1.3] Figure 1.1.5. Structure of Methane
 1.2. Elements
Elements are the simplest substance which are made
only of atoms.

The periodic table

There are 118 elements discovered over the years.
Elements are put into a chart called the periodic
table. It is arranged in groups (I, II, III, etc.) as rows
and periods (1, 2, 3, etc.) as columns. There are 18
groups and 7 periods. From left to right along the
group, the elements have greater electron affinity

O
(likeliness of electron by atom). Atomic size
increases (more shells are added) down the period.

VIIB
The elements in the same group have the same
valency.

VIB
Group IA elements are called Alkali metals and
include lithium, sodium and potassium with valency

VB
of 1. They are metals and have the lowest electron
affinity meaning they want to get rid of the only

IVB
electron in their outermost shells.
Group IIA elements are called alkaline earth metals
IIB IIIB
and include barium, magnesium and calcium with
valency of 2.
Group VIIB elements are halogens and include
IB

fluorine, chlorine and iodine with valency of 1. They

are non-metals and have the highest electron affinity.
VIA VIIA ———-VIII———

Whenever there is an electron, they want to accept it

and add it to their missing one in outermost shell for
stability since to fulfill their Octet, they only need
one electron.

Metals and non-metals

Elements are classified into metals and non-metals
depending on their properties. In the periodic table,
metals lie on the left side of the staircase line and the
VA

non-metals on the right.

IVA

Metals have positive valencies and are written with

positive sign in front of the number. For sodium,
IIIA

valency is +1. For calcium, it is +2. The reason for

this is that metals lose their electrons when forming a
IIA

compound. Before losing, there are electrons in the

outermost shells that are not paired. In case of
sodium, there is 1 extra electron in outermost shell
IA

which has to be given to other atom for stability.

Non-metals have negative valencies and are written
1

with negative sign. For chlorine, it is -1.

Hydrogen is a non-metal with valency of +1.
Figure 1.2.1. The periodic table
Metallic bond
Metallic bonding is the bonding between metal and
metal. Since metal atoms are larger and can easily
lose their valence electrons, the electrons on their
outer shell can be pooled and be distributed evenly
with other metal atoms. Electrons in the metallic
bonding are delocalized which means that the
electrons can move freely through the metal. This
give the conductivity of metals.
1.3. Chemical bonds
Ionic bond or electrostatic bond
Ionic bond or electrostatic bond exists between
metal and non-metals.
In ionic bonding, the electron from a metal is
completely transferred to a non-metal resulting in the
formations of ions, cations and anions.
Ions are atoms which is either short of electron or
electrons or extra electron or electrons than they
Figure 1.3.1. Ionic bond (NaCl)
should have. For example, normally sodium has one
electron in the outermost shell and the electronic
structure is 2.8.1. Chlorine has seven electrons in the
outermost shell and the electronic structure is 2.8.7.
During formation of ionic bond, one electron from
Na is transferred to Cl. Na becomes a cation which
has lost its one electron and donated as Na1+. Cl
becomes Cl1-, an anion. Then, a new product is
formed which is sodium chloride, NaCl molecule.

Covalent bond Figure 1.3.2. Non-polar covalent bond (Cl2)

A covalent bond exists between non-metals. An

electron or groups of electrons are shared between
each atom, not transferred completely from one to
another.
For example, chlorine gas or Cl2 is a covalently
bonded molecule. Chlorine atom is lacking one
electron in its outermost shell. The two atoms of
chlorine share their electrons with each other to form
Figure 1.3.5. Pauling scale of electronegativity of
a stable chlorine molecule.
some common elements in the periodic table
Electronegativity
Electronegativity represents the ability of an atom to
attract the shared pair of electrons towards itself. The
atom of greater electronegativity in that case would
have partial negative charge (δ-) and the other partial
positive charge (δ+). This creates a dipole in a
molecule.
For example, in water molecule, oxygen is more Figure 1.3.3. (µ) shows dipole moment which is a
electronegative than two hydrogen atoms. The measurement of electronegativity difference
electrons deviate to it. The bond between two between two atoms. The net direction of dipole
hydrogen and oxygen is polar covalent bond. moment of water is towards oxygen atom.
But, the bond between two chlorine atoms is a non-
polar covalent bond because there is dipole
formation between them
The dipole-dipole interaction exists between two
molecules with dipole. This is a bond between
molecules and is one of the intermolecular forces or
bondings.

Hydrogen bond
Figure 1.3.4. Hydrogen bond shown in
Hydrogen bond exists between an electronegative
dotted line between two water molecules
atom and a hydrogen bonded to either nitrogen,
fluorine or oxygen. It is often described as strong
dipole-dipole interaction.
1.4. Carbon
All living matters are made up of carbon as their Figure 1.4.1. Carbon showing atomic
element. All organic compounds contain this number on left corner and atomic
element. mass below the symbol.

Chemical properties
Carbon is a small element belonging to Group IVB in
the periodic table of period 2. Its atomic size or
radius is relatively small and thus can have many
forms without taking much space.
Carbon has two shells. Its atomic number is 6 thus it Figure 1.4.2. Allotropes of carbon showing
has 2.4 structure. Atomic number is number of molecular arrangement of carbon atoms.
protons or electrons in an atom. Carbon has valency
of 4 therefore it can form four bonds.

Physical properties
Carbon exists in the earth crust as coal, charcoal,
fossils. It has a density of 2.2 g/cm3 at 20oC. Its
melting point is 3652oC and its boiling point is
4827oC.
Carbon has two allotropic forms, crystalline and
amorphous. Crystalline carbons are diamonds and
graphites with flat shiny surfaces. Amorphous
carbons are coal, charcoal and coke with black
color.
Figure 1.4.3. Different functional groups of organic
compounds. For example, a compound with (-O-) is
Organic compounds an ether. This is ethyl ether with its ethyl groups
connected by ether group (CH3-O-CH3). This gives
All organic compounds have at least carbon, oxygen this compound properties of ether.
and hydrogen in them. All organic compounds have
core or backbone structure with carbon chain and
one or more functional groups attached to it.
Functional groups give characteristics of the organic
compounds. Some functional groups found
commonly in organisms are alcohol (-OH), amino Figure 1.4.4. A. Structure of methane. B. Structure
of carbon dioxide. C. Structure of carbon
group (-NH2), phosphate (-PO4) and carboxylic
monoxide.
group (-COOH). These groups can be attached to
carbon or other atoms on the backbone by bonds.

Carbon and organic compounds

Carbon containing molecules can be of many
shapes, ring, sheets, curved, etc. This is because
carbon can form a single bond, double bond and
triple bond with other atoms.
Methane (CH4) has one carbon bonded to four
hydrogen with four single bonds.
Carbon dioxide (CO2) has one carbon bonded to two
oxygen by two double bonds.
Carbon monoxide (CO) has one carbon bonded to
one oxygen by one triple bond.
[See figure 1.4.4 for methane, carbon dioxide and
carbon monoxide. Check the complete dot-cross
structure as shown in figure1.3.1 to see if all atoms
are in Octet.]
Figure 1.4.5. Different forms of carbon containing compounds.
(a) long straight chain (b) short molecule (c) ring shaped
1.5. Water
Water is the major component of all living things.
Water takes up about 60% of the human body.

Chemical properties Figure 1.5.1. Water molecule

Water is a molecule with one oxygen and two

hydrogen atoms bonded by two single polar covalent
bondings. Water is a polar compound which means
it tends to attract other molecules that comes close to
it provided that they are polar, too. That is why salt,
NaCl is attracted by the water molecule which
breaks it down eventually into Na and Cl ion
dissolving it. Fat on the other does not dissolve in
water because it is not polar. Polarity may be
different for different molecules. Water can form
hydrogen bondings with many polar compounds.

Physical properties
Water is a clear transparent substance that exists as
liquid at room temperature. Its density is 100g/cm3.
The more dense substance sinks in water compared
to water density and the less dense substance floats. Figure 1.5.2. Dissolving salt (NaCl) in water. NaCl is a compound
Its melting point is 0oC and boiling point is 100oC. with Na and Cl atoms joined together by ionic bonds. When
water intervenes, its partial negative charge of oxygen attracts
positive Na and partial positive charge of hydrogen attracts
Water in biological system negative Cl. NaCl has been dissociated.
Water plays a major role in organisms.
1. Water is a universal solvent. Almost all
substances dissolve in water.
2. Water acts as a medium for transport of
substances in the body.
3. Water takes up most part of the organism’s
body.
4. Many chemical reactions take place in
solutions. Water gives the dissociation state
of many large and complex compounds.
Large compounds are broken down into
smaller substances by reacting with water.
This is known as hydrolysis.
5. Water acts as coolant. Water has high heat
capacity and latent heat of vaporization. Figure 1.5.3
6. Water protects the body from
freezing due to its high latent
heat of solidification.
7. Water gives buoyancy in
some organisms such as fish
so that they swim in the
water without drowning.
8. Water acts as lubricant
providing slipperiness.
Water is usually used to breakdown
large substances as well as in
synthetic process. When joining two
o r g a n i c c o m p o u n d s , wa t e r i s
released. This process is called
condensation or hydration and is
common in synthesis and breakdown Figure 1.5.4. Synthesis and breakdown of carbohydrates
of carbohydrate.
1.6. Biomolecules
There are four basic biomolecules; carbohydrate,
lipid, protein and nucleic acid. Smaller substances
called monomers join together to form larger and
complex molecules called polymers.

Carbohydrate
Carbohydrate is a macromolecule made of carbon,
hydrogen and oxygen. It can be classified as
monosaccharide (simple sugar), disaccharide and
polysaccharide. Monosaccharides include glucose
fructose, galactose, mannose, etc. Disaccharide is
formed when two monosaccharides are joined by a
glycosidic bond. It include lactose, milk sugar
(glucose and galactose), sucrose, common sugar Figure 1.6.1. Different types of carbohydrates
(glucose and fructose) and maltose (two glucose
molecules). Polysaccharide is formed when millions
of monosaccharides are joined. It may be in straight
chain or branched. For example, starch.
Carbohydrate form the major source of energy for
the body. They also contribute to structural role as in
A B
cellulose of plants.

Lipids
Lipid consists of fats and oils, and wax. Fats and oils
are made of two monomers, glycerol and fatty acids.
Depending on the length and presence of double
bonds in fatty acid chain, fats and oils differ.
C
Triglyceride is an example of fat which is made of
one glycerol and three fatty acids. Some fats have
sphingosine molecule instead of glycerol. The bond Figure 1.6.2. A. Glycerol B. Fatty acid C. Triglyceride
between lipid monomers are ester bonds.
Lipids also act as energy source for the body. They
also incorporate in structural functions.

Proteins
Proteins are made of amino acids, monomers.
Proteins contain carbon, hydrogen, oxygen and
nitrogen generally. In some proteins, sulfur can be
found. When two amino acids join together by
peptide bond, they form a dipeptide. If more than 50 Figure 1.6.3.
amino acids are linked together, they form a protein,
a polymer.
Proteins play a major in body structure.

Nucleic acids
Nucleic acids are large molecules with carbon,
hydrogen, oxygen, nitrogen and phosphate.
Nucleotides are the monomers. Nucleotide is formed
from a five-carbon ring sugar (ribose) with its carbon
A B
number one attached to a nitrogenous base by
glycosidic bond and carbon number five attached to
a phosphate by ester bond. When nucleotides are
linked together, they form nucleic acid such as DNA
and RNA. Figure 1.6.4. A. Nucleotide B. Nucleic acid
Nucleic acids are the genetic materials that carry
hereditary informations.
1.7. Monosaccharides and disaccharides
Monosaccharides are the simple sugar that make up
larger carbohydrate molecules. They are monomers
of carbohydrate.

Classification
All monosaccharides have a general structure with
carbon, hydrogen and oxygen. The chemical formula
being CnH2nOn. If the monosaccharide contains six
carbons, the formula is C6H12O6.
The number of carbon may varies with one another.
Those with five carbons are called pentoses. Those
with six carbons are called hexoses. Hexoses may
also have various shapes. Those which are pentagon
are called furanose. Those which are hexagon are
called pyranose.
Glucose is a hexose and have pyran ring. Galactose Figure 1.7.1. Monosaccharides
is also a hexose and pyranose. They are similar and
the only difference is the position of hydroxy, OH
group at C4. They are epimers, two molecules with
similar chemical formula and structure with the only
difference being at one side. Fructose on the other
hand is a hexose but a furanose.
Ribose is a pentose. Other include xylose, arabinose,
deoxyribose, etc.

Glycosidic bonds
When two monosaccharides are joined, glycosidic
bond forms resulting disaccharide as end product.
When glucose and fructose are joined, sucrose is
formed. When glucose and galactose are joined,
lactose is formed. When two glucose molecules are
joined, maltose is formed.

Synthesis and breakdown

When two monosaccharides react with each other, a
disaccharide is formed. Hydrolysis of disaccharide
gives two monosaccharides.

Reducing sugars
Sugars when exist in straight chain form contains
aldehyde or ketone group. The carbon that used to
Figure 1.7.2. Disaccharides showing glycosidic bonds
part of aldehyde or ketone in straight chain now in
ring form is called anomeric carbon. When OH
group and O-R (R= functional group) are attached to
anomeric carbon, it is called hemiacetal.
Sugars with hemiacetal are reducing sugars because
cam reduce metal salts like Cu2+ in Benedict’s
solution. Glucose, fructose, maltose and lactose are
reducing sugars. Sucrose is not a reducing sugar. Figure 1.7.3. Reducing sugar. Galactose is opened
to show its aldehyde group. The blue arrow is
pointing anomeric carbon of hemiacetal.
 1.8. Polysaccharides
S i m p l e s u g a r s l i k e m o n o s a c ch a r i d e s a n d
disaccharides are usually soluble in water and taste
sw e e t . B u t c o m p l e x c a r b o hy d ra t e s l i k e
polysaccharides are usually insoluble in water and
they do not taste sweet. Examples are starch,
glycogen, cellulose and chitin.

Storage forms of carbohydrates

Starch and glycogen are storage forms of
carbohydrates usually glucose.
Starch is found in plant cells. Starch is made of
millions of glucose molecules. Starch consists of two
main groups, water soluble amylopectin and water
less soluble amylose.
Amylose comprises of long chain glucose residues
joined by α-1,4 glycosidic bond. It makes up about Figure 1.8.1. Amylose and amylopectin
20 to 30% of starch. The number glucose residues
ranges from 300 to 3,000. Amylopectin comprises of
2,000-20,000 glucose residues joined by α-1,4
glycosidic bond. Branching occurs in amylopectin
every 8 to 12 units. The branch point is connected by
α-1,6 glycosidic bond. About 24 to 30 glucose units
are contained in a branch.
Starch can be tested by iodine liquid. The liquid
turns blue if starch is present.
Glycogen is found in animal cells especially liver
and muscles. Its structure is similar to that of
amylopectin. Glycogen contains about 120,000
glucose molecules.

Structural role of polysaccharides Figure 1.8.2. Structural comparison of starch,

glycogen and cellulose
Cellulose is found in plant cell walls. It is made up of
thousand and millions of glucose linked together by
β-1,4 glycosidic bond into long chain. It gives
integrity to plant cells.
Chitin is a polysaccharide consisting primarily of Starch
glucose and is found in exoskeleton of arthropods. Amylase

Synthesis and breakdown

Starch is broken down by enzyme called amylase.
Hydrolysis of starch produces maltose. Maltose is
then hydrolyzed by maltase into glucose. Amylase is Maltose Maltase
found in saliva.
Glycogen is formed only when there is excess in
glucose than the body’s need for fuel. Synthesis of
glycogen is called glycogenesis. When there is too
little glucose or the body needs more glucose, Glucose
glycogen is broken down to supply glucose. This is
called glycogenolysis.
Figure 1.8.3. Hydrolysis of starch
Cellulose is part of dietary fiber. Cellulose is
indigestible by human and passes out in feces. It
prevents constipation.
1.9. Fatty acids
Fatty acids are carboxylic acids with straight carbon
chain containing from 4 to more than 20 carbons. Common name Number of carbon
They are usually found as structures combined with
Caprylic acid 8
polar group containing compounds such as sugar.
Fatty acids are non-polar and therefore can not exist Capric acid 10
in body fluids. When they bind to compounds with
Lauric acid 12
polar groups, the new compound formed can exist in
both water soluble and water insoluble states. This is Myristic acid 14
called amphipathic property of lipids. Palmitic acid 16
Fatty acids have a general chemical formula of
CH3(CH2)nCOOH where n is 2 or more. If the fatty Stearic acid 18
acid contains 4 carbons, the chemical formula is Arachidic acid 20
CH3CH2CH2COOH where n is 2.
Behenic acid 22

Classification of fatty acids Lignoceric acid 24

Cerotic acid 26
According to length, there are
1) Short chain fatty acids with five or fewer Table 1.9.1. Saturated fatty acids
carbons.
2) Medium chain fatty acids with 6 to 20 carbons. Common name Number of double bonds
3) Long chain fatty acids with 13 to 21 or more Oleic acid 1
carbons.
Linoleic acid 2
According to saturation, there are α-Linolenic acid 3
1) Saturated fatty acids
Saturated fatty acids do not have any Arachidonic acid 4
double bonds between carbon because they are
Table 1.9.2. Unsaturated fatty acids
fully saturated with hydrogens.
2) Unsaturated fatty acids
Unsaturated fatty acids contain one or more
double bonds between the carbons. Presence of
double removes one hydrogen.
There are two different forms with similar
chemical structure, trans and cis. Trans-form fatty
acids have the two hydrogens on either side of
the double bond. Thus, trans-form fatty acids
have similar configuration to that of saturated fat.
Cis-form fatty acids have the two hydrogens on
the same side of double bond. This causes the
chain to bend.

According to synthesis in the body, there are

1) Essential fatty acids Figure1.9.1. Saturation of fatty acids
These fatty acids cannot be synthesized in the
body and must be supplied in the diet. Linoleic,
and linolenic acids are two essential fatty acids.
2) Non-essential fatty acids
These fatty acids can be synthesized in the
body and need not be supplied by the diet. Fatty
acids except linoleic and linolenic acids are non-
essential fatty acids.

Fatty acid esters

Esters are formed when acids react with alcohols.
When fatty acids react with alcohol or alcohol-
containing compounds (glycerol), they form fatty
acid esters. Esters are not amphipathic.
1.10. Complex lipids
Lipids include fats and fat derivatives.
Fats comprise of fatty acid molecules and an alcohol.
Fatty acids can vary in length and saturation. Alcohol
can be glycerol or sphingosine.

Triglycerides
Triglyceride is composed of one glycerol molecule
and three fatty acids hence the name. Two of these
fatty acids are usually unsaturated. The bond
between glycerol, alcohol and fatty acid, acid is
called ester bond. Triglyceride is amphipathic.
Triglyceride is a major storage form of fat in adipose
tissues.

Phospholipids A
Phospholipid is composed of one glycerol molecule,
two fatty acids, a phosphate group and a base. A
glycerol, two fatty acids and phosphate form the
phosphatidic acid.
Phospholipid resembles the structure of a hair pin. It
is amphipathic and has a hydrophobic or water B
insoluble part or tail and hydrophilic or water loving
part or head. Hydrophobic tail is the fatty acid part
and the hydrophilic head is the glycerol, phosphate
and a base.
Phospholipids are named according to the types of
base attached. There are three bases, choline, serine,
ethanolamine. The most common phospholipid is
phosphatidylcholine or lecithin.
They are the major component of cell membrane
because they are amphipathic. They form a bilayer in
body fluid where the hydrophobic tails facing each
other in the interior and hydrophilic heads facing the
water and cytoplasm of cells.

Glycolipids
Glycolipid is a mixed compound of carbohydrate C
and lipid. It consists of a sphingosine, one fatty acid
and a carbohydrate. Carbohydrate is attached to
sphingosine.
They are usually found in the nervous system.
Cerebroside is a glycolipid with monosaccharide.

Fat derivatives Figure 1.10.1. A. Triglyceride B. Phospholipid (R= base)

Fat derivatives include cholesterol and eicosanoids. C. Cholesterol
Cholesterol exists as cholesterol ester bounded by
fatty acid in the cell membrane. Cholesterol is
important in providing integrity of cell membrane
and it is a component of many steroid hormones.
Eicosanoids are synthesized from arachidonic acids.
They involve in inflammatory response, immune
response and other important functions.
1.11. Amino acids
Amino acids are monomers of proteins, the building
blocks of life. They are about 300 amino acids in
nature but only 20 are used in the body for synthesis
of protein. Amino acid has a general structure with a
carbon linked to four different groups, hydrogen, a
straight chain or ring, an amino group on the left, a
carboxylic group on the right. The R or variable
group gives amino acids their characters. Figure 1.11.1. General Figure 1.11.2. Imino acid proline
R can be polar straight chain, non-polar straight formula of amino acid
chain, polar ringed, non-polar ringed, positively
charged or negatively charged. Among the 20,
proline is an imino acid.
There are ten essential amino acids, alanine, leucine,
lysine, histidine, isoleucine, tyrosine, valine,
methionine, phenylalanine and tryptophan.

Isoelectric pH
Amino acids exist as zwitterion (ion with both
positive and negative charge) at isoelectric pH. At
the pH below isoelectric point, the amino acid will
have net positive charge. At the pH above it, it will
have net negative charge. This effects the properties
of amino acids.
Figure 1.11.3. At isoelectric pH (middle diagram), the amino
acid contains both positive and negative charges and hence
electrically neural in nature. At lower pH (left diagram) when
there is plenty of H+, the zwitterion becomes positively
charged. At higher pH (right diagram) when there is plenty of
OH-, it exists as negatively charged ion.

Figure 1.11.4. List of 19 amino acids (highlighted part shows different R groups)
1.12. Peptides and proteins
Peptide bonds
When two amino acids are linked together, they
form a bond called peptide bond. The product is a
dipeptide molecule. The carboxyl end of one amino
acid reacts with the amino end of another giving off
water and the two molecules are joined.
Polypeptide is formed when more amino acids join
together. The left side of the peptide molecule will Figure 1.12.1. Formation of peptide bond
always have an amino group while the right will
always have a carboxyl group. The left side is termed
as N-terminal end and the right as C-terminal end.
When another amino acid comes, it reacts at the C-
terminus.

Proteins
Proteins are made up of many polypeptide chains.
Proteins play a major in body building such as tissue
formations.
A protein has four levels of structural organizations.
1) Primary structure
It is the sequence of amino acids. Each of the
molecule is linked only by peptide bonds.
2) Secondary structure
The polypeptide chain forms α helix or β
sheet. At about every five molecules, the first
amino acid forms hydrogen bond with the fifth
between the hydrogen and oxygen of C-terminus
and the fifth is bend nearer to the first. This forms
the secondary structure of proteins.
3) Tertiary structure
Proteins become functional as the polypeptide
chain begins to fold into a 3D shape. The folding
is caused by the bonding between the side chain
molecules of amino acids. The bonds include
hydrophobic interaction, hydrogen bond, ionic
bond and disulfide bond.
4) Quaternary structure
More than one polypeptide chains are linked
together into one unit by non-covalent bonds
and disulfide bonds.
According to products of proteins breakdown and
destruction, there are
(a) Simple proteins
On hydrolysis they yield only the amino acids
and occasional small carbohydrate compounds. Figure 1.12.2. Structural organization of proteins
Examples are: albumins, globulins and histones.
(b) Conjugated proteins
These are simple proteins combined with
some non-protein material in the body. Non-
protein substance is called prosthetic group.
Examples are: nucleoproteins, glycoproteins,
hemoglobins.
(c) Derived proteins
These are proteins derived from simple or
conjugated proteins by physical or chemical Figure 1.12.3. Hemoglobin with heme, prosthetic group
means. Examples are: peptides.
1.13. Enzymes
Enzymes are a form of protein that have special
functions. They are also known as biological
catalysis or catalytic proteins. Enzymes possess
tertiary or quaternary structures.

Properties of enzymes
Enzymes catalyze chemical reactions. Enzymes
make the reactions proceed faster i.e. they increase
the rate of chemical reactions. They do this by
lowering the transition energy, maximum energy Figure 1.13.1. Chemical reactions with enzyme and
required for a chemical reaction to occurs. At this without enzyme indicating the change in transition state.
point (transition energy), the substances that enzyme
catalyze are just converted to products.
If the substance is to be broken down, the enzyme
lower the transition energy at which is this substance
is broken down into its respective products. Amylase
is an enzyme that catalyzes the breakdown of starch
into maltoses.
Without enzymes, it would takes a long time for a
reaction to occur or it would not occur at all.
Enzymes are very specific on their targets, too.

Mechanism of enzymatic reactions

The substance that the binds to enzyme for catalysis Figure 1.13.2. Lock and Key Model
is called a substrate which will later forms products.
Enzymes have two main properties: catalytic
property and specificity.
Specificity of enzyme is important and that is why
enzymes found in certain place cannot catalyze
other reactions.
Catalytic property is when enzyme causes the
reactions to proceed faster. Enzyme has active site
where substrate binds to it. The active site and the
substrate must be complement in both shape and
size otherwise the substrate would not fit. This is
called Lock-and-Key model.
Even though enzymes may be involved, they are not
completely changed in the reaction i.e. enzymes Figure 1.13.3. Lock and Model showing enzymatic
may be changed during the reaction but remain the reactions
same before and after the reactions.

Coenzymes
Coenzymes are non-protein organic substances that
help the activities of enzymes. Coenzymes are
usually derivatives of vitamin B complex such as
NAD/NADH (NADH is just a reduced form of NAD).
Enzyme without coenzyme in it is called
apoenzyme. After binding of coenzyme, it is called
holoenzyme. Not all enzymes require coenzymes
though.

Figure 1.13.4. Alcohol dehydrogenase enzyme requires

NAD as coenzyme in order to convert alcohol into
acetaldehyde. NAD is converted into NADH.
 1.14. Nucleotides
Nucleotides are monomers of nucleic acids which is
made up of carbon, hydrogen, oxygen, nitrogen and
phosphate. A nucleotide comprises of ribose or
deoxyribose sugar, nitrogenous base and phosphate.

Nitrogenous bases
Nitrogenous bases that are included in nucleotides
are of two groups; purine: adenine (A), thymine (T)
and pyrimidine: cytosine (C), guanine (G) and uracil
(U). They are attached to the C1 of ribose by N-
glycosidic bond.

Nucleosides
The ribose-base complex is called nucleoside. If the
base is adenine, the nucleoside is called adenosine.
If it is thymine, it is called thymidine. If it is cytosine,
it is cytidine and if it is guanine, it is guanosine.

Nucleotides
The phosphate group is attached to C5 of ribose by
ester bond. When there is one phosphate, it is called
mononucleotide. When there are two phosphate
groups, it is called dinucleotide and trinucleotide
when there are three.
The nucleotides are named by their nucleoside and
number of phosphate attached. Mononucleotides
include adenosine monophosphate (AMP), Figure 1.14.1.Nucleosides
thymidine monophosphate (TMP), cytosine
monophosphate (CMP) and guanosine
monophosphate (GMP). [Figure out the names of the
dinucleotides and trinucleotides]
If the sugar is deoxyribose, the nucleosides will be
called with deoxy- in front of the names listed above.

Adenosine triphosphate (ATP)

Adenosine triphosphate or ATP is an important
nucleotide in the body. [Figure out its structure] ATP
is the major currency in the body because it carries a
lot of energy which is needed in order for a cell to Figure 1.14.2.Nucleotide
function properly. The last phosphate is bonded to
the second phosphate by a very high energy bond.
ATP makes the energy-dependent reactions happen.
When it is needed, it breaks off its last chemical
bond to the substance that needs energy or
sometimes the entire phosphate group.
ATP is resynthesized when the ADP and P reacts
during respiration where the energy is produced. This
energy is again used in other reactions.
Endergonic reactions require ATP in order to proceed
and they are usually catabolic pathways. Exergonic
reactions release ATP during their reactions and they
are usually anabolic.
1.15. Nucleic acids
When the nucleotides are joined together into long
chains, they form nucleic acids.

Nucleic acid chain

One nucleotide can be linked to another by a special
bond called phosphodiester bond. The phosphate
group of C5 of a nucleotide is linked to the OH of
C3 of another nucleotide by ester bond.
The long nucleotide chain runs in a direction which
is denoted as 3’ where the OH of C3 is and 5’ where
the phosphate of C5 is located. Thus, the bond is
also called 5’,3’-phosphodiester bond.

Figure 1.15.1.DNA (one side)

Deoxyribonucleic acid
Deoxyribonucleic acid or DNA is a double helical
polynucleotide chains that run parallel but in
opposite directions. Each nucleotide is composed of
a deoxyribose sugar, a base and a phosphate. DNA is
the genetic material that carries hereditary
informations.
The sugar and phosphate forms the backbone of the
structure. The base sequence forms the genetic
information. The sequence varies with each
individuals. Adenine from one polynucleotide chain
always pairs up with guanine from another chain.
Thymine pairs up with cytosine. These base pairs are
linked by weak hydrogen bonds. There are two
hydrogen bonds between A and T, and three
hydrogen bonds between C and G.

Ribonucleic acid
The differences from DNA include
1) RNA having single polynucleotide chain,
2) Uracil instead of thymine which pairs with Figure 1.15.2. DNA
cytosine,
3) Does not involve in heredity but transfers the
genetic material of DNA for protein synthesis.

Figure 1.15.3.DNA and RNA

Practice Questions
I. Choose the correct answers for each statements.

1.5. Water
1. What is true about water?
A. Two hydrogens are covalently bounded
to an oxygen by hydrogen bonds.
B. Water has dipole and is polar.
C. Water has very heavy compared to fat
due to its polarity.
D. Water and salt forms dipole-dipole
interaction.
2. Water is very important for living things
because
A. It can help maintain body temperature.
B. It can protects the body from freezing.
C. It react with many molecules and allows
chemical reactions to occur.
D. It fights off foreign substances.
1.6/1.11/1.12. Proteins
1.6/1.7/1.8. Carbohydrates
1. Chemistry of carbohydrates
A. Hexose: five carbon sugar
B. Hexose: sugar with six carbons
C. Hexose: sugar with hexagon ring
D. Pentose: six carbon sugar
2. Carbohydrates metabolism
A. Glycogen is the storage form of glucose.
B. Starch is the storage form of glucose.
C. Glycogenolysis occurs when there is low
amount of glucose.
D. Glucose molecules are linked by α-1,4
glycosidic bond to form glycogen.
3. Functions of carbohydrates
A. Energy source
B. Structure of cell wall
C. Immunity
D. Growth and differentiation
4. Glucose
A. Is a reducing sugar.
B. And fructose forms lactose.
C. And galactose are linked by α-1,4
glycosidic bond to form maltose.
D. Is stored as glycogen in plants.
1.6/1.9/1.10. Lipids
1. Importance of lipids
A. They are primary source of energy in the
body.
B. They participate in structural role.
C. They involve in inflammation.
D. They play a role as hormones.
2. Fatty acids are
A. Monomers of TAG.
B. Major form of energy among lipids.
C. Stored as TAG in adipose tissues.
D. Unsaturated if double bond is present
between carbons.
3. Which is/are not true?
(Y)+(N) fatty acids+(Z)= (X)
A. Y= Glycerol, N= 2, Z= Phosphate+Base
X= Phospholipid
B. Y= Sphingosine, N= 1, Z= Sugar
X= Glycolipid
C. Y= Sphingosine, N= 2, Z= Sugar
X= Glycolipid
D. Y= Glycerol, N= 2, Z = Phosphate
X= Phosphatidic acid
1. There are plenty of proteins in our body with
varying functions. But the determination of
protein function is at
A. Primary level
B. Secondary level
C. Tertiary level
D. Quaternary level
2. Zwitterion
A. Amino acid, glutamic acid exists as both
cation and anion at pH 4.
B. At pH 9, glycine exists as anion.
C. At pH 2.4, valine exists as cation.
D. Lysine is positively charged amino acid.
3. Protein or carbohydrate diet
A. If you need energy, protein should be
taken.
B. If you need energy, carbohydrate should
be taken.
C. Proteins give amino acids, the building
blocks.
D. Protein does not give energy.
4. Keratin is a protein found in hair and skin.
Which of the following might be true about
keratin?
A. It is not water soluble.
B. It has either tertiary or quaternary
structure.
C. It is made up of amino acids.
D. It forms protective structure of hair and
skin.
1.13. Enzymes 4. State the metabolism of carbohydrates.

1. Which of the following is/are not properties 1.6/1.9/1.10. Lipids

of enzymes?
A. Enzymes are very specific.
B. Enzymes act on random substrate.
C. Enzymes are energetic.
D. Enzymes take part in chemical reactions.
2. Enzymes are so important because
A. They give energy.
B. They speeds the reactions up.
C. They lower the transition energy.
D. They do not change the substrate.
3. Specificity of enzyme may be due to
A. Compartmentation of enzymes
B. Substrate binding affinity
C. Number of enzymes
D. Number of substrate
5. List five functions of lipids.
6. Draw different types of sphingosine based
lipids generally. [chemical structure need not
be drawn]
1.6/1.11/1.12. Proteins
7. State the structure and functions of protein.
8. Explain why proteins are not used as energy
suppliers.
1.13. Enzymes
9. Explain why enzymes are essential for life.

1.6/1.14/1.15. Nucleic acids 1.6/1.14/1.15. Nucleic acids

1. What is/are true about ATP? 10. State the structure of RNA.
A. It carries a lot of energy.
B. It takes part in DNA synthesis.
C. It is the major source of energy.
D. It gives rise to AMP during respiration.
2. DNA has these functions that RNA does not
which are
A. Protein synthesis
B. Genetic transcription
C. Replication
D. Translation
E. Transfer genetic materials
3. According to Chargoff’s rule which states that
number of purine is always equal to number
of pyrimidine, so if there is 30% of base A,
there is ——— of base C.
A. 30%
B. 40%
C. 60%
D. 20%
4. Which represents “nucleoside”.
A. Adenine
B. DNA
C. AMP
D. Cytosine

II. Write short paragraphs for each question.

1.5. Water
1. State the physical, chemical and biological
properties of water.
2. Draw and explain the molecular structure of
water.

1.6/1.7/1.8. Carbohydrates
3. Name three monosaccharides that you know.
Classify them as hexose or pentose.