TOPIC 3

MOLECULES OF LIFE

LEARNING OUTCOMES
3.1 WATER

a) Explain structure,
properties /roles as
constituent of life and
solvent
b) Described properties
of water-

WATER
Structure of a water
molecule
A water molecule
consist of an oxygen
atom and two
hydrogen atoms
The two hydrogen
atoms are combined
with the oxygen atom
by sharing of electrons

 The three atoms

form a triangle,
not a straight line

 The water molecule

is electrically
neutral, but there is
a net negative
charge on the
oxygen atom and a
net positive charge
on both hydrogen
atoms.

 A molecule carrying such an unequal

distribution of electrical charge is called a
polar molecule.

 The positively
charged hydrogen
atoms of one water
molecule are
attracted to the
negatively charged
oxygen atoms of
nearby water
molecules by
forces called
hydrogen bonds.
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 Hydrogen bonds are weaker than covalent

bonds.
But there are strong enough to hold water
molecules together.

10

 Because of their hydrogen bonds,

water molecules are attracted to
charged particles or charged
surfaces.
In fact, hydrogen bonds largely
account for the unique properties
of water.

11

Properties of water as vital

constituent of life

12

Water as a universal solvent

powerful solvent for polar substances.

These include ionic substances like

sodium chloride (Na+ and Cl-), and also
organic molecules with ionized groups
(such as the carboxyl group COO- , and
amino group NH3+).
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 These cations (negatively charged ions)

and anions (positively charged ions)
become surrounded by a shell of
orientated water molecules.

14

 Soluble organic molecules like sugars

dissolve in water due to the formation of
hydrogen bonds between the water
molecules and the slightly charged
hydroxyl (-OH) groups in these organic
molecules.
Once dissolve, the molecules of a
substance are free to move around.

15

 This makes them more reactive chemically

than when they form part of an undissolve
solid.

16

 At the same time, non-polar substances

are repelled by water, as in the case of oil
on the surface of water. Non-polar
substances are hydrophobic.

17

Viscosity of water
It has a low viscosity
This unique property makes it suitable
medium of transportation in living
organisms.

18

Specific heat capacity

A lot of energy is required to raise the
temperature of water.
This is because, much energy is needed
to break the hydrogen bonds that restrict
the movement of water molecules.

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 This property of water is known as its specific

heat capacity.
The specific heat capacity of water is the highest
of any known substance.
Consequently, aquatic environments like stream
and rivers, ponds, lakes and seas are all very
slow to change temperature when the
surrounding air temperature changes.
20

 Aquatic environments have more stable

temperatures than terrestrial environments do.
Another consequence is that cells and the
bodies of organisms do not change temperature
readily.
Bulky organisms particularly tend to have a
stable body temperature in the face of a
fluctuating surrounding temperature, whether in
extremes of heat or cold.
21

Latent heat of vaporization of water

The hydrogen bonds between water
molecules make it difficult for them to be
separated and vaporized.
This means that much energy is needed
to turn liquid water into water vapor.

22

 This amount of energy known as the

latent heat of vaporization, and for
water it is very high.
Consequently, the evaporation of
water in sweat on the skin, or in
transpiration from green leaves,
causes marked cooling because the
escaping molecules take a lot of
energy with them.
23

 And since a great deal of heat is lost

within the evaporation of a small
amount of water, cooling by
evaporation of water is also
economical on water.

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 The amount of heat energy needed to

melt ice is very high, and the amount
of heat that must be removed from
water to turn into ice is also great.

26

 This amount of heat energy is known as

the latent heat of fusion.
Again, it is very high for water. This means
that both the contents of cells and the
water in the environment are slow to
freeze when it very cold.

27

Effect of temperature on water

density
Most liquids contract on cooling, reaching their
maximum density at their freezing point.
Water is unusually reaching its maximum density
at 4C.
As water freezes, the ice formed is less dense
than the cold water around it. The ice floats on top.
The floating layer of ice insulates the water below.
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 This is why the bulk of ponds, lakes or the

sea rarely freeze solid.
Aquatic life can generally survive a freezeup.

29

Surface tension- adhesive and

cohesive forces
Water adheres strongly to most surfaces
and can be drown up into long columns
through narrow tubes like the xylem
vessels of plant stems, without the water
column breaking.

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 Compared with other liquids, water has

extremely strong adhesive and cohesive
properties that prevent the column
breaking under tension.

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 The outermost molecules of water form

hydrogen bonds with water molecules below
them.
This gives a very high surface tension to waterhigher than that of any other liquid except
mercury. Surface skate.
The insects waxy cuticle prevents wetting of its
body, and the mass of the insect is not great
enough to break through the surface.
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33

pH as measure of hydrogen ion in

aqueous solution
pH scale which ranger from 0 -14
compress the range of H+ and OHconcentration by employing logarithms.
The pH of a solution is defined as the
negative logarithms (base 10) of the
hydrogen ion concentration:
pH = - log [ H+ ]
34

 pH declines as H+ concentration
increases.
An acid is a substance that increases the
hydrogen ion concentration of a solution.
A base is a substance that reduces the
hydrogen ion concentration of a solution,
therefore it has a higher concentration of
hydroxyl ions.
35

CARBOHYDRATE

carbohydrates

monosaccharides

carbonyl group

disaccharides

hydroxyl group

polysaccarides

starch

glycogen

cellulose

36

Use of carbohydrates:
Source of energy
Storage of energy
Structural component of cell membranes
and cell walls

37

Three main groups

1. Monosaccharides single sugars
2. Disaccharides double sugars
3. Polysaccharides- many sugars

All are composed of carbon, hydrogen and

oxygen atoms.
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MONOSACCHARIDES

Characteristic:
1. Small
2. Sweet
3. Readily soluble in water

General formula : ( CH2O)n

(glucose C6H12O6)

Carbonyl group and hydroxyl group

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TYPE
1. Triosa sugar contains 3 carbon atoms
(glyceraldehydes)
2. Pentose sugar contains 5 carbon
atoms (ribose)
3. Hexose sugar contains 6 carbon atoms
(glucose)
40

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FUNCTIONAL GROUP
i.

Ketose , e.g fructose

ii. Aldose, e.g glucose

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Two types of glucose

- glucose and - glucose
With six carbon atoms numbered
Are said to be isomers (different
compounds with the same molecular
formula.
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DISACCHARIDES
Small, sweet and soluble.
Monosaccharides may join together to
give a double sugar molecule a
disaccharide.
Joined together to form it by a
condensation reaction.
46

 The bond between two carbon atoms is

called a glycosidic bond.
All condensation reactions can be
reversed by adding water to the glycosidic
bond this is known as hydrolysis.

47

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POLYSACCHARIDES

Are formed when many hundreds of

monosaccharides condense (join) to form
chains.

The chains formed may be:

1.
2.
3.
4.

Variable in length
Branched or unbranched
Folded ideal for energy storage
Straight or coiled
50

Characteristic of polysaccharides:
1. large,
2. not sweet
3. Insoluble in water

51

Starch

Used as storage of glucose in plants.

1. Amylose
2. Amylopectin

52

Amylose
Made from -glucose molecules
Forming unbranched helical chain of 300
units in length.
Each -glucose is joined by a glycosidic
bond between neighbouring C1 and C4
atoms.
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Amylopectin
Made from -glucose molecules
Forming branched chains of up to 1500 units
Branches occur every 30 units and are formed
between neighbouring C1 and C6 atoms which
are then held together by glycosidic bond.

56

Glycogen
Is the only carbohydrate energy store
found in animals.
Found in liver and muscle tissue and
made up of short branched chains of glucose units.

57

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Cellulose
Important structural materials in plants
Long chains of -glucose units which are
unbranched but parallel strands of
cellulose are linked by means of hydrogen
bonds, making the cell wall a very stable
structure.

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LIPIDS
General term for any water-insoluble organic
molecules that can be extracted from cells
by ethers, benzene, or other nonpolar
solvents.

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3 MAJOR CLASSES OF LIPIDS

1.

TRIGLYCERISES
e.g. Fat & oil

2.

PHOSPHOLIPIDS
e.g. Lecithin

3.

STEROIDS
e.g. Cholesterol & Testosterone
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FORMATION VIA CONDENSATION

Breakdown By Hydrolysis

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IMPORTANCE OF LIPIDS
1.
2.
3.
4.
5.

Energy storage
Component of cell membrane
Insulation : blubber
Emulsifiers
Important carriers or precursors of
important flavor and odor compounds.
6. Transports fat-soluble vitamins
7. Immune system
8. Contributes to obesity, coronary heart
disease and other health problems.

65

TRYGLYCERIDE
Composed of 3 fatty acid molecules attached
to a glycerol backbone

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FATTY ACIDS
Long linear hydrocarbon chains
One end - contains a carboxylic acid group
The other end is the methyl, "n" or omega
end.

68

Classification of fats based on fatty acids

1. Saturated fat : saturated fatty acid
2. Unsaturated fat : unsaturated fatty acid

69

Classification fatty acids

Based on the number of double bonds at the
hydrocarbon chain :
1. Saturated fatty acid [ CnH2O2 ] .
E.g. Stearic acid.
2. Unsaturated fatty acid [ CnH2nO2 ].
E.g. Oleic acid.
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PHOSPHOLIPIDS
Example : Lecithin (in cell membrane structure).

72

Importance of lecithin in cell membrane

structure:1. Polarization leads to solubility in water. It act
as a permeability barrier, so that exchanges
across this membrane are very limited and
very slow.
2. Permeable to water molecules, but not to
ions such as Na+, K+, and Cl-.
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STEROIDS
Examples : Cholesterol & Testosterone.

Structure of Steroids.
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Structure of Cholesterol.

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Structure of testosterone.
Testosterone :
Male sex hormone
that stimulates sperm
formation, promotes
the development of
the male duct system
in the fetus, and is
responsible for
secondary sex
characteristics such
as facial hair growth.
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Steroid abuses
Effect of anabolic steroids abuses :
1. Impotent
2. Liver tumors
3. Renal failure

Effect of topical corticosteroids: clinical

examples of abuses.
1. Iatrogenic Cushing syndrome
2. Ichthyosiform scaling.
3. Itchy skin lesion

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 Other effects of steroids abuses :

Cardiovascular disease : heart attack & stroke.
Cause male-pattern baldness, cysts, acne, and oily hair
and skin.
Affect your mood - angry &hostile for
no reason.
There are recorded cases of murder attributed to intense
anger from steroid use.
Increase the risk of infection from sharing needles or
using dirty needles to inject steroids puts you at risk for
diseases such as HIV/AIDS & hepatitis.
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IMPORTANCE OF
CHOLESTEROL IN HEALTH
Increase the membrane permeability
of non-polar solutes. The presence of
the steroids moves the polar heads
further apart, giving greater access of
non-polar substances to the lipid
layers, plus these materials also tend
to be soluble in the steroids
themselves.
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PROTEIN
Are always composed of nitrogen, carbon,
hydrogen and oxygen and sometimes sulphur
and phosphorus.

80

Function of protein:
1. Nutrition digestive enzymes.
2. Transport of respiratory gases
haemoglobin.
3. Immunity antibodies.
4. Co-ordination hormomes.
5. Growth and repair membrane proteins.
6. Support and movement myosin/actin,
keratin.
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Protein molecule
Each different proteins molecule is made under the direction
of its own gene and performs its precise function.
The shape of it is determined by its amino acids sequence.
Amino acids are the building blocks from which protein are
made.
There are about 20 commonly occuring amino acids in protein.
All have the same basic structure but differ in their
RESIDUAL CHAIN ( R ).
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Formation of Polypeptides
Two amino acids can be joined by a condensation reaction
to form a dipeptide.
If any amino acids are joined together by peptide bonds
then a polypeptide is formed.
A polypeptide usually contains hundreds of amino acids.
The repeated sequence (-N-C-C-N-) is the polypeptide
backbone.
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Structure of proteins
A typical protein consists of one or more polypeptide
chains which may be folded, branched and crosslinked at intervals.
Each proteins has a specific three-dimensional shape.
In describing the structure of a protein, it is usual to
refer to four separate levels of organization.
Primary, secondary, tertiary and quaternary.
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Primary structure
This describe the sequence of amino acids in
the protein and usually determines its eventual
shape and biological function.
The twenty commonly occuring amino acids
can be arranged in an enoromous variety of
different ways in giving rise to many different
proteins.
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Secondary structure
Once a linear chain of amino acids is formed it
spontaneously folds to form a helix or a
pleated sheet.
Hydrogen bonds holds the secondary structure
together.

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Tertiary structure
Once they have been folded by hydrogen
bonds, polypeptides may then fold into a
globular shape which is maintained by
hydrogen bonds, ionic bonds and covalent
bonds between sulphur atoms in the residual
chains of the amino acids.

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Quaternary structure
Some proteins consists of more than one
polypeptide chain.
Human haemoglobin is an example.
It consists of four chains (two -polypeptide
chains and two -polypeptide chains) wrapped
around an iron haem group.
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NUCLEIC ACID
Nucleic Acids are very Large and Complex Organic
Molecules that STORE Important Information in the Cell.
(Genetic or Heredity Information)
Nucleic Acids use a System of FOUR Compounds to
store Heredity Information. A Sequence of the four
compounds arranged in a certain order acts as a Code
for Genetic Instructions of the Cell.
DEOXYRIBONUCLEIC ACID, OR DNA, contains
information that is essential for almost all Cell Activities,
Including Cell Division.
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 RIBONUCLEIC ACID, OR RNA, Stores

and Transfers Information essential for the
Manufacturing of Proteins.
Both DNA and RNA are Polymers,
composed of thousands of linked
Monomers called NUCLEOTIDES.

104

STRUCTURE OF DNA AND RNA

Each Nucleotide is made of THREE Main
Components:
A PHOSPHATE GROUP,
A FIVE-CARBON SUGAR,
A RING SHAPED NITROGEN BASE

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Pentose
The sugar found in the nucleotides of DNA is
deoxyribose.
Ribose is found in RNA.
Deoxyribose and ribose are pentose sugars
(containing 5 carbon atoms).
The carbon atoms are numbered for orientation
and "primes" are used to distinguish the atoms
of the sugars from the atoms of the nitrogenous
bases in nucleotides.

107

Pentose
Note that the 5' ("five prime") carbon atom is not
a part of the ring.
The fifth atom of the ring is an oxygen.
The only difference between deoxyribose and
ribose is that deoxyribose lacks a hydroxyl group
at the 2' position.
Thus, the deoxyribose found in nucleic acids is
more properly known as 2'-deoxyribose.

108

PENTOSE SUGAR

109

Bases
The nitrogenous bases of nucleotides are ring structures of
nitrogen and carbon with other organic side chains attached
at specific locations.
Bases classified as purines have a double structure and,
depending on the organic side chains attached, may be
either adenine or guanine.
Bases classified as pyrimidines have a single ring structure
and may be cytosine, uracil, or thymine.
The numbering shown around the generalized structures in
these figures are used for orientation.
Purines are adenine and guanine
Pyrimidines are thymine, cytosine and uracil

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Formation of nucleotide
Pentose, phosphate group and bases link up to
form a nucleotide via condensation reaction.
Base is joined to carbon atom 1 of the pentose
molecule.
Phosphate group attached to the sugar molecule
at atom 5.
Two molecules of water are removed in the
process.
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Formation of polynucleotide
Nucleotides are combinded end-to-end to form a
single strand of nucleic acid.
In a single strand, nucleotides are linked by a
phosphodiester bond, a covalent bond, between
the alpha phosphate of one nucleotide to the 3'
carbon of the adjacent nucleotide.
At one end of the stand, a free (unattached) 5'
phosphate group from the terminal nucleotide is
found.
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Polynucleotide sequences are referenced

in the 5' to 3' direction.
Typically, polynucleotides will contain a 5'
phosphate and 3' hydroxyl terminal groups.
The common representation of polynucleotides
is as an arrow with the 5' end at the left and
the 3' end at the right.

120

Structure of DNA
In most living organisms (except for viruses), genetic
information is stored in the molecule deoxyribonucleic
acid, or DNA.
DNA is made and resides in the nucleus of living cells.
DNA gets its name from the sugar molecule contained in
its backbone(deoxyribose); however, it gets its
significance from its unique structure.
Four different nucleotide bases occur in DNA: adenine
(A), cytosine (C), guanine (G), and thymine (T).
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 The DNA molecule is a double helix, as

shown at right.

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 The two strands are held together by

hydrogen bonds that form between the
nitrogenous bases of opposite strands.
E.g; adenine pairs with thymine and form
two hydrogen bonds, cytosine pairs with
guanine and form three hydrogen bonds.
This known as complementary base
pairing.
124

Structure of RNA
Single strand-stranded molecule.
Sugar ribose is found in the nucleotide.
Adenine, guanine, cytosine and uracil.
Three types; mRNA, rRNA and tRNA.
125

 Functions of RNA:
mRNA directs the translation of proteins,
RNAs of ribosomes (1/3 protein and 2/3 RNA)
probably have functional as well as structural
roles,
tRNA delivers amino acids to the ribosomes
during translation,

126

Features

DNA

RNA

Basic unit

Deoxyribonucleotide

Ribonucleotide

Pentose

Deoxyribose

Ribose

Nitrogenous base

Adenine, Guanine,
Cytosine, Thymine

Adenine, Guanine,
Cytosine, Uracil

Structure

double helix consisting of single strand

two chains (STRANDS)
of nucleotides coiled
around each other

Size

Large molecule

Relatively small molecule

Location

In the nucleus

In the nucleus and

cytoplasm

Type

One

Three
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End of this topic

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