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TOPIC 3
MOLECULES OF LIFE
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LEARNING OUTCOMES
3.1 WATER
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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
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The three atoms
form a triangle,
not a straight line
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6
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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.
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A molecule carrying such an unequal
distribution of electrical charge is called a
polar molecule.
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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.
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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.
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Properties of water as vital
constituent of life
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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 NH
3
+
).
Water as a universal solvent
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These cations (negatively charged ions)
and anions (positively charged ions)
become surrounded by a shell of
orientated water molecules.
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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.
16
This makes them more reactive chemically
than when they form part of an undissolve
solid.
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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.
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Viscosity of water
It has a low viscosity
This unique property makes it suitable
medium of transportation in living
organisms.
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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.
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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.
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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.
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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.
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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.
27
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.
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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 freeze-
up.
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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 water-
higher 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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pH as measure of hydrogen ion in
aqueous solution
pH scale which ranger from 0 -14
compress the range of H
+
and OH
-
concentration by employing logarithms.
The pH of a solution is defined as the
negative logarithms (base 10) of the
hydrogen ion concentration:
pH = - log [ H
+
]
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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.
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CARBOHYDRATE
carbohydrates
monosaccharides disaccharides polysaccarides
carbonyl group hydroxyl group starch glycogen cellulose
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Use of carbohydrates:
Source of energy
Storage of energy
Structural component of cell membranes
and cell walls
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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)
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FUNCTIONAL GROUP
i. Ketose , e.g fructose
ii. Aldose, e.g glucose
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Two types of glucose
E - glucose and F- 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.
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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.
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POLYSACCHARIDES
Are formed when many hundreds of
monosaccharides condense (join) to form
chains.
The chains formed may be:
1. Variable in length
2. Branched or unbranched
3. Folded ideal for energy storage
4. Straight or coiled
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Characteristic of polysaccharides:
1. large,
2. not sweet
3. Insoluble in water
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Starch
Used as storage of glucose in plants.
1. Amylose
2. Amylopectin
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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.
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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.
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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 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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1. TRIGLYCERISES
e.g. Fat & oil
2. PHOSPHOLIPIDS
e.g. Lecithin
3. STEROIDS
e.g. Cholesterol & Testosterone
3 MAJOR CLASSES OF LIPIDS 3 MAJOR CLASSES OF LIPIDS
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FORMATION VIA CONDENSATION FORMATION VIA CONDENSATION
Breakdown By Hydrolysis
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IMPORTANCE OF LIPIDS IMPORTANCE OF LIPIDS
1. Energy storage
2. Component of cell membrane
3. Insulation : blubber
4. Emulsifiers
5. 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.
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TRYGLYCERIDE TRYGLYCERIDE
Composed of 3 fatty acid molecules attached
to a glycerol backbone
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FATTY ACIDS FATTY ACIDS
Long linear hydrocarbon chains
One end - contains a carboxylic acid group
The other end is the methyl, "n" or omega end.
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Classification of fats based on fatty acids
1. Saturated fat : saturated fatty acid
2. Unsaturated fat : unsaturated fatty acid
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Classification fatty acids Classification fatty acids
Based on the number of double bonds at the
hydrocarbon chain :
1. Saturated fatty acid [ C
n
H
2
O
2
] .
E.g. Stearic acid.
2. Unsaturated fatty acid [ C
n
H
2n
O
2
].
E.g. Oleic acid.
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PHOSPHOLIPIDS
Example : Lecithin (in cell membrane structure).
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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 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.
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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 cross-
linked 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.
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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.
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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.
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PENTOSE SUGAR
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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.
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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.
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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.
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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,
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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
two chains (STRANDS)
of nucleotides coiled
around each other
single strand
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