SUBTOPIC :

1.1 Water
1.2 Carbohydrates
1.3 Lipids
1.4 Protein
1.5 Nucleic acids
1.1 WATER
At the end of this topic, students should be able to:

explain the structure of water molecule

describe the properties of water and its importance

Structure of a water molecule

A water molecule consist of an oxygen atom and two hydrogen atom

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.

Hydrogen bonds largely account for the unique properties of water. weaker than
covalent bonds.

But -> strong enough to hold water molecules together.

Because of their hydrogen bonds, water molecules are attracted to charged particles
or charged surfaces.
Properties of water as vital constituent of life
1. 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

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

This makes them more reactive chemically than when they form part of an undissolve
solid.

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.

2. Low viscosity of water

This unique property makes it suitable medium of transportation in living organisms.

Helps in movement of food substances

It also can act as a lubricants in joints

3. High specific heat capacity

A lot of energy is required to raise the temperature of water.

Because, much energy is needed to break the hydrogen bonds .

The head capacity of water is the amount of head required to raise the temperature of
1g of water by 1oC per calorie (cal) or 1 cal/g of water per oC

This property of water is known as its high specific heat capacity.

The specific heat capacity of water is the highest of any known substance.

Aquatic environments like stream , lakes and seas are all very slow to change
temperature when the surrounding air temperature changes.
4. Latent heat of vaporization of water

When pure water is heated to 100oC, it boils

The water molecules gain sufficient kinetic energy to escape into the air as water
vapor

The heat energy that is being used to produce this change is called the latent heat of
vaporization

Water has a high latent heat of vaporization

Because 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.

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.

Many living organism use this feature of water as cooling mechanism.

For example, human sweat the liquid water in sweat absorbs heat energy from the
skin or in transpiration from green leaves to stop the leaves temperature from rising too
high on a hot day
5. 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.

This is why the bulk of ponds, lakes or the sea rarely freeze solid.

Aquatic life can generally survive a freeze-up.

6. High Surface Tension - adhesive and cohesive forces

Water adheres strongly to most surfaces

It can be drown up into long columns through narrow tubes like the xylem vessels of
plant stems, without the water column breaking.

Compared with other liquids, water has extremely strong adhesive and cohesive
properties that prevent the column breaking under tension.

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.
1.2 CARBOHYDRATES
Learning Outcomes:
At the end of the lesson, student should be able to explain:
1. Describe various forms and classes
2. Describe the formation and breakdown of maltose
3. Structures and functions of starch, glycogen and cellulose.
Introduction

Organic molecule containing the element carbon, hydrogen and oxygen in a 1:2:1
ratio

Written as (CH2O)n ; n = number of carbon

Use of carbohydrates:

Source of energy

Storage of energy

Structural component of cell membranes and cell walls

Carbohydrates can be classified into three classes:

1. monosaccharides :- single sugars
2. disaccharides :- double sugars
3. polysaccharides :- many sugars
MONOSACCHARIDES
Physical Characteristic:
1. Small
2. White
3. Sweet
4. Soluble
5. Can be crystallized
Chemistry Characteristic
1. reducing Benedict test

2. condensation reaction to form disaccharide or polysaccharide

Greek words, monos = simple; sacchar = sugar, generally have molecular formula
that are some multiple of CH2O --> (CH2O)n For example, glucose has the formula C6H12O6.

Most names for sugars end in -ose.

basic unit or monomer

It can be classified by two ways :

1.By the number of carbons in the backbone
2.By the functional group
Classification by the number of carbon in the backbone

Three carbon (3C) triose sugars . Example : glyseraldehyde and dihydroxyaceton

Five carbon (5C) pentose sugars. Example : ribose and ribulose

Six carbon (6) hexose sugars Example : glucose and fructose

Ring Structure for pentose
Importance as synthesis of nucleic acid (RNA and DNA)

Ring Structure for hexose

Importance as source of energy in cell respiration
Classification by the functional group
Example :

Aldehyde group glyseraldehyde, ribose and glucose

Ketone group dihydroxyaceton, ribulose and fructose

Functional Groups

Differences between aldehyde and ketone group

All sugar contain the C = O. This is called a carbonyl group

The monosaccharides which have a aldehyde group is called aldose sugar

The monosaccharides which have ketone group is called ketose sugar

Carbonyl Groups
If the location of carbonyl group is in the middle backbone of the corbon, it call ketose
Reducing sugar

Aldehydes are reducing agents.

So aldose sugar have reducing agents, and are called reducing sugar.

Ketose sugars do not have reducing agents, but in monosaccride form, it react as
reducing agents because hydroxyl in functional group have free.
Benedicts test

Benedicts reagent contains copper (II) ions, which give a blue colour to the
Benedicts solution.

When heated with a reducing sugar, the copper (II) ions are reduced to copper (I)
ions, and an orange-red precipitate of copper (I) oxide is formed:
reducing + Cu2+ oxidised + Cu+
sugar
(oxidised) sugar
(reduced)
ISOMER

Isomer = molecules which have same chemical formula but with different structure

Example : glucose and fructose C6H12O6

and isomers

Example : - glucose and - glucose

With six carbon atoms numbered.

At Carbon 1 ,
glucose has OH down
glucose has OH up
DISACCHARIDES

Disaccharides are formed when two monosaccharide joined together

Physic characteristic
- Sweet
- soluble in water.
- Can be crystallized

Chemistry characteristic
- Reducing Benedict test (except sucrose)

A monosaccharide able joined together to form it by a condensation reaction.

By hydrolysis reaction to form monosaccharide.

Types of Disaccharide
Maltose : Malt sugar, an ingredient for brewing beer, reducing sugar.
Sucrose :Source sugar-cane, in plant (main form that is transportation in plant), nonreducing sugar.
Lactose :found in milk and, important energy source for young mammals, can only be
digested slowly.
Formation of disaccharide

The two monosaccharide joined together by a condensation reactions in which water

is removed

The bond formed between two monosaccharide as a result of condensation is called

glycosidic bond

A glycosidic bond can also be broken down to release separate monomer units. This
is called hydrolysis because water is needed to split up the bigger molecule

Maltose, malt sugar glucose + glucose

Sucrose, table sugar glucose + fructose .

Lactose, milk sugar glucose + galactose

Formation of disaccharide : Maltose
lactose

Milk sugar, is found exclusively in milk and is an important energy source for young
mammals

It can only be digested slowly, so gives a slow steady release of energy.

Lactose = glucose + galactose

Formation of disaccharide : Sucrose
Reducing sugar

All monosaccharides and some disaccharide (maltose and lactose) are type of
chemical reaction knows as reduction.

Sucrose (non reducing sugar) and polysaccharide cant reducing Benedict test.

Reducing sugar : maltose

Non reducing sugar : sucrose

POLYSACCHARIDES

Are formed when many hundreds of monosaccharides condense (join) to form

chains.

The chains formed may be:

- Variable in length
- Branched or unbranched
- Folded ideal for energy storage
- Straight or coiled
Characteristic of polysaccharides:
- large,
- not sweet
- Insoluble in water

Polysaccharides are polymers of hundreds to thousands of monosaccharides joined

by glycosidic linkages.

Function is as an energy storage macromolecule that is hydrolyzed as needed.

Others serve as building materials for the cell or whole organism.

STARCH

Starch is a storage polysaccharide in plants.

monomers are joined by 1-4 linkages between the glucose, known as -1,4
glycosidic bond .

unbranched form of starch amylose forms a helix.

Branched forms amylopectin.

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.
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.
amylose
amylopectin
Glycogen

Animals also store glucose in a polysaccharide called glycogen.

Glycogen is highly branched, like amylopectin.

Found in liver and muscle tissue and made up of short branched chains of -glucose
units.
Cellulose

Major component of the tough wall of plant cells.

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.

The enzymes that digest starch cannot hydrolyze the beta linkages in cellulose.
Cellulose in our food passes through the digestive tract and is eliminated in feces as
insoluble fiber.
As it travels through the digestive tract, it abrades the intestinal walls and stimulates the
secretion of mucus.
Some microbes can digest cellulose to its glucose monomers through the use of cellulase
enzymes.
Herbivores, like cows , have symbiotic relationships with cellulolytic microbes, allowing them
access to this rich source of energy.
Cows do have enzymes amylases, which can break - 1,4 glicosidic bonds in starch but
which cannot recognize - 1,4 glicosidic bonds in cellulose,
the bacteria in the rumen do produce enzymes called cellulles which can recognize and break

 - 1,4 glicosidic bonds in cellulose

Edited on Mei, 31 2011

Retold by,

Amran Md Said
Matriculation College of Pahang.

TOPIC 1 : MOLECULES OF LIFE

Retold by,

Amran Md Said
Matriculation College of Pahang

1.3 LIPIDS

They contain carbon, hydrogen and oxygen, with far more hydrogen and carbon compared
with oxygen than in carbohydrates;
They are insoluble in water .

IMPORTANCE OF LIPIDS

Energy storage
Component of cell membrane
Insulation : blubber
Emulsifiers

Important carriers or precursors of important flavor and odor compounds.

Transports fat-soluble vitamins
Immune system
Contributes to obesity, coronary heart disease and other health problems.

TRYGLYCERIDE

Triglycerides with reletively short fatty acid chains, or with unsaturated fatty acids, tend to be
liquid at normal temperaturated and called oils.
Triglycerides with longer fatty acid chains, or with saturated fatty acid, are more likely to be
solid and are called fats.
Triglycerides, like all lipids, are insoluble in water. This is because they have no dipoles and
no charges which can attract water molecules.
Are especially useful as energy stores, because they contain much energy per gram than
either carbohydrates or proteins.

FATTY ACIDS

Classification fatty acids

Classification of essential
Essential fatty acids
- Body cant produce own fatty acids, so its needed from food.
Non-essential fatty acids.
Body can synthesise fatty acids itself

PHOSPHOLIPIDS

Example : Lecithin (in cell membrane structure).

Importance of lecithin in cell membrane
structure:-

Polarization leads to solubility in water. It act as a permeability barrier, so that exchanges

across this membrane are very limited and very slow.
Permeable to water molecules, but not to ions such as Na+, K+, and Cl-.
STEROIDSExamples : Cholesterol & Testosterone.
Structure of Steroids.

PROTEIN

Protein are polymers whose molecules are made from many amino acid molecules linked
together.
Protein consists of carbon, hydrogen, oxygen and nitrogen.
Function of protein:
- Enzymatic catalysis .
- Transport of respiratory gases and storage.
- Structure and support
- Contacts or co-ordination (hormones)
- Immunity.
- Growth and development membrane proteins.
- Heredity

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 ).
Amino Acid Structure
An amino acid is a molecule containing an amino group (-NH2), a carboxyl group (-COOH),
and a hydrogen atom.

Amino group (-NH2) has characteristics such as basic.

Carboxyl group (-COOH) has characteristics such as acidic.
Each amino acid has unique chemical properties determine by the nature of the side group
(indicated by R).

For example, when the side group is CH2OH, the amino acid (serine) is polar, but when the
side group is CH3, amino acid (alanine) is nonpolar.
Type of amino acid, Base on side chain group
- Polar eg. Serine (Ser)
- Non polar eg. Glycine (Gly)
- Acidic eg. Aspartic acid (Asp)
- Basic eg. Lysine (Lys).

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.

amino acids are structure of protein

The twenty commonly occurring amino acids can be arranged in an enormous variety of
different ways in giving rise to many different proteins
A plant can synthesis all amino acids as needed from simple component.
But an animal cant synthesis apart of amino acids
Base on essential, amino acids divide 2 categories
i) Essential amino acid eg. Methionine, lysine and Valine
ii) Non-essential amino acid eg. Glycine, alanine and Cysteine.

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.

Primary structure
This discribe the sequence of amino acids in the protein and usually determines its eventual
shape and biological function.

Secondary structure
Once a linear chain of amino acids is formed it spontaneously folds to form helix or
pleated sheet.
Hydrogen bonds holds the secondary structure together.

alfa helix
beta plaeated sheet

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
- disulphide bridge
Example myoglobin.

Hydrogen bond bond between polar side chains

Ionic bond bond between positively and negatively charged side chains
disulphide bridge (covalent bonds between sulphur atoms in the residual chains of the amino
acids.)
Hydrophobic interactions & van der Waals interactions Nonpolar R group with another
nonpolar R group

Quaternary structure

Consists of more than one polypeptide chains to form a single functional molecule
Held together by hydrophobic interactions, hydrogen bonds, ionic bonds and disulfide bridges
Associated with non-protein groups into a large complex protein molecule

Human haemoglobin is an example.

It consists of four chains (two -polypeptide chains and two -polypeptide chains) wrapped
around an iron hem group.

Effect of pH and temperature on structure of protein

Structure of protein maintain by hydrogen bond ( 2 , 3 and 4); ionic bond, hydrophobic

interaction, disulfide bridge and van de waals interaction ( 3, 4)

Breakage the bond causes loss of specific three-dimensional shape of a protein molecule
They change may be temporary or permanent

But amino acid sequence remains unaffected

Change shape of protein denaturation
Denaturation occurs under extreme conditions such as extreme pH and temperature.
Molecule unfolds and can no longer perform its normal biological function

If the temperature or pH exceeds a proteins range of tolerance, its polypeptide chains will
unwind or change shape, causing to lose its conformation and hence its ability to function

Example: Proteins are easily damaged by heat (temperatures greater than 40 0C) due to
breakage of their cross linkages
This cause the protein molecules to open up, straighten the folds and assume a random
configuration

For some proteins, denaturation might be reserved when normal conditions are restored

Classifation base on structure

Divided by 3 classification base on structure.
- Conjugated protein
- Globular protein
- Fibrous protein

Conjugated Protein

protein joined with non protein component/ prosthetic group

Protein structure merge with with non protein group (prosthetic group)
Eg. Haemoglobin contains the prosthetic group containing iron, which is the haem. It is with in
the haem group that carries the oxygen molecule through the binding of the oxygen molecule
to the iron ion (Fe2+) found in the haem group

Globular Protein

Mostly, that protein related in tertiary and quaternary structure.

Usually water soluble (can to form colloid)
Long polypeptide with helix to form globular or spherical
example: globulin (blood serum), enzymes, antibody, hormone

Fibrous Protein

Mostly, that protein related in secondary structure.

Insoluble in water and very strong because its make from long polypeptide
example: collagen, myosin, fibrin and keratin

Differences between fibrous protein and globular proteins

Properties of protein

Amphoteric
Buffering capacity
Colloidal properties
Denaturation

Note :

Properties of Protein, just for extra knowledge

Properties of protein

1. Amphoteric

In aqueous as neutral (pH 7), amino acid such as dipole, its called zwitterions
Amphoteric because have characteristic both acidic and basic.
In aqueous acidic (< pH 7), protein receive H+ and make its positive charge.
In aqueous alkaline (>pH 7), donate H+ and make its negative charge.

Charge at zwitterions depend on pH

pH at amino acid as neutral like electric its call isoelectric
All amino acids have own characteristic as isoelectric point (pI).

2. Buffering capacity

Amphoteric characteristic of amino acids, its make such as buffer

A buffer solution is one which resist the tendency to alter its pH even when small amounts of
acid or alkali are added to.
That mean a buffer solution cant change spontaneously, while added pH increase (basic) .
Amino acids will donate hydrogen ionic.
While pH reduce (acidic), amino acids will receive hydrogen ionic.

4.Denaturation

The structure of a protein can be change if the bonds which hold it in shape are broken. This
process is called Denaturation.

High temperatures break hydrogen bond and van der Waals forces. In a globular protein a
long chain instead of a curled-up ball. The molecules will no longer be soluble in water.
Extremes of pH break ionic bond, because they alter the charges on R groups.
Reducing agents break disulphide bond. This is made use of when perming hair. Keratin, from
which hair is made, contains disulphide bond that hold the shape in shape.

NUCLEIC ACID

Topic distinguish

At the end of the lesson, students should be able to:

Describe the structure of nucleotide as the basic composition of nucleic acid (DNA and RNA)
Describe the structure of DNA based on the Watson and Crick Model.
State the type and function of RNA
State the differences of DNA and RNA

Nucleic acids
The amino acid sequence of a polypeptide is programmed by a gene.
A gene consists of regions of DNA, a polymer of nucleic acids.
DNA (and their genes) is passed by the mechanisms of inheritance.

Nucleic acid
Structure of nucleotide
Nucleic acids are polymers of monomers called nucleotides.
Each nucleotide consists of three smaller molecules. These are :

A phosphate group
A pentose sugar
A nitrogenous base

Phosphate group
Pentose sugar
Nitrogenous base

DNA

RNA
rRNA
tRNA
mRNA

- The End -