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CHAPTER 1:
MOLECULES OF LIFE
(7 HRS)

1.0 Molecules Of Life (7 hrs)


1.1 Water

(1)

1.2 Carbohydrates

(1)

1.3 Lipids

(1)

1.4 Proteins

(2)

1.5 Nucleic Acids

(1)

Learning outcomes
a) Explain the structure of water molecule
b) Describe the properties of water and its
importance

Learning Outcomes :
1.1 (a) Explain the structure of water molecule

O
H

Structure:

1 oxygen atom & 2 hydrogen atoms (H2O)


Joined together by sharing electrons ~ covalent bond
3 atoms ~ arranged to form a triangle

Angle ~ 104.5

Learning Outcomes :
1.1 (a) Explain the structure of water molecule

2O
+

The sharing of electrons between O & H atoms are not equal


O atom ~ slightly negative charge (-)
H atoms ~ slightly positive charge (+)
Unequal charge distribution within a molecule ~ polar
molecule

Learning Outcomes :
1.1 (a) Explain the structure of water molecule

+ H atom of one water


molecule is attracted to the
- O atom of nearby water
molecules

2+
+

Hydrogen
bond

Water molecules are held


together by hydrogen bonds

H bond is weak,
represented by dotted lines

2+

Learning Outcomes :
1.1 (a) Explain the structure of water molecule

1 water molecule can


form maximum of 4
hydrogen bonds with 4
water molecules

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

Properties of water
1.
2.
3.
4.
5.
6.

Universal solvent
High specific heat capacity
High latent heat of vaporization
High surface tension
Maximum density at 4C
Low viscosity

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

1. Universal Solvent
Powerful solvent for ionic & polar substances (eg: NaCl)

NaCl are held together by ionic bonds between Na+ & Cl-

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

1. Universal Solvent
Water is a polar molecule
The O atoms has a slightly negative charge & H atoms has a
slightly positive charge
O atoms are attracted to the positively charged sodium ions
H atoms are attracted to the negatively charged chloride ions

Ionic bonds between NaCl molecules become weaker

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

1. Universal Solvent

Water molecules gather around the Na+ & Cl- to form a


hydration shell, separating them from one another
Pulling these ions away from the salt crystal
Causes these ions to separate & dissolve

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

1. Universal Solvent
Importance:

Act as transport medium for solutes (eg: dissolved


nutrients are carried throughout the body in blood
plasma)
Water facilitates chemical reaction (solutes are more
reactive when dissolved)

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

2. High specific heat capacity


Definition : amount of energy needed to increase the
temperature of 1 g of a substance by 1C
Large amount of energy is needed to increase the
temperature of 1 g of water by 1oC
Heat is absorbed to break the H bonds between water
molecules
Value = 1 cal/g (most substances have lower value)
A large body of water (ocean/lakes) has a relatively constant
temperature although its surrounding temperature changes
(temperature rises & falls slowly)

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

2. High specific heat capacity


Importance:
Organisms can maintain their normal body
temperature
Aquatic organisms can live in a relatively stable
temperature (protected from rapid temperature
changes)

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

3. High latent heat of vaporization


Definition : Amount of energy needed to change 1 g of a
substance from liquid phase to vapor
A lot of energy is needed to change 1 g of water from
liquid state to vapor
Heat is absorbed to break the H bonds between water
molecules before they can move faster & vaporized
Value = 540 cal/g

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

3. High latent heat of vaporization


Importance:
Cooling effect in organisms due to sweating (animals) or
transpiration (plants)
Explanation:

As water absorbs heat, its energy increases


When water evaporates, it takes a lot of heat energy
away lowering the temperature of the organism

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

4. High surface tension


H bonds make water molecules stick to each other
cohesion
On the surface, water has greater attraction for each other
than for molecules in the air

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

4. High surface tension


Water are also pulled downward
by other water molecules
beneath them
Produce a strong layer on the
surface, hard to break the water
surface create high surface
tension
Water molecules can also stick to
other substances adhesion

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

4. High surface tension


Importance:
Allow some organisms to move on water (eg: water strider)

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

5. Maximum density at 4C
As water cools, the
molecules get closer
together
Reach maximum density
at 4C
At temperature below 4C,
water molecules expand
until it freezes/solidifies
(at 0C)

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

5. Maximum density at 4C

H bonds in ice space the water molecules far apart &


become stable

Ice is less dense than cold water floats

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

5. Maximum density at 4C
Importance:
Allow aquatic life to live under the frozen surface of water
in cold climate region
Explanation:
The floating layer of ice insulates the water below, prevent
them from losing heat & from freezing

Learning Outcomes :
1.1 (b) Describe the properties of water and its importance

6. Low viscosity
Weak H bonds between water molecules are constantly
breaking & reforming.
Water molecules can slide easily over each other
It flows with less friction through narrow vessels.
Importance:
Act as medium of transportation in living organisms
(eg: blood easily flow in the circulatory system)
Act as a good lubricant to reduce friction within body
(eg: mucus facilitates movement of feces through the bowel)

1.0 Molecules Of Life (7 hrs)


1.1 Water

(1)

1.2 Carbohydrates

(1)

1.3 Lipids

(1)

1.4 Proteins

(2)

1.5 Nucleic Acids

(1)

Learning outcomes
a) Describe various forms & classes of carbohydrates
b) Describe the formation & breakdown of maltose
c) Describe the structures & functions of starch,
glycogen and cellulose

Learning Outcomes :
1.2 (a) Describe various forms and classes of carbohydrates

Introduction
Composed of carbon, hydrogen & oxygen atoms
Ratio of C, H & O ~ approximately 1:2:1 (CH2O)n
n = number of C atoms

Learning Outcomes :
1.2 (a) Describe various forms and classes of carbohydrates

Classes of carbohydrates:

Classification

Monosaccharide
1 sugar unit

Disaccharide

Polysaccharide

2 sugar units

Many sugar units

Learning Outcomes :
1.2 (a) Describe various forms and classes of carbohydrates

MONOSACCHARIDES
1 sugar molecule; simple sugar (3-7 carbon atoms)
Characteristics:

1.
2.
3.
4.
5.
6.

Small
Sweet
Soluble in water
Can crystallized
White / colourless
Reducing sugar

Learning Outcomes :
1.2 (a) Describe various forms and classes of carbohydrates

Classes of monosaccharide:
Classification

Based on the position


of functional group

Aldose

Ketose

Based on no. of C atom

Triose 3C

Pentose 5C

Hexose 6C

Learning Outcomes
Outcomes ::
Learning
1.2 Describe
(a) Describe
various
forms
classes
of carbohydrates
(a)
various
forms
andand
classes
of carbohydrates

Classes of monosaccharide:
based on the position of functional group

Functional group ~ carbonyl group (C=O)


1. Aldose sugar
Carbonyl group is located at the end of carbon chain
Eg: glucose
2. Ketose sugar
Carbonyl group is located in the middle of carbon
chain
Eg: fructose

Numbering of carbon chain begins with the carbon nearest to


carbonyl group

Learning Outcomes :
1.2 (a) Describe various forms and classes of carbohydrates

Learning Outcomes :
1.2 (a) Describe various forms and classes of carbohydrates

Classes of monosaccharide:
based on the number of carbon atom

3 classes:
1. Triose sugar (3 C atoms)
Eg: glyceraldehyde & dihidroxyacetone; C3H6O3
2. Pentose sugar (5 C atoms) will be discussed in
nucleic acid
Eg: ribose, ribulose; C5H10O5, & deoxyribose; C5H10O4
3. Hexose sugar (6 C atoms)
Eg: glucose, galactose, fructose; C6H12O6

When dissolved in water, pentose & hexose form ring


structure; which is more stable

Learning Outcomes :
1.2 (a) Describe various forms and classes of carbohydrates

Hexose sugar (6 C atoms)

Same molecular formulas but


different arrangements of atoms
~ isomers

Glucose ~ blood sugar, moderate


sweetness, found in fruits &
vegetables

Galactose ~ less sweet, found in


milk & yoghurt

Fructose ~ fruit sugar, sweetest,


found in fruits & honey

Linear and ring forms of glucose. To form the glucose


ring, carbon 1 bonds to the oxygen attached to carbon 5.

Learning Outcomes :
1.2 (a) Describe various forms and classes of carbohydrates

Glucose

Each of these structure is glucose (C6H12O6)


a. All carbon atoms are clearly shown
b. The carbon atoms are omitted
c. The hydrogen atoms are omitted

Learning Outcomes :
1.2 (a) Describe various forms and classes of carbohydrates

Glucose

2 isomeric forms, according to the position of OH group at C1

above the ring plane = -glucose


below the ring plane = -glucose

Learning Outcomes :
1.2 (a) Describe various forms and classes of carbohydrates

Function of Monosaccharides

Energy source

Glucose ~ major respiratory substrate, primary energy source

Basic building units or monomers for disaccharide &


polysaccharide

Learning Outcomes :
1.2 (b) Describe the formation and breakdown of maltose

DISACCHARIDES
2 sugar molecules or two monosaccharides

Joined together by a condensation process (removal of a

water molecule)
Form covalent bond glycosidic bond
Can be broken down into monomers by hydrolysis process
(addition of water molecule)
Characteristics:
Disaccharide
1. Sweet
2. Soluble in water
3. Can crystallized
Maltose Sucrose Lactose
4. White / colourless

Learning Outcomes :
1.2 (b) Describe the formation and breakdown of maltose

CONDENSATION PROCESS
Condensation

HYDROLYSIS PROCESS
Hydrolysis

Learning Outcomes :
1.2 (b) Describe the formation and breakdown of maltose

MALTOSE
Malt sugar
Monomers : -glucose + -glucose
Joined together by -1,4 glycosidic bond (between C1 of one

glucose molecule and C4 of another molecule)


+
condensation
condensation

hydrolysis
hydrolysis
-1,4
glycosidic
bond

-glucose
(C6H12O6)

-glucose
(C6H12O6)

Maltose
(C12H22O11)

Learning Outcomes :
1.2 (c) Describe the structures and functions of starch, glycogen and cellulose

POLYSACCHARIDES
Many sugar molecules; polymer (vary in length)

Joined together by condensation process (removal of a water

molecules)
Form covalent bond glycosidic bond
Formation of polymer (large molecules made up of repeating
units of monomers) polymerization
Can be broken down into monomers by hydrolysis process
(addition of water molecules)
Polysaccharide
Characteristics:
1. Large molecule
Starch Glycogen Cellulose
2. Not sweet
3. Insoluble in water (form colloid)
Amylose

Amylopectin

Learning Outcomes :
1.2 (c) Describe the structures and functions of starch, glycogen and cellulose

STARCH
Energy storage in plants
Plants convert excess glucose into starch for storage in chloroplast

Monomers: -glucose molecules


Broken down by hydrolysis process with the help of amylase enzyme
Starch is a mixture of:

Amylose
Amylopectin

Learning Outcomes :
1.2 (c) Describe the structures and functions of starch, glycogen and cellulose

AMYLOSE
Monomers: -glucose molecules

Joined together by -1,4 glycosidic bond


Helical, due to the formation of H bonds
Unbranched chain (variable length of monomers)

Folded ~ very compact (ideal for storage)


6
CH2OH

6
CH2OH
5

5
4 OH
O

6
CH2OH

2
OH

-glucose

4 OH

6
CH2OH

4 OH

1
2
OH

-glucose

2
OH

-glucose

-1,4 glycosidic bond

4 OH

1
O

1
2
OH

-glucose

Learning Outcomes :
1.2 (c) Describe the structures and functions of starch, glycogen and cellulose

AMYLOPECTIN
Monomers: -glucose molecules
Joined together by -1,4 glycosidic bond & -1,6 glycosidic bond

Helical, branched chain (variable length of monomers)


Branches occur within 30 units
Folded & branched ~ very compact (ideal for storage)

Learning Outcomes :
1.2 (c) Describe the structures and functions of starch, glycogen and cellulose

AMYLOPECTIN
6
CH2OH

6
CH2OH

5
4 OH
O

4 OH

-1,6 glycosidic bond

OH

OH

6
CH2OH

4 OH
3

6
C

6
CH2OH

2
OH

-glucose

4 OH

6
CH2OH

4 OH

1
2
OH

-glucose

2
OH

-glucose

-1,4 glycosidic bond

4 OH

1
O

1
2
OH

-glucose

Learning Outcomes :
1.2 (c) Describe the structures and functions of starch, glycogen and cellulose

DIFFERENCES BETWEEN AMYLOSE &


AMYLOPECTIN
Features

Amylose

Amylopectin

Monomers

-glucose

-glucose

Bond

-1,4 glycosidic bond

-1,4 glycosidic bond


-1,6 glycosidic bond

Shape

Helical, unbranched

Helical, branched (within


30 units)

Function

Ideal for energy storage


(insoluble, coiled, compact)

Learning Outcomes :
1.2 (c) Describe the structures and functions of starch, glycogen and cellulose

GLYCOGEN
Energy storage in animals (in liver & muscle)
Structure ~ similar to amylopectin

More branched than amylopectin

Learning Outcomes :
1.2 (c) Describe the structures and functions of starch, glycogen and cellulose

CELLULOSE
Major component of plant cell wall
Monomers: -glucose

Bond: -1,4 glycosidic bond


Broken down by hydrolysis with the help of cellulase enzyme
Unbranched, long straight chain
6
CH2OH

6
CH2OH
5

5
4 OH
3

6
CH2OH

1
2
OH

-glucose

4 OH
3

6
CH2OH

1
2
OH

-glucose

4 OH
3

1
2
OH

-glucose

-1,4 glycosidic bond

4 OH
3

1
2
OH

-glucose

Learning Outcomes :
1.2 (c) Describe the structures and functions of starch, glycogen and cellulose

CELLULOSE

-1,4 glycosidic bond

Learning Outcomes :
1.2 (c) Describe the structures and functions of starch, glycogen and cellulose

CELLULOSE
Straight chains are arranged parallel to one another
Linked together by hydrogen bonds (form microfibril)
Very stable & tough structure ~ provide support to plant cell

Learning Outcomes :
1.2 (c) Describe the structures and functions of starch, glycogen and cellulose

Functions of Polysaccharides
Energy Storage ~ eg: starch (in plant) & glycogen (in animals)
Major component of cell walls ~ provide structural support to

plant cell ~ eg: cellulose

1.0 Molecules Of Life (7 hrs)


1.1 Water

(1)

1.2 Carbohydrates

(1)

1.3 Lipids

(1)

1.4 Proteins

(2)

1.5 Nucleic Acids

(1)

Learning outcomes
a) State the types of lipid
b) Describe the structure of glycerol & fatty acids
c) Describe the formation & breakdown of
triglycerides

Learning Outcomes :
1.3 (a) State the types of lipid: fats, phospholipids and steroids

LIPIDS
Consist of mainly carbon & hydrogen atoms; few oxygen atom
Group of hydrophobic molecules ~ insoluble in water
3 major types:

LIPIDS

Fats

Phospholipids

Steroids

Eg: oil, butter

Eg: lecithin

Eg: cholesterol

Learning Outcomes :
1.3 (a) State the types of lipid: fats, phospholipids and steroids

FATS
Most abundant
Also known as (a.k.a) : Triglyceride / Triacylglycerol

Building block

1 Glycerol

3 Fatty acids

Saturated

Unsaturated

a) Structure of glycerol and b) general structure of fatty acids

Learning Outcomes :
1.3 (b) Describe the structure of glycerols and fatty acids

Glycerol
.

A.k.a : glycerine
3C alcohol with 3 OH groups (soluble in water)

H
H

OH

OH

OH

Learning Outcomes :
1.3 (b) Describe the structure of glycerols and fatty acids

Fatty Acids
.

Has 2 regions:
Hydrophilic head (a carboxyl group, COOH at 1 end ) ~

acid
Hydrophobic tail ~ long unbranched hydrocarbon chain
(known as side chain, R)
O
HO

C1 C
R2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 H
H

Carboxyl group

Hydrocarbon chain

Learning Outcomes :
1.3 (b) Describe the structure of glycerols and fatty acids

Fatty Acids
.

Hydrophobic tail vary in length


Different fatty acids has different number of C atoms

(usually 16 or 18)

O
HO

C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17 C18 H


H

Eg: Stearic acid (stearate) C18H36O2

Learning Outcomes :
1.3 (b) Describe the structure of glycerols and fatty acids

Classification of Fatty Acids


Based on the presence of double bonds within hydrocarbon

chain:
Saturated fatty acids
~ no double bond between C atoms; eg: stearic acid
Unsaturated fatty acids
~ has double bonds between C atoms; eg: oleic acid
O
HO

C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17 C18 H


H

Eg: Stearic acid (stearate) C18H36O2

Learning Outcomes :
1.3 (b) Describe the structure of glycerols and fatty acids

SATURATED FATTY ACID


Has maximum number

. of H atoms
Straight chain, fatty

acids can be closely


packed
Solid at room
temperature

Learning Outcomes :
1.3 (b) Describe the structure of glycerols and fatty acids

SATURATED FATTY ACID


Fats that consist of saturated fatty acids ~ saturated fat

. Mostly animal fats (eg: butter, lard)

Learning Outcomes :
1.3 (b) Describe the structure of glycerols and fatty acids

SATURATED FATTY ACID

Learning Outcomes :
1.3 (b) Describe the structure of glycerols and fatty acids

UNSATURATED FATTY ACID


Double bond causes

bending in
unsaturated fatty
acids
Fatty acids cannot be

closely packed
Liquid at room

temperature

Learning Outcomes :
1.3 (b) Describe the structure of glycerols and fatty acids

UNSATURATED FATTY ACID


Fats that consist of unsaturated fatty acids ~ unsaturated fat
Mostly plant & fishes fats (eg: oil)

Fatty acids stearic acid (saturated fat) and oleic acid (unsaturated fat).

Learning Outcomes :
1.3 (b) Describe the structure of glycerols and fatty acids

Classification of Fatty Acids


Based on the ability to be synthesized in the body:

.
Essential fatty acids

~ cannot be synthesized in the body


~ must be present in the diet
~ eg: linoleic, linolenic and arachidonic acids
Non-essential fatty acids

~ can be synthesized in the body


~ eg: stearic acid & others

Learning Outcomes :
1.3 (a) State the types of lipid: fats, phospholipids and steroids

PHOSPHOLIPIDS
Major component of cell membrane; eg: lecithin
Amphipathic molecule
i.e one end hydrophilic polar, another end hydrophobic non-polar

Building block

1 Glycerol

2 Fatty acids

Phosphate group

Learning Outcomes :
1.3 (a) State the types of lipid: fats, phospholipids and steroids

PHOSPHOLIPIDS

Learning Outcomes :
1.3 (c) Describe the formation & breakdown of triglycerides

TRIGLYCERIDE
Composed of 3 fatty acids & 1 glycerol backbone
Fats are formed when 3 condensation reaction occurs ~ also

known as esterification
Water is removed by extracting the OH from the carboxyl

group (of fatty acid) and H from the glycerols hydroxyl group
Triglyceride can be broken down by hydrolysis

Learning Outcomes :
1.3 (c) Describe the formation & breakdown of triglycerides

Formation of Triglycerides
H
H

O
OH

HO

O
O

O
H

OH

HO

OH

HO

C
O

H
1 glycerol

Condensation
Hydrolysis

O
H

3 fatty acids

Triglyceride

Ester bond

R
Ester bond

R
Ester bond

R
+ 3H2O

Learning Outcomes :
1.3 (c) Describe the formation & breakdown of triglycerides

Importance of Lipids
Main energy storage in animals (due to higher number of

hydrogen atom)
1 g of fat has > twice energy than same weight of starch
Lighter ~ hydrophobic nature, doesnt associates with

water
Improve buoyancy in aquatic animals
Provide better thermal insulation of mammals
Act as padding for internal organs
Phospholipid ~ major component of plasma membrane
Steroid ~ some are hormones that regulates metabolism

1.0 Molecules Of Life (7 hrs)


1.1 Water

(1)

1.2 Carbohydrates

(1)

1.3 Lipids

(1)

1.4 Proteins

(2)

1.5 Nucleic Acids

(1)

Learning outcomes
a) Describe the basic structure of amino acids
b) Explain how amino acids are grouped

c) Describe the formation and breakdown of dipeptide


d) Explain primary, secondary, tertiary & quaternary levels of
proteins & the types of bonds involved

e) Classify proteins according to their structure


f)

Explain the effect of pH & temperature on the structure of


protein

Learning Outcomes :
1.4 (a) Describe the basic structure of amino acids

PROTEIN

Polymer
Building blocks ~ amino acids
Joined together to form a long chain ~ polypeptide

Protein consist of 1 or more polypeptide chains which folded &


coiled into specific conformation
Mostly composed of C, H, O, N & sometimes S

Learning Outcomes :
1.4 (a) Describe the basic structure of amino acids

BASIC STRUCTURE OF AMINO ACIDS


Amino acids consist of 4 components attached to a central
carbon
These components include:
a. a hydrogen atom
b. a carboxyl group
c. an amino group
d. a variable R group (or side chain).
R

amino group

H2N

C
H

COOH carboxyl group

Learning Outcomes :
1.4 (a) Describe the basic structure of amino acids

BASIC STRUCTURE OF AMINO ACIDS


2 functional groups:
i. COOH (carboxyl group)
ii. NH2 (amino group)

: acidic
: basic

Amino acids are amphoteric; have both acidic & basic


properties
R
amino group

H2N

C
H

COOH carboxyl group

Learning Outcomes :
1.4 (b) Explain how amino acids are grouped

GROUP OF AMINO ACIDS


20 types of amino acids commonly found in proteins
All have the same basic structure but differ in the side chain, R
Amino acids are grouped based on the properties of R group

R
amino group

H2N

C
H

COOH carboxyl group

Learning Outcomes :
1.4 (b) Explain how amino acids are grouped

4 groups

Non-polar
Hydrophobic

Glycine (gly)

Polar

Hydrophilic

Acidic

Basic

Has COOH group Has NH2 group

Serine (ser)
Aspartic acid (asp)

Lysine (Lys)

Learning Outcomes :
1.4 (b) Explain how amino acids are grouped

GROUP OF AMINO ACIDS


i.

Essential amino acids (for human)


Cannot be synthesized in sufficient amount, must be
obtained through food or supplement intake
8 amino acids; eg: isoleucine, leucine, lysine, methionine,
phenylalanine, threonine, tryptophan, valine
For infants : histidine

ii. Non-essential amino acids


Can be synthesized in the body
Eg: alanine, arginine, asparagine, aspartic acid, cysteine,
glutamic acid, glycine, proline, serine, tyrosine, glutamine

Learning Outcomes :
1.4 (c) Describe the formation and breakdown of dipeptide

Formation of the dipeptide


2 amino acids are joined by condensation process to
form a dipeptide
By removal of a hydroxyl group from the carboxyl end of
one amino acid and a hydrogen from the amino group of
another amino acid.
Form a covalent bond ~ peptide bond

Learning Outcomes :
(c) describe the formation and breakdown of dipeptide
Learning Outcomes :
1.4 (c) Describe the formation and breakdown of dipeptide

Formation & breakdown of the dipeptide


H

R1

OH

Condensation

N-terminal

OH

Hydrolysis

H 2O
R1

R2

H2O
R2

Peptide bond

OH

C-terminal

Learning Outcomes :
1.4 (c) Describe the formation and breakdown of dipeptide

Breakdown of dipeptide
Dipeptide is hydrolysed into 2 amino acids by hydrolysis
process (addition of water).

Peptide bond is broken down and produces 2 amino acids.

Learning Outcomes :
1.4 (c) Describe the formation and breakdown of dipeptide

Formation of polypeptide
Many amino acids are joined by condensation process to form
a polypeptide
Bond ~ peptide bonds
Polypeptide backbone ~ repeated sequence of (-N-C-C-)

R1

OH

R2

Peptide bond

OH

Peptide bond

R3

OH

Learning Outcomes :
1.4 (c) Describe the formation and breakdown of dipeptide

Formation of tripeptide

Learning Outcomes :
1.4 (d) Explain primary, secondary, tertiary & quaternary levels of proteins & the types of bonds involved

Classification of Protein
Two ways based on:Level of protein structure
i. Primary
ii. Secondary
iii. Tertiary
iv. Quaternary
Structure
i. Fibrous
ii. Globular
iii. Conjugated

Learning Outcomes :
(d) explain primary, secondary, tertiary and quaternary levels of proteins and the types of bonds
Learning Outcomes :
involved
1.4 (d) Explain primary, secondary, tertiary & quaternary levels of proteins & the types of bonds involved

Learning Outcomes :
1.4 (d) Explain primary, secondary, tertiary & quaternary levels of proteins & the types of bonds involved

Primary structure
Refers to the linear sequence of amino acids joined by
peptide bonds within a polypeptide chain
Each protein has a unique sequence of amino acids,
determined by specific DNA code
Different sequence results in the formation of different bonds
between amino acids

Causes a polypeptide chain to fold & coil into a unique 3


dimensional shape of protein

Eg : lysozyme & all protein that has been sequenced

Learning Outcomes :
1.4 (d) Explain primary, secondary, tertiary & quaternary levels of proteins & the types of bonds involved

Primary structure

Learning Outcomes :
1.4 (d) Explain primary, secondary, tertiary & quaternary levels of proteins & the types of bonds involved

Secondary structure
Linear chain of amino acids will coil or fold spontaneously
Due to the formation of H bonds between the backbones
(between H of the NH groups & O of the C=O groups of
amino acids in the primary chain)
2 types
-helix

-pleated sheet

Learning Outcomes :
1.4 (d) Explain primary, secondary, tertiary & quaternary levels of proteins & the types of bonds involved

Secondary structure

Learning Outcomes :
1.4 (d) Explain primary, secondary, tertiary & quaternary levels of proteins & the types of bonds involved

-helix
Helical coil
H bonds is formed between 1 amino
acid & the 4th amino acid away from it
Can stretch under tension ~ provide
elasticity
Because the hydrogen bonds can be
reformed
Eg: keratin in hair, nails & wool

|
S

|
S

S
|

S
|

Learning Outcomes :
1.4 (d) Explain primary, secondary, tertiary & quaternary levels of proteins & the types of bonds involved

-pleated sheet
Zig-zag pattern ~ provide strength & flexibility
Eg: silk, spider web

Learning Outcomes :
1.4 (d) Explain primary, secondary, tertiary & quaternary levels of proteins & the types of bonds involved

Tertiary structure
1 polypeptide chain in secondary structure may further coiled
into a globular shape which is maintained by bonds and
interactions among R groups

Globular shape unique to each polypeptide chain


Mantained by 4 interactions between R groups: Disulfide bonds (covalent bonds) between R groups with
sulfhydryl groups
Ionic bonds between +ve & -ve charged R groups
Hydrogen bonds between + & - charged R groups
Hydrophobic / Van der Waals interaction between nonpolar R groups

Learning Outcomes :
1.4 (d) Explain primary, secondary, tertiary & quaternary levels of proteins & the types of bonds involved

Tertiary structure

Learning Outcomes :
1.4 (d) Explain primary, secondary, tertiary & quaternary levels of proteins & the types of bonds involved

Tertiary structure
Eg: enzymes, hormones, antibodies
Type of bonds exist in different levels of protein:
Features

Primary

Secondary

Tertiary

Type of
bond exist

i. Peptide
bond

i. Peptide bond
ii. H bond (between
C=O & NH group of
backbone)

i. Peptide bond
ii. H bond (between C=O
& NH group of
backbone)
iii. Disulfide bond
iv. Ionic bond
v. H bond (between R
groups)
vi. Hydrophobic (van der
Waals) interaction

Learning Outcomes :
1.4 (d) Explain primary, secondary, tertiary & quaternary levels of proteins & the types of bonds involved

Quaternary structure
Refers to a single protein that is formed when two or more
polypeptide chain joins
Bonds exist ~ same as tertiary structure
Eg: hemoglobin (consist of 4 polypeptide chains, two chains
and two chains)

Learning Outcomes :
1.4 (d) Explain primary, secondary, tertiary & quaternary levels of proteins & the types of bonds involved

4 Levels of Protein

Learning Outcomes :
1.4 (e) Classify proteins according to their structure

Classification of Protein
Based on Structure

Fibrous

Globular

Conjugated

FIBROUS
Mostly secondary structure
Form long parallel filaments or strands
Insoluble & stable
Function : mechanical & structural support
Eg:
Keratin, actin, myosin, collagen, silk

Learning Outcomes :
1.4 (e) Classify proteins according to their structure

Globular Protein
Mostly tertiary/quaternary structure
Folded to form compact spherical shaped
Relatively unstable
Relatively soluble ~ colloid
Function : metabolic & chemical process
Eg:
Enzyme

Hormone

Antibodies

Hemoglobin

Learning Outcomes :
1.4 (e) Classify proteins according to their structure

Conjugated Proteins
Protein that can function well if it joins with other compound
Non-protein compound ~ prosthetic group
Conjugated Protein

Prosthetic group

Location

Glycoprotein

Polysaccharide

Component of cell membrane


Mucin (in saliva)

Lipoprotein

Lipid

Component of cell membrane


Lipid transported in blood
plasma

Chromoprotein

Pigment

Myoglobin, hemoglobin

Nucleoprotein

Nucleic acid

Chromosome, ribosome

Learning Outcomes :
1.4 (f) Explain the effect of pH and temperature on the structure of protein

Effect of pH and Temperature


Structure of protein is affected by:1. pH
2. temperature
Globular protein is relatively unstable because it is maintained
by weak ionic bonds, hydrogen bonds & hydrophobic
interactions
When protein is heated or exposed to an extreme pH
changes, those bonds are broken
Causes it to uncoiled & change its conformation
Lose its biological function ~ denatured protein coagulate
Usually irreversible (sometimes, renaturation may occur)

Learning Outcomes :
1.4 (f) Explain the effect of pH and temperature on the structure of protein

Effect of pH and Temperature

Factor

Effect to the protein structure

Heat or radiation

Increased kinetic energy


Protein atoms vibrate
H & ionic bonds, van der Waals interaction break

Strong acids &


alkali

H & ionic bonds, van der Waals interaction break


Breakdown of peptide bonds occur if exposed very long

1.0 Molecules Of Life (7 hrs)


1.1 Water

(1)

1.2 Carbohydrates

(1)

1.3 Lipids

(1)

1.4 Proteins

(2)

1.5 Nucleic Acids

(1)

Learning outcomes
a) Describe the structure of nucleotide as the monomer
of nucleic acid (DNA & RNA)
b) Describe the structure of DNA based on the Watson
& Crick Model
c) State the types & function of RNA
d) State the differences of DNA & RNA

Learning Outcomes :
1.5 (a) Describe the structure of nucleotide as the monomer of nucleic acid (DNA and RNA)

Introduction
Nucleic acid is polynucleotide ~ polymer of nucleotides
Building blocks ~ nucleotide
Mostly composed of C, H, O, P & N

Learning Outcomes :
1.5 (a) Describe the structure of nucleotide as the monomer of nucleic acid (DNA and RNA)

NUCLEIC ACIDS
2 types

Deoxyribonucleic Acid
(DNA)

Ribonucleic Acid
(RNA)

Learning Outcomes :
1.5 (a) Describe the structure of nucleotide as the monomer of nucleic acid (DNA and RNA)

Structure of nucleotides
Each nucleotide has 3 components:Nucleotide

Pentose sugar

Ribose
(in RNA)

Deoxyribose
(in DNA)

Nitrogenous base

Phosphate group

Learning Outcomes :
1.5 (a) Describe the structure of nucleotide as the monomer of nucleic acid (DNA and RNA)

Pentose Sugar (5 C sugars)

C5H10O4

C5H10O5

Ribose
~ component of RNA nucleotide
Deoxyribose ~ component of DNA nucleotide
At 2nd carbon atom
~ in deoxyribose; one H atom

~ in ribose; one OH group

Learning Outcomes :
1.5 (a) Describe the structure of nucleotide as the monomer of nucleic acid (DNA and RNA)

Nitrogenous base
Based on the number of C ring

2 groups
Double rings

Single ring

Pyrimidine

Cytosine (C)

Purine

Uracil (U)

Thymine (T)

In RNA

In DNA

Guanine (G)

Adenine (A)

Learning Outcomes :
Learning Outcomes :
(a) Describe the structure of nucleotide as the basic composition of nucleic acid (DNA and
1.5 (a) Describe the structure of nucleotide as the monomer of nucleic acid (DNA and RNA)
RNA)

Nitrogenous base
Nitrogenous base in DNA:
i. Guanine
ii. Adenine
iii. Thymine
iv. Cytosine

Nitrogenous base in RNA:


i. Guanine
ii. Adenine
iii. Uracil
iv. Cytosine

Learning Outcomes :
Learning Outcomes :
(a) Describe the structure of nucleotide as the basic composition of nucleic acid (DNA and
1.5 (a) Describe the structure of nucleotide as the monomer of nucleic acid (DNA and RNA)
RNA)

DNA nucleotide

RNA nucleotide

Nitrogenous
Base

Phosphate
Group
OH
HO

P
O

Nitrogenous
Base

Phosphate
Group
OH

CH2

HO

deoxyribose

H
3

OH

Pentose Sugar ~
deoxyribose

P
O

CH2

ribose

H
3

OH

OH

Pentose Sugar ~
ribose

In a nucleotide :
nitrogenous base is joined to the 1st carbon of the pentose
phosphate group is joined to the 5th carbon of the pentose

Learning Outcomes :
1.5 (a) Describe the structure of nucleotide as the monomer of nucleic acid (DNA and RNA)

FORMATION OF DINUCLEOTIDE
2 nucleotides are combined by condensation process ~
dinucleotide
Between OH group in phosphate group (of 1 nucleotide)
and the OH group at the 3rd carbon in pentose sugar (of
the other nucleotide)
Joined together by phosphodiester bond

Learning Outcomes :
1.5 (a) Describe the structure of nucleotide as the monomer of nucleic acid (DNA and RNA)

FORMATION OF DINUCLEOTIDE
OH
HO

P O
O

OH
5

CH2

HO

deoxyribose

P O

OH

P O
O

H
2

H
O

CH2

HO

deoxyribose

H
2

OH

condensation

OH

HO

deoxyribose

CH2

P O
O

phosphodiester
bond

CH2

deoxyribose

H
2

OH

Learning Outcomes :
1.5 (a) Describe the structure of nucleotide as the monomer of nucleic acid (DNA and RNA)

FORMATION OF POLYNUCLEOTIDE
Many nucleotides
joined together ~
polynucleotide
Elongation ~ from 5
to 3
Forming a backbone
with repeating sugarphosphate units
Breakdown by
hydrolysis process
3

Learning Outcomes :
1.5 (b) Describe the structure of DNA based on the Watson & Crick Model

DNA Structure
Based on Watson & Crick Model

Learning Outcomes :
1.5 (b) Describe the structure of DNA based on the Watson & Crick Model

DNA Structure
Consist of 2 polynucleotide chains
Both polynucleotide chains are twisted to
form a double helix
Each polynucleotide chain is made up of
nucleotide
Nucleotides are joined together by
phosphodiester bond

Each full turn of a double helix has 10 base


pairs

Learning Outcomes :
1.5 (b) Describe the structure of DNA based on the Watson & Crick Model

DNA Structure
5'

2 polynucleotide chains
are arranged in opposite
direction (antiparallel)
One strand ends with a 3
hydroxyl group while the
other strand ends with a
5 phosphate group

3'

3'
5'

Learning Outcomes :
1.5 (b) Describe the structure of DNA based on the Watson & Crick Model

DNA Structure
Sugar-phosphate forms the backbone

The 2 backbones are on the outside,


the nitrogenous bases are paired
inside the helix

Learning Outcomes :
1.5 (b) Describe the structure of DNA based on the Watson & Crick Model

DNA Structure
5'

Both chains are held together


by hydrogen bonds between
complementary base pair;
Adenine with Thymine,
Cytosine with Guanine
Between Adenine & Thymine
~ 2 hydrogen bonds
Between Cytosine & Guanine
~ 3 hydrogen bonds
Specific base-pairing rule
~ the numbers of A=T, G=C

3'

3'
5'

Learning Outcomes :
1.5 (b) Describe the structure of DNA based on the Watson & Crick Model

DNA
Importance:

As genetic material which carries


genetic information that control all
activities of a cell

Learning Outcomes :
1.5 (c) State the types & function of RNA

RNA
Single stranded polynucleotide
Pentose sugar ~ ribose
Nitrogenous bases ~ Guanine, Adenine, Cytosine, Uracil
3 types:
RNA

Messenger RNA
(mRNA)

Ribosomal RNA
(rRNA)

Transfer RNA
(tRNA)

Learning Outcomes :
1.5 (c) State the types & function of RNA

mRNA
Function :
Carries genetic information copied from DNA which act
as a template for protein synthesis

Learning Outcomes :
1.5 (c) State the types & function of RNA

rRNA
Function :
Forms ribosomal subunits (together with proteins)

Learning Outcomes :
1.5 (c) State the types & function of RNA

tRNA
Function :
Transfer specific amino acids to ribosome during protein
synthesis

Learning Outcomes :
1.5 (c) State the types & function of RNA

RNA

Learning Outcomes :
1.5 (d) State the differences of DNA & RNA

Differences between DNA & RNA


DNA

RNA

2 polynucleotide chains

1 polynucleotide chain

pentose sugar ~ deoxyribose

pentose sugar ~ ribose

nitrogenous base ~ G, A, T, C

nitrogenous base ~ G, A, C, U

shape ~ double helix

shape ~ linear (mRNA)

longer chain / larger molecular


mass

shorter chain / smaller molecular


mass

Only 1 type

Has 3 types : mRNA, rRNA &


tRNA

Reference
Campbell N.A & Reece, J.B., Biology, 6th ed.
(2002), Pearson Education, Inc.
Solomon E.P & Berg, L.R, Biology, 7th ed. (2005)
Thomson Learning, Inc.
Mader, S.S Biology, 8th ed. (2004) McGraw-Hill
Companies, Inc.