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Chapter 4

Chemical Composition of the Cell


4.1 Chemical composition of the cell
4.2 Carbohydrates-loq-ferissa
4.3 Lipids-aishah-foto
4.4 Proteins-mariah-gigi kilat
4.5 Enzymes-kecil-reena-tak datang
adlina
4.6 Nucleic Acids-2 tangan-zabreeee
4.7 Water-minah-idzmir

4.1
Chemical composition of the cell
- Elements & chemical compounds
- Importance of Organic compounds,
Inorganic compounds (water)

Element
= a substance that composed of
only 1 type of atom
25 essential elements which are important to living organisms
Most common
elements found in
living cells 96%
C - Carbon
H - Hydrogen
O - Oxygen
N - Nitrogen

Other elements in cells


4%
S Sulphur
K Potassium*
Na Sodium*
Cl Chlorine*
Mg Magnesium*
Ca Calcium*
P - Phosphorus
Fe Ferum / Iron*

Trace elements
< 0.01%
Cu Copper
I Iodine
Zn - Zinc

* Mineral ions - Exist as ions in the cell

Chemical compounds
= consist of >1 types of atoms
Common elements combined with each
other to form various chemical compounds
in the cell.
Divided into:
organic compounds & inorganic compounds.

Chemical
compounds

Does not
contain carbon

Inorganic
compound

Obtained from
external
environment

Contain
carbon

Organic
compounds

Water

Carbohydrates

Lipids

H, O

C, H, O

C, H, O

Synthesized by
living cells

Nucleic
Acids

Proteins
C, H, O, N, (S)

C, H, O, N, P

Handouts
1. Function of elements in animal cell and
plant cell
2. Importance of chemical compounds in
the cell

Importance of water
1.
2.
3.
4.
5.
6.
7.
8.

Universal solvent
Medium for biochemical reactions
As transport medium
Maintain body temperature
Provide support
Maintain osmotic pressure & turgidity
High surface tension & cohesion
Provide moisture & lubrication

Organic compounds

Carbohydrate

Lipid

Nucleic acid

Protein Enzyme

Monomer
Monomer
= small molecules that build a polymer.
= cannot be broken down into smaller units.
Examples of monomer:
Monosaccharide, amino acid, glycerol, fatty acid
Process of condensation to produce polymer is
known as polymerization.

Polymer
Consists of repeating units of monomers
joined together by chemical bonds
through condensation / polymerisation.

Class

Monomer

Dimer

Polymer

Nucleic acids

Nucleotide

Polynucleotide

Carbohydrates

Monosaccharide

Disaccharide Polysaccharide

Proteins

Amino acid

Dipeptide

Polypeptide

Fat / Oil /
Lipids

Fatty acid,
Glycerol

Triglyceride /
Fats / Lipids

Carbohydrate

4.2

Carbohydrates

- Elements in carbohydrates
- Types of carbohydrates:
Monosaccharides, Disaccharides,
Polysaccharides
- Formation and Breakdown of
Disaccharides and Polysaccharides

Carbohydrates
Carbon

Water

H2O

Elements:
C:H:O
Ratio:
1:2:1
Empirical formula: (CH2O)n , n3

4 types of Carbohydrates
1. Monosaccharide
one
sugar

3. Oligosaccharide
3-7
sugar

2. Disaccharide
two
sugar

4. Polysaccharide
multiple sugar

Class of
carbohydrates

Examples

Characteristics

Importance /
Functions

Monosaccharide

Glucose
Fructose
Galactose

Soluble in water
Tastes sweet
All are reducing sugar
(able to reduce Cu II
sulphate into Cu I
oxide)

Instant source of energy


Building block
(as monomers) of
carbohydrates

Maltose
Lactose
Sucrose

Soluble in water
Tastes sweet
All are reducing sugar
except sucrose

No specific function
As intermediate
substances in digestion
of carbohydrates

Glycoprotein
Glycolipid

Found on the plasma


membrane of the cell

As a marker for
cell recognition &
cell communication

Polysaccharide

Starch

(also known as
complex sugars)

Glycogen

Insoluble in water
Not sweet-tasting
All are non-reducing
sugar

Food (Energy) storage


in plant cell
Food (Energy) storage
in animal cell
Structural component in
the plant cell wall

(also known as
simple sugars)

Disaccharide
(also known as
complex sugars)
Oligosaccharide
(also known as
complex sugars)

Cellulose

Monosaccharides

Monosaccharides
Examples: Glucose, Fructose, Galactose
Characteristics:
Soluble in water
Tastes sweet
All are reducing sugar
(able to reduce Cu II sulphate into Cu I oxide)

Monosaccharide
Importance:
Instant source of energy
Building block (as monomers) of carbohydrates

Test for Reducing Sugar


2.
Benedicts
solution

1. Glucose
solution

For solid food sample


- add distilled water
- crushed using
mortar & pestle

3. Heat in
water bath
Brick red precipitate

Blue
Cu 2+
Copper (II) sulphate

efrom
glucose

Cu +
Copper (I) oxide

DISACCHARIDES
Examples of disaccharides:
Glucose + Glucose Maltose + Water
Glucose + Galactose Lactose + Water
Glucose + Fructose Sucrose + Water

Disaccharides are formed through a


process called condensation where one
water molecule is produced / expelled.

WORD EQUATION
Monomer

Condensation

Dimer

Monomer

Hydrolysis

Water

2 units of monomer

CARBOHYDRATES
Monosaccharide

Condensation
Disaccharides

+
Monosaccharide

Hydrolysis

2 units of sugar

Water

Test for Non-Reducing Sugar


4.
Benedicts
solution

1. Sucrose
solution

2. HCl
Sucrose
Glucose + Fructose
3. Sodium
bicarbonate

5. Heat in
water bath
Brick red precipitate

Blue

To neutralise the excess


acid

Cu 2+

Copper (II) sulphate

efrom
glucose &
fructose

Cu +
Copper (I) oxide

Sucrose
D-glucose

D-Fructose

Glycosidic linkage

Glycosidic linkage

Linkages depending on
how the OH group on
the anomeric carbon is
oriented.

POLYSACCHARIDES
Storage polysaccharides
= Starch, Glycogen.
Structural polysaccharides
= Cellulose, Chitin.

Polyccharides

Starch

Glycogen

Glycogen

Cellulose

Lipids

4.3

Lipids

Elements in lipids
Types of lipids
Components of Fats and Oils
Formation and Breakdown of Triglyceride
Saturated Fat and Unsaturated Fat

Lipids
Elements: C : H : O
- no fixed ratio
Unsaturated fat - Double bond between
C=C
Saturated fat - Single bond between C-C

Types of Lipids
Lipid

Function

Fats & Oils

Energy storage, insulation,


protection

Wax

A waterproof layer on the cuticle of


leaves

Phospholipid

Main component of plasma


membrane

Steroid
1. Cholesterol Make plasma membrane more rigid
2. Hormone
Controls secondary sex
characteristics

Lipid
Condensation
Glycerol

3 Fatty acid

Triglyceride
Hydrolysis

3 Water

Examples of Lipids

Structure of Lipids
1. Textbook pg 68
Figure 4.8
Condensation and hydrolysis of
triglycerides
2. Textbook pg 69
Figure 4.9
- Saturated & unsaturated fatty acids

Fats & Oils


Saturated fat contains
saturated fatty acids
condensed with glycerol.

Unsaturated fat contains


unsaturated fatty acids
condensed with glycerol.

Saturated fatty acid


= fatty acid with single
bond between carbon
atoms

Unsaturated fatty acid


= fatty acid 1 double
bonds between carbon
atoms.

Nucleic acid
DNA
RNA

Monomer of DNA = Nucleotide

DNA A, T, G, C
RNA A, U, G, C
DNA Deoxyribose
RNA - Ribose

DNA = Deoxyribonucleic acid

Monomer = Nucleotide
Polymer =Polynucleotide

Nitrogen bases:
Adenine
Thymine
Guanine
Cytosine
Uracil

2 types of Nucleic Acids


DNA = Deoxyribonucleic acid
Double stranded polynucleotide

RNA = Ribonucleic acid


Single stranded polynucleotide

Nucleotide consists of:


Nucleotide consists of:
Deoxyribose + Phosphate group + Ribose + Phosphate group +
Nitrogenous base.
Nitrogenous base.
Found in nucleus, mitochondrion,
chloroplast
1.

Function:
Store genetic information of
an organism

Found in nucleus, cytoplasm,


ribosome
1.

2.
1 type of DNA

Function:
Copies information carried
by DNA for the use of
protein synthesis.
Genetic material in some
viruses.
3 types of RNA

Polymer = Polynucleotide
Sugar is joined to
phosphate group
forming the
backbone of the
polynucleotide
molecule.

Pairing of bases is specific.

Double helix DNA is like a twisted ladder.


Sugar-phosphate backbone makes the sides of the ladder.
Base pairs are held by hydrogen bonds makes the steps of the ladder.

3 types of RNA
- involved in Protein Synthesis
1. mRNA = messenger RNA
2. rRNA = ribosomal RNA
3. tRNA = transport RNA

Protein synthesis
stage 1 Transcription: genetic codes of DNA are copied into mRNA
stage 2 Translation: tRNA amino acids

Translation of mRNA
into Amino acids by tRNA
3 bases = 1 genetic code
= 1 codon
codes for 1 amino acid

mRNA bind to ribosome.


Ribosome can read the
genetic codes on mRNA.
tRNA transport suitable
amino acids

Proteins

4.4 Proteins
Elements, Structure
Formation & Breakdown of Dipeptides
Amino acids: Essential, Non-Essential

Proteins
Elements:

C, H, O, N, S

Monomer = Amino acid


Polymer = Polypeptide = Protein
(linear, 2D)

(3D)

Amino acid
R = (CH3)n = Methyl group

R
H2N
Amino group
- basic

C
H

COOH
Carboxylic group
- acidic

WORD EQUATION
Condensation
Monomer

Monomer

Dimer
Hydrolysis

Water

2 units of monomer

PROTEINS
Condensation
Amino
acid

Amino
acid

Dipeptide
Hydrolysis

2 units of amino acids

Water

Formation of Dipeptide
Amino acids are joined together by
peptide bond through condensation process.

Word equation:

Amino acid

Amino acid

Dipeptide

+ Water

Structural equation:

N C

OH

H H
R
H

N C

H
R

O
C

H H

Peptide bond

OH

OH

H2O

Refer: Textbook pg66


20 types of amino acids required by human

Types of Amino acids


Essential amino acids
(9)

Non-essential amino acids


(11)

Must be obtained from food / Not necessary to be


diet.
obtained from diet.
Reason: Can be derived
from other amino acids.
Cannot be synthesized by
the body / cell.

Can be synthesized by the


body / cell.

Examples:
Leucine, Isoleucine, Lysine

Examples:
Alanine, Asparagine,
Aspartic acid

4 Levels of
the Structures
of Proteins
Draw in Notebook
Textbook pg 66
Figure 4.7

Structure of Protein
1.

Primary structure = Linear structure

2.

Secondary structure:
a) Coiled structure = Alpha-helix
- helix
b) Folded structure = Beta-pleated sheets
pleated sheets

3.

Tertiary structure = 3 Dimensional shape


- 1 polypeptide chain folded or coiled into 3D shape
- example: Hormone, enzyme, antibodies.

4.

Quarternary structure
- 2 tertiary chains joined together
- example: Haemoglobin

Tertiary structure
1 polypeptide coiled & folded
into 3-dimensional structure
with specific function.

Examples:
Enzyme, antibodies, plasma protein

Enzymes

4.5 Enzymes
Definition, Naming, Characteristics, Roles
Synthesis of enzymes :
Intracellular & Extracellular Enzymes
Mechanism of Enzyme Reaction:
Lock-and-Key Hypothesis
Factors that affect the Activity of Enzymes
Uses of Enzymes in Industry

Definition of Enzyme
Enzyme = Biocatalyst
= Protein produced by living cells which can
speed up biochemical reactions.

Naming of enzymes
Most enzymes have a name derived by adding
the suffix ase at the end of the name of their
substrates.
Substrate

Enzyme

Lactose

Lactase

Sucrose

Sucrase

Maltose

Maltase

Lipid

Lipase

2. Enzymes lower the activation energy needed by the


biochemical reactions to occur,
thus speed up biochemical reactions.

Characteristics of Enzymes
3. Remained unchanged at the end of the
reactions, thus can be reused.
4. Small amount of enzymes can catalyzed large
amount of substrates. Reason: (3)

Mechanism of enzyme reaction

Lock-and-Key Hypothesis

5. Highly specific each enzyme can catalyze 1


type of reaction or 1 type of substrate. Reason:
Specific active site of enzyme only binds to
specific substrate.
6. Most reactions catalyzed by enzymes are
reversible (forward & backward).

6. Many enzymes require cofactor (helper molecule)


to function.
7. Enzyme activities can be slowed down or stopped by
inhibitors (heavy metals like mercury Hg, lead Pb).

Mechanism of enzyme reaction


Enzyme has a 3-D shape which is highlyspecific.
Polypeptide chains folded to form a pocket
called active site.
Active site has a distinctive shape and
charges that complement to its substrate.

Mechanism of enzyme reaction

Lock-and-Key Hypothesis

++

ES

Enzyme + Substrate

Enzyme-Substrate
complex

Enzyme + Product

The way an enzyme binds to its substrate can be


explained by the lock-and-key hypothesis.

Lock represents enzyme; Key represents substrate.

1.

A specific substrate molecule arrives at the active site


of the enzyme molecule.

2.

Substrate molecule binds to the active site to form an


enzyme-substrate complex, like a key fits into a lock.
E-S complex is unstable.

3.

- Enzyme catalyses the substrate to form products.


- Products leave the active site of enzyme.
- Enzyme is free to bind to another substrate and
catalyze another reaction (can be reused).

Biochemical Reactions
in living cell / organism

Metabolism = all biochemical reactions occurring in living


cells.

Most of these biochemical reactions are catalyzed by


enzymes.

1.

Metabolism includes:
Anabolism
= Synthesis of large complex molecules from smaller,
simpler molecules Requires / Absorbs energy

2.

Catabolism
= Breakdown of large complex molecules into smaller,
simpler molecules Release energy

Intracellular Enzyme

Extracellular Enzyme

= Enzymes which are


produced & retained in the
cell for the use of the cell
itself.

= Enzymes which are


produced in the cell but
secreted from the cell to
function externally.

These enzymes are found in:


Cytoplasm, nucleus,
mitochondrion, chloroplast

These enzymes are found:


Outside the cell
(tissue fluid, blood)

Example:
Oxidoreductase catalyses
biological oxidation &
reduction in the
mitochondrion.

Example:
Digestive enzymes secreted
by pancreas but not used by
pancreas cells.
These enzymes are
transported to duodenum
which is the actual site of
enzymatic reaction.

Synthesis of Enzymes
Intracellular enzyme
Extracellular enzyme

3 types of RNA
- involved in Protein Synthesis
1. mRNA = messenger RNA
2. rRNA = ribosomal RNA
3. tRNA = transport RNA

Protein synthesis
stage 1 Transcription: genetic codes of DNA are copied into mRNA
stage 2 Translation: tRNA amino acids

Translation of mRNA
into Amino acids by tRNA
3 bases = 1 genetic code
= 1 codon
codes for 1 amino acid

mRNA bind to ribosome.


Ribosome can read the
genetic codes on mRNA.
tRNA transport suitable
amino acids

Factors that affect activity of enzymes


1.
2.
3.
4.

Temperature
pH
Concentration of substrate
Concentration of enzyme

* Refer handouts Essay

1. Temperature
Optimum temperature
= temperature at which an enzyme
catalyses a reaction at the maximum rate.
Most human enzymes have an optimum
temperature at around 37oC.
Most plants enzymes have an optimum
temperature at around 25oC.

Textbook Pg 73 Figure 4.12

Textbook Pg 73 Figure 4.12


At low temperature, enzymes are inactive
and reaction takes place slowly.
Rate of reaction doubles with every 10oC.
Rate of reaction increases proportional
to the temperature increase until the
optimum temperature.
Rate of reaction is the highest at the
optimum temperature.

Denaturation
Textbook pg73 Figure 4.12
Beyond the optimum temperature (>37 oC),
increase in temperature will no longer
increase the rate of reaction.
At 40 oC, rate of reaction decreases due to
denaturation of enzymes.
At 60 oC, rate of reaction = 0 (stop)
Reason: All enzymes are denatured.

At high temperature:
1. Chemical bonds that hold enzyme
together begin to break.
2. 3D shape of enzymes are altered.
3. Active sites are destroyed.
4. Substrates can no longer fit in the active
site.
5. Enzymes are denatured Irreversible
As a result, rate of reaction = 0

2. pH
Optimum pH
= pH at which the rate of reaction is at the
maximum.
Optimum pH for most enzymes ranges
between pH 6-8.
Effect of pH on enzymes are normally
reversible.

Rate of reaction
Trypsin

Change of pH can:
1. Alter the charges on the active sites.
2. Reduce the ability of enzyme & substrate
to bind with each other.

As a result, rate of reaction decreases

When pH reverts to optimum, charges on


active sites are restored, enzyme can
resume its normal function = Reversible

3. Enzyme concentration

4. Substrate concentration

Uses of Enzymes
Zymase
Protease

Convert sugar to ethanol in beer / wine-making industry

Amylase

Break down starch to sugar in syrup making


in detergent / washing powder - remove starch which is used as
stiffener of fabrics.

Lipase
Rennin
Trypsin
Cellulase

Ripening of cheese (dairy products)

Tenderizes the meat in food processing industry


Remove the skin of fish
in detergent / washing powder remove stain by breaking down
proteins

Solidify milk proteins in making dairy products


Remove hair from animal hides in leather- making
Breakdown cellulose of seed coat from cereal grains
Breakdown cell wall to extract agar from seaweed