Chapter 4Chemical 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
4.1Chemical 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
Most common elements found in living cells 96%
Other elements in cells
4%
Trace elements
< 0.01%
C - Carbon
H - Hydrogen
O - Oxygen
N - Nitrogen
S – Sulphur
K – Potassium*
Na – Sodium*
Cl – Chlorine*
Mg – Magnesium*
Ca – Calcium*
P - Phosphorus
Fe – Ferum / Iron*
Cu – Copper
I – Iodine
Zn - Zinc
* Mineral ions - Exist as ions in the cell
25 essential elements which are important to living organisms
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
Inorganic compound
Organic compounds
Water
H, O
Carbohydrates
C, H, O
Lipids
C, H, O
Nucleic Acids
C, H, O, N, P
Proteins
C, H, O, N, (S)
Contain carbon
Does not contain carbon
Obtained from external environment
Synthesized by living cells
Handouts
1. Function of elements in animal cell and plant cell
2. Importance of chemical compounds in the cell
Importance of water
1. Universal solvent2. Medium for biochemical reactions3. As transport medium4. Maintain body temperature5. Provide support6. Maintain osmotic pressure & turgidity7. High surface tension & cohesion8. 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
• Elements: C : H : O
• Ratio: 1 : 2 : 1
• Empirical formula: (CH2O)n , n≥3
Carbon Water
C H2O
4 types of Carbohydrates
1. Monosaccharide
one sugar
2. Disaccharide
two sugar
3. Oligosaccharide
3-7 sugar
4. Polysaccharide
multiple sugar
Class of carbohydrates
Examples Characteristics Importance /Functions
Monosaccharide
(also known as simple sugars)
GlucoseFructose
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
Disaccharide
(also known as complex sugars)
MaltoseLactoseSucrose
• Soluble in water• Tastes sweet
• All are reducing sugarexcept sucrose
• No specific function• As intermediate
substances in digestion of carbohydrates
Oligosaccharide
(also known as complex sugars)
GlycoproteinGlycolipid
• Found on the plasma membrane of the cell
• As a marker for cell recognition &
cell communication
Polysaccharide
(also known as complex sugars)
Starch
Glycogen
Cellulose
• 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
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
1. Glucose solution
For solid food sample - add distilled water- crushed using mortar & pestle
2. Benedict’s
solution
3. Heat in water bath
Blue Brick red precipitate
Copper (II) sulphate Copper (I) oxide
Cu 2+ Cu + + e-
from glucose
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.
Monomer
Monomer
+ Dimer
Condensation
Hydrolysis
Monosaccharide
+Disaccharides
Condensation
HydrolysisMonosaccharide
+ Water
+ Water
2 units of sugar
WORD EQUATION
2 units of monomer
CARBOHYDRATES
Test for Non-Reducing Sugar
1. Sucrose solution
4. Benedict’s
solution
5. Heat in water bath
Blue Brick red precipitate
Copper (II) sulphate Copper (I) oxide
Cu 2+ Cu +
2. HCl
Sucrose Glucose + Fructose
3. Sodium bicarbonate
To neutralise the excess acid + e-
from glucose &fructose
Sucrose
Glycosidic linkage
D-glucose D-Fructose
Linkages depending on how the –OH group on the anomeric carbon is oriented.
Glycosidic linkage
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 LipidsLipid 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
2. Hormone
Make plasma membrane more rigid
Controls secondary sex characteristics
Lipid
Glycerol + Triglyceride
Condensation
Hydrolysis
3 Fatty acid + 3 Water
Examples of Lipids
Structure of Lipids
1. Textbook pg 68Figure 4.8
– Condensation and hydrolysis of triglycerides
2. Textbook pg 69Figure 4.9
- Saturated & unsaturated fatty acids
Fats & Oils
• Saturated fat contains saturated fatty acids condensed with glycerol.
• Saturated fatty acid
= fatty acid with single bond between carbon atoms
• Unsaturated fat contains unsaturated fatty acids condensed with glycerol.
• Unsaturated fatty acid
= fatty acid ≥ 1 double bonds between carbon atoms.
Nucleic acid
DNA
RNA
Monomer of DNA = Nucleotide
DNA – Deoxyribose
RNA - Ribose
DNA – A, T, G, C
RNA – A, U, G, C
DNA = Deoxyribonucleic acid
• Monomer = Nucleotide• Polymer =Polynucleotide
• Nitrogen bases:Adenine
Thymine
Guanine
Cytosine
Uracil
DNA = Deoxyribonucleic acid RNA = Ribonucleic acid
Double stranded polynucleotide Single stranded polynucleotide
Nucleotide consists of: Deoxyribose + Phosphate group + Nitrogenous base.
Nucleotide consists of:
Ribose + Phosphate group + Nitrogenous base.
Found in nucleus, mitochondrion, chloroplast
Found in nucleus, cytoplasm, ribosome
Function:
1. Store genetic information of an organism
Function:
1. Copies information carried by DNA for the use of protein synthesis.
2. Genetic material in some viruses.
1 type of DNA 3 types of RNA
2 types of Nucleic Acids
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.
1. mRNA = messenger RNA
2. rRNA = ribosomal RNA
3. tRNA = transport RNA
3 types of RNA- involved in Protein Synthesis
Protein synthesisstage 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
H2N
H
COOH
R
C
R = (CH3)n = Methyl group
Carboxylic group
- acidic
Amino group
- basic
Monomer Monomer+Dimer
Condensation
Hydrolysis
Dipeptide
Condensation
Hydrolysis
+ Water
+ Water
2 units of amino acids
WORD EQUATION
2 units of monomer
PROTEINS
Amino acid
Amino acid
+
Formation of Dipeptide
• Amino acids are joined together by
peptide bond through condensation process.
C
O
OHN
H
R
C
H
H
H
R
CN
H
H C
O
OH +
+ H2O
Word equation: Amino acid + Amino acid Dipeptide + Water
Structural equation:
C
O
OHN
H
R
C
HH
R
CN
H
H C
O
Peptide bond
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 / diet.
Not necessary to be 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 66Figure 4.7
Structure of Protein1. Primary structure = Linear structure
2. Secondary structure:a) Coiled structure = Alpha-helix
α - helixb) Folded structure = Beta-pleated sheets
β – 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 highly-specific.
• 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
+
E + S ES E + P
+ +
Enzyme + Substrate Enzyme + ProductEnzyme-Substrate complex
1 32
• 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.
• Metabolism includes:1. 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
1. mRNA = messenger RNA
2. rRNA = ribosomal RNA
3. tRNA = transport RNA
3 types of RNA- involved in Protein Synthesis
Protein synthesisstage 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. Temperature2. pH3. Concentration of substrate4. 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.
Trypsin
Rate of reaction
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 EnzymesZymase Convert sugar to ethanol in beer / wine-making industry
Protease Tenderizes the meat in food processing industryRemove the skin of fishin detergent / washing powder – remove stain by breaking down proteins
Amylase Break down starch to sugar in syrup makingin detergent / washing powder - remove starch which is used as stiffener of fabrics.
Lipase Ripening of cheese (dairy products)
Rennin Solidify milk proteins in making dairy products
Trypsin Remove hair from animal hides in leather- making
Cellulase Breakdown cellulose of seed coat from cereal grainsBreakdown cell wall to extract agar from seaweed
