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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

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

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 .

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

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

Glycerol - Triglyceride / Fats / Lipids .Class Monomer Dimer Polymer Nucleic acids Nucleotide - Polynucleotide Carbohydrates Monosaccharide Disaccharide Polysaccharide Proteins Amino acid Dipeptide Polypeptide Fat / Oil / Lipids Fatty acid.

Carbohydrate .

Elements in carbohydrates .4.2 Carbohydrates .Types of carbohydrates: Monosaccharides. Polysaccharides .Formation and Breakdown of Disaccharides and Polysaccharides . Disaccharides.

Carbohydrates Carbon C Water H2O • Elements: C:H:O • Ratio: 1:2:1 • Empirical formula: (CH2O)n . n≥3 .

Oligosaccharide 3-7 sugar 2.4 types of Carbohydrates 1. Monosaccharide one sugar 3. Polysaccharide multiple sugar . Disaccharide two sugar 4.

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 .

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

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

add distilled water . Benedict’s solution 1. Glucose solution For solid food sample . Heat in water bath Brick red precipitate Blue Cu 2+ Copper (II) sulphate + efrom glucose Cu + Copper (I) oxide .Test for Reducing Sugar 2.crushed using mortar & pestle 3.

.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. 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 solution 2. HCl Sucrose  Glucose + Fructose 3. Sodium bicarbonate 5. Benedict’s solution 1.

Sucrose D-glucose D-Fructose Glycosidic linkage .

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

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

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 .

protection Wax A waterproof layer on the cuticle of leaves Phospholipid Main component of plasma membrane Steroid 1. Hormone Controls secondary sex characteristics .Types of Lipids Lipid Function Fats & Oils Energy storage. Cholesterol Make plasma membrane more rigid 2. insulation.

Lipid
Condensation
Glycerol

+

3 Fatty acid

Triglyceride
Hydrolysis

+

3 Water

Examples of Lipids

9 .Saturated & unsaturated fatty acids .8 – Condensation and hydrolysis of triglycerides 2. Textbook pg 68 Figure 4. Textbook pg 69 Figure 4.Structure of Lipids 1.

• Saturated fatty acid = fatty acid with single bond between carbon atoms • Unsaturated fatty acid = fatty acid ≥ 1 double bonds between carbon atoms. • Unsaturated fat contains unsaturated fatty acids condensed with glycerol. .Fats & Oils • Saturated fat contains saturated fatty acids condensed with glycerol.

.

Nucleic acid DNA RNA .

G. G. T. U.Ribose .Monomer of DNA = Nucleotide DNA – A. C DNA – Deoxyribose RNA . C RNA – A.

DNA = Deoxyribonucleic acid • • Monomer = Nucleotide Polymer =Polynucleotide • Nitrogen bases: Adenine Thymine Guanine Cytosine Uracil .

ribosome 1. Function: Store genetic information of an organism Found in nucleus. Nitrogenous base. cytoplasm. Found in nucleus. 1 type of DNA Function: Copies information carried by DNA for the use of protein synthesis. 2. chloroplast 1. 3 types of RNA . Genetic material in some viruses.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. mitochondrion.

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

Pairing of bases is specific. .

Base pairs are held by hydrogen bonds makes the steps of the ladder.Double helix DNA is like a twisted ladder. Sugar-phosphate backbone makes the sides of the ladder. .

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

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

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

Proteins .

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

O. 2D) (3D) . S • Monomer = Amino acid • Polymer = Polypeptide = Protein (linear.Proteins • Elements: C. H. N.

acidic .Amino acid R = (CH3)n = Methyl group R H2N Amino group .basic C H COOH Carboxylic group .

.

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: H R O N C C OH + H H H R H N C R O N C C H H R O N C C H H 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. Can be synthesized by the body / cell. Reason: Can be derived from other amino acids. Examples: Leucine. Asparagine. obtained from diet. Aspartic acid . Cannot be synthesized by the body / cell. Isoleucine. Lysine Examples: Alanine.

7 .4 Levels of the Structures of Proteins Draw in Notebook Textbook pg 66 Figure 4.

Quarternary structure . enzyme. 4. antibodies. Primary structure = Linear structure 2.Structure of Protein 1.helix b) Folded structure = Beta-pleated sheets β – pleated sheets 3.1 polypeptide chain folded or coiled into 3D shape .example: Hormone.example: Haemoglobin . Tertiary structure = 3 Dimensional shape .≥2 tertiary chains joined together . Secondary structure: a) Coiled structure = Alpha-helix α .

.

antibodies. plasma protein . • Examples: Enzyme.Tertiary structure • 1 polypeptide coiled & folded into 3-dimensional structure with specific function.

Enzymes .

4. Characteristics. Naming.5 Enzymes • Definition. 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. .

Substrate Enzyme Lactose Lactase Sucrose Sucrase Maltose Maltase Lipid Lipase .Naming of enzymes • Most enzymes have a name derived by adding the suffix –ase at the end of the name of their substrates.

Enzymes lower the activation energy needed by the biochemical reactions to occur.2. thus speed up biochemical reactions. .

Remained unchanged at the end of the reactions. Reason: (3) . 4. thus can be reused. Small amount of enzymes can catalyzed large amount of substrates.Characteristics of Enzymes 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. Most reactions catalyzed by enzymes are reversible (forward & backward). 6. Reason: Specific active site of enzyme only binds to specific substrate.

Enzyme activities can be slowed down or stopped by inhibitors (heavy metals like mercury Hg. .6. lead Pb). 7. Many enzymes require cofactor (helper molecule) to function.

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 ++ E + + S ES Enzyme + Substrate Enzyme-Substrate complex 1 2 E + P Enzyme + Product 3 .

.Products leave the active site of enzyme. Key represents substrate. 2. .Enzyme catalyses the substrate to form products. . 1. • Lock represents enzyme. like a key fits into a lock. A specific substrate molecule arrives at the active site of the enzyme molecule. Substrate molecule binds to the active site to form an enzyme-substrate complex. 3.• The way an enzyme binds to its substrate can be explained by the “lock-and-key” hypothesis.Enzyme is free to bind to another substrate and catalyze another reaction (can be reused). . E-S complex is unstable.

Metabolism includes: Anabolism = Synthesis of large complex molecules from smaller. • Most of these biochemical reactions are catalyzed by enzymes. • 1. simpler molecules  Release energy . Catabolism = Breakdown of large complex molecules into smaller.Biochemical Reactions in living cell / organism • Metabolism = all biochemical reactions occurring in living cells. simpler molecules  Requires / Absorbs energy 2.

blood) Example: Oxidoreductase catalyses biological oxidation & reduction in the mitochondrion. . These enzymes are transported to duodenum which is the actual site of enzymatic reaction. = Enzymes which are produced in the cell but secreted from the cell to function externally. nucleus. These enzymes are found in: Cytoplasm. Example: Digestive enzymes secreted by pancreas but not used by pancreas cells. chloroplast These enzymes are found: Outside the cell (tissue fluid. mitochondrion.Intracellular Enzyme Extracellular Enzyme = Enzymes which are produced & retained in the cell for the use of the cell itself.

Synthesis of Enzymes • Intracellular enzyme • Extracellular enzyme .

mRNA = messenger RNA 2. rRNA = ribosomal RNA 3. tRNA = transport RNA .involved in Protein Synthesis 1.3 types of RNA .

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

•tRNA transport suitable 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.

Temperature pH Concentration of substrate Concentration of enzyme * Refer handouts  Essay .Factors that affect activity of enzymes 1. 3. 4. 2.

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

12 .Textbook Pg 73 – Figure 4.

12 • At low temperature. . • Rate of reaction is the highest at the optimum temperature. enzymes are inactive and reaction takes place slowly.Textbook Pg 73 – Figure 4. • Rate of reaction doubles with every 10oC. • Rate of reaction increases proportional to the temperature increase until the optimum temperature.

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

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

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

Rate of reaction Trypsin .

Change of pH can: 1. Alter the charges on the active sites. Reduce the ability of enzyme & substrate to bind with each other. rate of reaction decreases • When pH reverts to optimum. charges on active sites are restored. enzyme can resume its normal function = Reversible . 2. • As a result.

3. Enzyme concentration .

4. Substrate concentration .

remove starch which is used as stiffener of fabrics.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 . 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 .