Chapter 3.2: Biomolecules

1. Carbohydrates

• Definition: Carbohydrates are polyhydroxy aldehydes or ketones, or substances that yield these on hydrolysis. They are the most important source of energy for living organisms. They are also known as saccharides.
• Classification:
  • Monosaccharides (Simple Sugars): Cannot be hydrolyzed further. General formula is (CH₂O)n.
    • Glucose: A six-carbon sugar (hexose) that is the primary source of energy for most living organisms. It is an aldohexose, meaning it has an aldehyde group at position 1.
    • Ribose: A five-carbon sugar (pentose) that is a component of ribonucleic acid (RNA). It is an aldopentose.
    • Deoxyribose: A modified five-carbon sugar that is a component of deoxyribonucleic acid (DNA). It is derived from ribose by the removal of an oxygen atom from the second carbon.
  • Disaccharides: Formed by the condensation of two monosaccharide units, joined by a glycosidic bond.
    • Maltose (Malt Sugar): Composed of two glucose units. It is a reducing sugar.
    • Lactose (Milk Sugar): Composed of glucose and galactose. It is a reducing sugar and is found in milk.
    • Sucrose (Cane Sugar): Composed of glucose and fructose. It is a non-reducing sugar and is the common table sugar.
  • Polysaccharides (Complex Carbohydrates): Long chains of monosaccharides linked by glycosidic bonds.
    • Glycogen: The main storage polysaccharide in animals, stored primarily in the liver and muscles. It is a branched polymer of glucose.
    • Starch: The main storage polysaccharide in plants. It is a mixture of two polymers: amylose (a linear polymer of glucose) and amylopectin (a branched polymer of glucose).
    • Cellulose: A structural polysaccharide that forms the cell wall of plants. It is a linear polymer of glucose with beta-1,4-glycosidic bonds, which makes it indigestible by most animals.
    • Inulin: A polymer of fructose, found in many plants, such as chicory. It is used as a prebiotic and a fat substitute.
    • Chitin: A structural polysaccharide found in the exoskeletons of arthropods and the cell walls of fungi. It is a polymer of N-acetylglucosamine.

2. Proteins

• Definition: Proteins are polymers of amino acids, linked by peptide bonds. They are the most abundant organic molecules in living systems and have a wide range of functions.
• Amino Acids:
  • Structure: An amino acid is a substituted methane, with four substituent groups occupying the four valency positions: a carboxyl group, an amino group, a hydrogen atom, and a variable group designated as R group.
    • Glycine: The simplest amino acid, with hydrogen as its R group.
    • Alanine: Has a methyl group as its R group.
    • Serine: Has a hydroxymethyl group as its R group.
  • Zwitter-ion: An amino acid can exist as a zwitter-ion, which is a molecule with both a positive and a negative charge. The amino group is protonated (-NH3+) and the carboxyl group is deprotonated (-COO-).
  • Types:
    • Acidic: Have an acidic R group (e.g., Aspartic acid, Glutamic acid).
    • Basic: Have a basic R group (e.g., Lysine, Arginine).
    • Neutral: Have a neutral R group (e.g., Glycine, Alanine, Valine).
    • Sulphur-containing: Contain a sulphur atom in the R group (e.g., Cysteine, Methionine).
  • Essential and Non-essential Amino Acids:
    • Essential: Cannot be synthesized by the body and must be obtained from the diet (e.g., Lysine, Leucine, Isoleucine).
    • Non-essential: Can be synthesized by the body (e.g., Glycine, Alanine, Serine).
• Levels of Protein Structure:
  • Primary Structure: The linear sequence of amino acids in a polypeptide chain.
  • Secondary Structure: The polypeptide chain is folded into regular structures like the α-helix and the β-pleated sheet. These structures are stabilized by hydrogen bonds.
  • Tertiary Structure: The overall three-dimensional shape of a polypeptide chain. It is stabilized by various types of bonds, including hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.
  • Quaternary Structure: The arrangement of multiple polypeptide chains (subunits) in a protein. e.g., Haemoglobin.
• Functions of Proteins:
  • Enzymes: Catalyze biochemical reactions.
  • Structural proteins: Provide support and shape to cells and tissues (e.g., collagen, keratin).
  • Transport proteins: Carry substances across cell membranes or in the blood (e.g., hemoglobin).
  • Hormones: Regulate physiological processes (e.g., insulin).
  • Antibodies: Defend the body against pathogens.

3. Lipids

• Definition: A diverse group of organic compounds that are insoluble in water but soluble in nonpolar organic solvents.
• Classification, Structure, and Functions of Fats and Oils:
  • Fats and Oils (Triglycerides): Composed of three fatty acid molecules esterified to a glycerol molecule.
    • Fats: Solid at room temperature and are generally of animal origin. They are rich in saturated fatty acids.
    • Oils: Liquid at room temperature and are generally of plant origin. They are rich in unsaturated fatty acids.
  • Functions:
    • Energy storage: They are the main form of energy storage in animals.
    • Insulation: They provide thermal insulation.
    • Protection: They protect vital organs from shock.
    • Source of fat-soluble vitamins: They are a source of vitamins A, D, E, and K.

4. Enzymes

• Definition: Biological catalysts that speed up the rate of biochemical reactions without being consumed in the reaction.
• General Properties:
  • Almost all enzymes are proteins.
  • They are highly specific for their substrates.
  • They work best at a specific temperature and pH (optimum temperature and pH).
  • They are required in small amounts.
• Nomenclature and Classification:
  • Nomenclature: Enzymes are usually named by adding the suffix "-ase" to the name of the substrate they act on (e.g., sucrase, lactase).
  • Classification: Classified into 6 classes based on the type of reaction they catalyze:
    1. Oxidoreductases: Catalyze oxidation-reduction reactions.
    2. Transferases: Catalyze the transfer of a functional group from one molecule to another.
    3. Hydrolases: Catalyze the hydrolysis of a bond.
    4. Lyases: Catalyze the removal of a group from a substrate to form a double bond.
    5. Isomerases: Catalyze the interconversion of isomers.
    6. Ligases: Catalyze the joining of two molecules.
• Co-factors: Non-protein constituents bound to the enzyme to make it catalytically active.
  • Prosthetic groups: Tightly bound to the enzyme (e.g., heme in hemoglobin).
  • Co-enzymes: Loosely bound to the enzyme (e.g., NAD, FAD).
  • Metal ions: Act as a bridge between the enzyme and the substrate (e.g., Zn2+, Mg2+).
• Factors Affecting Enzyme Activity:
  • Temperature: Enzyme activity increases with temperature up to an optimum temperature, after which it denatures.
  • pH: Each enzyme has an optimum pH at which its activity is maximum.
  • Substrate concentration: The rate of reaction increases with substrate concentration until the enzyme is saturated with the substrate.
• Competitive Inhibitors:
  • A substance that competes with the substrate for the active site of the enzyme. It has a similar structure to the substrate.

5. Secondary Metabolites

• Definition: Organic compounds that are not directly involved in the normal growth, development, or reproduction of an organism. They are often produced as by-products of metabolism and have important ecological functions.
• Examples:
  • Alkaloids: Morphine, Codeine (pain relievers)
  • Terpenoids: Monoterpenes (e.g., menthol), Diterpenes (e.g., gibberellins)
  • Essential oils: Lemon grass oil (used in aromatherapy and as an insect repellent)
  • Toxins: Abrin, Ricin (highly toxic proteins)
  • Lectins: Concanavalin A (a protein that binds to carbohydrates)
  • Drugs: Vinblastin (an anticancer drug), Curcumin (an anti-inflammatory agent)
  • Polymeric substances: Rubber, Gums, Cellulose