Exercises
What are macromolecules? Give examples.
Answer
Macromolecules are large, complex molecules formed by the polymerization of smaller repeating units called monomers. They have high molecular weight (generally greater than 10,000 daltons) and are also called polymers or high-molecular-weight compounds.
Examples
1. Proteins: Polymers of amino acids linked by peptide bonds (e.g., haemoglobin, enzymes, collagen).
2. Nucleic acids: Polymers of nucleotides (e.g., DNA, RNA).
3. Polysaccharides: Polymers of monosaccharides (e.g., starch, cellulose, glycogen).
4. Lipids: Though not strictly polymers, large lipid molecules (e.g., triglycerides, phospholipids) are sometimes included.
These macromolecules are the main components of living cells and are involved in virtually all biological processes.
What is meant by tertiary structure of proteins?
Answer
The tertiary structure of a protein refers to the three-dimensional folding of a polypeptide chain that has already acquired secondary structure (α-helices and β-pleated sheets). It is the overall three-dimensional shape of the entire polypeptide chain.
This folding occurs due to interactions between the R-groups (side chains) of amino acids that are far apart in the primary sequence:
1. Hydrogen bonds between R-groups
2. Ionic interactions (salt bridges) between oppositely charged R-groups
3. Hydrophobic interactions — nonpolar R-groups cluster toward the interior, away from water
4. Disulfide bridges (covalent bonds) between cysteine residues
5. Van der Waals forces
The tertiary structure determines the biological activity (function) of the protein. For example, enzymes have an active site with a specific shape determined by tertiary structure that allows them to bind substrates.
Find and write down structures of 10 interesting small molecular weight biomolecules. Find if there is any industry which manufactures the compounds by isolation. Find out who are the buyers.
Answer
Ten interesting small molecular weight biomolecules and their industrial relevance:
1. Glucose (C₆H₁₂O₆): A monosaccharide; hexagonal ring structure. Pharmaceutical/food industry manufactures it. Buyers: food industry, hospitals (IV drips), sports nutrition.
2. Cholesterol (C₂₇H₄₆O): A sterol lipid with four fused carbon rings and a hydroxyl group. Produced by chemical synthesis and isolation. Buyers: pharmaceutical industry (steroid synthesis), cosmetics industry.
3. ATP (Adenosine triphosphate): Nucleotide with adenine + ribose + three phosphate groups. Produced by fermentation/biotechnology. Buyers: research laboratories, pharmaceutical companies.
4. Ascorbic acid (Vitamin C): Lactone structure; antioxidant. Manufactured by Reichstein process or fermentation. Buyers: pharmaceutical, food and beverage industry.
5. Caffeine (C₈H₁₀N₄O₂): Methylxanthine; extracted from tea/coffee or synthesized. Buyers: food and beverage industry, pharmaceutical industry.
6. Alanine (C₃H₇NO₂): An amino acid; NH₂-CH(CH₃)-COOH. Produced by fermentation. Buyers: food supplements, pharmaceutical industry.
7. Ribose (C₅H₁₀O₅): A pentose monosaccharide (open chain and ring form). Produced by fermentation. Buyers: pharmaceutical and food industry.
8. NAD⁺ (Nicotinamide adenine dinucleotide): Coenzyme; complex structure with nicotinamide and adenine. Manufactured for research. Buyers: research labs, health supplement companies.
9. Testosterone (C₁₉H₂₈O₂): A steroid hormone; four fused rings with hydroxyl group. Produced by chemical synthesis. Buyers: pharmaceutical companies (hormone therapy).
10. Palmitic acid (C₁₆H₃₂O₂): A saturated fatty acid; long carbon chain with COOH group. Isolated from palm oil. Buyers: cosmetics, soap, food industry.
Find out and make a list of proteins used as therapeutic agents. Find other applications of proteins (e.g., Cosmetics etc.)
Answer
Proteins used as therapeutic agents:
1. Insulin: Used in treatment of diabetes mellitus (Type I). Produced by recombinant DNA technology.
2. Human growth hormone (HGH/Somatotropin): Used for growth hormone deficiency in children.
3. Erythropoietin (EPO): Stimulates RBC production; used in anemia treatment.
4. Interferons: Antiviral proteins used against hepatitis B, C and multiple sclerosis.
5. Monoclonal antibodies: Used in cancer treatment (e.g., Herceptin for breast cancer).
6. Tissue Plasminogen Activator (tPA): Dissolves blood clots; used in heart attacks and strokes.
7. Vaccines: Protein-based vaccines (e.g., Hepatitis B surface antigen).
8. Clotting factors: Factor VIII for hemophilia A treatment.
9. Albumin: Used to replace blood volume loss.
10. Streptokinase: Enzyme used as a clot-dissolving agent.
Other applications of proteins
• Cosmetics: Collagen and keratin in anti-aging creams, hair care products; silk (fibroin) in hair conditioners.
• Food industry: Casein (cheese), gluten (baking), whey protein (supplements).
• Textile industry: Silk (fibroin) and wool (keratin) fibers.
• Industrial enzymes: Proteases in detergents, amylases in baking.
• Research tools: Restriction enzymes, DNA polymerase, antibodies.
Explain the composition of triglyceride.
Answer
A triglyceride (also called triacylglycerol or fat) is composed of:
1. One molecule of glycerol (a three-carbon alcohol with three –OH groups)
2. Three molecules of fatty acids (long-chain carboxylic acids, typically 12–20 carbon atoms)
The three fatty acids are attached to the three carbon atoms of glycerol by ester bonds (formed between the –OH of glycerol and the –COOH of each fatty acid, releasing three water molecules — condensation reaction).
General structure
Glycerol-C1 — O — CO — R₁ (fatty acid 1)
Glycerol-C2 — O — CO — R₂ (fatty acid 2)
Glycerol-C3 — O — CO — R₃ (fatty acid 3)
The three fatty acids may be same (simple triglyceride) or different (mixed triglyceride). Fatty acids can be saturated (no double bonds, e.g., palmitic acid, stearic acid — found in animal fats, solid at room temperature) or unsaturated (one or more double bonds, e.g., oleic acid, linoleic acid — found in plant oils, liquid at room temperature).
Triglycerides are the main form of stored energy (fat) in animals, stored in adipose tissue.
Can you attempt building models of biomolecules using commercially available atomic models (Ball and Stick models)?
Answer
Yes, commercially available ball and stick models can be used to build models of biomolecules. These models represent atoms as colored balls and bonds as sticks of specific lengths and angles.
For building biomolecule models
• Amino acids: Use balls for C, N, O, H atoms and sticks for bonds; build the central carbon with amino group (–NH₂), carboxyl group (–COOH), hydrogen, and R-group attached.
• Glucose: Build the six-carbon ring (pyranose form) with OH groups on each carbon.
• DNA double helix: Simplified models can show nucleotide pairs (A-T, G-C) with a twisted ladder structure.
• Triglyceride: Model glycerol backbone with three fatty acid chains attached via ester bonds.
These models help visualize spatial arrangement of atoms, bond angles, and the three-dimensional shapes of molecules, which are crucial for understanding their biological functions (e.g., enzyme-substrate complementarity).
Draw the structure of the amino acid, alanine.
Answer
Alanine is a non-polar, aliphatic amino acid. Its structure:
Structural formula of Alanine
The central carbon (α-carbon) is attached to:
— Amino group: –NH₂
— Carboxyl group: –COOH
— Hydrogen: –H
— R-group (side chain): –CH₃ (methyl group)
Molecular formula: C₃H₇NO₂
IUPAC name: 2-aminopropanoic acid
Structure (written linearly): H₂N–CH(CH₃)–COOH
At physiological pH (~7.4), alanine exists as a zwitterion (both NH₃⁺ and COO⁻ forms): ⁺H₃N–CH(CH₃)–COO⁻
Alanine is one of the most common amino acids found in proteins and is important in glucose-alanine cycle (gluconeogenesis).
What are gums made of? Is Fevicol different?
Answer
Natural plant gums are complex polysaccharides (heteropolysaccharides) that are secreted by plants in response to injury or stress. They are composed of monosaccharide units and their derivatives linked by glycosidic bonds.
Examples:
• Gum Arabic (acacia gum): Made of arabinose, galactose, rhamnose, and glucuronic acid.
• Guar gum: Made of galactose and mannose.
• Xanthan gum: Made of glucose, mannose, and glucuronic acid (produced by bacteria).
• Gum tragacanth: Contains arabinose, xylose, galactose, and galacturonic acid.
These gums are water-soluble or form viscous solutions/gels.
Fevicol is chemically different from natural gums. Fevicol is a synthetic polymer adhesive — it is a polyvinyl acetate (PVA) emulsion-based glue. When Fevicol dries, the water evaporates and the polymer chains interlock, creating a strong bond. It does not contain carbohydrates or polysaccharides. Thus, while natural gums are carbohydrate polymers of biological origin, Fevicol is a synthetic organic polymer with no relation to biomolecules.
Find out a qualitative test for proteins, fats and oils, amino acids and test any fruit juice, saliva, sweat and urine for them.
Answer
Qualitative tests for biomolecules:
1. Proteins — Biuret test: Add NaOH followed by dilute CuSO₄ solution. A violet/purple color indicates peptide bonds (proteins). Alternatively, Ninhydrin test (pink/purple for amino acids and proteins).
2. Fats and oils — Sudan III/IV test: Add Sudan III dye; fats stain orange-red. Alternatively, grease spot test: put a drop on paper; translucent spot indicates fat.
3. Amino acids — Ninhydrin test: Amino acids react with ninhydrin to give a purple/blue color. Free amino acids give purple; proline gives yellow.
Results for biological fluids
• Fruit juice: Contains sugars (positive Benedict's test); may have small amounts of proteins and amino acids.
• Saliva: Contains the enzyme salivary amylase (protein) — positive Biuret test.
• Sweat: Contains amino acids and small amounts of proteins — faint positive Ninhydrin and Biuret tests.
• Urine: Normally no significant proteins (proteinuria indicates kidney disease); may contain urea; positive Biuret only in disease.
• Fats in urine: Not normally present; lipiduria indicates disease.
Note: This is an activity-based question; actual results should be observed in a laboratory setting.
Find out how much cellulose is made by all the plants in the biosphere and compare it with how much paper is manufactured by man and hence what is the consumption of plant material by man annually. What a loss of vegetation!
Answer
This is a data-gathering and reflection activity. Key facts:
• Global cellulose production by plants: Approximately 100–200 billion tonnes of cellulose are produced annually by all plants in the biosphere through photosynthesis and cell wall synthesis. Cellulose is the most abundant organic compound on Earth.
• Global paper production by humans: Approximately 400 million tonnes of paper and paperboard are produced annually worldwide (as of recent estimates). Each tonne of paper requires roughly 2–3 tonnes of wood (which is ~40–50% cellulose).
• Wood consumed for paper: Approximately 800 million – 1.2 billion tonnes of wood are consumed for paper production annually.
• Cellulose consumed for paper: Approximately 400–600 million tonnes of cellulose is used for paper annually — a tiny fraction of total plant cellulose production, but still representing destruction of enormous amounts of forests and vegetation.
Observation: This enormous consumption of plant biomass for paper, timber, and fuel represents a significant loss of vegetation and biodiversity. It is a major driver of deforestation. Conservation, recycling of paper, and use of alternative materials are essential to reduce this loss.
Describe the important properties of enzymes.
Answer
Properties of enzymes:
1. Chemical nature: Enzymes are proteins (though some RNA molecules called ribozymes have enzymatic activity). They have a specific three-dimensional structure critical for function.
2. Catalytic efficiency: Enzymes are highly efficient catalysts — they increase the rate of biochemical reactions by 10⁶ to 10¹² times compared to uncatalyzed reactions.
3. Specificity: Enzymes are highly specific — they act on a specific substrate (lock-and-key model or induced fit model). For example, urease only acts on urea.
4. Not consumed in the reaction: Enzymes are not used up in the reaction; they can be used repeatedly. They lower the activation energy without being permanently changed.
5. Sensitive to temperature: Enzymes have an optimal temperature (usually 35–40°C in humans). At very high temperatures, they denature; at very low temperatures, they become inactive.
6. Sensitive to pH: Each enzyme works best at a specific pH (e.g., pepsin at pH 2, trypsin at pH 8). Extreme pH values cause denaturation.
7. Reversibility: Most enzyme-catalyzed reactions are reversible; the enzyme catalyzes both forward and reverse reactions, though the equilibrium position is not altered.
8. Cofactor requirement: Many enzymes require non-protein cofactors (metal ions or coenzymes) for activity. The enzyme without cofactor is called apoenzyme; with cofactor it is the holoenzyme.
9. Inhibition: Enzyme activity can be inhibited by competitive inhibitors (similar to substrate), non-competitive inhibitors (bind at an allosteric site), or end-product inhibition (feedback inhibition).
10. Saturation kinetics: At high substrate concentrations, all enzyme molecules are occupied and the reaction rate reaches maximum (Vmax). The substrate concentration at which the reaction rate is half of Vmax is the Michaelis constant (Km).
Important Extra Questions
What is the difference between a nucleoside and a nucleotide?
Answer
Nucleoside: Consists of a nitrogenous base + pentose sugar (ribose or deoxyribose). Examples: adenosine, thymidine, guanosine.
Nucleotide: Consists of a nitrogenous base + pentose sugar + one or more phosphate groups. Examples: AMP, ADP, ATP, dATP.
In short: Nucleotide = Nucleoside + Phosphate group(s).
Nucleotides are the monomers of nucleic acids (DNA and RNA).
What are the biological functions of carbohydrates?
Answer
1. Energy source: Glucose is the primary fuel for cellular respiration (ATP production).
2. Energy storage: Starch (plants) and glycogen (animals) store energy.
3. Structural role: Cellulose forms plant cell walls; chitin forms fungal cell walls and arthropod exoskeletons.
4. Cell recognition: Glycoproteins and glycolipids on cell surfaces are involved in cell-cell recognition and signaling.
5. Nucleic acid backbone: Ribose (in RNA) and deoxyribose (in DNA) are part of nucleotides.
6. Lubrication: Mucin (glycoprotein) lubricates joints and digestive tract.
What is the primary structure of a protein? How is it different from secondary structure?
Answer
Primary structure: The linear sequence of amino acids in a polypeptide chain, linked by peptide bonds. It is determined by the gene (DNA sequence). Example: Gly-Ala-Val-Leu...
Secondary structure: Regular folding of the polypeptide chain into α-helices or β-pleated sheets, stabilized by hydrogen bonds between CO and NH groups of the peptide backbone (not R-groups).
Difference: Primary structure is about the sequence (1D), while secondary structure is about local regular folding (2D/3D conformations). Primary structure determines secondary structure, which in turn contributes to tertiary and quaternary structures.
Define enzyme cofactors and their types.
Answer
Cofactors are non-protein components associated with an enzyme that are essential for its catalytic activity.
Types:
1. Prosthetic groups: Tightly bound cofactors (covalently or very tightly non-covalently). Example: heme in hemoglobin and cytochromes, FAD in succinate dehydrogenase.
2. Coenzymes: Loosely bound organic cofactors (transiently associated). Example: NAD⁺, NADP⁺, CoA — these carry chemical groups between enzymes.
3. Metal ion cofactors (activators): Metal ions required for enzyme activity. Example: Zn²⁺ in carboxypeptidase, Fe²⁺ in catalase, Mg²⁺ in hexokinase.
Apoenzyme (inactive protein) + Cofactor = Holoenzyme (active enzyme).
What are essential and non-essential amino acids? Give examples.
Answer
Essential amino acids: Amino acids that cannot be synthesized by the human body and must be obtained from the diet. There are eight to ten essential amino acids in humans.
Examples: Valine, Leucine, Isoleucine, Threonine, Methionine, Phenylalanine, Tryptophan, Lysine (+ Histidine and Arginine in children).
Non-essential amino acids: Amino acids that can be synthesized by the human body from other metabolic precursors, so they are not required in the diet.
Examples: Glycine, Alanine, Serine, Aspartate, Glutamate, Glutamine, Asparagine, Tyrosine, Cysteine, Proline.
A diet lacking essential amino acids leads to protein-energy malnutrition (e.g., kwashiorkor, marasmus).