Biomolecules

Given/Concept: Macromolecules are large molecular weight biomolecules (generally >10,000 Da) found in living systems. They are polymers made up of repeating monomeric units.

Answer:
Macromolecules are very large molecules with high molecular weights, formed by the polymerisation of smaller units called monomers. They are found in the acid-insoluble fraction of living tissues.

Types and Examples:

| Macromolecule | Monomer Units |
|---|---|
| Proteins | Amino acids |
| Nucleic acids (DNA, RNA) | Nucleotides |
| Polysaccharides (starch, glycogen, cellulose) | Monosaccharides (e.g., glucose) |

Note: Lipids are also found in the macromolecular fraction because of their association with membranes, although they are not strictly polymers.

Conclusion: Thus, the three principal classes of true macromolecules in living systems are proteins, nucleic acids, and polysaccharides.

Given/Concept: Proteins exhibit four levels of structural organisation — primary, secondary, tertiary, and quaternary.

Tertiary Structure of Proteins:

The tertiary structure refers to the three-dimensional (3-D) folding of the entire polypeptide chain, including all its secondary structural elements (α-helices, β-pleated sheets, and random coils), into a compact, specific, and biologically active conformation.

Key Points:
1. It arises due to interactions between R-groups (side chains) of amino acids that may be far apart in the primary sequence but come close together in 3-D space.
2. The interactions responsible for maintaining tertiary structure include:
- Disulphide bonds (covalent)
- Hydrogen bonds
- Ionic bonds (electrostatic interactions)
- Hydrophobic interactions
- Van der Waals forces
3. The tertiary structure determines the shape of the active site of enzymes and hence their biological function.
4. Disruption of tertiary structure (denaturation) leads to loss of biological activity.

Example: The globular shape of haemoglobin and the specific folding of an enzyme like lysozyme are examples of tertiary structure.

Conclusion: Tertiary structure is the overall 3-D shape of a polypeptide chain, critical for its biological function.

Given/Concept: Small molecular weight biomolecules have molecular weight less than 1000 Da. They include amino acids, sugars, nucleotides, vitamins, fatty acids, etc.

Ten Interesting Small Molecular Weight Biomolecules:

1. Glucose ($C_6H_{12}O_6$) — A monosaccharide (aldohexose); ring structure (pyranose form). *Industry:* Corn-starch hydrolysis industry. *Buyers:* Food industry, pharmaceutical companies (IV drips).

2. Adenosine Triphosphate (ATP) — Nucleotide with adenine + ribose + 3 phosphate groups. *Industry:* Fermentation-based biotech companies. *Buyers:* Research laboratories.

3. Alanine (Amino acid) — $CH_3$-$CH(NH_2)$-$COOH$. *Industry:* Fermentation/chemical synthesis. *Buyers:* Pharmaceutical and food industries.

4. Cholesterol — Steroid with 4 fused rings + hydroxyl group. *Industry:* Extracted from animal sources/synthesised. *Buyers:* Pharmaceutical companies (steroid hormone synthesis).

5. Ascorbic acid (Vitamin C) — Lactone ring structure. *Industry:* Reichstein process / fermentation. *Buyers:* Nutraceutical and pharmaceutical companies.

6. Ribose ($C_5H_{10}O_5$) — Pentose sugar; component of RNA. *Industry:* Fermentation. *Buyers:* Biotech and pharmaceutical companies.

7. Palmitic acid ($CH_3(CH_2)_{14}COOH$) — Saturated fatty acid (C16). *Industry:* Saponification of palm oil. *Buyers:* Soap, cosmetic, and food industries.

8. Nicotinamide (Niacin/Vitamin B3) — Pyridine ring with amide group. *Industry:* Chemical synthesis. *Buyers:* Pharmaceutical and food fortification industries.

9. Glycerol ($C_3H_8O_3$) — Three-carbon polyol. *Industry:* By-product of soap/biodiesel manufacture. *Buyers:* Cosmetic, pharmaceutical, and food industries.

10. Urea ($CO(NH_2)_2$) — End product of nitrogen metabolism. *Industry:* Haber-Bosch related synthesis. *Buyers:* Fertiliser industry, pharmaceutical companies.

Note: Students are encouraged to draw the full structural formulae of each compound from their textbook/reference material.

Given/Concept: Proteins have diverse functions in living systems and many are exploited commercially for therapeutic and other purposes.

Proteins Used as Therapeutic Agents:

| Protein | Therapeutic Use |
|---|---|
| Insulin | Treatment of diabetes mellitus |
| Erythropoietin (EPO) | Treatment of anaemia |
| Interferon | Antiviral and anticancer therapy |
| Streptokinase / Urokinase | Dissolving blood clots (thrombolysis) |
| Factor VIII | Treatment of haemophilia A |
| Monoclonal antibodies (e.g., Herceptin) | Cancer therapy |
| Human Growth Hormone (HGH) | Treatment of growth disorders |
| Tissue Plasminogen Activator (tPA) | Treatment of heart attacks and strokes |
| Albumin | Plasma volume expander in surgery |
| Vaccines (protein antigens) | Immunisation against diseases |

Other Applications of Proteins:

1. Cosmetics: Keratin proteins used in hair-strengthening treatments; collagen used in anti-ageing creams and skin moisturisers.
2. Food Industry: Casein (milk protein) used in cheese making; gluten used in baking.
3. Textile Industry: Silk (fibroin protein) and wool (keratin) used as fibres.
4. Adhesives: Casein-based glues.
5. Enzymes in Industry: Proteases in detergents (e.g., subtilisin); amylases in paper and textile industries.
6. Diagnostics: Antibodies used in ELISA and other diagnostic tests.

Conclusion: Proteins are indispensable not only as therapeutic agents but also in cosmetics, food, textiles, and industrial processes.

Given/Concept: Triglycerides (also called triacylglycerols) are the most common form of dietary fats and oils. They belong to the class of lipids.

Composition of a Triglyceride:

A triglyceride is composed of:
1. One molecule of Glycerol — a three-carbon alcohol with three hydroxyl (–OH) groups.
2. Three molecules of Fatty Acids — long-chain carboxylic acids (may be saturated or unsaturated).

Formation:
Each fatty acid is joined to glycerol by an ester bond (–COO–) formed by a condensation (dehydration) reaction between the –COOH group of the fatty acid and the –OH group of glycerol, releasing water.

$$\text{Glycerol} + 3\text{ Fatty Acids} \xrightarrow{\text{esterification}} \text{Triglyceride} + 3H_2O$$

Structural Representation:
$$\begin{array}{l}$$
CH_2 - OOC - R_1 \\
| \\
CH \;\; - OOC - R_2 \\
| \\
CH_2 - OOC - R_3
\end{array}

Where $R_1$, $R_2$, and $R_3$ are hydrocarbon chains of fatty acids (they may be the same or different).

Key Points:
- If all three fatty acids are saturated (no double bonds), the triglyceride is a fat (solid at room temperature), e.g., butter.
- If one or more fatty acids are unsaturated (contain double bonds), the triglyceride is an oil (liquid at room temperature), e.g., olive oil.
- Triglycerides serve as the major energy storage molecules in animals.

Conclusion: A triglyceride consists of one glycerol molecule esterified with three fatty acid molecules through three ester bonds.

Activity-Based Question:

Concept: Ball and Stick models are three-dimensional physical models where:
- Balls represent atoms (different colours for different elements: black for Carbon, white for Hydrogen, red for Oxygen, blue for Nitrogen, yellow for Sulphur, etc.).
- Sticks represent covalent bonds between atoms.

Suggested Biomolecules to Model:

1. Glucose ($C_6H_{12}O_6$) — Build the open-chain and ring (pyranose) form.
2. Alanine (amino acid) — Show the central carbon, amino group, carboxyl group, and methyl side chain.
3. A dipeptide — Show the peptide bond (–CO–NH–) formed between two amino acids.
4. A nucleotide — Show the phosphate group, pentose sugar, and nitrogenous base.
5. A fatty acid (e.g., palmitic acid) — Show the long hydrocarbon chain and carboxyl group.

Steps to Build a Model:
1. Identify the molecular formula and structural formula of the chosen biomolecule.
2. Select appropriate coloured balls for each atom.
3. Connect them with sticks according to the valency of each atom (Carbon = 4, Oxygen = 2, Nitrogen = 3, Hydrogen = 1).
4. Ensure correct bond angles (e.g., tetrahedral ~109.5° for $sp^3$ carbon).

Conclusion: Yes, ball and stick models can be effectively built for biomolecules. This activity helps visualise the 3-D arrangement of atoms, bond angles, and the overall shape of molecules, which is crucial for understanding their biological function. *(This is a practical/activity-based question; students are encouraged to perform this activity in the laboratory.)*

Given: Alanine is a non-polar, aliphatic amino acid. It is the simplest amino acid with a methyl group as its R (side chain) group.

Molecular Formula: $C_3H_7NO_2$

Structure of Alanine:

Alanine has the general amino acid structure with:
- An amino group ($-NH_2$) — basic group
- A carboxyl group ($-COOH$) — acidic group
- A hydrogen atom ($-H$)
- A methyl group ($-CH_3$) as the R (side chain) group

All four groups are attached to the central α-carbon.

$$\underset{\displaystyle\text{Alanine}}{\begin{array}{c} H_2N - \underset{|}{\overset{|}{C}} - COOH \\ \quad\quad\quad H \\ \quad\quad CH_3 \end{array}}$$

More clearly written as:

$$H_2N - \underset{\displaystyle CH_3}{\overset{\displaystyle H}{C}} - COOH$$

Or in standard structural notation:

$$\begin{array}{c} COOH \\ | \\ H_2N - C - H \\ | \\ CH_3 \end{array}$$

Key Features:
- The α-carbon of alanine is a chiral centre (asymmetric carbon).
- Naturally occurring alanine is the L-form.
- It is a non-essential amino acid (can be synthesised by the human body).

Conclusion: Alanine is a simple amino acid with a methyl side chain attached to the α-carbon, which also bears an amino group and a carboxyl group.

Given/Concept: Gums are natural substances exuded by plants, while Fevicol is a synthetic adhesive.

What are Gums Made of?

Plant gums are heteropolysaccharides — complex carbohydrates made up of different types of monosaccharide units and their derivatives.

Composition:
- They are composed of sugar residues such as galactose, arabinose, glucuronic acid, mannose, rhamnose, etc., linked by glycosidic bonds.
- They also contain uronic acids (oxidised sugars).
- Examples:
- Gum Arabic (from *Acacia senegal*): composed of arabinose, galactose, rhamnose, and glucuronic acid.
- Guar gum: composed of galactose and mannose.
- Xanthan gum: a microbial polysaccharide.

Properties of Natural Gums:
- Soluble or dispersible in water.
- Form viscous solutions or gels.
- Used as thickeners, stabilisers, and adhesives in food, pharmaceutical, and textile industries.

Is Fevicol Different?

Yes, Fevicol is completely different from natural gums.
- Fevicol is a synthetic polymer-based adhesive.
- It is made of polyvinyl acetate (PVA) emulsion — a synthetic organic polymer, not a carbohydrate.
- It is a man-made (artificial) adhesive, not derived from biological polysaccharides.
- It works by forming a strong film upon drying that bonds surfaces together.

Conclusion: Natural gums are heteropolysaccharides of plant origin, whereas Fevicol is a synthetic polyvinyl acetate-based adhesive — they are chemically entirely different.

Given/Concept: Various qualitative biochemical tests are used to detect the presence of biomolecules in biological samples.

Qualitative Tests:

1. Test for Proteins — Biuret Test:
- Reagents: Sodium hydroxide (NaOH) solution + dilute copper sulphate ($CuSO_4$) solution.
- Procedure: Add 2–3 drops of NaOH to the sample, then add 1–2 drops of dilute $CuSO_4$.
- Positive Result: Development of a violet/purple colour indicates the presence of peptide bonds (proteins).
- Principle: $Cu^{2+}$ ions form a complex with peptide bonds in alkaline conditions.

2. Test for Fats and Oils — Sudan III / Grease Spot Test:
- Sudan III Test: Add Sudan III (or Sudan IV) dye to the sample. Fats stain red/orange.
- Grease Spot Test: Rub the sample on brown paper. A translucent (greasy) spot that does not disappear on drying indicates fat.
- Emulsification Test: Add ethanol to the sample, then pour into water — a milky white emulsion indicates fat.

3. Test for Amino Acids — Ninhydrin Test:
- Reagent: Ninhydrin solution.
- Procedure: Add ninhydrin solution to the sample and heat gently.
- Positive Result: Development of a purple/violet colour (Ruhemann's purple) indicates the presence of free amino acids.
- Note: Proline gives a yellow colour with ninhydrin.

Testing Biological Samples:

| Sample | Protein (Biuret) | Fat (Sudan III) | Amino Acids (Ninhydrin) |
|---|---|---|---|
| Fruit juice | Negative/Trace | Negative | Positive (traces) |
| Saliva | Positive (mucin, amylase) | Negative | Positive (traces) |
| Sweat | Positive (trace proteins) | Trace | Positive (urea, amino acids) |
| Urine (normal) | Negative | Negative | Positive (urea, traces) |

Note: Presence of protein in urine (proteinuria) may indicate kidney disease. Students should perform these tests under teacher supervision in the laboratory.

Conclusion: Biuret test detects proteins, Sudan III/grease spot test detects fats, and ninhydrin test detects amino acids. Saliva tests positive for proteins due to enzymes like salivary amylase and mucin.

Given/Concept: Cellulose is the most abundant organic polymer on Earth, synthesised by plants. Paper is manufactured primarily from plant cellulose (wood pulp).

Cellulose Production by Plants:
- It is estimated that plants in the biosphere produce approximately $1.5 \times 10^{11}$ tonnes (150 billion tonnes) of cellulose per year through photosynthesis and cell wall synthesis.
- Cellulose constitutes about 33% of all plant matter and is the most abundant organic compound on Earth.

Paper Manufacture by Man:
- Global paper and paperboard production is approximately 400–420 million tonnes per year (as per recent estimates).
- Paper is made primarily from wood pulp (which is ~40–50% cellulose after removal of lignin and hemicellulose).
- To produce 1 tonne of paper, approximately 2–3 tonnes of wood are required.
- Therefore, annual wood consumption for paper ≈ $400 \times 2.5 = 1000$ million tonnes = $10^9$ tonnes of wood per year.

Comparison:
$$\frac{\text{Cellulose used for paper}}{\text{Total cellulose produced}} = \frac{\sim 2 \times 10^8 \text{ tonnes}}{1.5 \times 10^{11} \text{ tonnes}} \approx 0.13\%$$

Implications:
- Although the fraction appears small, the rate of deforestation far exceeds the rate of forest regeneration.
- Millions of hectares of forest are cleared annually for paper, timber, agriculture, and urbanisation.
- This leads to loss of biodiversity, soil erosion, disruption of water cycles, and contribution to climate change.
- Recycling paper and using alternative materials can significantly reduce this loss.

Conclusion: While plants produce enormous quantities of cellulose, human consumption of plant material for paper alone runs into hundreds of millions of tonnes annually, contributing significantly to deforestation and loss of vegetation. This underscores the urgent need for sustainable practices and paper recycling.

Given/Concept: Enzymes are biological catalysts, mostly proteinaceous in nature (except ribozymes), that catalyse biochemical reactions in living cells.

Important Properties of Enzymes:

1. Catalytic Power:
- Enzymes are highly efficient catalysts. They can catalyse reactions at a rate $10^6$ to $10^{12}$ times faster than uncatalysed reactions.
- They lower the activation energy of a reaction, thereby increasing the rate without being consumed.
$$\text{Enzyme} + \text{Substrate} \rightarrow \text{Enzyme-Substrate Complex} \rightarrow \text{Enzyme} + \text{Products}$$

2. Specificity:
- Enzymes are highly specific — each enzyme catalyses only one particular reaction or acts on one type of substrate.
- This is explained by the Lock and Key model (Fischer) and the Induced Fit model (Koshland).
- Example: Urease acts only on urea; maltase acts only on maltose.

3. Effect of Temperature:
- Enzyme activity increases with temperature up to an optimum temperature (usually 37°C in humans).
- Beyond the optimum, activity decreases sharply due to denaturation of the protein structure.
- At very low temperatures, enzymes are inactive but not denatured (activity resumes on warming).

4. Effect of pH:
- Each enzyme has an optimum pH at which it shows maximum activity.
- Example: Pepsin works best at pH ~2 (acidic); trypsin at pH ~8 (alkaline); salivary amylase at pH ~7 (neutral).
- Extreme pH values cause denaturation.

5. Reversibility:
- Enzymes catalyse both forward and reverse reactions; they do not alter the equilibrium of a reaction, only the rate at which equilibrium is reached.

6. Requirement of Cofactors:
- Many enzymes require non-protein components called cofactors for their activity.
- Prosthetic groups: Tightly bound organic compounds (e.g., haem in peroxidase).
- Co-enzymes: Loosely bound organic molecules, often vitamins (e.g., NAD, NADP).
- Metal ions: e.g., $Zn^{2+}$ in carboxypeptidase, $Mg^{2+}$ in many kinases.
- The protein part without the cofactor is called apoenzyme; the complete active enzyme is called holoenzyme.
$$\text{Apoenzyme} + \text{Cofactor} = \text{Holoenzyme (active)}$$

7. Denaturation:
- Enzymes are denatured (lose their 3-D structure and activity) by high temperatures, extreme pH, heavy metal ions, and certain chemicals.

8. Inhibition:
- Enzyme activity can be inhibited by inhibitors:
- Competitive inhibitors: Structurally similar to substrate; compete for the active site.
- Non-competitive inhibitors: Bind to a site other than the active site (allosteric site), changing the enzyme's shape.

9. Colloidal Nature:
- Enzymes are colloidal in nature (large protein molecules) and are sensitive to agents that affect colloids.

10. Activity in Small Amounts:
- A small amount of enzyme can catalyse the transformation of a large amount of substrate (high turnover number).

Conclusion: Enzymes are highly specific, efficient, and regulated biological catalysts that are sensitive to temperature, pH, and inhibitors. Their activity depends on the integrity of their three-dimensional structure and, in many cases, on the presence of cofactors.