Biological Molecules

🟢 Lite — Quick Review (1h–1d)

Rapid summary for last-minute revision before your exam.

Biological Molecules — Key Facts for MDCAT

Living organisms are composed of four major classes of biomolecules. Each has specific structures, functions, and importance in biological systems.

1. Carbohydrates:

• General formula: (CH₂O)$_n$ (where n = number of carbon atoms)

• Monosaccharides (simple sugars — cannot be hydrolysed further):

  • Trioses (n=3): Glyceraldehyde, dihydroxyacetone
  • Pentoses (n=5): Ribose (RNA), Deoxyribose (DNA)
  • Hexoses (n=6): Glucose (blood sugar), Fructose (fruit sugar), Galactose

• Disaccharides (two monosaccharides):

  • Sucrose = Glucose + Fructose (table sugar)
  • Lactose = Glucose + Galactose (milk sugar)
  • Maltose = Glucose + Glucose (malt sugar)
  • Bond: Glycosidic bond

• Polysaccharides (many monosaccharides):

  • Starch: Plant storage; amylose (linear, α-1,4) + amylopectin (branched, α-1,6)
  • Glycogen: Animal storage; highly branched; stored in liver and muscles
  • Cellulose: Plant structural; β-1,4 linkages; humans cannot digest (cellulose = dietary fibre)

2. Lipids:

• Insoluble in water (hydrophobic); soluble in organic solvents
• Fats and oils: Glycerol + 3 fatty acids → Triglycerides
  • Saturated fatty acids: No C=C bonds (solid at room temperature, e.g., butter)
  • Unsaturated fatty acids: ≥1 C=C bonds (liquid at room temperature, e.g., vegetable oils)
  • Essential fatty acids: Linoleic acid (ω-6), α-linolenic acid (ω-3)
• Phospholipids: Glycerol + 2 fatty acids + phosphate group → Cell membrane component
• Steroids: Cholesterol (cell membranes), Hormones (testosterone, oestrogen, cortisol)
• Waxes: Ester of fatty acid + long-chain alcohol (protective coatings)

3. Proteins:

• Made of amino acids linked by peptide bonds
• 20 standard amino acids; 9 essential (must be obtained from diet)
• Structure levels:
  1. Primary: Amino acid sequence (peptide bonds)
  2. Secondary: α-helix (right-handed) and β-pleated sheet (H-bonds)
  3. Tertiary: 3D shape (hydrophobic interactions, disulfide bridges, ionic bonds)
  4. Quaternary: Multiple polypeptide subunits (e.g., haemoglobin — 4 subunits)

4. Nucleic Acids:

• DNA (deoxyribonucleic acid): Double helix; deoxyribose sugar; A, T, G, C
• RNA (ribonucleic acid): Single strand; ribose sugar; A, U, G, C
• Nucleotide = Sugar + Phosphate + Nitrogenous base

⚡ Exam tip: Carbohydrates provide ~4 kcal/g, fats provide ~9 kcal/g, and proteins provide ~4 kcal/g. This is important for understanding energy balance. In dehydration synthesis (building), water is REMOVED. In hydrolysis (breaking down), water is ADDED. Remember: Glucose is the universal fuel of cells; ATP is the energy currency.

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🟡 Standard — Regular Study (2d–2mo)

Standard content for students who want genuine understanding.

Biological Molecules — Complete Study Guide

Carbohydrate Classification:

Type	Examples	Function
Monosaccharides	Glucose, fructose	Immediate energy source
Disaccharides	Sucrose, lactose, maltose	Transport form of sugar
Polysaccharides	Starch, glycogen, cellulose	Storage (plants) and structural (cellulose)

Lipid Functions:

• Energy storage (triglycerides — most concentrated energy source: 9 kcal/g)
• Structural (phospholipids in cell membranes)
• Hormonal (steroid hormones)
• Protective (wax coatings on leaves, fur)
• Insulating (adipose tissue under skin)
• Vitamins A, D, E, K are fat-soluble (stored in fat)

Protein Functions:

• Enzymatic: Catalyse biochemical reactions (e.g., pepsin, amylase)
• Structural: Collagen (connective tissue), keratin (hair, nails)
• Transport: Haemoglobin (O₂ transport), channel proteins
• Contractile: Actin and myosin (muscle contraction)
• Hormonal: Insulin, growth hormone
• Defensive: Antibodies (immunoglobulins)
• Storage: Casein (milk), ovalbumin (egg white)

Enzyme Basics:

• Lower activation energy; not consumed in reaction
• Lock and key model: Substrate fits into enzyme’s active site (specific)
• Induced fit model: Enzyme changes shape to fit substrate better
• Factors affecting enzyme activity: Temperature, pH, substrate concentration, inhibitors

Nucleic Acid Structure:

Feature	DNA	RNA
Sugar	Deoxyribose (C₅H₁₀O₄)	Ribose (C₅H₁₀O₅)
Bases	Adenine, Thymine, Guanine, Cytosine	Adenine, Uracil, Guanine, Cytosine
Structure	Double helix (antiparallel)	Usually single stranded
Base pairing	A=T (2 H-bonds), G≡C (3 H-bonds)	A=U, G≡C
Location	Nucleus, mitochondria	Nucleus, ribosomes, cytoplasm
Stability	More stable (deoxyribose, fewer OH groups)	Less stable (ribose, 2’ OH attacks phosphodiester bond)

ATP — The Energy Currency:

• Adenosine triphosphate: Adenine + Ribose + 3 phosphate groups
• Breaking the terminal phosphate bond: $ATP + H_2O \rightarrow ADP + P_i + 30.5 \text{ kJ/mol}$
• ATP is continually synthesised and hydrolysed — the “ATP cycle”

⚡ Common mistakes: Confusing the function of starch (plant storage) with glycogen (animal storage). Forgetting that cellulose has β-1,4 linkages which humans cannot break (no cellulase enzyme). Confusing the number of rings in glucose (6-membered/pyranose) vs deoxyribose (5-membered/furanose). Thinking steroid hormones are not lipids — they ARE, because they’re hydrophobic and derived from cholesterol.

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🔴 Extended — Deep Study (3mo+)

Comprehensive coverage for students on a longer study timeline.

Biological Molecules — Advanced Notes

Carbohydrate Metabolism — Glycolysis:

• Occurs in cytoplasm
• Glucose (6C) → 2 pyruvate (3C) + 2 ATP + 2 NADH
• Key steps: Hexokinase (glucose → glucose-6-phosphate), Phosphofructokinase (rate-limiting step), Pyruvate kinase
• Fate of pyruvate: Aerobic → acetyl-CoA → Krebs cycle; Anaerobic → lactate (animals) or ethanol + CO₂ (yeast)

Beta-Oxidation of Fatty Acids:

• Occurs in mitochondria
• Fatty acid → Acetyl-CoA units (each round produces 1 NADH + 1 FADH₂ + 1 acetyl-CoA)
• For stearic acid (C₁₈): 9 rounds → 9 acetyl-CoA + 9 NADH + 9 FADH₂
• More ATP per carbon than glucose oxidation

Protein Structure — Amino Acids:

• General structure: NH₂-CH(R)-COOH
• Classification by R group:
  • Nonpolar (hydrophobic): Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline
  • Polar (hydrophilic): Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine
  • Charged: Aspartic acid (negative), Glutamic acid (negative), Lysine (positive), Arginine (positive), Histidine (positive)

Enzyme Kinetics — Michaelis-Menten: $$v = \frac{V_{max}[S]}{K_m + [S]}$$

• $K_m$ = substrate concentration at which $v = V_{max}/2$
• $K_m$ is an inverse measure of substrate affinity — lower $K_m$ = higher affinity
• $V_{max}$ depends on enzyme concentration

Enzyme Inhibition:

• Competitive: Inhibitor competes with substrate at active site; increases $K_m$, $V_{max}$ unchanged; reversed by more substrate (e.g., sulfanilamide competes with PABA in folic acid synthesis)
• Non-competitive: Inhibitor binds elsewhere (allosteric site); decreases $V_{max}$, $K_m$ unchanged; cannot be overcome by more substrate
• Irreversible inhibition: Covalent binding (e.g., aspirin irreversibly inhibits cyclooxygenase)
• Feedback inhibition: End product inhibits enzyme early in pathway (e.g., isoleucine inhibits threonine deaminase)

Nucleic Acid Replication:

• DNA replication is semi-conservative (each new DNA has one old strand + one new strand)
• DNA polymerase III: Main replicating enzyme; adds nucleotides 5’→3’
• Leading strand: Synthesised continuously
• Lagging strand: Synthesised discontinuously as Okazaki fragments; later joined by DNA ligase
• Telomeres: G-rich repeats at chromosome ends; telomerase (reverse transcriptase) maintains them in germ cells and cancer cells

Central Dogma of Molecular Biology: $$DNA \xrightarrow{\text{transcription}} RNA \xrightarrow{\text{translation}} Protein$$

• Reverse transcription (RNA → DNA): Retroviruses (HIV), telomerase
• Translation occurs on ribosomes (rRNA + proteins) in cytoplasm

Water — The Biological Solvent:

• Properties: High specific heat, high heat of vaporisation, cohesion, adhesion, excellent solvent
• pH: pH = -log[H⁺]; neutral = 7; acidic < 7; basic > 7
• Buffer systems: Bicarbonate buffer (blood), phosphate buffer (intracellular), protein buffer

MDCAT Question Patterns: MDCAT Pakistan biological molecules questions frequently test: (1) classifying biomolecules and their monomers/polymers, (2) distinguishing saturated vs unsaturated fatty acids, (3) protein structure levels and their bonds, (4) DNA vs RNA structure, (5) enzyme kinetics (Michaelis-Menten), (6) carbohydrate classification and functions, (7) ATP structure and function, (8) water properties. 2–3 questions per paper. Carbohydrate classification, protein structure, and enzyme kinetics are very high-yield.

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