Biochemical Processes and the Chemistry of Life
🟢 Lite — Quick Review (1h–1d)
Rapid summary for last-minute revision before your exam.
Biochemistry — Key Facts for Sri Lanka A/L Examination
The Four Major Biomolecules:
| Biomolecule | Monomer | Role | Examples |
|---|---|---|---|
| Carbohydrates | Monosaccharides | Energy, structural | Glucose, starch, cellulose |
| Proteins | Amino acids | Enzymes, structure | Enzymes, keratin, haemoglobin |
| Lipids | Fatty acids + glycerol | Energy storage, membranes | Fats, oils, phospholipids |
| Nucleic acids | Nucleotides | Genetic information | DNA, RNA, ATP |
Key Chemical Reactions in Plants:
- Photosynthesis: CO₂ + H₂O → C₆H₁₂O₆ + O₂ (light energy)
- Respiration: C₆H₁₂O₆ + O₂ → CO₂ + H₂O + ATP (energy release)
- Protein synthesis: Amino acids → polypeptide chains
Water Properties:
- Polar molecule with hydrogen bonding
- Excellent solvent (universal solvent)
- High specific heat capacity
- Cohesion and adhesion (capillary action in xylem)
- Density of ice < liquid water (floats, insulates aquatic life)
⚡ A/L Exam Tip: Water’s properties are essential for life — cohesion allows water transport in xylem via transpiration pull!
🟡 Standard — Regular Study (2d–2mo)
Standard content for students with a few days to months.
Biochemistry — Detailed Study Guide
Carbohydrates
Classification:
| Type | Examples | Function |
|---|---|---|
| Monosaccharides | Glucose, fructose | Simple sugar, energy |
| Disaccharides | Sucrose, maltose | Transport sugar in plants |
| Polysaccharides | Starch, cellulose | Storage (plants) / Structure |
Key Sugars in Plants:
- Glucose: Primary energy currency, produced in photosynthesis
- Sucrose: Transport form of carbohydrate in phloem (glucose + fructose)
- Starch: Storage form in amyloplasts (amylose + amylopectin)
- Cellulose: Structural component of plant cell walls (β-1,4-glucan)
⚡ A/L PYQ: “Why is cellulose unsuitable as a storage compound in plants?” Answer: Cellulose has β-1,4-glycosidic bonds that form rigid microfibrils — it cannot be rapidly mobilised for energy, unlike starch which has α-1,4 and α-1,6 bonds allowing easy hydrolysis.
Carbohydrate Tests:
| Test | reagent | Positive Result | Substance |
|---|---|---|---|
| Benedict’s | Copper(II) sulphate (blue) | Orange/red precipitate | Reducing sugars (glucose) |
| Iodine | Iodine solution (brown) | Blue-black colour | Starch |
| Molisch | α-naphthol + H₂SO₄ | Purple ring | All carbohydrates |
Proteins
Amino Acid Structure:
- General formula: NH₂-CH(R)-COOH
- Central carbon bonded to: amino group, carboxyl group, hydrogen, and R group (variable)
- 20 standard amino acids determine protein diversity
Protein Structure:
| Level | Description | Bonds/Forces |
|---|---|---|
| Primary | Amino acid sequence | Peptide bonds |
| Secondary | α-helix, β-pleated sheet | H-bonds |
| Tertiary | 3D folding | H-bonds, ionic, hydrophobic, disulfide |
| Quaternary | Multiple polypeptide subunits | Same as tertiary |
Enzymes:
- Active site: Region where substrate binds (lock and key / induced fit)
- Cofactors: Non-protein helpers (coenzymes, metal ions)
- Vitamins (coenzymes in humans): B-complex — thiamine (B1), riboflavin (B2), niacin (B3), B6, B12
- Inhibitors: Competitive (similar substrate) and non-competitive (alters active site)
Enzyme Kinetics:
- Activation energy: Energy needed to start a reaction
- Rate affected by: Temperature, pH, substrate concentration, enzyme concentration
- Optimum conditions: Peak activity for specific enzyme
⚡ A/L Important: Enzyme denaturation — high temperature or extreme pH destroys the tertiary/quaternary structure, inactivating the enzyme permanently.
Lipids
Types:
| Type | Examples | Function |
|---|---|---|
| Fats & Oils | Triglycerides | Energy storage (plants: seeds — coconut, rice bran) |
| Phospholipids | Lecithin | Cell membrane structure (hydrophilic head, hydrophobic tails) |
| Waxes | Cutin, suberin | Waterproofing (leaf cuticle, Casparian strip) |
| Steroids | Cholesterol, plant hormones | Membranes, signalling (gibberellins are steroids) |
Significance of Lipids in Plants:
- Phospholipid bilayer: Cell membrane structure (selective permeability)
- Waxes: Epidermal cuticle prevents water loss (transpiration)
- Suberin: Casparian strip in endodermal cell walls
- Cutin: Leaf surface wax coating
Lipid Tests:
| Test | Method | Positive Result |
|---|---|---|
| Sudan III | Stain fat droplets | Red-orange staining |
| Emulsion test | Ethanol + water | Cloudy white emulsion |
Nucleic Acids and ATP
DNA Structure:
- Double helix (Watson & Crick, 1953)
- Antiparallel strands
- Complementary base pairing: A-T (2 H-bonds), G-C (3 H-bonds)
- Deoxyribose sugar, thymine present
RNA Structure:
- Single stranded (usually)
- Ribose sugar, uracil replaces thymine
- Types: mRNA, tRNA, rRNA
ATP (Adenosine Triphosphate):
- Structure: Adenine + ribose + 3 phosphate groups
- Function: Universal energy currency of the cell
- Energy release: ATP → ADP + Pi (hydrolysis releases ~30.5 kJ/mol)
- Regeneration: ADP + Pi → ATP (via respiration or photophosphorylation)
⚡ A/L Key Point: Photosynthesis produces O₂ as a byproduct because water is split during photolysis, not because CO₂ is converted to O₂!
🔴 Extended — Deep Study (3mo+)
Comprehensive coverage for students on a longer study timeline.
Biochemistry — Complete Notes for A/L Sri Lanka
Enzyme Mechanism in Detail
Lock and Key vs Induced Fit Model:
| Model | Description | Evidence |
|---|---|---|
| Lock and key | Active site rigid, exact fit | X-ray crystallography shows static shape |
| Induced fit | Active site changes shape on binding | Enzyme-substrate complex studies |
Enzyme-Substrate Complex:
E + S → [ES complex] → E + P
(transition state, lower activation energy)Factors Affecting Enzyme Activity:
| Factor | Effect | Mechanism |
|---|---|---|
| Temperature ↑ | Rate ↑ to optimum, then ↓ | More collisions, then denaturation |
| pH | Rate peaks at optimum | H⁺/OH⁻ disrupt ionic bonds |
| Substrate concentration | Rate ↑, then levels off | Saturation of active sites |
| Enzyme concentration | Rate proportional (at low [E]) | More active sites available |
Enzyme Classification (IUBMB):
| Class | Reaction Type | Example |
|---|---|---|
| 1. Oxidoreductases | Redox reactions | Dehydrogenases |
| 2. Transferases | Group transfer | Transaminases |
| 3. Hydrolases | Hydrolysis | Amylase, lipase |
| 4. Lyases | Addition/removal of groups | Decarboxylases |
| 5. Isomerases | Isomerisation | Phosphoglucose isomerase |
| 6. Ligases | Bond formation (ATP) | DNA ligase |
⚡ A/L Important: Named plant enzymes frequently tested: RuBisCO (carbon fixation), nitrate reductase (nitrogen assimilation), amylase (starch hydrolysis in germinating seeds).
Metabolic Pathways
Photosynthesis Summary:
Light Reactions (Thylakoid):
2H₂O → 4H⁺ + O₂ + 4e⁻ (photolysis)
NADP⁺ + H⁺ → NADPH (reduction)
ADP + Pi → ATP (photophosphorylation)
Calvin Cycle (Stroma):
CO₂ + RuBP → 2 × 3-PGA (fixation by RuBisCO)
3-PGA + ATP + NADPH → G3P (reduction)
G3P → glucose + RuBP (regeneration)
Net: 6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂Respiration:
Glycolysis (cytoplasm):
Glucose → 2 pyruvate + 2 ATP + 2 NADH
Link reaction (mitochondrial matrix):
Pyruvate → Acetyl-CoA + CO₂ + NADH
Krebs cycle (mitochondrial matrix):
Acetyl-CoA → 2CO₂ + 3 NADH + FADH₂ + GTP
Electron transport chain (inner mitochondrial membrane):
NADH → ~2.5 ATP
FADH₂ → ~1.5 ATP
O₂ + 4e⁻ + 8H⁺ → 2H₂O
Total yield: ~36-38 ATP per glucose⚡ A/L Common Mistake: Students confuse the location of processes. Glycolysis is in the cytoplasm; Krebs cycle and ETC are in mitochondria. Light reactions are in thylakoids; Calvin cycle is in the stroma.
Water and Mineral Nutrition
Water as a Solvent:
- Polar molecules: Water dissolves ionic compounds (salts, minerals) and other polar substances
- Non-polar substances: Lipids repel water (hydrophobic effect — basis of membrane structure)
- Capillary action: Water rises in narrow tubes due to adhesion (water-wall) and cohesion (water-water)
Mineral Ion Functions:
| Ion | Plant Function | Deficiency |
|---|---|---|
| NO₃⁻ | Nitrogen source for amino acids | Stunted, yellow leaves |
| NH₄⁺ | Nitrogen source (wetland plants) | Acidifies soil |
| PO₄³⁻ | Phosphorus for ATP, nucleic acids | Purple leaves, poor roots |
| K⁺ | Stomatal function, enzyme activation | Scorched leaf margins |
| Mg²⁺ | Chlorophyll porphyrin ring | Interveinal chlorosis |
| Ca²⁺ | Cell wall middle lamella | Deformed young leaves |
| Fe³⁺ | Chlorophyll synthesis | Young leaves yellow |
| S²⁻ | Cysteine, methionine (proteins) | Young leaves yellow |
GCE A/L Sri Lanka Past Paper Tips
Common Structured Questions:
- “Describe the lock and key hypothesis of enzyme action” (6 marks)
- “Explain the factors that affect the rate of an enzyme-catalysed reaction” (10 marks)
- “Describe the role of water in plant physiology” (8 marks)
- “Compare the structure of DNA and RNA” (8 marks)
- “Explain how ATP acts as an energy currency in cells” (6 marks)
Calculation Questions:
- Limiting factor questions in photosynthesis (light, CO₂, temperature)
- Water potential calculations (Ψ = Ψs + Ψp)
- Enzyme kinetics (Michaelis-Menten)
Diagram Questions:
- Draw the lock and key enzyme model (4 marks)
- Draw chemical structure of water molecule showing hydrogen bonding (5 marks)
- Draw labelled diagram of ATP molecule (4 marks)
⚡ A/L Strategy: For biochemistry questions involving plant examples, use Sri Lankan crops (rice, coconut, mango) to illustrate concepts — e.g., starch storage in rice endosperm, oil in coconut kernel, sucrose transport in phloem.
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