Biochemistry

🟢 Lite — Quick Review (1h–1d)

Rapid summary for last-minute revision before your exam.

Biochemistry — Key Facts for MDCAT

Biochemistry is the study of the chemical substances and processes that occur within living organisms. For MDCAT, focus on the four major classes of biomolecules and their roles.

Carbohydrates:

• Monosaccharides: Simple sugars — glucose (C₆H₁₂O₆, aldohesox; found in blood), fructose (ketohexose; found in fruits), ribose (C₅H₁₀O₅; in RNA)
• Disaccharides: Two monosaccharides — sucrose (glucose + fructose, Table sugar), lactose (glucose + galactose; milk sugar), maltose (glucose + glucose; malt sugar)
• Polysaccharides: Many monosaccharides — starch (plant storage; amylose + amylopectin), glycogen (animal storage; highly branched, in liver and muscles), cellulose (plant structural; β(1→4) linkages, humans cannot digest)

Key Test: Benedict’s test for reducing sugars (glucose, fructose, maltose) — blue → green → yellow → brick-red precipitate on heating. Sucrose is NON-reducing.

Lipids:

• Fats and oils (triglycerides): glycerol + 3 fatty acids
• Saturated fatty acids: no C=C bonds (butter, solid; e.g., stearic acid C₁₇H₃₅COOH)
• Unsaturated fatty acids: ≥1 C=C bonds (oils, liquid; e.g., oleic acid)
• Phospholipids: major component of cell membranes (hydrophilic head + hydrophobic tails)
• Steroids: cholesterol (animal cell membranes), hormones (testosterone, oestrogen)

Proteins:

• Made of amino acids linked by peptide bonds
• Essential amino acids (9): must come from diet — histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine
• Protein structure: Primary → Secondary (α-helix, β-pleated sheet) → Tertiary → Quaternary
• Denaturation: Heat, pH, alcohol — disrupts tertiary/quaternary structure (not primary)

⚡ Exam tip: Carbohydrate classification: (CH₂O)$_n$ where n = 3 (triose), 4 (tetrose), 5 (pentose), 6 (hexose), 7 (heptose). Glucose is a ALDOhexose; fructose is a KETOhexose. The distinction between α and β glycosidic bonds determines whether starch (α-1,4, digestible) vs cellulose (β-1,4, not digestible by humans) can be digested.

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🟡 Standard — Regular Study (2d–2mo)

Standard content for students who want genuine understanding.

Biochemistry — Complete Study Guide

Enzymes — Biological Catalysts:

• Lower activation energy but DO NOT change $\Delta G$
• Most are proteins (some RNA enzymes = ribozymes, e.g., ribonuclease P)
• Enzyme nomenclature: names usually end in “-ase” (e.g., lactase, amylase, kinase)
• Lock and key model vs Induced fit model

Enzyme Kinetics — Michaelis-Menten Equation: $$v = \frac{V_{max}[S]}{K_m + [S]}$$ Where $V_{max}$ = maximum velocity, $[S]$ = substrate concentration, $K_m$ = Michaelis constant (substrate concentration at which $v = V_{max}/2$).

Factors Affecting Enzyme Activity:

• Temperature: Optimal ~37°C (human enzymes); denaturation above ~50–60°C
• pH: Each enzyme has optimal pH (pepsin ~2, trypsin ~8, amylase ~7)
• Substrate concentration: Follows Michaelis-Menten kinetics
• Inhibitors: Competitive (mimic substrate, increase $K_m$, $V_{max}$ unchanged), Non-competitive (bind elsewhere, decrease $V_{max}$, $K_m$ unchanged)

Nucleic Acids — DNA and RNA:

Feature	DNA	RNA
Sugar	Deoxyribose (C₅H₁₀O₄)	Ribose (C₅H₁₀O₅)
Bases	A, T, G, C	A, U, G, C
Strands	Double helix	Usually single strand
Location	Nucleus, mitochondria	Nucleus, ribosomes, cytoplasm
Function	Genetic information storage	Protein synthesis (mRNA, tRNA, rRNA)

DNA Structure (Watson-Crick):

• Antiparallel strands (5’ → 3’ and 3’ → 5’)
• Complementary base pairing: A = T (2 H-bonds), G ≡ C (3 H-bonds)
• Double helix width = 2 nm; one turn = 10 base pairs
• Major groove and minor groove on the helix surface

ATP — The Energy Currency: Adenosine triphosphate (ATP): adenine + ribose + 3 phosphate groups $$ATP + H_2O \rightarrow ADP + P_i + \text{energy (30.5 kJ/mol)}$$ ATP is synthesised by: oxidative phosphorylation (in mitochondria), photophosphorylation (in chloroplasts), substrate-level phosphorylation (in glycolysis).

⚡ Common mistakes: Confusing DNA replication (unwinds, each strand serves as template for new DNA) with transcription (DNA → RNA). Thinking enzymes are used up in reactions (they are NOT — they are recycled). For Benedict’s test, forgetting that sucrose is non-reducing because its glycosidic bond is between the anomeric carbons of both glucose and fructose.

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🔴 Extended — Deep Study (3mo+)

Comprehensive coverage for students on a longer study timeline.

Biochemistry — Advanced Notes

Carbohydrate Metabolism:

• Glycolysis: Glucose → 2 pyruvate (in cytoplasm)

  • Net: $Glucose + 2NAD^+ + 2ADP \rightarrow 2pyruvate + 2ATP + 2NADH$
  • Key enzymes: hexokinase (phosphorylates glucose), phosphofructokinase (rate-limiting step), pyruvate kinase
  • ATP yield: 2 ATP (substrate-level) directly; 2 NADH → 5 ATP via ETC

• Krebs Cycle (Citric Acid Cycle): Pyruvate → Acetyl-CoA enters cycle

  • Occurs in mitochondrial matrix
  • Per acetyl-CoA: 3 NADH, 1 FADH₂, 1 GTP (ATP) → ~12 ATP total per cycle
  • One glucose = 2 pyruvate = 2 acetyl-CoA → ~24 ATP from Krebs + ETC

• Electron Transport Chain (Oxidative Phosphorylation):

  • NADH → Complex I → Q → Complex III → Cyt c → Complex IV → O₂ → H₂O
  • FADH₂ → Complex II → Q → Complex III → Cyt c → Complex IV → O₂
  • ATP synthase produces ~2.5 ATP per NADH, ~1.5 ATP per FADH₂
  • Total theoretical yield: ~30–32 ATP per glucose (modern calculation ~28–30)

Beta-Oxidation of Fatty Acids: Fatty acids are broken down in mitochondria to acetyl-CoA units:

• Stearic acid (C₁₈): 9 acetyl-CoA produced
• Each round of β-oxidation produces: 1 NADH, 1 FADH₂, 1 acetyl-CoA
• Beta-oxidation releases MORE energy per carbon than glucose oxidation

Gluconeogenesis: Synthesis of glucose from non-carbohydrate sources (lactate, amino acids, glycerol). Occurs mainly in liver during fasting. Not simply the reverse of glycolysis — some irreversible steps are bypassed.

Photosynthesis: $$6CO_2 + 6H_2O \xrightarrow{\text{light}} C_6H_{12}O_6 + 6O_2$$

• Light reactions (thylakoid membrane): Photophosphorylation — produces ATP and NADPH
• Calvin cycle (stroma): Carbon fixation by RuBisCO — CO₂ + RuBP → 2 × 3-PGA → glucose
• C₃ plants: Rice, wheat, oats — CO₂ first fixed into 3-carbon compound (3-PGA)
• C₄ plants: Maize, sugarcane — spatial separation of CO₂ fixation and Calvin cycle (Kranz anatomy)
• CAM plants: Cacti, pineapple — temporal separation (night vs day)

Nitrogen Metabolism:

• Nitrogen fixation: N₂ → NH₃ (by nitrogenase enzyme in legumes, Rhizobium bacteria)
• Ammonification: Organic N → NH₃ (decay by decomposers)
• Nitrification: NH₃ → NO₂⁻ → NO₃⁻ (by Nitrosomonas and Nitrobacter)
• Denitrification: NO₃⁻ → N₂ (returns N₂ to atmosphere)

MDCAT Question Patterns: MDCAT Pakistan biochemistry questions frequently test: (1) distinguishing monosaccharides/disaccharides/polysaccharides, (2) lock and key vs induced fit enzyme models, (3) factors affecting enzyme activity (competitive/non-competitive inhibition), (4) DNA structure (base pairing rules), (5) ATP as energy currency, (6) glycolysis overview and end products, (7) photosynthesis light vs dark reactions. 2–3 questions per paper. Enzyme kinetics and metabolic pathways are high-yield.

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