Biochemistry Study Guide

📖 Core Concepts Biochemistry – study of chemical processes in living organisms; links chemistry of cells to whole‑organism physiology. Four major biomolecule classes – carbohydrates, lipids, proteins, nucleic acids; each can be a polymer of monomers linked by dehydration synthesis. Dehydration synthesis vs. Hydrolysis – polymer formation releases H₂O; polymer breakdown adds H₂O. Structural hierarchy of proteins – primary (sequence) → secondary (α‑helix, β‑sheet) → tertiary (3‑D fold) → quaternary (multiple subunits). Enzyme catalysis – lowers activation energy; can increase rates up to $10^{11}$‑fold; activity modulated by inhibitors/activators & covalent modifications. Central dogma – DNA → RNA → protein; nucleic acids provide genetic info (DNA) and functional/energetic roles (RNA, ATP). Metabolic overview – glycolysis (anaerobic) → pyruvate → either lactate/ethanol (no O₂) or acetyl‑CoA → citric‑acid cycle → ETC → ATP (32 per glucose). --- 📌 Must Remember Carbohydrate formula: $CnH{2n}On$ (≈ 1:2:1 ratio). Glucose – $C6H{12}O6$, key monosaccharide. Lactose intolerance – lack of lactase → cannot hydrolyze lactose. Saturated fatty acid – no C=C double bonds; unsaturated – one or more C=C. Essential amino acids (humans): Ile, Leu, Lys, Met, Phe, Thr, Trp, Val. Base pairing: A–T (DNA) / A–U (RNA) (2 H‑bonds); C–G (3 H‑bonds). Glycolysis net gain: 2 ATP, 2 NADH per glucose. Aerobic respiration total ATP: ≈ 32 ATP per glucose. Key enzymes in urea cycle – convert toxic NH₃ → urea for excretion. --- 🔄 Key Processes Dehydration Synthesis (Polymerization) Align monomer’s –OH (from carboxyl) with another monomer’s –H (from hydroxyl). Form covalent bond (e.g., peptide, glycosidic, phosphodiester). Release one H₂O molecule. Hydrolysis (Polymer Breakdown) Add H₂O across the polymer bond. –OH attaches to one fragment, –H to the other → monomers regenerated. Glycolysis (simplified) Energy investment: 2 ATP phosphorylate glucose → Fructose‑1,6‑bisphosphate. Cleavage: Split into 2 glyceraldehyde‑3‑phosphate (G3P). Energy payoff: Each G3P → 2 ATP (substrate‑level) + 1 NADH → net 2 ATP, 2 NADH per glucose. Aerobic Oxidation of Pyruvate Pyruvate + CoA + NAD⁺ → acetyl‑CoA + CO₂ + NADH. Acetyl‑CoA enters citric‑acid cycle → 2 ATP, 6 NADH, 2 FADH₂ per glucose. NADH/FADH₂ donate electrons to ETC → proton gradient → ATP synthase → ≈ 30‑34 ATP. Transamination (amino‑group transfer) Amino acid + α‑keto acid ↔ new amino acid + new α‑keto acid (catalyzed by transaminase). Enables non‑essential amino acid synthesis & ammonia handling. --- 🔍 Key Comparisons Saturated vs. Unsaturated Fatty Acids Saturated: no C=C bonds → straight chains → pack tightly → higher melting point. Unsaturated: one or more C=C → kinked chains → lower melting point. DNA vs. RNA DNA: deoxyribose sugar, thymine (T), double‑stranded, long‑term storage. RNA: ribose sugar, uracil (U), usually single‑stranded, roles in expression & catalysis. Furanose vs. Pyranose Rings (monosaccharide cyclic forms) Furanose: 5‑membered ring (4 carbons + O). Pyranose: 6‑membered ring (5 carbons + O). Enzyme Inhibition Types Competitive: inhibitor resembles substrate → binds active site → effect overcome by high substrate. Non‑competitive: inhibitor binds elsewhere → Vmax ↓, Km unchanged. --- ⚠️ Common Misunderstandings “All sugars are sweet.” – Many polysaccharides (cellulose, glycogen) are not sweet; sweetness depends on monomer type and solubility. “Lipids are only fats.” – Lipids also include phospholipids, sterols, waxes; many are amphiphilic, not purely non‑polar. “Proteins are always enzymes.” – Only a subset are catalytic; many are structural, signaling, or transport molecules. “ATP hydrolysis always yields 30 kJ/mol.” – Actual free energy varies with cellular conditions (≈ ‑30 to ‑50 kJ/mol). --- 🧠 Mental Models / Intuition Polymer‑Water Analogy: Building a polymer is like snapping LEGO bricks together (water released); breaking it is like pulling them apart with water as “glue”. Energy Flow in Metabolism: Think of glucose as a “fuel tank” → glycolysis = “spark‑plug” → citric cycle = “engine” → ETC = “generator”. Enzyme as a “shortcut”: The reaction coordinate diagram shows the enzyme lowering the peak (activation energy) but not changing start/end points. --- 🚩 Exceptions & Edge Cases Lactose digestion: Only infants/most mammals have high lactase; adult deficiency → lactose intolerance. Unsaturated fatty acids: Cis double bonds are common; trans fats (industrial) behave more like saturated fats (higher melting point). Glycolysis in red blood cells: No mitochondria → pyruvate always reduced to lactate (no aerobic path). --- 📍 When to Use Which Identify a biomolecule class: Contains glycerol + fatty acids → lipid. Polymer of nucleotides → nucleic acid. Polymer of amino acids → protein. Polymer of saccharides → carbohydrate. Choose analytical technique: Separate by size → gel filtration chromatography. Separate by charge → ion‑exchange chromatography. Determine 3‑D structure → X‑ray diffraction or NMR (small vs. large molecules). Select metabolic pathway: Low O₂ or intense exercise → anaerobic glycolysis → lactate. Adequate O₂ → aerobic respiration (full ATP yield). Need glucose during fasting → gluconeogenesis (use amino acids, glycerol). --- 👀 Patterns to Recognize “+2 ATP, +2 NADH” → hallmark of glycolysis net yield. “3‑C, 2‑C, 1‑C” → typical carbon loss pattern in citric‑acid cycle (CO₂ releases). “Hydrophobic tail + hydrophilic head” → amphiphilic lipids → form bilayers/micelles. “Alpha‑helix: i → i+4 H‑bond” – recognize secondary‑structure hydrogen‑bond pattern. --- 🗂️ Exam Traps Confusing substrate‑level phosphorylation with oxidative phosphorylation. Trap: attributing ATP from glycolysis to the electron transport chain. Why wrong: glycolytic ATP is generated directly by kinase enzymes, not by ETC. Misidentifying the “energy‑rich” bond in ATP. Trap: saying the bond itself stores energy. Why wrong: the high‑energy phosphate bond releases energy because products (ADP + Pi) are more stable. Assuming all disaccharides are digestible. Trap: treating sucrose and lactose the same. Why wrong: lactose requires lactase; deficiency leads to intolerance. Mixing up DNA vs. RNA base pairing rules. Trap: pairing A with T in RNA or with U in DNA. Why wrong: DNA uses T, RNA uses U. Overlooking the role of water in hydrolysis. Trap: thinking polymers break spontaneously. Why wrong: hydrolysis requires water (and often enzymes) to cleave bonds. ---