Biochemistry BZO6T16

Syllabus topics (RTMNU)

• Classification and general properties of carbohydrates: monosaccharides, oligosaccharides and polysaccharides; solubility, sweetness, reducing nature, mutarotation and basic reactions of sugars
• Structure and biological functions of glucose, fructose, sucrose, lactose, starch, glycogen and cellulose; role in energy storage and structural support
• Application of carbohydrates in foods: sugars, starch polysaccharides, non-starch polysaccharides
• Overview of carbohydrate metabolism: glycolysis, glycogenesis, glycogenolysis and gluconeogenesis (introductory)

Classification and general properties of carbohydrates

Carbohydrates are polyhydroxy aldehydes or ketones, or compounds that give these on hydrolysis; general formula C_n(H₂O)_n.

• Monosaccharides: simple sugars that cannot be hydrolysed further. By number of carbons — trioses (glyceraldehyde), tetroses, pentoses (ribose, deoxyribose), hexoses (glucose, fructose, galactose); by functional group — aldoses (glucose) and ketoses (fructose).
• Oligosaccharides: 2–10 monosaccharide units joined by glycosidic bonds — disaccharides (sucrose, lactose, maltose), trisaccharides (raffinose).
• Polysaccharides: many units — homopolysaccharides (starch, glycogen, cellulose, chitin) and heteropolysaccharides (hyaluronic acid, heparin, chondroitin sulphate).

General properties:

• Solubility and sweetness: mono- and disaccharides are crystalline, water-soluble and sweet (fructose sweetest, then sucrose, glucose; lactose least); polysaccharides are insoluble or form colloids and are not sweet.
• Optical activity and isomerism: have asymmetric carbons; D and L forms (natural sugars are mostly D); epimers (glucose and galactose differ at C-4).
• Reducing nature: sugars with a free aldehyde/ketone group (glucose, fructose, maltose, lactose) reduce Cu²⁺ to red Cu₂O — positive Benedict's and Fehling's tests; sucrose is non-reducing (both anomeric carbons bound).
• Mutarotation: the change in specific rotation of a freshly made sugar solution until equilibrium, due to interconversion of α and β anomers via the open chain: α-D-glucose (+112°) and β-D-glucose (+19°) → equilibrium +52.5° (about 36% α, 64% β).
• Basic reactions: oxidation (to gluconic/glucuronic acids), reduction (to sugar alcohols — sorbitol), osazone formation with phenylhydrazine (crystal shapes identify sugars), glycoside formation, fermentation by yeast, Molisch's test (violet ring, all carbohydrates), Seliwanoff's test (ketoses — red), iodine test (starch — blue).

Structure and biological functions

• Glucose (C₆H₁₂O₆, aldohexose): exists mainly as a six-membered pyranose ring (Haworth structure) with α and β anomers at C-1. "Blood sugar" (normal fasting about 70–100 mg/dL); main fuel of cells, especially brain and RBCs.
• Fructose (ketohexose, "fruit sugar"): five-membered furanose ring in sucrose; found in fruits, honey and seminal fluid (energy for sperm).
• Sucrose (cane sugar): α-D-glucose + β-D-fructose by α1→β2 glycosidic bond; non-reducing; hydrolysed by invertase/sucrase into "invert sugar".
• Lactose (milk sugar): β-D-galactose + D-glucose by β1→4 bond; reducing; digested by lactase (deficiency → lactose intolerance).
• Starch (plant storage): amylose (unbranched, α1→4, helical, blue with iodine, about 20–25%) + amylopectin (branched with α1→6 every 24–30 units, about 75–80%).
• Glycogen (animal starch): stored in liver and muscle; like amylopectin but more highly branched (every 8–12 units), red-brown with iodine; rapid source of glucose.
• Cellulose: unbranched β1→4 glucose chains forming H-bonded microfibrils; structural material of plant cell walls; cannot be digested by human enzymes (dietary fibre), digested by microbes in ruminants and termites.

Roles: energy source and storage (glucose, glycogen, starch); structural support (cellulose, chitin of arthropod exoskeleton, glycosaminoglycans of connective tissue); components of nucleic acids (ribose, deoxyribose), coenzymes (NAD, ATP); cell recognition (glycoproteins, glycolipids, blood group antigens); lubricants (hyaluronic acid); anticoagulant (heparin).

Applications of carbohydrates in foods

• Sugars: sweetening; preservation (high sugar lowers water activity — jams, jellies, syrups); fermentation (bread, alcohol); browning and flavour (caramelisation, Maillard reaction with proteins); texture and moisture (honey, invert sugar syrup in confectionery); glucose syrups, high-fructose corn syrup; sugar alcohols (sorbitol, xylitol) in sugar-free products.
• Starch polysaccharides: thickening and gelling (gelatinisation on heating with water — sauces, custard, soups); binder and filler (sausages, snacks); modified starches (resistant to heat/acid, freeze–thaw stable); maltodextrins; retrogradation causes staling of bread.
• Non-starch polysaccharides: pectin (gelling agent in jams and jellies), agar and carrageenan (from seaweeds — gels, dairy desserts, microbiological media), alginates (ice cream stabiliser), gum arabic, guar and xanthan gums (thickeners, emulsion stabilisers), cellulose derivatives (CMC, methylcellulose), inulin (prebiotic fibre). Dietary fibre aids bowel movement and lowers cholesterol and glycaemic response.

Overview of carbohydrate metabolism

• Glycolysis (Embden–Meyerhof–Parnas pathway, cytosol): glucose → 2 pyruvate in 10 steps; net gain 2 ATP and 2 NADH. Key regulatory enzymes: hexokinase, phosphofructokinase-1 (rate-limiting), pyruvate kinase. Under aerobic conditions pyruvate → acetyl-CoA → Krebs cycle (total about 30–32 ATP per glucose); under anaerobic conditions pyruvate → lactate (muscle) or ethanol (yeast).
• Glycogenesis: synthesis of glycogen from glucose in liver and muscle: glucose → glucose-6-P → glucose-1-P → UDP-glucose; glycogen synthase adds α1→4 units; branching enzyme makes α1→6 branches; stimulated by insulin (fed state).
• Glycogenolysis: breakdown of glycogen by glycogen phosphorylase to glucose-1-P (→ glucose-6-P); debranching enzyme removes branches; in liver glucose-6-phosphatase releases free glucose into blood; stimulated by glucagon and adrenaline (fasting, stress).
• Gluconeogenesis: formation of glucose from non-carbohydrate sources — lactate (Cori cycle), glycerol, glucogenic amino acids (alanine) — mainly in liver (and kidney) during fasting; bypasses three irreversible glycolytic steps using pyruvate carboxylase, PEP carboxykinase, fructose-1,6-bisphosphatase and glucose-6-phosphatase.

Likely exam questions

1. (Long, 8 marks) Classify carbohydrates with examples. Describe the structure and functions of starch, glycogen and cellulose.
2. (Long, 8 marks) Give an overview of carbohydrate metabolism: glycolysis, glycogenesis, glycogenolysis and gluconeogenesis.
3. (Short, 4 marks) What is mutarotation?
4. (Short, 4 marks) Why is sucrose a non-reducing sugar?
5. (Short, 4 marks) Write the uses of non-starch polysaccharides in food.

Syllabus topics (RTMNU)

• Amino acids: structure and properties; classification based on side chains; physical and chemical properties; zwitterionic nature and isoelectric point
• Levels of protein organisation and functions: primary, secondary (α-helix and β-sheet), tertiary and quaternary structures; types of bonds; biological functions of proteins
• Overview of amino acid metabolism: transamination, deamination, ammonia transport and urea cycle
• Enzymes and enzyme kinetics: classification and nomenclature; active site and ES complex; lock-and-key and induced-fit models; Km concept; enzyme inhibition (competitive, non-competitive, irreversible); factors affecting enzyme activity

Amino acids — structure and properties

An α-amino acid has a central α-carbon bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen and a variable side chain (R). All except glycine are optically active; proteins contain L-amino acids. 20 standard amino acids are coded by the genetic code.

Classification by side chain:

• Non-polar (hydrophobic): glycine, alanine, valine, leucine, isoleucine, proline, methionine, phenylalanine, tryptophan.
• Polar, uncharged: serine, threonine, cysteine, tyrosine, asparagine, glutamine.
• Acidic (negative): aspartic acid, glutamic acid.
• Basic (positive): lysine, arginine, histidine.
• Nutritional: essential (must come from diet) — valine, leucine, isoleucine, threonine, methionine, phenylalanine, tryptophan, lysine, histidine (arginine semi-essential in children); others non-essential.

Properties: white crystalline, water-soluble, high melting points. In solution they exist as zwitterions (dipolar ions, ⁺H₃N–CHR–COO^–), so they are amphoteric — act as acids and bases (buffers). The isoelectric point (pI) is the pH at which the amino acid has no net charge and does not move in an electric field; solubility is least at pI (e.g. glycine pI about 6.0). Chemical reactions: ninhydrin test (purple, Ruhemann's purple; proline yellow), peptide bond formation, xanthoproteic test (aromatic), Millon's test (tyrosine), reactions of –SH (cysteine forming disulphide bonds).

Levels of protein organisation and functions

• Primary structure: linear sequence of amino acids joined by peptide bonds (–CO–NH–); determined by genes; one change can cause disease (sickle-cell anaemia — glutamate → valine at position 6 of β-globin).
• Secondary structure: regular folding of the backbone held by hydrogen bonds — α-helix (right-handed coil, 3.6 residues per turn, H-bond between C=O of residue n and N–H of n+4; e.g. keratin) and β-pleated sheet (extended strands side by side, parallel or antiparallel; e.g. silk fibroin); also β-turns and random coils; collagen has a special triple helix.
• Tertiary structure: three-dimensional folding of the whole polypeptide, stabilised by side-chain interactions — hydrophobic interactions, hydrogen bonds, ionic (salt) bridges, van der Waals forces and covalent disulphide bonds; e.g. myoglobin; gives the active site.
• Quaternary structure: association of two or more polypeptide subunits — e.g. haemoglobin (2α + 2β), with cooperative O₂ binding.

Bonds in protein structure: peptide (covalent, primary), disulphide (covalent), hydrogen, ionic, hydrophobic and van der Waals (non-covalent). Denaturation (heat, pH, urea) breaks the non-covalent bonds and destroys function without breaking peptide bonds.

Functions of proteins: enzymes (catalysis), structural (collagen, keratin, elastin), transport (haemoglobin, albumin, membrane carriers), storage (ferritin, casein, ovalbumin), contractile (actin, myosin), hormones (insulin, growth hormone), defence (antibodies, fibrinogen), receptors and signalling, regulation of genes (transcription factors), energy source.

Overview of amino acid metabolism

• Transamination: transfer of the α-amino group from an amino acid to an α-keto acid (usually α-ketoglutarate → glutamate) by aminotransferases (transaminases) with pyridoxal phosphate (vitamin B₆) as coenzyme. E.g. alanine + α-ketoglutarate ⇌ pyruvate + glutamate (ALT/SGPT); aspartate + α-KG ⇌ oxaloacetate + glutamate (AST/SGOT). Serum ALT and AST rise in liver/heart damage.
• Deamination: removal of the amino group as ammonia — oxidative deamination of glutamate by glutamate dehydrogenase (NAD⁺) in mitochondria of liver: glutamate → α-ketoglutarate + NH₃. The carbon skeletons enter glycolysis/Krebs cycle (glucogenic or ketogenic amino acids).
• Ammonia transport: ammonia is toxic (especially to the brain), so it is carried as glutamine (from most tissues, by glutamine synthetase) and as alanine from muscle (glucose–alanine cycle) to the liver.
• Urea cycle (Krebs–Henseleit cycle, liver, partly mitochondrial and partly cytosolic): NH₃ + CO₂ → carbamoyl phosphate (carbamoyl phosphate synthetase I, 2 ATP) → + ornithine → citrulline → + aspartate → argininosuccinate → arginine + fumarate → arginine is split by arginase into urea + ornithine. Uses about 3 ATP (4 high-energy bonds) per urea. Animals excreting urea are ureotelic (mammals, amphibians); fish are mostly ammonotelic; birds and reptiles uricotelic.

Enzymes and enzyme kinetics

Enzymes are biological catalysts, mostly proteins (some RNA — ribozymes), that speed up reactions by lowering the activation energy without being consumed; highly specific; work under mild conditions; regulated. Many need cofactors — metal ions or organic coenzymes (NAD⁺, FAD, CoA); protein part = apoenzyme, complete enzyme = holoenzyme.

Classification (IUBMB/Enzyme Commission, 7 classes, each with an EC number): 1 Oxidoreductases (dehydrogenases), 2 Transferases (kinases, transaminases), 3 Hydrolases (amylase, lipase, proteases), 4 Lyases (aldolase, decarboxylases), 5 Isomerases (phosphohexose isomerase), 6 Ligases/synthetases (DNA ligase), 7 Translocases (membrane transport, added 2018). Names usually end in "-ase" and indicate substrate and reaction.

Active site and enzyme–substrate complex: the active site is a small cleft with binding and catalytic residues; E + S ⇌ ES → E + P.

• Lock-and-key model (Emil Fischer, 1894): active site has a rigid shape exactly complementary to the substrate — explains specificity.
• Induced-fit model (Koshland, 1958): the active site is flexible; substrate binding induces a change in enzyme shape for a tighter fit — explains broader specificity and allosteric effects.

Kinetics: at low [S] the rate rises almost linearly; at high [S] it reaches a maximum (V_max) as all enzyme is saturated (hyperbolic curve). Michaelis–Menten equation: v = V_max[S]/(K_m + [S]). K_m (Michaelis constant) = substrate concentration at which v = ½V_max; a low K_m means high affinity of the enzyme for the substrate. The Lineweaver–Burk (double reciprocal) plot 1/v vs 1/[S] gives a straight line: intercept 1/V_max on y-axis and −1/K_m on x-axis.

Example: if K_m = 2 mM and [S] = 2 mM, v = V_max × 2/(2 + 2) = 0.5 V_max; at [S] = 18 mM, v = 18/20 = 0.9 V_max.

Enzyme inhibition:

Factors affecting enzyme activity: temperature — rate rises to an optimum (about 37 °C for human enzymes), then falls due to denaturation; pH — each enzyme has an optimum (pepsin about 2, salivary amylase about 6.8, trypsin about 8); enzyme concentration — rate proportional to [E] when substrate is in excess; substrate concentration — hyperbolic saturation curve; also activators, inhibitors and product concentration.

Likely exam questions

1. (Long, 8 marks) Describe the levels of protein organisation and the bonds involved.
2. (Long, 8 marks) Explain the mechanism of enzyme action and Michaelis–Menten kinetics. Describe the types of enzyme inhibition.
3. (Short, 4 marks) What is a zwitterion? Define isoelectric point.
4. (Short, 4 marks) Write a note on the urea cycle.
5. (Short, 4 marks) Explain transamination with an example.

Syllabus topics (RTMNU)

• Classification and biological importance of lipids: simple, compound and derived lipids; structure and functions of fatty acids, triglycerides, phospholipids and steroids; roles in energy storage and membrane structure
• Fatty acids and storage lipids: saturated and unsaturated fatty acids; triacylglycerols as energy reserves; essential fatty acids
• Lipid metabolism (overview): digestion, absorption and transport of lipids; activation and transport of fatty acids; β-oxidation (basic concept)
• Lipids in biological regulation: lipids as signalling molecules and membrane components; cholesterol and its physiological significance

Classification and biological importance of lipids

Lipids are a varied group of organic compounds insoluble in water but soluble in non-polar solvents (ether, chloroform, benzene), mostly esters of fatty acids or substances able to form such esters (Bloor's classification).

• Simple lipids: esters of fatty acids with alcohols — fats and oils (triacylglycerols, with glycerol) and waxes (with long-chain alcohols, e.g. beeswax, cerumen).
• Compound (conjugated) lipids: fatty acid esters with an extra group — phospholipids (glycerophospholipids such as lecithin/phosphatidylcholine, cephalin; sphingomyelin), glycolipids (cerebrosides, gangliosides), lipoproteins (chylomicrons, VLDL, LDL, HDL).
• Derived lipids: products of hydrolysis — fatty acids, glycerol, steroids (cholesterol, bile acids, steroid hormones, vitamin D), fat-soluble vitamins (A, D, E, K), ketone bodies, eicosanoids.

Structures in brief: fatty acid — long hydrocarbon chain with a terminal –COOH; triglyceride — glycerol esterified with three fatty acids; phospholipid — glycerol + 2 fatty acids (hydrophobic tails) + phosphate and a polar head (choline, ethanolamine, serine) — amphipathic; steroid — four fused rings (cyclopentanoperhydrophenanthrene nucleus).

Biological roles: most concentrated energy store (about 9 kcal/g vs 4 kcal/g for carbohydrates and proteins); insulation and protection of organs (adipose tissue); membrane structure (phospholipid bilayer, cholesterol, glycolipids); precursors of hormones and vitamins; signalling; myelin sheath; carry fat-soluble vitamins; waterproofing (waxes).

Fatty acids and storage lipids

• Saturated fatty acids: no C=C double bonds; straight chains pack closely; solid at room temperature — palmitic (C16:0), stearic (C18:0); abundant in animal fats, ghee, coconut oil.
• Unsaturated fatty acids: one (monounsaturated — oleic C18:1) or more (polyunsaturated — linoleic C18:2, α-linolenic C18:3, arachidonic C20:4) double bonds, usually cis, producing kinks; liquid oils (vegetable and fish oils). Trans fats (from partial hydrogenation, vanaspati) raise heart disease risk. Nomenclature: ω-3 and ω-6 families by the position of the first double bond from the methyl end.
• Triacylglycerols (TAGs): neutral fats stored in adipocytes as large droplets; anhydrous and highly reduced, so they store about six times more energy per gram of tissue than hydrated glycogen; hydrolysed by lipases to fatty acids and glycerol when energy is needed; also thermal insulation (blubber) and buoyancy.
• Essential fatty acids (EFAs): polyunsaturated fatty acids that mammals cannot synthesise (lack desaturases beyond C-9) and must take in food — linoleic acid (ω-6) and α-linolenic acid (ω-3); arachidonic acid becomes essential if linoleic is deficient. Sources: vegetable oils, nuts, flaxseed, fish. Roles: membrane fluidity, precursors of eicosanoids, brain and retina (DHA). Deficiency: scaly dermatitis, poor growth, poor wound healing.

Lipid metabolism — overview

• Digestion: mainly in the small intestine; bile salts emulsify fats into small droplets; pancreatic lipase (with colipase) hydrolyses TAG to 2-monoacylglycerol and free fatty acids; phospholipase A₂ and cholesterol esterase act on other lipids.
• Absorption: products form mixed micelles with bile salts that carry them to the enterocyte surface; inside the cells TAGs are re-synthesised and packed with cholesterol, phospholipids and apoproteins into chylomicrons, which enter lymph (lacteals) and then blood. Short-chain fatty acids go directly into portal blood.
• Transport: as lipoproteins — chylomicrons (dietary TAG to tissues), VLDL (liver-made TAG), LDL ("bad cholesterol" — carries cholesterol to tissues), HDL ("good cholesterol" — reverse cholesterol transport to liver); free fatty acids travel bound to albumin. Lipoprotein lipase on capillary walls releases fatty acids for uptake.
• Activation and transport of fatty acids: in the cytosol fatty acids are activated to fatty acyl-CoA by acyl-CoA synthetase (thiokinase) using ATP (→ AMP + PPi). Long-chain acyl-CoA cannot cross the inner mitochondrial membrane, so the acyl group is transferred to carnitine (carnitine acyltransferase/CPT-I), carried across by a translocase and transferred back to CoA inside (CPT-II) — the carnitine shuttle.
• β-oxidation (mitochondrial matrix; Knoop): repeating cycle of four steps — oxidation (FAD → FADH₂), hydration, oxidation (NAD⁺ → NADH), thiolysis — each removing a two-carbon unit as acetyl-CoA from the carboxyl end (β-carbon is oxidised). Palmitate (C16) undergoes 7 cycles giving 8 acetyl-CoA, 7 FADH₂ and 7 NADH, which yield about 106 ATP net (older books 129). Acetyl-CoA enters the Krebs cycle or forms ketone bodies in the liver during fasting.

Lipids in biological regulation

• Membrane components: phospholipid bilayer (fluid mosaic model, Singer and Nicolson, 1972) with cholesterol (regulates fluidity) and glycolipids (cell recognition); sphingolipids in myelin and lipid rafts.
• Signalling molecules: steroid hormones (cortisol, aldosterone, testosterone, oestrogen, progesterone) act through intracellular receptors to regulate genes; eicosanoids from arachidonic acid — prostaglandins (inflammation, pain, fever, uterine contraction), thromboxanes (platelet aggregation), leukotrienes (bronchoconstriction, allergy); membrane-derived second messengers — IP₃ and DAG from PIP₂ (phospholipase C), sphingosine-1-phosphate; platelet-activating factor; vitamin D (calcitriol) regulates calcium; fat-soluble vitamins; juvenile hormone and ecdysone in insects.
• Cholesterol: a 27-carbon sterol with a hydroxyl group, a steroid nucleus and a hydrocarbon side chain; made mainly in the liver from acetyl-CoA (rate-limiting enzyme HMG-CoA reductase, inhibited by statins) and taken in from animal foods. Significance: component of animal cell membranes, precursor of bile acids (fat digestion), steroid hormones and vitamin D₃; carried by LDL and HDL. Normal total blood cholesterol is commonly given as below 200 mg/dL. High LDL cholesterol deposits in artery walls → atherosclerosis, coronary heart disease and stroke; gallstones.

Likely exam questions

1. (Long, 8 marks) Classify lipids with examples and describe their biological importance.
2. (Long, 8 marks) Describe the digestion, absorption and transport of lipids. Give the basic concept of β-oxidation of fatty acids.
3. (Short, 4 marks) What are essential fatty acids?
4. (Short, 4 marks) Write the physiological significance of cholesterol.
5. (Short, 4 marks) Distinguish between saturated and unsaturated fatty acids.

Syllabus topics (RTMNU)

• Structure and functions of nucleic acids: DNA and RNA; types of RNA (mRNA, tRNA, rRNA) and their roles
• Introduction to bioenergetics: thermodynamics in biological systems; Gibbs free energy change and its significance; redox reactions in metabolism
• ATP and high-energy compounds: structure and role of ATP; ATP synthesis and hydrolysis; high-energy phosphate bonds
• Oxidative phosphorylation and electron transport chain (overview): organisation of ETC in mitochondria; chemiosmotic hypothesis and ATP synthase; inhibitors of electron transport

Structure and functions of nucleic acids

Nucleic acids are polymers of nucleotides; each nucleotide = nitrogenous base + pentose sugar + phosphate (nucleoside = base + sugar). Bases: purines (adenine, guanine) and pyrimidines (cytosine, thymine in DNA, uracil in RNA). Nucleotides are joined by 3′,5′-phosphodiester bonds, giving a sugar–phosphate backbone with 5′ and 3′ ends.

DNA (deoxyribonucleic acid): Watson–Crick double helix (1953) — two antiparallel strands coiled right-handedly; bases inside paired by hydrogen bonds (A=T two, G≡C three) — complementary; diameter 2 nm, one turn 3.4 nm with about 10 bp; major and minor grooves; Chargaff's rule A + G = T + C. Functions: stores genetic information, replicates for inheritance, directs protein synthesis via transcription, undergoes mutation and recombination (variation and evolution).

RNA (ribonucleic acid): usually single-stranded, contains ribose and uracil, folds into hairpins; less stable than DNA.

Other RNAs: snRNA (splicing), miRNA and siRNA (gene silencing), viral RNA genomes.

Introduction to bioenergetics

Bioenergetics is the study of energy transformations in living systems. Living cells are open systems that exchange energy and matter with surroundings.

• First law of thermodynamics: energy can neither be created nor destroyed, only converted (e.g. light → chemical energy in photosynthesis; chemical → mechanical in muscle).
• Second law: every spontaneous process increases the entropy (disorder) of the universe; living organisms maintain order by taking in free energy and releasing heat and simple molecules.
• Gibbs free energy (G): the energy available to do useful work at constant temperature and pressure: ΔG = ΔH − TΔS. If ΔG < 0 the reaction is exergonic and spontaneous; ΔG > 0 endergonic (needs energy input); ΔG = 0 at equilibrium. Standard free energy change ΔG°′ (pH 7) is related to the equilibrium constant: ΔG°′ = −RT ln K′_eq. ΔG says whether a reaction can occur, not how fast (rate depends on enzymes).
• Coupling: endergonic reactions are driven by coupling with exergonic ones (usually ATP hydrolysis), since free energy changes are additive — e.g. glucose + Pi → glucose-6-P (+13.8 kJ/mol) coupled with ATP → ADP + Pi (−30.5 kJ/mol) gives net −16.7 kJ/mol.
• Redox reactions: oxidation = loss of electrons (or hydrogen), reduction = gain; they occur together. Tendency to accept electrons is given by the standard reduction potential E°′; electrons flow from lower (more negative, e.g. NAD⁺/NADH −0.32 V) to higher potential (O₂/H₂O +0.82 V). ΔG°′ = −nFΔE°′. In metabolism fuels are oxidised and electrons are carried by NAD⁺, NADP⁺ and FAD to the electron transport chain, releasing energy for ATP synthesis.

ATP and high-energy compounds

ATP (adenosine triphosphate) = adenine + ribose + three phosphate groups (α, β, γ) linked by one phosphoester and two phosphoanhydride bonds. It is the energy currency of the cell — formed in energy-yielding reactions and used for muscle contraction, active transport (Na⁺/K⁺ pump), biosynthesis, nerve impulses and signalling.

• Hydrolysis: ATP + H₂O → ADP + Pi, ΔG°′ = −30.5 kJ/mol (−7.3 kcal/mol); ATP → AMP + PPi, −45.6 kJ/mol. The terminal bonds are called high-energy bonds (written ~P) — not because the bond itself is unusually strong, but because hydrolysis releases much free energy owing to relief of charge repulsion between phosphates, resonance stabilisation and better solvation of products.
• Synthesis: (1) substrate-level phosphorylation — direct transfer of phosphate from a high-energy substrate (1,3-bisphosphoglycerate, phosphoenolpyruvate in glycolysis; succinyl-CoA in Krebs cycle); (2) oxidative phosphorylation in mitochondria (most ATP); (3) photophosphorylation in chloroplasts.
• Other high-energy compounds (ΔG°′ of hydrolysis more negative than about −25 kJ/mol): phosphoenolpyruvate (−61.9), 1,3-bisphosphoglycerate (−49.4), creatine phosphate (−43.0; energy reserve in vertebrate muscle; arginine phosphate in invertebrates), acetyl-CoA and other thioesters (−31.4), GTP, UTP, CTP. Low-energy phosphates: glucose-6-phosphate (−13.8), glycerol-3-phosphate. ATP is intermediate in this scale, so it can accept phosphate from higher compounds and donate it to lower ones.

Oxidative phosphorylation and electron transport chain (overview)

Electron transport chain (ETC) — located in the inner mitochondrial membrane (cristae). NADH and FADH₂ from glycolysis, link reaction, Krebs cycle and β-oxidation pass electrons through a series of carriers of increasing redox potential to oxygen:

1. Complex I (NADH–CoQ reductase, NADH dehydrogenase with FMN and Fe–S) — accepts electrons from NADH; pumps 4 H⁺.
2. Complex II (succinate dehydrogenase, FAD) — passes electrons from FADH₂/succinate to CoQ; pumps no protons.
3. Coenzyme Q (ubiquinone) — mobile lipid-soluble carrier.
4. Complex III (cytochrome bc₁) — CoQH₂ → cytochrome c; pumps 4 H⁺ (Q cycle).
5. Cytochrome c — mobile protein carrier in the intermembrane space.
6. Complex IV (cytochrome c oxidase, cytochromes a and a₃, Cu) — transfers electrons to O₂, forming H₂O; pumps 2 H⁺.

Chemiosmotic hypothesis (Peter Mitchell, 1961; Nobel 1978): the energy of electron flow pumps protons from the matrix to the intermembrane space, creating a proton-motive force (pH gradient + membrane potential). Protons flow back into the matrix through ATP synthase (Complex V, F₀F₁-ATPase): F₀ is the membrane proton channel (rotor) and F₁ the catalytic knob that makes ATP from ADP + Pi by rotational catalysis (Boyer's binding-change mechanism). About 2.5 ATP are made per NADH and 1.5 per FADH₂ (older values 3 and 2).

Inhibitors of electron transport and oxidative phosphorylation (overview): Complex I — rotenone (fish poison/insecticide), amytal (barbiturate); Complex III — antimycin A; Complex IV — cyanide, carbon monoxide, azide, H₂S (block electron transfer to O₂, causing rapid death); ATP synthase — oligomycin; uncouplers — 2,4-dinitrophenol and thermogenin (UCP-1 of brown fat) let protons leak back without making ATP, so energy is released as heat (non-shivering thermogenesis in hibernating animals and newborns).

Likely exam questions

1. (Long, 8 marks) Describe the organisation of the electron transport chain and explain the chemiosmotic hypothesis of ATP synthesis.
2. (Long, 8 marks) Describe the structure and functions of DNA and the types of RNA.
3. (Short, 4 marks) Explain the concept of Gibbs free energy change in biological reactions.
4. (Short, 4 marks) Why is ATP called the energy currency of the cell?
5. (Short, 4 marks) Name the inhibitors of the electron transport chain and their sites of action.