Unit 4: Metabolism I

Metabolism is the sum of enzyme-catalysed reactions that harvest, store and spend chemical energy. This unit deals with carbohydrate metabolism, organised around the currencies of energy (ATP) and reducing power (NADH, NADPH, FADH₂) and the pathways that generate or consume glucose. All later pathways trade in the properties set out below.

• Catabolism vs anabolism: Catabolism degrades fuels to release energy (glycolysis, glycogen breakdown); anabolism builds molecules and consumes energy (gluconeogenesis, glycogen synthesis).
• Free energy sign: A reaction proceeds when ΔG < 0. Cells couple unfavourable steps to ATP hydrolysis (ΔG°′ ≈ −30.5 kJ·mol⁻¹) to force them forward.
• Reduced carriers: NADH and FADH₂ feed the electron transport chain for ATP synthesis; NADPH supplies reductive biosynthesis. They are kept in separate pools.
• Reciprocal regulation: Opposing pathways (glycolysis/gluconeogenesis, glycogen synthesis/breakdown) are controlled so both are never fully active at once, avoiding futile cycles.
• Compartmentation: Glycolysis, fermentation and the pentose phosphate pathway occur in the cytosol; gluconeogenesis begins in the mitochondrion and finishes in the cytosol.

II. ATP and Electron Carriers — the energy and redox currencies

Energy metabolism moves phosphoryl groups and electrons between a small set of recyclable carriers rather than storing energy in bulk.

A. ATP as phosphoryl donor

• Structure: Adenine + ribose + three phosphates linked by two phosphoanhydride bonds.
• High transfer potential: Hydrolysis of the terminal bond is favourable because of charge repulsion relief, resonance stabilisation of Pᵢ, and greater solvation of products.
• Coupling equation:
  
  TEXT

  ATP + H₂O → ADP + Pᵢ      ΔG°′ = −30.5 kJ·mol⁻¹

• Cellular ΔG: In vivo ΔG is nearer −50 kJ·mol⁻¹ because [ATP]/[ADP][Pᵢ] is far from equilibrium.

B. NAD⁺/NADH and FAD/FADH₂ — catabolic carriers

• NAD⁺ reduction: Accepts a hydride (2e⁻ + 1H⁺) at C4 of the nicotinamide ring: NAD⁺ + 2H → NADH + H⁺.
• FAD reduction: Accepts two hydrogen atoms to give FADH₂; tightly bound to its enzyme as a prosthetic group.
• Yield on oxidation: Each NADH yields ≈ 2.5 ATP and each FADH₂ ≈ 1.5 ATP via oxidative phosphorylation.

C. NADPH — the anabolic carrier

• Same reaction, different role: Differs from NADH only by a 2′-phosphate on the adenine ribose, which enzymes read to distinguish the two pools.
• Function: Donor of reducing power for fatty-acid and nucleotide synthesis; supplied largely by the pentose phosphate pathway.

III. Glycolysis — splitting glucose to pyruvate

Glycolysis oxidises one glucose to two pyruvate in ten cytosolic steps, netting ATP and NADH without oxygen.

A. Overall reaction and stages

• Net equation:
  
  TEXT

  Glucose + 2 NAD⁺ + 2 ADP + 2 Pᵢ →
  2 Pyruvate + 2 NADH + 2 H⁺ + 2 ATP + 2 H₂O

• Investment phase (steps 1–5): Spends 2 ATP to phosphorylate and cleave glucose into two glyceraldehyde-3-phosphate.
• Payoff phase (steps 6–10): Produces 4 ATP and 2 NADH, giving the net yield of 2 ATP.

B. Key regulated steps

• Hexokinase (step 1): Glucose + ATP → glucose-6-phosphate; traps glucose in the cell; inhibited by its product G6P.
• Phosphofructokinase-1 (step 3): Fructose-6-P + ATP → fructose-1,6-bisphosphate; the committed, rate-limiting step; activated by AMP and fructose-2,6-bisphosphate, inhibited by ATP and citrate.
• Pyruvate kinase (step 10): PEP + ADP → pyruvate + ATP; substrate-level phosphorylation; activated by fructose-1,6-bisphosphate (feed-forward).

C. Substrate-level phosphorylation and NADH balance

• GAPDH (step 6): Oxidises glyceraldehyde-3-P to 1,3-bisphosphoglycerate, reducing NAD⁺ to NADH and inserting Pᵢ.
• Regeneration need: The NAD⁺ used at step 6 must be regenerated (by respiration or fermentation) or glycolysis halts.

IV. Fermentation — regenerating NAD⁺ anaerobically

Fermentation reoxidises glycolytic NADH so glycolysis continues when oxygen is unavailable, producing no extra ATP itself.

A. The two main routes

1. Lactate fermentation: In muscle and lactic-acid bacteria.
   
   TEXT

      Pyruvate + NADH + H⁺ → Lactate + NAD⁺   (lactate dehydrogenase)

2. Alcoholic fermentation: In yeast, two steps.
   
   TEXT

      Pyruvate → Acetaldehyde + CO₂          (pyruvate decarboxylase)
      Acetaldehyde + NADH + H⁺ → Ethanol + NAD⁺ (alcohol dehydrogenase)

B. Significance and limits

• Redox purpose: Both routes restore NAD⁺; the net ATP yield stays at 2 per glucose.
• Cori cycle: Muscle lactate travels to the liver, is reconverted to glucose by gluconeogenesis, and returns—shifting the energy cost to the liver.

V. Gluconeogenesis — synthesising glucose from non-carbohydrates

Gluconeogenesis builds glucose from pyruvate, lactate, glycerol and glucogenic amino acids, mostly in liver, to maintain blood glucose during fasting.

A. Relationship to glycolysis

• Not simple reversal: Seven glycolytic steps are reversible and shared, but the three irreversible steps are bypassed by distinct enzymes.
• Energy cost: Making one glucose consumes 4 ATP + 2 GTP + 2 NADH, versus the 2 ATP glycolysis yields.

B. The three bypass reactions

• Pyruvate → PEP: Two steps via pyruvate carboxylase (needs biotin, ATP, makes oxaloacetate) then PEP carboxykinase (uses GTP, releases CO₂).
• Fructose-1,6-bisphosphate → Fructose-6-P: Fructose-1,6-bisphosphatase removes Pᵢ; opposes PFK-1.
• Glucose-6-P → Glucose: Glucose-6-phosphatase in the ER lumen; present only in liver and kidney, so only they export free glucose.

C. Reciprocal regulation with glycolysis

• Fructose-2,6-bisphosphate: Activates PFK-1 and inhibits fructose-1,6-bisphosphatase, so high levels favour glycolysis and low levels favour gluconeogenesis.
• Hormonal control: Glucagon lowers fructose-2,6-bisphosphate, promoting glucose synthesis; insulin does the reverse.

VI. Pentose Phosphate Pathway — NADPH and pentose supply

The pentose phosphate pathway diverts glucose-6-phosphate to make NADPH and ribose-5-phosphate rather than ATP, operating entirely in the cytosol.

A. Oxidative phase

• Committed step: Glucose-6-P dehydrogenase (G6PD) oxidises G6P, generating the first NADPH; rate-limiting and inhibited by NADPH.
• Products: Two NADPH and one CO₂ per G6P, yielding ribulose-5-phosphate.
  
  TEXT

  Glucose-6-P + 2 NADP⁺ + H₂O →
  Ribulose-5-P + 2 NADPH + 2 H⁺ + CO₂

B. Non-oxidative phase

• Reversible interconversions: Transketolase (moves 2-carbon units, needs thiamine pyrophosphate) and transaldolase (moves 3-carbon units) interconvert 3-, 4-, 5-, 6- and 7-carbon sugars.
• Flexibility: Lets the cell balance ribose-5-phosphate for nucleotides against fructose-6-P and glyceraldehyde-3-P that re-enter glycolysis.

C. Physiological role

• NADPH uses: Reductive biosynthesis and defence against oxidative stress via glutathione; G6PD deficiency causes red-cell haemolysis.
• Ribose-5-phosphate: Precursor for DNA, RNA, ATP, NAD⁺ and coenzyme A.

VII. Glycogen Breakdown — glycogenolysis

Glycogenolysis releases glucose units from stored glycogen to fuel muscle contraction or restore blood glucose.

A. Phosphorolytic cleavage

• Glycogen phosphorylase: Cleaves α-1,4 bonds using Pᵢ (not water), releasing glucose-1-phosphate; needs pyridoxal phosphate.
  
  TEXT

  Glycogen(n) + Pᵢ → Glycogen(n−1) + Glucose-1-P

• Energy saving: Phosphorolysis yields an already-phosphorylated sugar, avoiding an ATP cost.

B. Debranching and entry to metabolism

• Debranching enzyme: Transfers a trisaccharide across and hydrolyses the α-1,6 branch, giving free glucose.
• Phosphoglucomutase: Converts glucose-1-P to glucose-6-P, which enters glycolysis (muscle) or is dephosphorylated for export (liver).

C. Regulation

• Covalent control: Phosphorylase is activated by phosphorylation (phosphorylase kinase, driven by glucagon/adrenaline via cAMP–PKA).
• Allosteric control: Muscle enzyme is activated by AMP and inhibited by ATP and glucose-6-P, linking breakdown to energy charge.

VIII. Glycogen Synthesis — glycogenesis

Glycogenesis stores excess glucose as branched glycogen when energy and glucose are abundant.

A. Activation and chain extension

• UDP-glucose formation: Glucose-1-P + UTP → UDP-glucose + PPᵢ (UDP-glucose pyrophosphorylase); PPᵢ hydrolysis makes it irreversible.
• Glycogen synthase: Adds UDP-glucose to a growing chain via α-1,4 bonds; the rate-limiting enzyme; requires a glycogenin primer.

B. Branching

• Branching enzyme: Transfers a ≈7-residue segment to form α-1,6 branches every 8–12 residues, increasing solubility and the number of non-reducing ends for rapid mobilisation.

C. Reciprocal regulation with breakdown

• Covalent control: Glycogen synthase is inactivated by phosphorylation and activated by dephosphorylation—the opposite pattern to phosphorylase.
• Hormonal integration: Insulin activates protein phosphatase-1, dephosphorylating both enzymes to switch on synthesis and switch off breakdown; glucagon and adrenaline reverse this, ensuring the two pathways never run simultaneously.