Metabolism, Cell Respiration and Photosynthesis — IB Biology HL Study Guide (HL Extension)

For: IB Biology HL candidates sitting IB Biology HL.

Covers: IB Topic 8 (HL only) — enzyme regulation by allosteric effectors, full mechanism of cell respiration (glycolysis, link reaction, Krebs cycle, ETC, chemiosmosis with ATP synthase), full mechanism of photosynthesis (light-dependent reactions, Calvin cycle), comparison.

You should already know: Cell biology (Topic 1), molecular biology (Topic 2), basic respiration & photosynthesis (SL).

A note on the practice questions: All worked questions in the "Practice Questions" section below are original problems written by us in the IB Biology HL style for educational use. They are not reproductions of past IBO papers.

1. Why Metabolism Matters in HL

Topic 8 is the molecular machinery behind life's two energy-handling pathways. About 6-9% of HL Paper 1+2 directly. The exam expects detailed knowledge of enzyme names, intermediates, and the location of each step (cytoplasm vs mitochondrial matrix vs cristae vs chloroplast stroma vs thylakoid).

2. Enzyme regulation

Competitive inhibition: inhibitor mimics substrate, competes for active site. Effect overcome by raising [substrate].

Non-competitive inhibition: inhibitor binds elsewhere (allosteric site), changes enzyme shape. Cannot be overcome by raising [substrate].

Allosteric regulation: regulator binds allosteric site → enzyme shape changes → activity altered. Allows complex feedback (end-product inhibits an early enzyme — homeostasis).

End-product inhibition: in a metabolic chain $A\to B\to C\to D$, the final product $D$ inhibits the enzyme catalysing the first step. Stops production once enough $D$ is made.

3. Cell respiration overview

Glucose + 6 O₂ → 6 CO₂ + 6 H₂O + ~30-32 ATP (cellular yield, not theoretical 38).

Four stages:

1. Glycolysis (cytoplasm): glucose → 2 pyruvate. Net: 2 ATP, 2 NADH.
2. Link reaction (mitochondrial matrix): pyruvate → acetyl-CoA + CO₂ + NADH.
3. Krebs cycle (matrix): acetyl-CoA + oxaloacetate → citrate → ... → oxaloacetate. Per acetyl-CoA: 1 ATP, 3 NADH, 1 FADH₂, 2 CO₂.
4. Electron transport chain (ETC) + chemiosmosis (inner membrane): NADH/FADH₂ donate electrons → pumping H⁺ into intermembrane space → H⁺ flows back through ATP synthase → ATP made.

4. Glycolysis details

10 enzymatic steps. Key features:

• Phosphorylation: 2 ATP used in early steps to "energize" glucose.
• Substrate-level phosphorylation: 4 ATP made directly. Net 2 ATP.
• 2 NAD⁺ reduced to NADH.

Endpoint: 2 pyruvate (3-carbon) per glucose (6-carbon).

If oxygen absent → fermentation (anaerobic): pyruvate → lactate (animals) or ethanol + CO₂ (yeast). NAD⁺ regenerated to keep glycolysis going.

5. Krebs cycle details

Each acetyl-CoA enters; passes through 8 steps regenerating oxaloacetate. Per turn:

• 3 NADH (from isocitrate, α-ketoglutarate, malate dehydrogenases).
• 1 FADH₂ (from succinate dehydrogenase, embedded in inner membrane).
• 1 ATP (substrate-level phosphorylation).
• 2 CO₂.

Per glucose (2 turns): 6 NADH, 2 FADH₂, 2 ATP, 4 CO₂.

6. Electron transport + chemiosmosis

NADH and FADH₂ are oxidised, donating electrons to a chain of carriers (cytochromes) in the inner mitochondrial membrane. Energy released pumps H⁺ from matrix to intermembrane space → proton gradient.

H⁺ flows back through ATP synthase (a rotary motor) → ATP made from ADP + Pi.

Final electron acceptor: O₂ + 4 H⁺ + 4 e⁻ → 2 H₂O.

Per NADH ≈ 2.5 ATP (3 H⁺ pumped sites). Per FADH₂ ≈ 1.5 ATP (2 sites — FADH₂ enters at site 2).

Total per glucose: ~30-32 ATP (varies by organism and shuttle).

7. Photosynthesis overview

6 CO₂ + 6 H₂O + light → C₆H₁₂O₆ + 6 O₂ (net).

Two stages in chloroplasts:

1. Light-dependent reactions (thylakoid membrane): light → split H₂O → produce ATP + NADPH + O₂.
2. Light-independent reactions / Calvin cycle (stroma): use ATP + NADPH to fix CO₂ into glucose.

8. Light-dependent reactions

Photosystem II (PSII) absorbs light → e⁻ excited → energy used to pump H⁺ into thylakoid lumen → H⁺ flows back through ATP synthase → ATP.

Excited e⁻ from PSII passes through plastoquinone, cytochrome complex, plastocyanin, reaching PSI. H₂O is split to replace e⁻ in PSII: 2 H₂O → 4 H⁺ + 4 e⁻ + O₂.

PSI absorbs light → e⁻ excited again → reduces NADP⁺ to NADPH.

Net products: ATP + NADPH (used in dark stage) + O₂ (released).

9. Calvin cycle (light-independent)

Three phases per turn:

1. Carbon fixation: enzyme RuBisCO attaches CO₂ to RuBP (5C) → 2 × 3-PGA (3C).
2. Reduction: ATP and NADPH reduce 3-PGA → G3P (3C).
3. Regeneration: most G3P used to regenerate RuBP (using ATP). 1 in every 6 G3P leaves as net product.

Per glucose: 6 turns of cycle, using 18 ATP + 12 NADPH.

10. Worked Example

A plant in a sealed chamber begins photosynthesising at dawn.

(a) Why does the O₂ concentration in the chamber rise? (b) Where does the O₂ come from molecularly? (c) If a chemical blocks H⁺ flow back through ATP synthase, what happens to ATP, NADPH, and O₂ production?

Solution.

(a) Photosynthesis splits water and releases O₂; net O₂ production exceeds consumption by respiration.

(b) From water, not from CO₂. PSII splits H₂O to extract electrons; O₂ is the byproduct.

(c) ATP production stops (no chemiosmotic ATP synthesis). H⁺ accumulates in lumen → gradient stops being dissipated → eventually e⁻ flow stops → NADPH production stops. O₂ production also stops since e⁻ can't flow from PSII. All three drop to zero.

11. Common Pitfalls

• Glycolysis location: cytoplasm. Krebs: matrix. ETC: inner membrane. Calvin: stroma. Light-dependent: thylakoid. AP graders test exact location.
• NADPH vs NADH: NADPH is for biosynthesis (Calvin); NADH is for energy harvesting (respiration). Different molecules.
• RuBisCO: most abundant enzyme on Earth; very slow but irreplaceable.
• Net ATP from glucose: ~30-32, NOT 38. Older textbooks have older estimates.

12. Practice Questions

1. List in order the molecules through which an electron from glucose travels to reach the final O₂.
2. A plant deprived of CO₂ but exposed to light. What will accumulate in the chloroplast and why?
3. Compare and contrast oxidative phosphorylation with photophosphorylation in chemical mechanism (chemiosmosis).

13. Quick Reference Cheatsheet

• Glycolysis: cytoplasm, glucose → 2 pyruvate, 2 ATP + 2 NADH net.
• Krebs: matrix, acetyl-CoA → CO₂. Per glucose: 6 NADH, 2 FADH₂, 2 ATP.
• ETC + chemiosmosis: inner membrane. ~30-32 ATP per glucose.
• O₂ in: respiration (final acceptor). O₂ out: photosynthesis (from H₂O split).
• Light-dependent: thylakoid, makes ATP + NADPH + O₂.
• Calvin: stroma, 18 ATP + 12 NADPH per glucose.
• RuBisCO: fixes CO₂ to RuBP.

14. What's Next

Topic 8 connects with Topic 11 (Animal Phys) for muscle metabolism and Topic 9 (Plant Bio) for plant transport relating to photosynthesis. Use Ollie for any specific pathway question or step-by-step ATP yield calculation.