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Cell Biology Unit 4: Energy, Mitochondria and Chloroplasts

This unit explains how cells capture energy: mitochondria oxidize fuels to build a proton gradient that makes ATP, and chloroplasts use light to do the same while also making NADPH to fix CO₂.

Covers: Free energy, ATP and redox reactions, Mitochondrial structure and the citric acid cycle, Electron transport chain, Chemiosmosis and ATP synthase, Respiratory control, inhibitors and uncouplers, Chloroplast light reactions, Calvin cycle and photorespiration

Study guide

Cells run on free energy. A reaction is favorable when ΔG is negative, and ΔG = ΔG°' + RT ln Q, so concentrations matter. ATP hydrolysis has ΔG°' of about −30.5 kJ/mol, but because cells keep ATP high and ADP low, the real ΔG is near −50 kJ/mol. Fuel oxidation is a series of redox reactions: electrons move from donors with low (negative) reduction potential to acceptors with higher potential, and ΔG°' = −nFΔE°'. NADH has E°' ≈ −0.32 V and O₂/H₂O has +0.82 V, so passing two electrons from NADH to O₂ releases about 220 kJ/mol.

Mitochondria have a porous outer membrane, an intermembrane space, a tightly sealed inner membrane folded into cristae, and the matrix. Pyruvate from glycolysis enters the matrix and is converted to acetyl-CoA, which the citric acid cycle oxidizes to CO₂, generating NADH, FADH₂ and GTP. The electron transport chain in the inner membrane passes electrons from NADH to complex I, from FADH₂ (via succinate) to complex II, then to ubiquinone, complex III, cytochrome c and complex IV, which reduces O₂ to water. Complexes I, III and IV pump H⁺ into the intermembrane space.

Mitchell's chemiosmotic theory says the pumped protons form a proton-motive force made of a voltage (matrix negative) and a pH difference (matrix alkaline), together about 200 mV. Protons flow back through ATP synthase, whose F₀ ring rotates and turns a central stalk inside the F₁ head; each turn makes 3 ATP by the binding-change mechanism. Roughly 4 H⁺ are used per ATP including transport, so NADH yields about 2.5 ATP and FADH₂ about 1.5, and a glucose yields about 30 to 32 ATP. Respiration is tightly coupled: blocking ATP synthase (oligomycin) slows electron transport, while uncouplers such as DNP or UCP1 in brown fat let electron transport run fast and release heat.

Chloroplasts have an outer and inner envelope, the fluid stroma, and stacked thylakoid membranes. In the light reactions, photosystem II absorbs light, its P680 passes excited electrons to plastoquinone, and water is split to replace them, releasing O₂. Electrons pass through the cytochrome b₆f complex, which pumps H⁺ into the thylakoid lumen, then to photosystem I (P700), which is re-energized by light and reduces NADP⁺ to NADPH. H⁺ flows from the lumen to the stroma through ATP synthase. Cyclic electron flow around PSI makes extra ATP without NADPH.

The Calvin cycle in the stroma uses ATP and NADPH to fix CO₂. Rubisco attaches CO₂ to ribulose-1,5-bisphosphate, the product splits into 3-phosphoglycerate, which is reduced to glyceraldehyde-3-phosphate, and most G3P is recycled to regenerate RuBP. Each CO₂ costs 3 ATP and 2 NADPH, so a hexose costs 18 ATP and 12 NADPH. Rubisco also reacts with O₂, especially when stomata close on hot, dry days, wasting energy in photorespiration. C₄ and CAM plants avoid this by concentrating CO₂ around rubisco. Mitochondria and chloroplasts share the same logic: electron transport builds a proton gradient that ATP synthase converts to ATP.

Key ideas

• Real ΔG depends on concentrations, which make ATP hydrolysis about −50 kJ/mol in cells.
• Electrons flow from negative to positive reduction potential, releasing energy (ΔG°' = −nFΔE°').
• The electron transport chain pumps H⁺ to create a proton-motive force across the inner membrane.
• ATP synthase is a rotary motor driven by H⁺ flowing back across the membrane.
• Inhibitors and uncouplers reveal that electron transport and ATP synthesis are coupled.
• Photosystems II and I use light to move electrons from water to NADP⁺ while pumping H⁺ into the thylakoid lumen.
• The Calvin cycle uses 3 ATP and 2 NADPH per CO₂, and photorespiration wastes energy when O₂ competes with CO₂.

Formulas and rules

Common mistakes

• Thinking the Krebs cycle runs in the intermembrane space or cytosol; it runs in the matrix.
• Saying mitochondria pump protons into the matrix; they pump them out to the intermembrane space.
• Mixing up uncouplers (electron transport continues, no ATP) with ATP synthase inhibitors (both stop).
• Forgetting that the Calvin cycle needs light-reaction products even though it does not use light directly.
• Using ΔG°' instead of actual ΔG for reactions under cell conditions.

Before the test, make sure you can

• Calculate ΔG from ΔG°' and concentrations, and ΔG°' from ΔE°'.
• Trace electrons from NADH and FADH₂ through the chain to O₂.
• Explain chemiosmosis and the rotary mechanism of ATP synthase.
• Calculate ATP yields per NADH, FADH₂ and glucose.
• Predict the effects of inhibitors and uncouplers on O₂ use and ATP synthesis.
• Describe linear and cyclic electron flow in the light reactions.
• Explain the Calvin cycle's ATP and NADPH costs and why photorespiration occurs.
• Compare proton gradients in mitochondria and chloroplasts.

Words to know

Redox potential (E°')

A measure of how strongly a molecule accepts electrons; electrons flow toward more positive E°'.

Matrix

The innermost mitochondrial compartment containing the citric acid cycle enzymes and mtDNA.

Cristae

Folds of the inner mitochondrial membrane that hold the electron transport chain and ATP synthase.

Ubiquinone

A lipid-soluble electron carrier that shuttles electrons from complexes I and II to complex III.

Cytochrome c

A small soluble protein in the intermembrane space that carries electrons from complex III to complex IV.

Complex IV

Cytochrome c oxidase; transfers electrons to O₂ and pumps H⁺.

Proton-motive force

The combined electrical and pH gradient of H⁺ across a membrane that drives ATP synthesis.

ATP synthase

A rotary enzyme (F₀F₁) that uses H⁺ flow to make ATP from ADP and Pi.

Uncoupler

A substance that lets H⁺ leak across the inner membrane, so electron transport continues without ATP synthesis.

Respiratory control

The dependence of electron transport rate on ADP availability and the proton gradient.

Thylakoid

Flattened membrane sacs in chloroplasts containing the photosystems and ATP synthase.

Photosystem II

Light-driven complex (P680) that splits water, releasing O₂ and passing electrons to plastoquinone.

Photosystem I

Light-driven complex (P700) that passes electrons to ferredoxin and NADP⁺.

Cyclic electron flow

Electron flow from PSI back to cytochrome b₆f that makes ATP but no NADPH.

Rubisco

The Calvin cycle enzyme that fixes CO₂ onto RuBP; also reacts with O₂.

Photorespiration

A wasteful pathway that occurs when rubisco uses O₂ instead of CO₂.

C₄ plants

Plants that first fix CO₂ into four-carbon acids in mesophyll cells to concentrate CO₂ around rubisco.

Sample practice questions

30 more questions like these, from level 1 to 5, are in the practice set.