Unit 3: Photosynthesis and Respiration

1. Photosynthetic pigments

Photosynthesis begins with light capture, not with carbon fixation. A pigment absorbs a photon and is raised to an excited state; that excitation energy is then transferred from molecule to molecule until it reaches the reaction centre. No pigment works alone: pigments are organised in light-harvesting complexes (LHC) embedded in the thylakoid membrane, so that hundreds of pigment molecules funnel energy to one reaction centre.

Chlorophyll a and chlorophyll b

Chlorophyll a (Chl a) absorbs strongly in the blue-violet region (around 430 nm) and in the red region (around 660–680 nm), and reflects green — which is why leaves look green. Chlorophyll b absorbs at slightly shifted wavelengths (around 453 nm in the blue and 642 nm in the red). The structural difference is small — chlorophyll b has a formyl group (–CHO) where chlorophyll a has a methyl group (–CH₃) on the porphyrin ring — but the absorption shift matters: together, a and b cover a wider range of wavelengths than either alone.

The decisive distinction is functional, not just spectral. Only chlorophyll a acts as the primary electron donor in the reaction centre. In Photosystem II the reaction-centre chlorophyll a is P680; in Photosystem I it is P700 (see Section 2). Chlorophyll b is never the reaction-centre pigment: it only harvests light and transfers excitation energy to chlorophyll a. An exam answer that calls chlorophyll b the primary donor is wrong — this is one of the traps in the Exam traps box below.

Carotenoids: carotene and xanthophylls

Carotenoids are yellow, orange and red pigments with a long conjugated chain of double bonds. They fall into two groups. Carotenes are pure hydrocarbons (for example, beta-carotene); xanthophylls are oxygenated carotenoids (for example, lutein, violaxanthin, zeaxanthin). Their roles are threefold:

• Accessory light harvesting: they absorb blue-green light (around 400–500 nm), wavelengths chlorophyll absorbs poorly, and transfer that energy to chlorophyll a.
• Photoprotection: they quench excess excitation energy and scavenge singlet oxygen and other reactive species, protecting chlorophyll from photo-oxidation in bright light. The xanthophyll cycle (violaxanthin to zeaxanthin) dissipates excess energy as heat.
• Structural role: they stabilise pigment–protein complexes in the thylakoid membrane.

In short: chlorophyll a does the chemistry; chlorophyll b and the carotenoids widen the harvest and protect the machinery. Without accessory pigments, photosynthesis would still work in red and blue light but would waste much of the visible spectrum and be far more vulnerable to light damage.

2. Photosystem I and II — reaction centres and antennae

Think of the antenna as a funnel and the reaction centre as the drain. Hundreds of antenna molecules — chlorophyll a, chlorophyll b and carotenoids bound to light-harvesting complex (LHC) proteins — absorb photons and pass excitation energy from one pigment to the next by resonance energy transfer. The energy arrives at a single special pair of chlorophyll a molecules in the reaction centre. Only there does a chemical event happen: the excited chlorophyll a donates an electron to an acceptor. That is the moment light energy becomes chemical energy.

P680 and P700: why the numbers matter

The numbers are absorption maxima, not arbitrary labels. P680 absorbs maximally at 680 nm; P700 at 700 nm. They are both chlorophyll a, but their protein environment shifts their absorption. The order of action is the reverse of the numbering, and that confuses students: PSII acts first in the non-cyclic (Z-scheme) flow, even though it is called II, because it was discovered second. PSII splits water and feeds electrons onwards; PSI then re-energises them to reduce NADP⁺.

Antenna vs reaction centre — the distinction to write in an exam: antenna molecules only transfer excitation energy; they never lose an electron themselves. The reaction centre is the only place where charge separation occurs — an electron is actually removed from chlorophyll a, leaving P680⁺ (a very strong oxidant, able to pull electrons from water) or P700⁺. If a question asks "where does photolysis happen?", the answer is at PSII, because only P680⁺ is oxidising enough to split water.

3. Electron transport and ATP synthesis

Photolysis of water

Water is split at the oxygen-evolving complex on the lumen side of PSII: 2H₂O → O₂ + 4H⁺ + 4e⁻. The electrons replace those lost by P680; the protons add to the lumen proton gradient; the oxygen is released as a by-product. This is the only source of the oxygen we breathe from photosynthesis, and it explains why oxygen evolution and PSII activity rise and fall together.

The Z-scheme: non-cyclic electron flow

The Z-scheme is named for the zig-zag shape of the energy diagram: electrons are boosted up twice (once at each photosystem) and fall downhill between them. Follow one electron:

Products of non-cyclic flow: ATP (from the proton gradient), NADPH, and O₂. Both ATP and NADPH are needed by the Calvin cycle, so non-cyclic flow is the main route in ordinary photosynthesis.

Cyclic electron flow

In cyclic flow, electrons from PSI return via ferredoxin to the cytochrome b₆f complex and plastoquinone, then back to PSI, instead of going to NADP⁺. No water is split, no oxygen is released, and no NADPH is made — but protons are still pumped, so ATP is still made. Cyclic flow therefore lets the chloroplast top up ATP when the Calvin cycle needs more ATP than NADPH (the Calvin cycle needs 3 ATP per NADPH, while non-cyclic flow gives a ratio closer to 1:1), and it operates when NADP⁺ is scarce.

Chemiosmosis and ATP synthesis: Mitchell, Jagendorf and Arnon

Photophosphorylation was demonstrated by Arnon and colleagues in 1954, who showed isolated chloroplasts could make ATP in light. The mechanism is chemiosmosis, proposed by Mitchell: the electron transport chain does not make ATP directly; it builds a proton gradient, and the gradient drives ATP synthesis.

Protons accumulate in the thylakoid lumen from three sources: photolysis of water, protons carried across by plastoquinone, and proton pumping by cytochrome b₆f. The result is a steep gradient: the stroma is about pH 8 (alkaline) while the lumen is about pH 5.5 (acidic). The decisive proof came from Jagendorf's acid-bath experiment: chloroplasts soaked in acid (so their lumen became acidic) and then transferred to an alkaline buffer made ATP in the dark, with no light at all — proving that the proton gradient alone, not light itself, drives ATP synthesis.

ATP synthase (the CF_o–CF₁ complex) sits in the thylakoid membrane. CF_o is the membrane-embedded proton channel; protons flowing down their gradient through CF_o rotate the complex. CF₁ is the stromal head that uses that rotation to join ADP + inorganic phosphate (Pi) into ATP. The same principle, with a mitochondrial F_o–F₁ ATP synthase, drives oxidative phosphorylation in respiration (Section 9) — learn chemiosmosis once and use it twice.

4. C3, C4 and CAM pathways of carbon fixation

The Calvin cycle (C3 pathway)

The Calvin cycle runs in the stroma and uses the ATP and NADPH from the light reactions. It has three phases. The overall requirement is 3 ATP and 2 NADPH per CO2 fixed (18 ATP and 12 NADPH per glucose, since 6 CO2 are needed).

The C4 pathway (Hatch–Slack pathway)

C4 plants — maize, sugarcane, sorghum — solve a problem of the C3 pathway: RuBisCO also binds oxygen (see photorespiration, Section 5), wasting fixed carbon in hot, bright conditions when stomata close and internal O2 rises relative to CO2. The C4 solution is spatial separation, supported by Kranz anatomy ("wreath" anatomy): mesophyll cells form a ring around large, chloroplast-rich bundle-sheath cells that surround the vascular bundle.

In mesophyll cells, CO2 is first fixed not by RuBisCO but by PEP carboxylase, which has a much higher affinity for CO2 (as bicarbonate) and no oxygenase activity. CO2 + phosphoenolpyruvate (PEP, 3C) → oxaloacetate (OAA, 4C), which is converted to malate (4C). The 4C acid is the first stable product — hence "C4". Malate moves into the bundle-sheath cells, where it is decarboxylated, releasing CO2 at a high concentration around RuBisCO. RuBisCO then runs the Calvin cycle there, with almost no oxygenase activity because CO2 now vastly outnumbers O2. The remaining 3C compound (pyruvate) returns to the mesophyll, where ATP regenerates PEP. This CO2-concentrating pump costs extra ATP (2 extra ATP per CO2), so C4 plants pay more energy per CO2 — but in hot, high-light environments they more than recover the cost by avoiding photorespiration.

CAM pathway (Crassulacean acid metabolism)

CAM plants — cacti, agaves, pineapples, many succulents — live where water is scarcer still. Opening stomata by day would lose too much water, so they separate the same two carboxylations by time, not by cell type, in the same mesophyll cell.

At night, stomata open when it is cool and humid. PEP carboxylase fixes CO2 into oxaloacetate, then malate, which is stored overnight in the large central vacuole as malic acid. By day, stomata close to conserve water. Malate leaves the vacuole and is decarboxylated, releasing CO2 inside the leaf; RuBisCO then runs the Calvin cycle using that internally released CO2, powered by the day's light reactions. CAM is therefore slow — growth is limited by how much malate can be stored overnight — but extremely water-efficient.

Comparison: C3 vs C4 vs CAM

5. Photorespiration

RuBisCO is an ancient, imperfect enzyme: it cannot fully distinguish CO2 from O2. When O2 binds instead of CO2, RuBP (5C) is split into one molecule of 3-PGA (3C), which re-enters the Calvin cycle, and one molecule of phosphoglycolate (2C), which cannot. The plant must salvage that 2C fragment, and the salvage pathway is photorespiration.

Salvage requires cooperation across three organelles. In the chloroplast, phosphoglycolate is dephosphorylated to glycolate and exported. In the peroxisome, glycolate is oxidised to glyoxylate and then transaminated to glycine. In the mitochondrion, two glycines combine to form one serine (3C) plus CO2 and ammonia (NH3) — this is where the CO2 is actually released. Serine returns via the peroxisome to the chloroplast, where it is converted back to 3-PGA and re-enters the Calvin cycle. Net result for two oxygenations: one 3-PGA recovered, one CO2 lost, plus ATP and NADPH consumed and toxic ammonia to detoxify. In C3 plants under hot, bright, dry conditions, photorespiration can reduce net photosynthesis by 25–50%.

Why C4 plants avoid it: the C4 pump (Section 4) concentrates CO2 around RuBisCO in bundle-sheath cells, so CO2 outcompetes O2 at the active site and oxygenase activity is negligible. CAM plants achieve a similar effect by releasing stored CO2 internally during the day. Photorespiration is therefore mainly a C3 problem, and it gets worse exactly when stomata close: internal CO2 falls, O2 from the light reactions accumulates, and the O2/CO2 ratio at RuBisCO rises.

Is photorespiration entirely wasteful? Exam answers should call it wasteful in net carbon and energy terms, but note that it also protects the photosynthetic apparatus by dissipating excess energy when CO2 is limiting, and it recovers most (about three-quarters) of the carbon in phosphoglycolate rather than losing it all. Do not write that it "produces energy" — it consumes it.

6. Glycolysis

Glycolysis is universal: it occurs in the cytoplasm of almost every living cell, plant or animal, aerobic or anaerobic. That universality is the point — it is the ancient, oxygen-independent first stage of respiration, and everything after it (TCA cycle, oxidative phosphorylation) depends on whether oxygen is available and on the pyruvate it produces.

The 10 steps in outline

Memorise the logic, not every enzyme name at first: an energy-investment phase (steps 1–5) spends ATP to split glucose, then an energy-payoff phase (steps 6–10) earns ATP back, twice over because the molecule has split in two.

The net vs gross trap: glycolysis makes 4 ATP in total (gross), but 2 ATP were spent to start it, so the net gain is 2 ATP. If a question asks "net gain", the answer is 2; if it asks "total ATP formed", the answer is 4. Writing 4 for a net-gain question loses the mark — see the Exam traps box.

What happens to pyruvate next depends on oxygen: with oxygen, pyruvate enters the mitochondrion, is oxidatively decarboxylated to acetyl-CoA, and enters the TCA cycle (Section 8). Without oxygen, pyruvate is fermented (Section 7) so that NAD⁺ can be regenerated and glycolysis can continue.

7. Anaerobic respiration and fermentation

The purpose of fermentation is easily misunderstood: it is not to make more ATP, but to recycle NAD⁺. Glycolysis needs NAD⁺ at step 6; without oxygen, the electron transport chain cannot re-oxidise NADH, so NAD⁺ would run out and glycolysis would stop. Fermentation solves this by dumping the electrons from NADH onto pyruvate or its derivative.

Alcoholic fermentation

In yeast and some plant tissues (for example, waterlogged roots), pyruvate is decarboxylated to acetaldehyde (releasing CO2), then reduced by NADH to ethanol. This is the basis of brewing and bread-making: ethanol in beer and wine, CO2 raising bread dough.

Lactic acid fermentation

In muscle cells under intense exercise and in lactic acid bacteria, pyruvate is reduced directly by NADH to lactate (lactic acid). No CO2 is released. In plants, lactic fermentation can occur transiently in flooded roots, but prolonged lactate accumulation acidifies the cytoplasm, which is why plants generally favour alcoholic fermentation under anoxia.

8. The TCA (Krebs) cycle

Entry: pyruvate to acetyl-CoA

Before the cycle starts, each pyruvate (3C) is transported into the mitochondrial matrix and oxidatively decarboxylated by the pyruvate dehydrogenase complex to acetyl-CoA (2C), releasing one CO2 and one NADH per pyruvate. This link reaction is not part of the TCA cycle itself, but exam totals must include it — it contributes 2 CO2 and 2 NADH per glucose.

The cycle, step by step

Per acetyl-CoA (one turn): 2 CO2, 3 NADH, 1 FADH2, 1 GTP. Per glucose (two turns, plus the link reaction and glycolysis): 6 CO2 from the cycle and link reaction in total (2 from the link reaction + 4 from two turns), 10 NADH in total (2 glycolysis + 2 link + 6 TCA), 2 FADH2, and 4 ATP equivalents by substrate-level phosphorylation (2 net from glycolysis + 2 GTP from the cycle). The NADH and FADH2 carry most of the energy onwards to oxidative phosphorylation — the TCA cycle itself makes very little ATP directly, and that is a common exam error to avoid.

9. Oxidative phosphorylation

The electron transport chain: complexes I–IV

Chemiosmosis and ATP synthase

As in the chloroplast (Section 3), the gradient is the point. Complexes I, III and IV pump protons from the matrix into the intermembrane space, making the intermembrane space acidic and positively charged relative to the matrix. Protons flow back into the matrix through the F_o channel of ATP synthase; the rotation drives the F₁ head to synthesise ATP from ADP + Pi. Roughly 4 protons are needed per ATP made (including the cost of importing ADP and Pi and exporting ATP).

ATP yield: the convention used on this page

Convention used throughout this page: 1 NADH = 2.5 ATP and 1 FADH2 = 1.5 ATP (modern P/O ratios). Older textbooks used 3 and 2, giving 36–38 ATP per glucose; modern values give about 30–32 ATP per glucose. The range comes from the shuttle used to move cytoplasmic NADH from glycolysis into the mitochondrion: the malate–aspartate shuttle delivers its electrons as mitochondrial NADH (giving 32 ATP in total), while the glycerol-phosphate shuttle delivers them as FADH2 (giving 30 ATP in total). State your convention in an exam if the question does not — a marker cannot fault a stated, consistent convention, but an unstated switch between 3 and 2.5 will look like an error.

Worked total (malate–aspartate shuttle, 2.5 / 1.5 convention): glycolysis net 2 ATP + 2 NADH (5 ATP) + link reaction 2 NADH (5 ATP) + TCA 6 NADH (15 ATP) + 2 FADH2 (3 ATP) + 2 GTP (2 ATP) = 32 ATP. With the glycerol-phosphate shuttle, the 2 cytoplasmic NADH give only 3 ATP, for a total of 30 ATP.

Poisons and uncouplers (brief)

Cyanide blocks complex IV (cytochrome c oxidase), so electrons cannot reach oxygen and ATP synthesis stops even though oxygen is present — the cell effectively suffocates. Uncouplers (for example, 2,4-dinitrophenol, DNP) make the inner membrane leaky to protons, so the gradient dissipates as heat without passing through ATP synthase: electron transport continues (and oxygen consumption may even rise), but ATP production falls. Brown fat uses a natural uncoupling protein (thermogenin) for the same purpose — heat production.

10. The glyoxylate cycle

Animals cannot convert fat into glucose net, because the two decarboxylation steps of the TCA cycle lose the acetyl-CoA carbons as CO2. Germinating oil seeds can, and the glyoxylate cycle is how. In seeds such as castor bean, stored fats are broken down by beta-oxidation to acetyl-CoA. If that acetyl-CoA entered the ordinary TCA cycle, its carbons would be lost as CO2 and no sugar could be built. Instead, in the glyoxysome, the cycle bypasses those steps.

The two signature enzymes are isocitrate lyase and malate synthase; if a question asks what makes the glyoxylate cycle distinct, name those two. The cycle fades once the seedling becomes photosynthetic and no longer needs to live off its fat reserves.

11. Oxidative pentose phosphate pathway (OPPP)

Respiration is usually taught as an ATP story, but cells also need reducing power for building molecules and 5-carbon sugars for DNA and RNA. The OPPP supplies both, without making ATP. Its oxidative phase converts glucose-6-phosphate → 6-phosphogluconate → ribulose-5-phosphate, releasing CO2 and producing 2 NADPH per glucose-6-phosphate. The non-oxidative phase then rearranges pentose phosphates back into glycolytic intermediates (fructose-6-phosphate and glyceraldehyde-3-phosphate), so carbon is not wasted.

Products and their uses: NADPH is used for fatty-acid synthesis, nitrogen assimilation (nitrate reduction), and maintaining reduced glutathione for antioxidant defence — note the contrast with NADH, which mainly feeds the electron transport chain for ATP. Ribose-5-phosphate is the backbone sugar for nucleotides (ATP, NAD⁺, DNA, RNA) and, in plants, feeds into the shikimate pathway for aromatic compounds. Where it runs: in plant cells the OPPP operates in the cytosol and in plastids (including chloroplasts in the dark, when the Calvin cycle is off and the chloroplast still needs NADPH); the plastid form is especially important in non-photosynthetic tissues such as roots. The key regulatory enzyme is glucose-6-phosphate dehydrogenase, which is inhibited by NADPH — a simple feedback loop: when NADPH is plentiful, the pathway slows.