New to photosynthesis? Start with the plant's big picture, then follow light into the chloroplast and carbon into new growth. Each stop has a quick check; the final lab asks you to explain real results.
Finish each game or your first flashcard deck to earn a bloom.
A plant takes in carbon dioxide (CO₂) from air and water (H₂O) from soil. Light supplies energy to build carbon-rich molecules from that CO₂. Splitting water releases oxygen gas (O₂). Most of the carbon in new plant tissue came from air, not soil.
This is a simplified net summary, not one reaction that instantly makes glucose. The pathway first produces G3P, a three-carbon molecule that cells can use to build sugars and other materials. The released O₂ comes from water.
Roots bring in water. Tiny leaf pores called stomata let CO₂ enter. Sunlight brings energy, but it does not supply the carbon atoms of sugar.
Inside leaf cells are chloroplasts. Their folded thylakoid membranes hold light-capturing pigments. The fluid around them is the stroma.
At the thylakoid, light reactions split water, release O₂ and make ATP and NADPH. ATP carries usable energy; NADPH carries high-energy electrons.
In the stroma, the Calvin–Benson cycle uses CO₂, ATP and NADPH to make G3P. Plants can use G3P to build sugars, starch and much of their biomass.
Two easy mix-ups: A stoma is a pore on a leaf; the stroma is fluid inside a chloroplast. The Calvin cycle depends on products of the light reactions; “light-independent” does not mean it normally runs only at night.
Plants still respire. Their cells use sugars for energy by day and by night. In good light, photosynthesis can outpace respiration, giving net CO₂ uptake and O₂ release.
Light supplies energy. CO₂ supplies carbon for G3P and plant growth; splitting H₂O supplies electrons and releases O₂.
Pigment: a molecule that absorbs certain colors of light. Chlorophyll: the main green photosynthetic pigment. Photon: one packet of light energy.
Thylakoid lumen: space inside a thylakoid where H⁺ builds up. Stroma: fluid around thylakoids where the Calvin cycle operates. Photosystem: a pigment-and-protein light catcher in the membrane.
Carbon fixation: moving carbon from CO₂ into an organic molecule. Rubisco: the enzyme that adds CO₂ in the Calvin cycle. G3P: a three-carbon sugar made later in the cycle.
Three passes: First, learn this map and try the games using each figure's “Look for” line. Next, return to the detailed captions and trace the mechanisms. Finally, explain the research cases without peeking and revisit due flashcards on later days.
Look for: The bottom axis is light color written as wavelength (nm); the taller the curve, the more strongly that pigment absorbs. Find blue and red peaks first.
Relative absorption versus wavelength. Redrawn from the McGraw-Hill figure on the slide by digitizing each curve against the original axes (sampled every 1–5 nm, tighter on steep flanks), then drawing a monotone curve through the points. Positional error is about ±1 nm and ±1 absorption unit. Hover or drag across the plot to read every pigment's value at a wavelength. Peak labels follow the original: chlorophyll a ≈ 425 and 673 nm, chlorophyll b ≈ 449 and 651 nm.
Look for: Chlorophyll a runs the reaction centers. Other pigments widen the colors collected or protect the cell from excess light.
| Pigment | Peaks in Fig. 1 (nm) | Typical λmax (nm) | Chemistry | Found in | Role |
|---|---|---|---|---|---|
| Chlorophyll a | 425, 673 | 430, 662 (ether) ~675–680 in vivo | Mg-chlorin (cyclic tetrapyrrole) with a phytol tail; methyl at C-7 | All oxygenic phototrophs: plants, algae, cyanobacteria | Primary pigment. Reaction-center special pairs P680 (PSII) and P700 (PSI) are chl a; also the bulk of core antenna. |
| Chlorophyll b | 449, 651 | 453, 642 (ether) | As chl a, but formyl (–CHO) at C-7; shifts Soret red and Qy blue | Land plants, green algae, euglenids | Accessory. Concentrated in LHCII; widens absorption into the blue and orange-red. |
| Carotenoids | ~407 (sh), 437, 466 | β-carotene: ~425 (sh), 450, 478 (hexane) | C40 isoprenoid polyene. Carotenes (hydrocarbons) and xanthophylls (oxygenated) | All phototrophs | Accessory absorption in 400–500 nm; photoprotection by quenching triplet chlorophyll and singlet O2; xanthophyll cycle drives NPQ. |
| Phycoerythrin | ~460, 525, 568 | R-PE: ~498, 545, 565 | Phycobiliprotein; open-chain tetrapyrrole (phycoerythrobilin) bound to cysteine by thioether | Red algae, many cyanobacteria, cryptophytes | Accessory. Captures green light (500–580 nm) that chlorophylls miss; in PE-containing phycobilisomes of red algae and cyanobacteria, it forms the outer rod segments. |
| Phycocyanin | 606 | C-PC: ~615–620 | Phycobiliprotein; phycocyanobilin chromophore | Cyanobacteria, red algae, glaucophytes | Accessory. Absorbs orange light; middle of the phycobilisome rod, passing energy to allophycocyanin (~650 nm) and then chl a. |
Why the figure's peaks don't match the literature exactly. Absorption maxima depend on environment. Chlorophylls in organic solvent absorb at shorter red wavelengths than when bound to proteins in the thylakoid, and phycobiliprotein spectra vary by species and assembly state. The "Typical" column gives commonly cited reference values; use the figure's positions for questions about this figure.
Look for: A leaf uses several pigments together. Compare the plant set with the PE/PC-containing set in the green wavelengths.
Mean relative absorption within each band, calculated from the Figure 1 curves (1-nm steps). Darker cells absorb more of that band. Band boundaries are conventional and approximate. Read down a column to see which pigment dominates a color; read across a row to see a pigment's "coverage."
The green gap. Each line is the highest single-pigment value at each wavelength (the upper envelope of Figure 1) for two pigment sets. It is a teaching proxy for where a set has strong absorbers, not a measured whole-cell spectrum, which would depend on pigment ratios and scattering. The plant set drops to under 10% between roughly 500 and 630 nm; phycoerythrin and phycocyanin fill that window.
Look for: Shorter wavelength means more energy per photon. Blue photons bring more energy than red ones, but their extra energy does not become an extra charge separation.
E = hc/λ, shown per mole of photons (NAhc = 119 627 kJ·nm·mol−1). Dashed lines mark the approximate excitation energies of the PSII and PSI reaction centers (P680 ≈ 176 kJ/mol, P700 ≈ 171 kJ/mol). A 680 nm photon carries about 176 kJ/mol; a 700 nm photon carries about 171. Blue photons carry more, but the extra energy is largely lost during relaxation.
Look for: Both blue and red absorption can end at the same lower excited state. From there, energy can drive chemistry, glow as fluorescence or become heat.
Simplified Jablonski diagram for chlorophyll. The two absorption bands of chlorophyll in Figure 1 correspond to two excited singlet states. A blue photon reaches S2 (Soret band) but relaxes to S1 within about 100 fs, releasing the difference as heat (Kasha's rule). Photochemistry happens only from S1, so a blue photon and a red photon each deliver one S1 excitation. That is why photosynthetic yield scales with photon number rather than photon energy.
Excitation migrates through antenna chlorophylls in femtoseconds to picoseconds and is trapped by charge separation at P680 or P700. This is the productive route.
Re-emission from S1 at slightly longer wavelength (~685 nm in vivo). It competes with photochemistry, which is why chlorophyll fluorescence is used to measure PSII efficiency.
Under excess light, non-photochemical quenching (including the xanthophyll cycle) dissipates S1 energy as heat before it can cause damage.
Intersystem crossing gives triplet chlorophyll, which can make singlet oxygen. Carotenoids next to chlorophylls quench both, a main reason carotenoids are essential.
Look for: Absorption asks what a pigment catches. Action asks how well a whole leaf photosynthesizes at each color. They need not have identical curves.
Absorption spectrum = how much light one pigment absorbs at each wavelength. Action spectrum = how much photosynthesis a leaf does per incident photon at each wavelength. The black curve is an approximate reconstruction of the averaged crop-leaf quantum-yield curve of McCree (1972), for shape comparison only. Three points stand out. Green light still drives about 70–80% of peak yield, because a whole leaf scatters light internally and accessory pigments absorb it even where isolated chlorophyll barely does. Blue yield is lower than chlorophyll's Soret peak suggests, because some blue is absorbed by carotenoids and non-photosynthetic compounds that transfer it inefficiently or not at all. Yield collapses beyond about 685 nm (the red drop).
Far-red light (>690 nm) is absorbed mainly by PSI, so on its own it gives low O2 yield. Adding shorter red light (~650 nm, which PSII can use) gives a higher rate than the two beams produce separately. Emerson's enhancement effect (1957) was the first evidence that two photosystems work in series, the basis of the Z-scheme.
Engelmann projected a spectrum onto a filament of Cladophora and watched aerobic bacteria cluster where O2 was produced. They crowded under blue and red light, producing the first action spectrum, which matched chlorophyll absorption.
Look for: Follow an arrow toward a reaction center. The upper lane is a PE-containing phycobilisome; the lower lane is a plant antenna.
Energy falls as wavelength increases. Excitation energy transfer (Förster resonance transfer) moves from pigments that absorb shorter wavelengths to those that absorb longer ones. Each step gives up a little energy as heat, which makes the transfer effectively one-way and delivers excitations to the reaction center. Energies are E = hc/λ at each pigment's main absorption peak.
Read the two lanes. A PE-containing phycobilisome passes excitation from phycoerythrin through phycocyanin and allophycocyanin to chlorophyll a; a plant antenna passes it from chlorophyll b to chlorophyll a. In either route, accessory pigments capture light and pass excitation toward a reaction center.
A caution on chromatic adaptation. Water absorbs red light strongly, so blue-green light dominates at depth, and red algae with phycoerythrin are often described as specialists for deep water (Engelmann's complementary chromatic adaptation hypothesis). Field distributions only partly support this: red algae grow at all depths, and light intensity matters as much as color. Cyanobacteria do show true complementary chromatic acclimation, adjusting their phycoerythrin to phycocyanin ratio to match ambient light color.
A PE-containing phycobilisome: phycoerythrin → phycocyanin → allophycocyanin → chlorophyll a. The plant antenna follows a different lane.
Look for: Electrons move from water through PSII, then PSI, to NADPH. Their trip builds an H⁺ gradient that powers ATP synthase. PSII acts first even though it is numbered II.
Simplified linear-flow budget for the c₁₄ ATP synthase shown below: about 12 lumenal H⁺ per O₂ divided by 14/3 H⁺ per ATP gives ~2.6 ATP. Cyclic electron flow can supply extra ATP without making NADPH.
Charge separation oxidizes P680 to P680⁺ (≈ +1.2 V), the strongest biological oxidant. The Mn₄CaO₅ oxygen-evolving complex cycles through S-states (Kok cycle), taking four electrons from two H₂O per O₂ and releasing 4 H⁺ into the lumen.
QB takes two electrons and two stromal H⁺, leaving as plastoquinol (PQH₂), a mobile carrier in the membrane.
Each PQH₂ oxidized at b₆f releases 2 H⁺ into the lumen. Across two Q-cycle turns, 4 H⁺ are released per 2 electrons delivered to plastocyanin; the other electrons recycle through cyt b₆ to reduce PQ. It is the rate-limiting step of linear flow.
A second photon re-energizes the electron. The electron passes through A₀, A₁ and Fe–S clusters to ferredoxin, and then FNR reduces NADP⁺ to NADPH in the stroma.
Lumen pH ≈ 5 against stroma ≈ 8 gives a proton-motive force that is mostly ΔpH. CF₀ rotation (c₁₄ ring, so ≈ 14 H⁺ per 3 ATP, about 4.7 H⁺/ATP) drives CF₁ catalysis by binding change.
Fd returns electrons to PQ (PGR5/PGRL1 or the NDH route), pumping H⁺ with no NADPH made. It tops up ATP, since the Calvin cycle needs 3 ATP : 2 NADPH, and it helps trigger NPQ.
Z-scheme logic. Two photosystems in series drive electrons uphill from H₂O (E°′ = +0.82 V) to NADP⁺ (−0.32 V), a span of about 1.1 V that one photon of ~680 nm cannot cover with useful efficiency. Herbicides like DCMU block QB binding, which stops linear flow and pushes up fluorescence.
PSII takes electrons from water. PSI re-energizes those electrons and sends them through ferredoxin and FNR toward NADPH.
Look for: CO₂ supplies carbon; ATP and NADPH pay the energy and electron costs. For every three CO₂ fixed, one G3P can leave while the rest regenerate the starting molecule.
Rubisco adds CO₂ to ribulose-1,5-bisphosphate (RuBP, 5C), making an unstable 6C intermediate that splits into 2 × 3-phosphoglycerate (3-PGA). Rubisco is slow (kcat ≈ 3 s⁻¹) and needs carbamylation of a lysine plus Mg²⁺, with Rubisco activase to keep it active.
3-PGA → 1,3-bisphosphoglycerate (ATP, phosphoglycerate kinase) → glyceraldehyde-3-phosphate (NADPH, GAPDH). This is where the light reactions' products are spent.
Five of every six G3P are reshuffled (aldolase, transketolase, FBPase, SBPase) back into three RuBP, using ATP at phosphoribulokinase. One G3P leaves for sucrose (cytosol) or starch (chloroplast).
Light raises stromal pH (≈ 8) and Mg²⁺, and reduced thioredoxin (via Fd–thioredoxin reductase) activates FBPase, SBPase and PRK. The cycle switches off in the dark, so it isn't truly "light-independent".
Photorespiration. Rubisco also reacts with O₂, making one 3-PGA plus 2-phosphoglycolate. Salvaging that 2-phosphoglycolate runs through the chloroplast, peroxisome and mitochondrion (glycine → serine releases CO₂ and NH₃). It costs ATP and reducing power and loses up to ~25% of fixed carbon. The problem gets worse at high temperature, because the CO₂:O₂ solubility ratio falls and Rubisco's specificity drops.
Three CO₂, nine ATP and six NADPH yield one exported G3P. G3P is a three-carbon sugar precursor, not a whole glucose molecule.
Look for: All three use the Calvin cycle. C₄ concentrates CO₂ by separating steps between cells; CAM separates CO₂ uptake and use between night and day.
| Feature | C₃ | C₄ | CAM |
|---|---|---|---|
| First stable product | 3-PGA (3C) | Oxaloacetate (4C) | Oxaloacetate → malate (night) |
| Initial carboxylase | Rubisco | PEP carboxylase (uses HCO₃⁻, no O₂ affinity) | PEP carboxylase |
| How CO₂ fixation is separated | None | In space: mesophyll → bundle sheath (Kranz anatomy) | In time: night uptake, day decarboxylation |
| Photorespiration | High in heat | Very low | Very low |
| Extra cost | — | +2 ATP per CO₂ (PPDK regenerates PEP) | ATP, and malate stored in the vacuole |
| Water-use efficiency | Low | Moderate to high | Highest (stomata close by day) |
| Examples | Rice, wheat, soybean, most trees | Maize, sugarcane, sorghum | Pineapple, cacti, Kalanchoe, agave |
Why C₄ wins in hot, bright habitats. PEP carboxylase has high affinity and ignores O₂, so it pumps CO₂ into the bundle sheath to ~10× atmospheric levels, which saturates Rubisco there. Below ~25 °C the ATP cost of the pump can make C₃ plants more efficient. Carbon isotopes often distinguish the pathways: bulk C₃ plant tissue is near δ¹³C ≈ −27‰ and C₄ tissue near −13‰, reflecting different carbon-discrimination pathways, not isolated enzyme values.
C₄ separates initial CO₂ fixation and the Calvin cycle between mesophyll and bundle-sheath cells. CAM collects CO₂ at night and uses it during the day.
A strong explanation traces where the atoms came from, where the energy went, and which step changed. Predict each result before opening the reasoning, then try the six-case field lab.
One leaf gets water marked with ¹⁸O. Another gets CO₂ marked with ¹³C. Under light, which label appears in released O₂, and which enters new carbon-rich material? Explain the reaction that moves each label.
O₂ made by photosynthesis carries oxygen from water split at PSII, so ¹⁸O-labelled water can produce labelled O₂. Rubisco fixes carbon from CO₂, so ¹³C enters G3P and later sugars and biomass. Light supplies energy, not carbon atoms.
A C₃ leaf closes its stomata during a hot, dry afternoon. Predict the change in internal CO₂, photorespiration and carbon gain. Then explain how C₄ and CAM plants reduce the same problem and what extra resource they spend.
Less incoming CO₂ raises Rubisco's relative use of O₂, so photorespiration increases and net carbon gain tends to fall. C₄ plants spend extra ATP to concentrate CO₂ in bundle-sheath cells. CAM plants store CO₂ fixed at night for daytime use, trading speed and storage capacity for water savings.
Expert check: Can you defend a prediction using the pathway rather than only name a pigment or cycle? The final cases revisit the same mechanism in new situations. A missed case gives a clue; explain your reasoning before trying again.
Start with the foundation cards, then work toward mechanisms. Try to answer out loud before revealing. Each answer pairs the science with a little memory petal. "Again" brings a card back in a few turns and makes it due now; "Got it" schedules it for a later day. Successful early practice leaves future review dates unchanged. Your dates stay on this device. Recall every card once for a flower.