Follow energy from pigment absorption through thylakoid electron transport into carbon fixation. Explore the spectra, connect them to the Calvin–Benson cycle and photorespiration, then practice with flower-earning mini-games and flashcards.
Every correct mini-game answer earns a bloom.
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.
| 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; outermost layer of the phycobilisome. |
| 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.
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.
E = hc/λ, shown per mole of photons (NAhc = 119 627 kJ·nm·mol−1). Dashed lines mark the excitation energies of the PSII and PSI reaction centers (P680 ≈ 176 kJ/mol, P700 ≈ 171 kJ/mol). Every visible photon carries at least that much; the surplus in a blue photon is not used.
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.
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.
Energy flows downhill in wavelength. 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.
Tie back to Figure 1. The pigment order along the funnel matches the order of their long-wavelength peaks: phycoerythrin (568) → phycocyanin (606) → chlorophyll b (651) → chlorophyll a (673). Accessory pigments are useful because they absorb where chlorophyll a is weak and then pass the energy on to chlorophyll a.
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.
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.
The Q-cycle oxidizes PQH₂ and releases 2 H⁺ per PQH₂ into the lumen, sending one electron to plastocyanin and recycling the other through cyt b₆. 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.
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.
| 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 tell the two apart: Rubisco discriminates strongly against ¹³C (δ¹³C ≈ −27‰), while PEPC discriminates weakly (≈ −13‰).
Say the answer out loud before you reveal it. "Again" sends a card to the back of the deck, and "Got it" retires it. Getting through the whole deck once earns a flower. Spacing beats cramming: come back tomorrow and run it again.