Photosynthesis
Photosynthesis: The Light Reactions
The light reactions are the act of a two-act play: they convert photons into two energy currencies — ATP and NADPH — that the Calvin cycle (CH23) will spend on CO2. The single organizing idea is the Z-scheme: two photon-driven uphill boosts (at Photosystem II and Photosystem I) separated by downhill electron flow, wired so that water is split, oxygen is released, a proton gradient is built, and NADPH is made. One molecular innovation, the Mn4CaO5 cluster that pries electrons off water, oxygenated the planet.
Every oxygen molecule you have ever breathed was once part of a water molecule, split apart at a single protein in a leaf. That protein is Photosystem II, and the moment it learned to pry electrons off water — roughly two and a half billion years ago — it rewrote the chemistry of the entire planet. The light reactions are how a chloroplast turns sunlight into two things a cell can actually spend: ATP and NADPH. Photosynthesis is a two-act play. Act one, the light reactions, makes the coins. Act two, the Calvin cycle, spends them on carbon dioxide. This chapter is act one.
The whole story comes down to one diagram, the Z-scheme: two uphill jumps powered by light, with a downhill electron slide in between. Get that shape into your head and the rest is bookkeeping.
Where it happens: a captured bacterium
The chloroplast is a double-membrane organelle, and that second membrane is a fossil. Inside the inner membrane sits the stroma, the soup where carbon gets fixed later. Floating in the stroma are flattened sacs called thylakoid membranes, stacked like poker chips into grana, each sac enclosing an interior space called the lumen. The light reactions run in and across the thylakoid membrane, and where the protons end up — the lumen — is the whole point, so keep that geography straight.
Why two membranes? Because about 1.5 billion years ago a eukaryotic cell engulfed a free-living cyanobacterium and never digested it. The evidence is hard to argue with: the double membrane (engulfer plus engulfed), the chloroplast’s own DNA, and bacterial-style 70S ribosomes inside it. Mitochondria carry the same scar from a separate engulfment. You are, in a real sense, a colony of domesticated bacteria.
A photon’s three fates
Light is energy in discrete packets, photons, each carrying E = hν. When a pigment absorbs one, an electron jumps to an excited state, and that excitation can go one of three ways.
It can simply fall back down, releasing the energy as fluorescence or heat. It can hand its energy to a neighboring pigment without the electron going anywhere — resonance energy transfer. Or, at one special spot, it can hand off the electron itself.
The second fate is where most students stumble, so slow down here. A light-harvesting complex packs 200 to 300 pigment molecules around a reaction center like a satellite dish. When a photon lands anywhere on that dish, the energy hops pigment to pigment toward the center, a bucket brigade in which no bucket actually moves. Energy travels by resonance; the electron transfers only at the reaction center. Confuse those two and the rest of the chapter dissolves.
At the reaction center, the third fate fires. An excited donor (D*) gives its electron to an acceptor (A), creating a separated pair of charges, D⁺ and A⁻. The surrounding protein holds them apart long enough that the electron can’t snap back. That photoinduced charge separation is the actual conversion of light into chemistry, and Deisenhofer and Michel won a Nobel for being the first to see its machinery, atom by atom.
The pigment that runs the whole show
The primary pigment is chlorophyll, a substituted tetrapyrrole built on the same ring skeleton as heme — but with a magnesium ion at its center instead of iron, plus a long greasy phytol tail that anchors it in the membrane. Chlorophyll a and b differ slightly and absorb slightly different colors, which is why leaves harvest a broad slice of sunlight. The reaction-center chlorophylls come as special pairs named for the wavelength they absorb best: P680 in Photosystem II, P700 in Photosystem I.
A small kitchen experiment makes the chemistry tangible. Boil greens too long and they go drab olive: acid swaps the central Mg²⁺ for two protons, converting chlorophyll into pheophytin, a sort of zombie chlorophyll. That same Mg-stripped molecule is no accident in the leaf — pheophytin is the very first electron acceptor in PSII.
The accessory pigments earn their keep too. Carotenoids absorb blue-green light chlorophyll misses, and they double as the plant’s built-in sunscreen: when light is too intense, they perform nonphotochemical quenching (NPQ), dumping dangerous excess energy as harmless heat. Those carotenoids were in the leaf all along, masked by chlorophyll. Autumn just removes the green and lets the reds and golds show.
Read the Z left to right and the story is honest about its bookkeeping: light pays twice. The first photon pries an electron off water — the only molecule on Earth's surface stubborn enough that it takes a +1.1 V oxidant (P680⁺) to do it — and the electron slides downhill, pumping protons into the lumen as it goes. The second photon lifts that same electron a second time, high enough to finally reduce NADP⁺. Two uphill boosts, one downhill valley between them; out the back come O₂, a proton gradient, and the NADPH that the Calvin cycle will spend. No light, no climb, no sugar.
The Z-scheme: two upstrokes and a downhill
Now the electron path, in order, because order is everything. Water → PSII (P680) → pheophytin → plastoquinone (QA → QB → QH₂) → cytochrome b6f → plastocyanin (a copper protein) → PSI (P700) → A₀ → A₁ (phylloquinone) → iron-sulfur clusters → ferredoxin → ferredoxin-NADP⁺ reductase (FNR, a FAD flavoprotein) → NADPH.
Plot that on an energy axis and it draws a Z. A photon hits P680 and kicks its electron sharply uphill (upstroke one); the electron then slides downhill through the carriers to plastocyanin; a second photon hits P700 and kicks it uphill again (upstroke two); then it runs downhill once more to NADPH. Two photon absorptions, two upstrokes, separated by downhill flow. The interactive above lets you fire each photon and watch the electron climb and fall.
The genius is at the bottom of the first upstroke. The instant excited P680* hands its electron to pheophytin, it leaves behind P680⁺ — at about +1.2 V, the strongest biological oxidant known — electron-hungry enough to rip electrons off water itself. That happens at the oxygen-evolving complex, a cluster of four manganese atoms, one calcium, and five oxygens (Mn₄CaO₅). It can’t grab all four electrons at once, so it counts: the S-state (Kok) cycle ratchets from S0 to S4, accumulating oxidizing power one photon at a time. At S4 it snaps, releasing O₂ and resetting. The net PSII reaction: 2 H₂O + 4 photons → O₂ + 4 H⁺ (into the lumen) + 4 e⁻.
Those lumen protons are half the energy story. Cytochrome b6f adds the rest: like Complex III in mitochondria, it runs a Q-cycle that pumps roughly 4 more H⁺ into the lumen per pair of electrons. At the top of the second upstroke, P700* lifts electrons high enough to reduce ferredoxin, biology’s strongest soluble reducing agent, and FNR uses it to make NADPH on the stromal side, exactly where the Calvin cycle waits.
A worthwhile pause: what if PSI worked but PSII didn’t? Toggle “Break PSII” in the widget and watch. PSI keeps lifting electrons, but nothing refills the supply from water. The chain starves, no O₂ appears, everything stalls. PSII acts first despite its name — the photosystems were simply discovered backwards.
Two products, two jobs. Linear flow is the only mode that splits water and reduces NADP⁺, so it has to run — it is where the O₂ and all the NADPH come from. But the protons it pumps buy slightly less than the 3 ATP the Calvin cycle spends for every 2 NADPH it consumes, so a leaf living on linear flow alone would slowly run out of ATP. Cyclic flow is the fix: route PSI's electrons back through b6f, pump protons without touching NADP⁺, and make ATP with no NADPH on the side. The chloroplast dials in just enough cyclic flow to balance the books at 3:2 — the same trick as topping up one currency without minting the other.
From gradient to ATP, and the planet it made
We now have a thylakoid lumen stuffed with protons, from water-splitting and from the Q-cycle. That gradient is potential energy, and in the next chapter it drives ATP synthase by chemiosmosis, the same proton-gradient logic Peter Mitchell proposed for mitochondria, run here in a chloroplast. Arnon showed isolated chloroplasts can make ATP two ways: non-cyclic photophosphorylation (the full linear path, yielding ATP, NADPH, and O₂) and cyclic photophosphorylation (electrons loop PSI → ferredoxin → b6f and back, making ATP only — handy when the cell needs ATP more than reducing power).
Step back and the scale is staggering. That one molecular innovation, the manganese cluster that splits water, flooded the ancient atmosphere with oxygen. The iron dissolved in the oceans rusted out as banded iron formations, an ozone layer formed, aerobic respiration became possible, and complex life followed. The Great Oxidation Event traces back to a protein in a pond. As Szent-Györgyi put it on Chris’s slide, “What drives life is a little electrical current, kept up by a little sunshine.”
With the coins minted — ATP and NADPH in the stroma — we are ready for act two. In CH23, the Calvin cycle, you’ll watch the cell spend exactly these currencies to pull carbon out of the air and build sugar.
How we measure it
X-ray crystallography of membrane proteins
Membrane proteins were long thought too greasy to crystallize, hiding roughly a third of all proteins from structure determination. Substituting detergents for natural lipids let Deisenhofer and Michel crystallize the bacterial photosynthetic reaction center — the first membrane protein ever solved — and read the exact mirrored arrangement of chlorophylls that channels light-driven electrons across the membrane. The same approach later gave us PSII, PSI, cytochrome b6f, and ATP synthase.
Absorption and action spectroscopy
Shine monochromatic light across the visible spectrum and measure either how much a pigment absorbs (absorption spectrum) or how fast photosynthesis runs (action spectrum). This is how chlorophyll a and b were distinguished, how the special-pair reaction centers were named for their absorption maxima (P680, P700), and how accessory carotenoids were shown to fill the blue-green gap chlorophyll misses.
The acid-bath / pH-jump experiment
Jagendorf and Uribe soaked chloroplasts at pH 4, then dropped them into pH 8 buffer in total darkness. The artificial proton gradient alone drove ATP synthesis with no light and no electron transport — the cleanest proof of Mitchell's chemiosmotic theory, showing that a proton gradient across the thylakoid membrane is the energy currency that powers ATP synthase.
Isolated-chloroplast photophosphorylation assays
Arnon's group stripped chloroplasts to naked lamellar membranes so ADP and phosphate could reach the thylakoids, then caught them making ATP from light alone. Running the reaction without oxygen (and erasing the apparent O2 requirement with added flavin mononucleotide) proved the ATP came from light, not from contaminating mitochondria — and separated cyclic from non-cyclic photophosphorylation.