Photosynthesis

A leaf takes in air, water, and a little sunlight, and quietly turns them into the sugar that ends up in every living thing on Earth. How it does this is one of the strangest pieces of chemistry the planet has ever discovered.

Stand in front of an oak tree on a summer afternoon. The leaves are doing nothing visible. And yet inside each leaf, hundreds of millions of green machines are running a chemical trick so unlikely that life had to wait two billion years for evolution to stumble into it. They are taking water apart with sunlight, pulling carbon dioxide out of the air, and stitching the two together into sugar — releasing oxygen as the waste.

Almost everything you have ever eaten is the output of this reaction. Almost every breath you take is its by-product.

The trick that runs the biosphere

The overall summary fits on a single line:

6 CO₂ + 6 H₂O + light  →  C₆H₁₂O₆ + 6 O₂

Six molecules of carbon dioxide, six of water, a dose of sunlight, and out comes one molecule of glucose — with oxygen on the side. Written like this, it sounds almost trivial: stitch the carbons in the air to the hydrogens in the water, and you have a sugar. In practice it is appallingly hard. Carbon dioxide is one of the most stable molecules in chemistry. Water is one of the hardest to take apart. Doing both reactions in the same room, at room temperature, using only the dilute energy of sunlight, is the sort of thing that should not work at all.

The whole thing happens inside a tiny organelle called the chloroplast. A typical leaf cell carries dozens of them. Each chloroplast is essentially a captured bacterium — an ancient cyanobacterium that some larger cell swallowed about a billion and a half years ago and never digested. We inherited photosynthesis as a kind of long-standing borrowing arrangement.

The light reactions — splitting water with sunlight

The first half of photosynthesis happens on the membranes of those green discs, called thylakoids. Embedded in them are two enormous protein machines, known prosaically as Photosystem II and Photosystem I. (They were numbered in the order they were discovered. Photosystem II is the one that comes first in the reaction, which makes the names slightly maddening.)

The job of Photosystem II is the audacious one: to take a molecule of water and rip it apart. This is, chemically, an absurd thing to attempt. Water is held together by some of the strongest bonds in everyday matter. Most reactions on Earth produce water; you don't normally see it going the other way. But sitting at the heart of Photosystem II is a tiny cluster of four manganese atoms and one calcium atom — a manganese cluster — that does it anyway. When a photon of light strikes a chlorophyll molecule nearby, the energy is funnelled to this cluster. After it has been hit four times, the cluster has pulled four electrons from two water molecules. The leftover is oxygen (O₂) and four loose protons (H⁺).

The oxygen, which to the plant is just waste, diffuses out through the leaf and joins the atmosphere. Every atom of oxygen you have ever breathed was, at some point, prised out of a water molecule by a cluster of manganese atoms inside a leaf or a cyanobacterium. The whole atmosphere is, in this sense, the long-running by-product of photosynthesis.

The four liberated electrons are then passed along a chain of carrier molecules — an electron transport chain — that uses their downhill movement to pump protons across the thylakoid membrane, building up a proton gradient. The gradient is then released through a turbine-like enzyme called ATP synthase, which spins as protons flow back through it and uses the rotation to make ATP — the cell's universal energy currency. A second hit of sunlight, at Photosystem I, gives the electrons a final upward kick and loads them onto a carrier called NADPH — the cell's universal currency of reducing power, which is to say, of spare electrons.

At the end of all this, the leaf has converted dilute sunlight into two tangible, useful things: ATP (energy) and NADPH (electrons). The oxygen is the price of doing business. So far, not a single carbon atom has been touched.

The Calvin cycle — turning CO₂ into sugar

The second half of photosynthesis happens in the fluid around the discs, the stroma. It is called the Calvin cycle, after Melvin Calvin, who worked it out at Berkeley in the late 1940s using radioactive carbon as a tracer. (He won the Nobel Prize for it in 1961, more or less alone, despite a great deal of work by his collaborators — an irritation in the history of biochemistry.)

The Calvin cycle uses the ATP and NADPH made by the light reactions to drag carbon atoms out of the air and weld them onto a growing sugar. The chemistry runs in a loop:

The first step — fixation — is done by an enzyme called RuBisCO, which has the distinction of being the most abundant protein on Earth. There is an awful lot of it: a typical leaf is about half RuBisCO by weight of soluble protein. It needs to be, because RuBisCO is also one of the slowest and clumsiest enzymes known. It will sometimes grab a molecule of oxygen by mistake instead of carbon dioxide, in which case the whole reaction goes into reverse and wastes energy. Evolution, apparently, was good enough but not good enough.

Three turns of the cycle pull in three CO₂ molecules and produce one molecule of G3P, a simple three-carbon sugar. Two G3Ps can be stitched together into a glucose. From glucose the plant builds starch (for storage), cellulose (for cell walls), and ultimately everything else — oils, vitamins, the wood of the trunk, the fragrance of the flower. Every gram of plant matter on Earth was, at some point, three carbon dioxide molecules pulled out of the air by RuBisCO and assembled into sugar.

What this means

The standard accounting of photosynthesis is that it converts about 1% of incoming sunlight into chemical energy. That sounds derisory until you remember the scale. Across the whole biosphere, plants, algae, and photosynthetic bacteria capture about 130 billion tonnes of carbon a year. That carbon, packaged as sugar, is the bottom of every food chain on the planet. A cow eating grass, a hawk eating a mouse, a human eating bread — all of it is, at the end of the chain, sunlight that a leaf turned into sugar through the chemistry above.

The same chemistry has rewritten the planet twice. Around two and a half billion years ago, cyanobacteria got good at splitting water and began belching out oxygen as waste. Iron in the oceans rusted out, then the atmosphere itself filled with O₂. This was the Great Oxygenation Event — the worst pollution disaster in Earth's history — and it nearly sterilized the biosphere. The survivors learned to breathe the pollutant; we are their descendants. The second rewrite is happening now, in reverse: hundreds of millions of years of buried photosynthetic carbon, as coal and oil, are being returned to the atmosphere faster than living leaves can pull it out again.

Photosynthesis is the trick the planet is built on. A green pigment, a manganese cluster, an enzyme that is a bit slow, and a stupendous amount of sunlight, working together inside captured bacteria inside leaves. It looks like nothing is happening. Everything is happening.