Energetics

The chloroplast separates the work into two stages. In the light reactions (on the thylakoid membranes), chlorophyll — a porphyrin ring with a single magnesium ion at its heart — funnels light to two reaction centres. At Photosystem II a manganese cluster (Mn₄CaO₅) splits water: 2 H₂O → O₂ + 4 H⁺ + 4 e⁻. The electrons run a "Z-scheme" (PSII → plastoquinone → cytochrome b6f → the copper protein plastocyanin → Photosystem I → ferredoxin), building NADPH, while the proton gradient drives ATP synthase to make ATP.

In the Calvin cycle (in the surrounding stroma), the enzyme RuBisCO attaches CO₂ to a five-carbon acceptor; the product splits into two molecules of 3-phosphoglycerate, which ATP and NADPH reduce to the three-carbon sugar G3P. That reduction is the exact moment solar energy becomes chemical-bond energy. It takes six turns (≈18 ATP + 12 NADPH) to net one extra sugar; five of every six G3P are recycled to regenerate the acceptor. The triose sugar is exported to the cytosol and assembled into sucrose, with surplus carbon banked as starch.

Common myth: the released O₂ does not come from CO₂ — it comes from the water that is split at Photosystem II.

The Calvin cycle — turning CO₂ into sugar (stroma):

1. CO₂from air
2. RuBisCO+ RuBP, fixation
3. 3-phosphoglycerate2 × C3
4. PGKATP
5. 1,3-bisphosphoglycerate
6. GAPDHNADPH → energy stored
7. G3Ptriose phosphate
8. 6 turns, then cytosol
9. glucose · sucrose

The actual building block isn't free glucose but UDP-glucose — "activated" glucose carrying its own reactive energy (made from sucrose by sucrose synthase, though recent work shows other routes can supply it too). Cellulose-synthase (CesA) proteins assemble into six-lobed rosettes in the plasma membrane — current evidence favours ≈18 subunits, built from three secondary-wall isoforms (conifers express the orthologous triplet in xylem). Each cycle adds one glucose to the non-reducing end, releasing UDP; because alternate units are flipped 180°, the true repeat is cellobiose, and the β linkage (not the α of starch) is exactly why cellulose is rigid and indigestible.

As the new fibril crystallises and anchors in the wall, the resistance pushes the enzyme forward through the fluid membrane — the machine walks while the fibril stays put. Cortical microtubules beneath the membrane act as guide rails (via the CSI1/POM2 tether), setting the grain of the wood. This is the headline contrast with the matrix sugars next door, which are made indoors in the Golgi.

Sugar to crystalline fibre, at the plasma membrane:

1. sucrosefrom the phloem
2. sucrose synthase+ UDP
3. UDP-glucoseactivated
4. CesA rosetteplasma membrane · β-1,4
5. β-1,4-glucan chain
6. H-bondingcrystallization
7. cellulose microfibril

First the cytosol builds a set of activated nucleotide sugars from the central hub UDP-glucose: UDP-galactose, UDP-glucuronic acid → UDP-xylose → UDP-arabinose, plus GDP-mannose from the fructose-6-phosphate pool. These are imported into the Golgi, where the chains are polymerised and decorated. The galactoglucomannan backbone is built by a cellulose-synthase-like enzyme (CSLA, using GDP-sugars) — but the xylan backbone is built by entirely different families (GT43/GT47), and the branches are added by yet others: galactose, 4-O-methyl-glucuronic acid (its methyl from the cofactor SAM), and arabinofuranose, plus O-acetyl groups from acetyl-CoA.

Worth knowing: all these sugars share the same (CH₂O)ₙ make-up, so a mannose-rich matrix is no more energy-dense than a xylose-rich one. Conifer wood burns hot because of its lignin and resin, not its hemicellulose.

Building the sugar toolkit (cytosol), then assembling in the Golgi:

1. UDP-glucosethe hub
2. UGD2 NAD⁺
3. UDP-glucuronic acid
4. UXS− CO₂ (decarboxylation)
5. UDP-xylose
6. 4-epimerase / mutase→ UDP-arabinose
7. UDP-Xyl · UDP-Ara · UDP-Gal · GDP-Mannucleotide sugars
8. Golgi glycosyltransferasesCSLA · GT43/47 · branches
9. galactoglucomannan · xylan

Stage 1 — make the amino acid. In plastids, the seven-step shikimate pathway condenses two photosynthetic intermediates (PEP and erythrose-4-phosphate) into the amino acid phenylalanine (its nitrogen drawn from soil). Animals lack this pathway — which is why phenylalanine is "essential" in our diet, and why the herbicide glyphosate, which blocks one shikimate enzyme, kills plants but not us.

Stage 2 — the phenylpropanoid trunk. PAL strips the amino group (→ cinnamic acid); a P450 enzyme adds a hydroxyl (→ p-coumaric acid, using O₂); 4CL attaches coenzyme A. Stage 3 — the monolignol branch. A methyl group from the cofactor SAM installs the single methoxyl that defines a guaiacyl unit, and two NADPH-driven reductions finish coniferyl alcohol. Softwoods make essentially no sinapyl (syringyl) alcohol because they lack the enzyme F5H — which is exactly why softwood lignin is guaiacyl-rich.

In the wall, copper laccases (using O₂) and iron peroxidases (using H₂O₂) pull one electron off each monomer's phenol, making a radical; two radicals couple — most often at the β-O-4 ether, also β-5, β-β, and 5-5. There's no DNA template, so the bonds form by chemistry alone, giving a different, irregular network every time — though "dirigent" proteins can steer specific couplings (such as the symmetric pinoresinol). Because lignin's aromatic rings are far more reduced than sugar rings, it is the most energy-dense major fraction of wood (~23–26 MJ/kg).

1. the monolignol pathway → coniferyl alcohol
2. phenylalaninefrom the shikimate pathway
3. PAL− NH₃
4. cinnamic acid
5. C4H · P450+ O₂
6. p-coumaric acid
7. 4CL+ CoA, ATP
8. p-coumaroyl-CoA
9. HCT → C3′H → CCoAOMT+ OCH₃ (from SAM) = guaiacyl
10. feruloyl-CoA
11. CCRNADPH
12. coniferaldehyde
13. CADNADPH
14. coniferyl alcoholthe softwood monolignol
15. laccase · peroxidaseO₂ / H₂O₂ · radical coupling
16. lignin network

Sugar is broken down to acetyl-CoA, and fatty acids are built inside the plastid by a bacteria-like assembly line. The committed step is acetyl-CoA carboxylase (making malonyl-CoA); condensing enzymes then add two carbons per cycle — each followed by NADPH-driven reductions — up to 16- and 18-carbon saturated chains. The first double bond, which makes oleic acid, is added by a separate soluble stearoyl-ACP Δ9 desaturase. The chains are then exported to the endoplasmic reticulum and assembled three-at-a-time onto a glycerol backbone (the Kennedy pathway) to make a triacylglycerol, stored in oil bodies. Conifers add an unusual signature: a Δ5 desaturase makes "pinolenic"-type fatty acids found almost nowhere else.

Why so energy-rich: combustion energy tracks how reduced a molecule is. Fats yield ~37–39 kJ/g versus ~16–17 kJ/g for carbohydrates, whose ring carbons already each carry an oxygen.

1. sugar → two-carbon units → fat
2. glucose
3. glycolysis → PDHin the plastid
4. acetyl-CoA2-carbon unit
5. ACCaseATP, + CO₂ (committed step)
6. malonyl-CoA
7. fatty-acid synthase7 cycles, NADPH
8. stearoyl-ACP18:0, saturated
9. stearoyl-ACP Δ9 desaturaseadds the double bond
10. oleic acid18:1
11. Kennedy pathway×3 on glycerol, at the ER
12. triacylglycerol

Terpenoids are built from a universal five-carbon unit (isopentenyl diphosphate) made by two routes — the MEP pathway in plastids and the MVA pathway in the cytosol. Joining these units gives a C10 precursor that terpene synthases cyclise into the pinenes (conifer versions unusually need manganese), and a C20 precursor that a bifunctional diterpene synthase folds into abietadiene; cytochrome P450 enzymes then oxidise it to resin acids like abietic acid. The finished oleoresin is stored under pressure in a network of resin ducts lined by living cells, and the whole system is switched up by wound signals (jasmonate) — making resin a regulated immune response. At ~40–44 MJ/kg, in the range of petroleum fuels, it is costly to make, so the tree is deliberately banking captured energy into a high-density defensive reserve.

From two-carbon and three-carbon units to the volatile (turpentine) and solid (rosin) fractions:

Each polymer has its own decomposition window. Hemicellulose is least stable and goes first (~220–315 °C); cellulose follows in a sharp burst (~315–400 °C, peak ~340 °C); and lignin decomposes slowly across a huge range (~160–900 °C), yielding ~40–45% of its mass as char. Cellulose pyrolysis is endothermic (it soaks up heat), while hemicellulose and lignin are exothermic.

1. waterdrying
2. hemicellulosechar ~23%
3. cellulosechar ~8%
4. ligninchar ~45%
5. ~100 °C300500700900 °C

About 70% of dry wood leaves as volatiles that feed the flame; the rest is char that glows and smolders. Burning efficiency is measured by the modified combustion efficiency (MCE): vigorous flaming runs ~0.95–0.99, while smoldering char drops to ~0.65–0.85, releasing more carbon monoxide and smoke. Char oxidation can account for roughly a third of the energy in vegetation fuels — but much char never fully burns. A pine charcoal is ~50–90% carbon and can persist in soils for decades to millennia, so fire both releases energy and banks a slow-cycling carbon residue.

Worth knowing: even a crown fire consumes only ~56–66% of the canopy foliage, and almost none of the bole — incomplete combustion is the rule, not the exception.

A ruminant (deer, elk) houses trillions of microbes that do make cellulases. In the rumen, microbes depolymerise cellulose to sugars and ferment them to volatile fatty acids — acetate, propionate, and butyrate (roughly 70:20:10 on browse) — which the animal absorbs through the gut wall and oxidises for energy. These VFAs supply ~70–80% of a ruminant's energy; the microbes themselves are then digested as protein. Termites do the same for wood, their gut symbionts removing 74–99% of the cellulose.

1. how a browser extracts wood energy
2. cellulose · hemicellulose
3. microbial cellulasesrumen / hindgut symbionts
4. sugars
5. fermentation→ acetate · propionate · butyrate
6. volatile fatty acidsabsorbed by the animal
7. β-oxidation · TCA · ox-phosin mitochondria
8. ATP~30–32 per glucose

Lignin's last trick: it passes through the gut almost untouched and physically shields the digestible sugars, which is why woody, lignin-rich tissue is poor forage — and why the easy calories are in young needles, sap, and seeds (fat at ~9 kcal/g vs ~4 for carbohydrate). Soluble sugars, starch, fat, and protein need no microbes — the animal's own enzymes handle them directly.

Decay speed tracks composition. Ponderosa needle litter turns over in ~6–13 years (k ≈ 0.08–0.18 yr⁻¹); a fallen white-fir log takes a half-life of ~14 years, and large conifer logs persist for 50–120 years. Gymnosperm wood decays roughly 2–3× slower than angiosperm wood (occasionally 10× for rot-resistant species), and standing dead snags decay far slower than logs on the moist ground. Of the carbon that is decomposed, ~70–90% is respired straight back to CO₂; the remainder becomes humus and soil organic matter — the forest's long-term carbon (and energy) savings account.

Full circle: the enzymes white-rot fungi use to take lignin apart are mechanistic cousins of the laccases and peroxidases the tree used to build it — the same oxidative chemistry, run in reverse.

Charring temperature sets the structure. Above ~400 °C the leftover carbon condenses into polycyclic aromatic clusters (often >7 fused rings); as temperature climbs the carbon content rises from ~48% in raw wood to ~85% at 600 °C and ~94% at 800 °C, shedding the oxygen-bearing "handles" enzymes need. The interior carbons are bonded only to other carbons, which is why condensed pyrogenic carbon is one of Earth's most decay-resistant organic pools — though it's a continuum, and lightly-charred material is far more labile (some field studies see surprisingly fast loss of that fraction).

Globally, fire converts ~256 Tg C/yr (≈12% of fire's carbon emissions) into pyrogenic carbon, which accumulates to roughly ~200 Pg C in soils and ~480–1440 Pg C in marine sediments. Buried and lithified, charcoal becomes inertinite, a coal maceral that is literally fossil wildfire: Carboniferous coals (≈359–299 Ma) are inertinite-rich (~15–20%, locally 40–50%). Because charcoal only forms and spreads when atmospheric oxygen sits in a "fire window" (≈16–35%), the inertinite in those coals also works as a paleo-oxygen gauge — pointing to a Late-Paleozoic O₂ peak around ~28–30%, well above today's 21%, which fed the era's intense, frequent fires.