HookTwo numbers decide how many mouths a field can feed
A field of wheat is a machine for turning sunlight into food, and it is a strikingly leaky one. Of the light that falls on a crop, only around 1 to 2% ends up as new plant material; the rest is reflected, misses the chlorophyll, or is the wrong wavelength to be used. Then, when an animal eats that plant, only around a tenth of the energy stored in it is built into the animal — the remainder is lost as heat from respiration, in droppings, and in the parts that are never eaten or digested. Two measurable numbers, roughly 1% and roughly 10%, decide how much food a given piece of land can ultimately provide.
Those numbers are why humanity is fed mostly on grain and not on beef: every step up a food chain throws most of the energy away, so a hectare feeds far more people as bread than as steak. Section 3.5 is the biology behind the two numbers — how photosynthesis captures light and fixes carbon, how respiration releases that energy again as ATP, how what survives flows through an ecosystem, and how the elements locked inside living things are cycled back by microorganisms so the whole system can run again. It is also heavily quantitative, so the marks reward clean, shown working: productivity budgets, percentage efficiencies, Rf values and respirometer volumes all live in this section.
MechanismPhotosynthesis I: the light-dependent reactions
Photosynthesis happens in the chloroplast, and its two halves happen in two places. The light-dependent reactions run on the thylakoid membranes, whose stacks (grana) give a huge surface area for the pigment chlorophyll. Light excites electrons in chlorophyll to a higher energy level, and they leave along an electron transport chain. To replace the lost electrons, water is split — photolysis:
\[ 2\mathrm{H_2O} \rightarrow 4\mathrm{H^+} + 4e^- + \mathrm{O_2} \]
which is where the oxygen you breathe comes from.
As the excited electrons pass down the chain they release energy that pumps protons into the thylakoid space; the protons then flow back through ATP synthase, driving photophosphorylation — the synthesis of ATP. At the end of the chain the electrons and protons reduce the coenzyme NADP to reduced NADP. The light-dependent stage therefore hands three things onwards: ATP, reduced NADP, and, as a waste product, oxygen.
MechanismPhotosynthesis II: the Calvin cycle
The light-independent reactions take place in the stroma and are known as the Calvin cycle. Carbon dioxide diffuses in and is fixed onto a five-carbon acceptor, ribulose bisphosphate (RuBP), by the enzyme rubisco. The unstable six-carbon product splits at once into two molecules of the three-carbon glycerate 3-phosphate (GP). Using the reduced NADP and ATP made in the light-dependent stage, GP is reduced to the three-carbon triose phosphate (TP).
Some TP leaves the cycle to build glucose — and from it starch, cellulose, amino acids and lipids — while most is recycled, using more ATP, to regenerate RuBP so the cycle can keep turning. The arithmetic is worth knowing: it takes three turns to yield one molecule of TP for export, and six turns — six molecules of carbon dioxide fixed — to build a single glucose. The overall rate is set by limiting factors: light intensity, carbon dioxide concentration and temperature, whichever is in shortest supply.
Account for a single glucose. Glucose has six carbons, so six molecules of carbon dioxide must be fixed — six turns of the Calvin cycle. Each turn fixes one carbon dioxide and spends 3 ATP and 2 reduced NADP, so one glucose costs \(6 \times 3 = 18\) ATP and \(6 \times 2 = 12\) reduced NADP. Those totals are exactly what the light-dependent reactions must supply, and they explain a classic exam graph: switch the light off, the ATP and reduced NADP supply stops, GP can no longer be reduced, so GP rises while TP and RuBP fall.
CaseSeeing it work: pigments and the Hill reaction — RP7 and RP8
Two required practicals make photosynthesis visible. In Required practical 7 you separate a leaf's pigments by chromatography: grind the leaf with a little solvent, spot the concentrated extract onto chromatography paper or a thin-layer plate, and let a solvent carry the pigments up. They separate because each pigment differs in how strongly it is attracted to the moving solvent versus the stationary paper, resolving into chlorophyll a, chlorophyll b and the accessory pigments carotene and xanthophyll. Each is identified by its Rf value — the distance the pigment moved divided by the distance the solvent front moved.
In Required practical 8 you measure the rate of the light-dependent reactions in chloroplasts extracted from a leaf. The dye DCPIP stands in for NADP: it is blue when oxidised and turns colourless when it accepts electrons, so the faster the light-dependent reactions run, the faster the blue fades — timed by eye or, better, as a falling absorbance in a colorimeter. The independent variable might be light intensity (vary the lamp distance) or wavelength; the dependent variable is the rate of colour loss; and controls include a tube of boiled chloroplasts (denatured, so no reaction) and one kept in the dark.
On a chromatogram the solvent front travels 80 mm. A carotene spot travels 68 mm and a chlorophyll b spot 40 mm. Their Rf values are \(R_f = \dfrac{68}{80} = 0.85\) and \(R_f = \dfrac{40}{80} = 0.50\). Carotene runs near the front because it is the most soluble in the moving organic solvent and least attracted to the paper. An Rf is always below 1 — a spot cannot overtake the solvent that carries it — so any value above 1 is an arithmetic slip. Matching an Rf against known values measured in the same solvent identifies the pigment.
MechanismRespiration: four stages from glucose to ATP
Respiration releases the energy in glucose in four stages. Glycolysis, in the cytoplasm and needing no oxygen, phosphorylates glucose using 2 ATP, then splits and oxidises it into two three-carbon pyruvate molecules, for a net yield of 2 ATP and 2 reduced NAD. Each pyruvate then enters a mitochondrion for the link reaction in the matrix: it is decarboxylated and dehydrogenated to a two-carbon acetyl group, carried on coenzyme A as acetyl-CoA, releasing carbon dioxide and reduced NAD.
The acetyl group joins a four-carbon acceptor to begin the Krebs cycle, also in the matrix; each turn gives off 2 carbon dioxide and produces 3 reduced NAD, 1 reduced FAD and 1 ATP — and there are two turns per glucose. The real payoff is oxidative phosphorylation on the inner membrane: electrons from all that reduced NAD and FAD pass down the electron transport chain, pumping protons whose return through ATP synthase makes most of the cell's ATP (chemiosmosis). Oxygen is the final electron acceptor, combining with electrons and protons to form water. Without oxygen the chain backs up, and cells fall back on anaerobic respiration — making lactate in animals, or ethanol and carbon dioxide in yeast and plants — simply to regenerate NAD so that glycolysis can limp on.
Add up the ATP from one glucose. Substrate-level phosphorylation gives 4 directly — 2 in glycolysis and 1 in each of the two Krebs turns. The rest comes from oxidative phosphorylation, fed by 10 reduced NAD (2 from glycolysis, 2 from the link reaction, 6 from Krebs) and 2 reduced FAD. Taking a modern yield of about 2.5 ATP per reduced NAD and 1.5 per reduced FAD gives \(10 \times 2.5 + 2 \times 1.5 = 28\), for a total near \(28 + 4 = 32\) ATP. Older specifications quote a theoretical maximum of 38 (using 3 and 2 instead); the real figure is lower still because protons leak and importing pyruvate and reduced NAD into the mitochondrion itself costs energy. State whichever assumption you use.
DataMeasuring respiration rate — Required practical 9
Required practical 9 measures how fast single-celled organisms such as yeast respire, using a respirometer. The organisms sit in a sealed tube connected to a manometer, and a chemical such as soda lime or potassium hydroxide absorbs the carbon dioxide they release. Because the carbon dioxide is mopped up, any change in gas volume is due to the oxygen consumed, so the manometer fluid moves toward the organisms by exactly that volume. A second respirometer holding glass beads instead of organisms acts as a control for changes in temperature and pressure, and the whole apparatus sits in a water bath to hold temperature — a major confounding variable — constant.
The independent variable might be temperature, substrate or organism; the dependent variable is the volume of oxygen used per minute, ideally corrected per gram of organism; controlled variables include the volume and concentration of the culture and the time allowed. If you remove the carbon-dioxide absorbent, the net movement of the fluid instead lets you find the respiratory quotient — the ratio of carbon dioxide given out to oxygen taken in — which is about 1.0 for carbohydrate and about 0.7 for lipid.
Read a respirometer. The manometer capillary has a bore of radius 0.5 mm, and in 6 minutes the coloured fluid moves 42 mm toward the yeast. The oxygen consumed is the volume of that cylinder of fluid: \(V = \pi r^2 l = \pi \times (0.5)^2 \times 42 = 33\ \text{mm}^3\). The rate is \(33 \div 6 = 5.5\ \text{mm}^3\,\text{min}^{-1}\); for 2 g of yeast that is \(2.75\ \text{mm}^3\,\text{min}^{-1}\,\text{g}^{-1}\). Without the control tube of glass beads you could not tell respiration from a stray change in room temperature, which would move the fluid just as convincingly.
DataEnergy through ecosystems: productivity and its losses
Producers capture light as chemical energy at a rate called gross primary production (GPP). Plants respire away a share of it, so what is left for growth — and for the animals that eat the plant — is the net primary production:
\[ \mathrm{NPP} = \mathrm{GPP} - R \]
where \(R\) is respiratory loss, measured in kJ m⁻² yr⁻¹. For consumers the equivalent bookkeeping is \(N = I - (F + R)\): the net production \(N\) is what is ingested (\(I\)) minus what is lost in faeces (\(F\)) and respiration (\(R\)).
Energy leaks at every step — as heat from respiration, in egested and excreted material, and in parts never eaten — so only around 10% of the energy at one trophic level is built into the next, and often much less. That is why food chains are short, and why farming is, at heart, an attempt to plug the leaks: simplifying food webs, using herbicides and pesticides to stop other organisms eating the crop, and rearing livestock so that less energy is wasted on movement and keeping warm. It raises yield — and it is why the diversity index of an intensive farm is so low.
Work through a grazed grassland. The grass has a gross primary production of 36 000 kJ m⁻² yr⁻¹ and respires away 16 000, so its net primary production is \(\mathrm{NPP} = 36\,000 - 16\,000 = 20\,000\) kJ m⁻² yr⁻¹.
Cattle grazing it ingest 2400 kJ m⁻² yr⁻¹, egest 600 in faeces and respire 1300, so their net production is \(N = 2400 - (600 + 1300) = 500\) kJ m⁻² yr⁻¹.
The efficiency of transfer from grass to cattle is \(500 \div 20\,000 = 0.025\), or 2.5%. Most of the grass's NPP is never eaten at all — it dies and passes to decomposers — which is why real herbivore efficiencies are often only a few per cent, well below the textbook 10%.
MechanismNutrient cycles: nitrogen, phosphorus and the microbes that drive them
Energy flows through an ecosystem and is lost, but the elements in living things are used again and again — and microorganisms run the recycling. Take the nitrogen cycle. Nitrogen fixation converts inert atmospheric nitrogen into ammonia, both by Rhizobium living mutualistically in the root nodules of legumes and by free-living soil bacteria. Ammonification by decomposers (saprobionts) turns the nitrogen in dead organisms and waste into ammonium. Nitrification, an aerobic process, is carried out by two bacteria in turn: Nitrosomonas oxidises ammonium to nitrite, then Nitrobacter oxidises nitrite to nitrate, the form plant roots absorb. Denitrification, by anaerobic bacteria in waterlogged soil, undoes the work, reducing nitrate back to nitrogen gas — which is why good farmers keep soil aerated and drained.
The phosphorus cycle has no gaseous stage. Phosphate ions are released by the weathering of rock, taken up by plant roots (often assisted by mycorrhizae — fungi that hugely increase the root surface area for absorption), passed along food chains, and returned to the soil when decomposers break down dead matter and waste. Farmers top both cycles up with fertilisers, but over-application has a cost: soluble nitrate and phosphate are washed by leaching into rivers and lakes, where they cause eutrophication — algal blooms that block light, followed by bacterial decay that strips the water of oxygen and kills fish.
VocabularyKey terms the mark scheme pays for
TrapsMisconceptions that cost marks
ExamWhat examiners want
Photosynthesis and respiration are marked as ordered sequences with the right molecule in the right place. Always attach a location — thylakoid membrane, stroma, cytoplasm, matrix, inner mitochondrial membrane — and the products of each stage, and never lose the coenzymes: reduced NADP and reduced NAD are the thread linking the stages, and 'ATP and reduced NADP' is the standard credit for the output of the light-dependent reactions.
The quantitative marks — at least 10% of the paper — cluster in this section: \(\mathrm{NPP} = \mathrm{GPP} - R\), net production \(N = I - (F + R)\), percentage efficiency between trophic levels, Rf values, and respirometer volumes from \(\pi r^2 l\). Always state the formula, substitute, and give the unit — kJ m⁻² yr⁻¹ or mm³ min⁻¹ — because the unit itself often carries a mark. On limiting-factor graphs, name which factor is limiting in each region rather than merely describing the line.
For the required practicals, be ready to state the independent, dependent and controlled variables and one real source of error with its fix — the beads control in the respirometer, boiled chloroplasts in the DCPIP assay, a pencil origin in chromatography. Six-mark extended answers are marked as a logical line of reasoning, so build the chain rather than listing facts. Evaluation questions on farming or fertiliser want both sides quantified: higher yield and productivity set against lost biodiversity, leaching and eutrophication. This is strongly synoptic material — expect it linked to enzymes, ATP structure and biodiversity in the Paper 3 essay.