Biology  by Bradford
support
IB BIOLOGY · THEME C · INTERACTION AND INTERDEPENDENCE

Light into sugar

Almost every meal you eat, and every breath of oxygen you take, starts with a leaf catching light. Here is how a plant splits water, pulls carbon out of the air and builds sugar from it, what slows it down, and how you can measure it on a bench.

IB Biology C1.3SL and HL3 hours SL, 6 HL15 chaptersdry lab

Start learningRun the dry labTeach it

Zoom into a leaf and watch light split water, oxygen leave and carbon dioxide become sugar.

01Learn

Fifteen chapters, the last eight for higher level. Read one, play its figure or change its settings, and make each prediction before you open the answer.

  1. 1Sunlight in, chemical energy out
  2. 2Carbon from the air, hydrogen from water
  3. 3More than one green
  4. 4Why some colours and not others
  5. 5Absorbed is not the same as used
  6. 6Whatever runs short sets the pace
  7. 7Tomorrow’s air, today
  8. 8Pigments in an array HL
  9. 9Water split, oxygen spare HL
  10. 10Protons downhill make ATP HL
  11. 11NADP reduced, and the thylakoid as a system HL
  12. 12Fixing carbon, slowly HL
  13. 13GP to TP, and RuBP made again HL
  14. 14Every carbon came this way HL
  15. 15Each half needs the other HL

C1.3.1 Light energy to chemical energy

Sunlight in, chemical energy out

Photosynthesis transforms light energy into chemical energy. In a leaf, pigments absorb light, and that energy ends up in the bonds of carbon compounds the plant builds: first sugars, then everything else it is made of. Light is not stored. It is changed into a different form, an energy transformation.

That chemical energy runs nearly every food chain. Plants, algae and cyanobacteria are producers. A rabbit eating grass, and a fox eating the rabbit, are living on energy the grass caught from the Sun. A few ecosystems, round deep-sea vents, run on chemical energy from the vent instead (C4.2 returns to this), but almost all the others depend on photosynthesis.

Cells need that energy for three kinds of work: building large molecules (anabolism, C1.1), moving substances against their gradients (active transport, B2.1), and movement, from muscle contraction to the pulling apart of chromosomes. Respiration (C1.2) releases the energy from carbon compounds and holds it in ATP, which pays for the work. At every step some energy leaves as heat. Energy flows through an ecosystem and is not recycled; carbon is (C4.2).

  • Photosynthesis transforms light energy into the chemical energy of carbon compounds.
  • Producers make the carbon compounds that every consumer in a food chain depends on.
  • Energy flows light, then chemical energy in sugar, then ATP, then work and heat.
Watch out Photosynthesis does not make energy; it changes light energy into chemical energy. And plants respire too, in the dark and in the light: they use some of the sugar they make.

The chemical energy in a slice of cheese: where did it first come from?

light energychemical energyin sugarcheese sandwichATPchemical energy in ATP
  1. Light energy from the Sun reaches a leaf.
  2. Photosynthesis turns it into chemical energy in the bonds of sugar.
  3. The cow lives on that energy, and stores some of it in milk.
  4. You release it in respiration, as ATP, and every step loses some as heat.

C1.3.2 C1.3.3 Carbon dioxide to glucose, with oxygen as a by-product

Carbon from the air, hydrogen from water

The word equation for photosynthesis is carbon dioxide + water → glucose + oxygen, with light energy and chlorophyll written over the arrow. In symbols it reads 6CO2 + 6H2O → C6H12O6 + 6O2, and the product that matters is glucose.

Look at the molecules. Carbon dioxide has carbon and oxygen but no hydrogen, and glucose needs plenty. The plant gets its hydrogen from water. It splits water using energy from the light that chlorophyll absorbs, a step called photolysis, and the hydrogen is added to carbon dioxide to build glucose. So glucose’s carbon and oxygen come from carbon dioxide, and its hydrogen comes from water. Most of a tree’s dry mass is carbon and oxygen taken from the air, not from the soil.

The oxygen gas a leaf gives off is a by-product. It comes from the water that was split, not from carbon dioxide. Every organism that photosynthesises this way gives off oxygen: plants, algae (from single cells to seaweeds) and cyanobacteria. Cyanobacteria were the first of them, as chapter 9 shows at higher level.

Adding hydrogen to a molecule is a reduction (C1.2). At higher level, chapters 8 to 13 follow the hydrogen from water to carbon dioxide, as electrons and protons carried by NADP.

How we know In 1941 Ruben and colleagues gave algae water made with a heavy form of oxygen. The oxygen gas the algae gave off was heavy too. When the heavy oxygen was in the carbon dioxide instead, the gas was not. The oxygen had come from the water.
  • Carbon dioxide + water → glucose + oxygen, with light energy and chlorophyll over the arrow.
  • Glucose’s carbon and oxygen come from carbon dioxide; its hydrogen comes from water.
  • The oxygen given off comes from the water that is split, and is a by-product.
Watch out “The oxygen comes from carbon dioxide” is the commonest slip, because the equation seems to say so. Carbon dioxide’s oxygen ends up in the glucose and in the water that is made again. And light does not split water by itself: chlorophyll catches the light first (chapter 9).

Where does the oxygen gas a leaf gives off come from?

6 carbon dioxideHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHOHHO12 wateroxygen leavesglucoseHHOHHOHHOHHOHHOHHOwater made againcarbon dioxide+water→glucose+oxygen
  1. What goes in: carbon dioxide from the air, water from the soil.
  2. Light energy splits water. The oxygen leaves as a by-product.
  3. The hydrogen is added to carbon dioxide, building glucose.
  4. carbon dioxide + water → glucose + oxygen. The bars show where each atom came from: green, carbon dioxide; pink, water.
Where did it come from?Six atoms or molecules to sortCame from carbon dioxideCame from waterThe carbon atomsin glucoseThe oxygen atomsin glucoseThe hydrogen atomsin glucoseThe oxygen gas aleaf gives offThe carbon in apotato’s starchHydrogen in the fatof an oil-seed plant

Pick a card (tap it, or Tab to it and press Enter), then pick the bin it belongs in.

0 of 6 sorted

Six atoms or molecules and two bins. Which molecule going in had the atom at all, and what tells you?
Zoom into a leaf and watch light split water, oxygen leave and carbon dioxide become sugar.

C1.3.4 Separation and identification of pigments by chromatography

More than one green

A leaf’s green is not one pigment but several, mixed. Chlorophyll a is the main one, blue-green. Chlorophyll b is yellow-green. Beside them are the yellow and orange carotenoids: carotenes and xanthophylls. All of them sit in the membranes of the chloroplast’s thylakoids.

Chromatography separates a mixture. A small, dark spot of leaf extract goes on a pencil line, the origin, near the bottom of a strip of chromatography paper (or a thin-layer plate, the stationary phase). The strip stands in a shallow layer of solvent (the mobile phase) below the spot, in a closed tube. The solvent climbs and carries the pigments with it.

Each pigment travels at its own speed. The more soluble it is in the solvent, and the less it clings to the paper, the further it goes. So the pigments end up as separate bands. The solvent front marks how far the solvent went, and the Rf value compares the two:

Rf = distance moved by the pigment ÷ distance moved by the solvent front, both from the origin, the pigment to the middle of its band.

Rf has no units and is always less than 1. You identify a pigment by its colour and its Rf, read against a table made with the same solvent and the same paper or plate. Thin-layer plates run faster and separate better than paper.

  • Pencil, not ink, for the origin: ink is a mixture and runs too.
  • A small, dark spot, built up by drying between drops.
  • Solvent below the origin, and a lid on the tube.
  • Take the strip out before the front reaches the top, and mark the front at once.
  • Work quickly: pigments fade in the light.
Watch out Measure from the origin line, not from the bottom of the paper, and to the middle of the band. And an Rf only means something beside a table made with the same solvent.
Why it matters Chromatography separates and identifies the substances in a biological mixture. The same idea separates amino acids and sugars.

The solvent front has moved 8.0 cm from the origin and a yellow band 5.7 cm. What is the band’s Rf?

1234originsolventsolvent front012345678cmpigment:5.7 cmsolvent:8.0 cm

0 to 10 min

Slide the time. The solvent climbs and the green spot pulls apart into numbered bands. At the end, the distances are measured from the origin line.
1 Grind2 Spot, then stand the strip in propanoneleaf, sand, propanoneorigin line, 2 cm uppropanone below itoriginfront01234567891011cm1234Your resultsBandColourDistance / mmRfPigment1234frontTable of known values: paper, propanonePigmentColourRfCaroteneorange-yellow0.95Phaeophytinolive grey0.83Xanthophyllyellow0.71Chlorophyll ablue-green0.65Chlorophyll byellow-green0.45
  1. Grind a leaf with a little sand and a few drops of propanone. Spot the extract on a pencil line 2 cm from the bottom of the strip, then stand the strip in propanone, below the line, with the lid on.
  2. Take the strip out before the solvent reaches the top and mark the front in pencil at once. The pigments have separated into bands. The table beside it lists known values for this solvent.
  3. Measure from the origin line to the middle of each band and to the front. Work out Rf for each band, then name each pigment from its colour and its Rf.

C1.3.5 Absorption of specific wavelengths by photosynthetic pigments

Why some colours and not others

Visible light is the band of wavelengths from about 400 nm (violet) to about 700 nm (red). White light is every one of them together, and the shorter the wavelength, the more energy each photon carries.

A pigment absorbs a photon only if the photon’s energy matches a jump one of its electrons can make to a higher energy level. The electron is then excited. Photons with other energies are not absorbed: they pass through the pigment or bounce off it, which is reflection.

Chlorophyll’s electrons can make jumps that match blue and red photons, so it absorbs those strongly and very little green. The green is reflected or passes through. That is why leaves look green: you see the light they did not use. The energy of the excited electron is what photosynthesis turns into chemical energy.

Accessory pigments, the carotenoids, absorb blue and blue-green light that chlorophyll a takes up less, and widen the range of light a leaf can use. In autumn the chlorophyll breaks down first, and the carotenoids show as yellow and orange. An absorption spectrum shows, wavelength by wavelength, how much of the light a pigment takes in. Draw it with both the wavelengths in nm and the colours along the horizontal axis.

The pigments are held together in arrays called photosystems (chapter 8).

  • Visible light runs from about 400 nm (violet) to about 700 nm (red).
  • A photon is absorbed only if its energy matches a jump an electron in the pigment can make.
  • Chlorophyll absorbs blue and red strongly and reflects green, so a leaf looks green.
  • The horizontal axis of an absorption spectrum carries wavelengths and colours.

Remember it The colours, longest wavelength first

  • RichardRedabout 700 nm, absorbed
  • OfOrangeabout 610 nm
  • YorkYellowabout 580 nm
  • GaveGreenabout 530 nm, mostly reflected
  • BattleBlueabout 450 nm, absorbed
  • InIndigoabout 440 nm
  • VainVioletabout 400 nm
Watch out A leaf is not green because chlorophyll makes green light. Green is the light it did not absorb.

Why does chlorophyll absorb red and blue light but very little green?

leaf (side view)white lightevery colour together050100400450500550600650700Wavelength / nmLight absorbed / %chlorophyll achlorophyll bcarotenoids leaf (side view)white lightevery colourtogether050100400500600700Wavelength / nmLight absorbed / %chlorophyll achlorophyll bcarotenoids
  1. White light is every colour together.
  2. Chlorophyll absorbs blue and red and reflects most green.
  3. An absorption spectrum: how much of each wavelength a pigment absorbs. These are for pigments dissolved in a solvent.
  4. Accessory pigments absorb where chlorophyll a absorbs least.
050100400450500550600650700Wavelength / nmLight absorbed / %

Drag each handle up to how much you think chlorophyll absorbs at that colour (or focus one and use the up and down keys). Then press Show me.

Sketch chlorophyll’s absorption spectrum: seven handles, one for each colour band. Chlorophyll a is the pigment to draw.

C1.3.6 Absorption and action spectra compared

Absorbed is not the same as used

An action spectrum plots how fast photosynthesis runs against the wavelength of the light a plant is given. You measure it by lighting the plant with one colour at a time, the same amount of light each time, and measuring the oxygen it gives off or the carbon dioxide it takes in. The rate of photosynthesis is the amount of oxygen produced (or carbon dioxide consumed) divided by the time taken, for example cm3 of oxygen ÷ 10 minutes, in cm3 min−1. Then plot rate against wavelength.

The two spectra are alike because the light a leaf uses is the light its pigments absorb: both peak in the blue and the red and dip in the green. They are not the same. The action spectrum’s green dip is shallower, because chlorophyll b and the carotenoids absorb some of those wavelengths and pass the energy on, and because in a thick leaf green light bounces about and more of it is absorbed in the end. And absorbing light is not always using it: some of the energy that carotenoids absorb in the blue is lost as heat, so the action spectrum’s blue peak is lower than the combined absorption there.

How we know In 1882 Theodor Engelmann lit a strand of a green alga with a spectrum from a prism and added bacteria that swim towards oxygen. They crowded where red and blue light fell. It was the first action spectrum, measured with living bacteria as oxygen detectors. The film below repeats it.
  • Rate of photosynthesis = oxygen produced (or carbon dioxide consumed) ÷ time.
  • Similar: both spectra peak in blue and red and dip in green.
  • Different: the action spectrum is a rate, its green dip is shallower, and its blue peak is lower than the absorption there.
Watch out An action spectrum is not “the light a plant absorbs”. It is what the plant does with each colour: its rate of photosynthesis.

Engelmann shone a spectrum along a strand of alga and added bacteria that swim towards oxygen. Where did the bacteria gather?

Oxygen collected from a sprig of pondweed in 10 minutes, at equal light of each wavelength
Wavelength / nmColourOxygen in 10 min / cm3Rate / cm3 min−1
425violet0.30
450blue0.30
500blue-green0.23
550green0.13
600orange0.24
650red0.35
675deep red0.35

Data from the dry lab’s model: a sprig in 5 % hydrogencarbonate at 25 °C, the same number of photons at every wavelength.

400450500550600650700Wavelength / nm0.000.010.020.030.04Rate of photosynthesis / cm3 min−1

Work out each rate: volume ÷ time. Then set each handle on the graph to its rate (drag it, or focus it and use the up and down keys).

Seven wavelengths of light, the oxygen a sprig gave off in 10 minutes in each, and empty axes. Rate = volume of oxygen ÷ time.
A strand of alga under a microscope, bacteria that seek oxygen, and a prism. Split the light and watch where the bacteria go.

C1.3.7 Varying light, carbon dioxide and temperature to test limiting factors

Whatever runs short sets the pace

Photosynthesis needs light, carbon dioxide and a suitable temperature all at once. When several factors affect a rate, the one in shortest supply holds it back. Raising that limiting factor speeds the process up, and raising the others does nothing, until one of them becomes the shortest. Blackman stated this as the law of limiting factors in 1905.

Light intensity limits the supply of energy for splitting water. The rate rises with light, then levels off when something else limits. Carbon dioxide concentration limits the fixing of carbon in the same way. Temperature acts on the enzymes (you saw why in C1.1): the rate rises to an optimum, about 25 to 30 °C for many temperate plants, then falls as the enzymes denature. In dim light, temperature matters little, because light is the limit. Where a curve levels off, another factor sets the height of the plateau: raise that one and the plateau rises.

To test each factor, vary it on its own. Move a lamp to change the light (the intensity falls roughly as 1 ÷ distance2, so use a light meter, with a heat shield between lamp and water). Dissolve sodium hydrogencarbonate in the water round pondweed or leaf discs to change the carbon dioxide (0 to 5 %). Use a water bath for temperature. Measure the rate by counting oxygen bubbles or collecting the gas, by the time leaf discs take to float, by the carbon dioxide taken up (hydrogencarbonate indicator), or by the gain in dry mass, which is slow and indirect.

A hypothesis is a provisional explanation that must be tested again and again. You can write it from theory before the experiment (“if carbon dioxide is the limiting factor, the rate will rise and then level off”), or from the evidence of a first run. Either way you name the independent variable (what you change), the dependent variable (what you measure) and the controlled variables (everything else, kept the same). Then test it on the bench, in the dry lab.

  • Limiting factor: the factor in shortest supply, which sets the rate.
  • Light, carbon dioxide and temperature are the three to know; raise the limiting one and the rate rises, until another takes over.
  • A hypothesis names the independent, dependent and controlled variables.

Remember it The three limiting factors

  • LazyLight intensitythe supply of energy for splitting water
  • CatsCarbon dioxide concentrationthe carbon to fix
  • ToastTemperaturethe speed of the enzymes, up to their optimum
Watch out A limiting factor is not “a factor that stops photosynthesis”. It is the one in shortest supply, setting the rate. Raise it and the rate rises, until another one takes over.

A plant at 15 °C is given more and more light until its rate levels off. Then it is warmed to 25 °C. What happens to the rate?

Stage 1 of 3 Rate against light intensity. Draw how you think the rate changes as the light gets brighter.

Light intensityRate of photosynthesis

Draw with a finger, a pen or the mouse (one stroke), then press Show me.

Sketch a hypothesis as a graph, then check it. Three stages: light, then temperature, then carbon dioxide at high and low light.

Sketch it: three tasks

Light intensityRate1: rate against light intensityLight intensityRate2: add a line for a low temperatureCarbon dioxideRate3: carbon dioxide, high and low light

The answers

Light intensityRatewarmLight intensityRatewarmcoolCarbon dioxideRatehigh lightlow light

C1.3.8 Carbon dioxide enrichment experiments

Tomorrow’s air, today

The air’s carbon dioxide has risen from about 280 parts per million before the industrial revolution to over 420 now, mostly from burning fossil fuels and clearing forests (D4.3 returns to this). Carbon dioxide is often a limiting factor, so will crops and forests grow faster in tomorrow’s air?

Carbon dioxide enrichment experiments grow plants in the carbon dioxide expected later this century (about 550 to 600 ppm) beside plants in today’s air, and compare photosynthesis, growth and yield. They ask whether the rate of photosynthesis rises and stays up, how much growth and yield gain, which plants gain most, and whether another factor (water, nitrogen or temperature) soon takes over as the limit.

In an enclosed greenhouse experiment, carbon dioxide from a gas cylinder holds the air at the chosen level. Temperature, light, water and nutrients can be controlled, so carbon dioxide is the only variable that differs. But pots restrict roots, the enclosure changes light and humidity, and only small plants fit. Commercial growers already enrich greenhouses to raise yields of crops such as tomatoes.

In free-air carbon dioxide enrichment (FACE), a ring of pipes up to about 20 to 30 m across stands in a field or a forest. A sensor in the middle measures the carbon dioxide, and a computer sets how much the upwind pipes release to hold the target level. Control rings with the same pipes but no added carbon dioxide stand nearby. The plants grow in real soil, weather and competition, and whole trees can be studied. But temperature, rain and light cannot be controlled, and the gas is costly.

Careful control of variables is part of designing an experiment. It is easier in a laboratory or greenhouse, but some questions can only be answered in the field. A controlled variable in a greenhouse is the temperature; in FACE it is the crop variety, the sowing date or the pipes in the control rings. Crops in FACE rings gained less yield from extra carbon dioxide than enclosure studies had predicted, probably because in a field another factor soon becomes limiting.

  • Enrichment experiments predict how plants will respond to the carbon dioxide of the future.
  • A greenhouse controls more variables; FACE keeps field conditions and real ecosystems.
  • Name a controlled variable for each: the greenhouse’s temperature, FACE’s crop variety and sowing date.
Watch out More carbon dioxide does not mean more growth for ever. It helps only while carbon dioxide is the limiting factor (chapter 6).

Crops given extra carbon dioxide gained less yield in FACE rings than in enclosures. What is the most likely reason?

GreenhouseFACE ring, from above550 ppmCO2​sensor: 550 ppmwindcontrol ring: no added CO2​Can it be controlled?temperaturetemperaturelightlightwaterwatersoilsoilweatherweatherroom for whole treesroom for whole treesWhat the field experiments foundExtra carbon dioxide raised crop yields in FACE rings,but by less than the enclosure experiments had predicted.The direction of the result only: no numbers are drawn.
  1. Two ways to grow plants in tomorrow’s air.
  2. A greenhouse controls more variables; a FACE ring keeps real field conditions.
  3. In the field, the gain in yield was smaller.
Greenhouse against FACE. Step 3 gives the direction of the result only, as reported by Long and colleagues (2006) in Science; no numbers are drawn.

C1.3.9 C1.3.10 Photosystems, and the advantage of the array

Pigments in an array

A photosystem is an array of a few hundred pigment molecules, chlorophylls and accessory pigments, held in fixed positions by proteins. Photosystems are always in a membrane: the thylakoid membranes of a chloroplast, or the internal membranes of a cyanobacterium. At the heart of each is the reaction centre, a special chlorophyll a.

Light absorbed by any pigment in the array excites an electron in that pigment. The energy, not the electron, passes from pigment to pigment, inwards, until it reaches the reaction centre. There an excited electron is emitted: it leaves the chlorophyll altogether, passing to an electron acceptor beside it in the membrane. There are two kinds of photosystem, photosystem II and photosystem I, numbered in the order they were discovered. Electrons pass through II first.

Why an array? A single chlorophyll molecule, even in sunlight, absorbs a photon only every so often, and its excitation lasts only a few billionths of a second. On its own, the energy is lost as heat or given out again as red light, and it cannot do any part of photosynthesis. In an array, hundreds of pigments collect light and funnel it to one reaction centre, which keeps it busy. Different pigments widen the range of wavelengths caught. And their fixed spacing lets energy jump from one to the next before it is lost.

Seeing it Chlorophyll extracted into propanone glows deep red under a bright light. Chlorophyll in a leaf hardly glows. In the leaf the energy is used. In the tube there is no array and no acceptor, so it comes straight back out as light.
  • A photosystem is an array of pigments round a reaction centre, always in a membrane.
  • Pigments pass on energy; only the reaction centre emits an excited electron.
  • One pigment alone could not do any part of photosynthesis.
Watch out Pigments in the array pass on energy, not electrons. Only the reaction centre emits an electron.

Chlorophyll dissolved in propanone glows red under a bright light. Chlorophyll in a leaf hardly glows at all. Why?

chlorophyll on its ownbright light in,a red glow outacceptora photosystemthylakoid membranereaction centreenergy hops frompigment to pigment,inwardsan excited electronleaves thereaction centrehundreds of pigments, one reaction centre
  1. On its own, chlorophyll gives the energy straight back, as red light.
  2. A photosystem: hundreds of pigments around a reaction centre, in a membrane.
  3. The energy hops from pigment to pigment, inwards.
  4. The reaction centre emits an excited electron.
  5. Many pigments, many colours, all feeding one reaction centre.

C1.3.11 Oxygen from the photolysis of water in photosystem II

Water split, oxygen spare

Photosystem II’s reaction centre has emitted its electrons, so it needs more. It takes them from water. The splitting of water, photolysis, is done by an enzyme on the lumen side of photosystem II. Two water molecules give four electrons, four protons and one oxygen molecule.

The electrons refill the reaction centre, so it can be excited again. The protons are released into the lumen, where they add to the proton gradient (chapter 10). Both are used. The oxygen is a waste product: it diffuses out of the chloroplast, the cell and the leaf. Light does not split water directly. It excites the reaction centre, and the electron-short reaction centre pulls electrons from water.

The advent of oxygen from photolysis had immense consequences on Earth. Cyanobacteria were the first organisms to split water. The oxygen they released first reacted with iron dissolved in the oceans, which settled as layers of iron oxide on the sea floor: the banded iron formations. When the iron was used up, oxygen built up in the air, in the Great Oxidation Event, about 2.4 billion years ago. Oxygen poisoned many anaerobic organisms. It formed the ozone layer, which screens ultraviolet light. And it made aerobic respiration possible, with its far higher yield of ATP (C1.2), on which large, active organisms depend.

  • Photolysis at photosystem II: 2 water give 4 electrons, 4 protons and 1 oxygen.
  • The electrons and protons are used; the oxygen is waste.
  • Light excites the reaction centre; the reaction centre takes electrons from water.

Remember it What photolysis gives

  • PleaseProtonsinto the lumen, for the gradient
  • EatElectronsback into photosystem II’s reaction centre
  • OrangesOxygenthrown away as waste
Watch out The protons and electrons from water are used; only the oxygen is waste. And it is photosystem II, not photosystem I, that splits water.

Cyanobacteria were splitting water for a long time before oxygen built up in the air. Where did their oxygen go at first?

LUMENSTROMATHYLAKOID MEMBRANEphotosystem IIHHOHHOtwo water molecules4 electrons refillthe reaction centre4 protons stayin the lumenwaste: out of the leaf2 water → 4 electrons, 4 protons, 1 oxygenelectrons and protons used; oxygen is waste
  1. Photosystem II has lost electrons.
  2. It takes more from water.
  3. Photolysis: electrons refill the reaction centre; protons stay in the lumen.
  4. The oxygen is a waste product.
0100Oxygen in the air, % of today'sGreat Oxidation Eventtodaybanded ironformations43210Billions of years ago
The shape of the rise is known better than the numbers, so only 0 and today’s level are marked. Banded iron formations are mostly older than about 1.8 billion years.

C1.3.12 ATP production by chemiosmosis in thylakoids

Protons downhill make ATP

The excited electron from photosystem II passes along a chain of electron carriers in the thylakoid membrane towards photosystem I, giving up energy at each step. One carrier uses that energy for proton pumping: it moves protons across the membrane from the stroma into the thylakoid lumen.

Protons come into the lumen two ways: pumped by the chain, and released by photolysis. The lumen is small, so their concentration rises fast, and the membrane does not let them back. That difference is the proton gradient. The only way back to the stroma is through ATP synthase, a protein that spans the membrane. Protons flowing down their gradient turn part of it, and the energy joins ADP and phosphate: ATP, made on the stroma side. Making ATP with energy from a proton gradient is chemiosmosis, and when light is the first source the whole process is photophosphorylation.

You met the same machine in mitochondria (C1.2). The difference is direction: a thylakoid pumps protons into its lumen and makes ATP outside it, in the stroma, while a mitochondrion pumps them out of the matrix and makes ATP inside it.

In non-cyclic photophosphorylation the electrons come from photosystem II, pass along the chain to photosystem I and on to NADP (chapter 11). In cyclic photophosphorylation, electrons excited at photosystem I go back to the chain, pump more protons and return to photosystem I. It makes ATP only: no reduced NADP, no water split, no oxygen. It tops up the ATP, because the Calvin cycle uses more ATP than reduced NADP.

  • Electrons along the chain pump protons from the stroma into the lumen; photolysis adds more.
  • Protons flow back through ATP synthase, which makes ATP on the stroma side.
  • Non-cyclic: electrons from photosystem II to NADP. Cyclic: electrons from photosystem I round the chain again, for ATP only.
Watch out Protons do not collect in an “intermembrane space”, as they do in a mitochondrion. In a chloroplast they collect in the thylakoid lumen.

In a working chloroplast, where do protons build up?

LUMENSTROMATHYLAKOID MEMBRANEATPsynthasephotosystem IIphotosystem Ichain ofcarrierstwo protons pumpedinto the lumenfrom photolysisa crowd of protonsin the small lumenADP + PATPback through ATP synthase:ATP made in the stromato NADP(chapter 11)no water split,no oxygenback round the chain:more protons pumped
  1. The thylakoid membrane: photosystems, a chain of carriers and ATP synthase.
  2. Electrons give up energy along the chain, which pumps protons into the lumen.
  3. Protons pile up in the small lumen: a proton gradient.
  4. They flow back through ATP synthase, which makes ATP in the stroma: chemiosmosis.
  5. Non-cyclic: on to NADP. Cyclic: back round the chain, for more ATP.
ADPPADPPATPNADPproton used upLUMEN: many H+STROMA: few H+membraneATP synthaserotorhead
  1. The lumen is crowded with protons; the stroma has few. That gradient is stored energy, and ATP synthase is the only way down.
  2. A proton enters the channel from the lumen side and takes a place on the rotor.
  3. Each proton that passes pushes the rotor one step round, like water on a turbine, and leaves into the stroma.
  4. The rotor turns the shaft inside the head. Each turn squeezes ADP and phosphate together: ADP is phosphorylated.
  5. ATP leaves into the stroma. NADP also takes up stroma protons when it is reduced, which keeps the gradient steep.
ATP synthase as a turbine: protons flowing down their gradient turn the rotor, and the rotor drives the phosphorylation of ADP.

C1.3.13 C1.3.14 NADP reduced by photosystem I, and the thylakoid as a system

NADP reduced, and the thylakoid as a system

Electrons arriving at photosystem I have given up energy along the chain. Light absorbed by photosystem I’s array excites them again, and from its reaction centre they pass, by a short carrier on the stroma side, to NADP. NADP picks up two electrons from photosystem I and one hydrogen ion (a proton) from the stroma, and becomes reduced NADP. This is a reduction, and taking that proton from the stroma steepens the gradient a little.

Reduced NADP carries the hydrogen, as electrons and a proton, to the Calvin cycle in the stroma, where it reduces carbon compounds (chapter 13). This is how the hydrogen from chapter 2 gets from water to carbon dioxide: water’s electrons go through photosystem II, the chain and photosystem I, to NADP.

A thylakoid is a system in which every part has its place. On the lumen side: photolysis at photosystem II, and the store of protons. In the membrane: the photosystems, the chain and ATP synthase, held in order so electrons pass from one to the next. On the stroma side: ATP is made and NADP is reduced, right where the Calvin cycle’s enzymes are. Thylakoids are stacked in grana, joined by single unstacked sheets of membrane that run through the stroma; the stacking gives a large area of membrane, and the small lumen builds a steep gradient fast. Nothing has to “move to the stroma”: ATP and reduced NADP are made in it.

  • NADP is reduced at photosystem I, by two electrons from it and a proton from the stroma.
  • Photolysis and the proton store are on the lumen side; ATP and reduced NADP are made on the stroma side.
  • Grana give a large area of membrane; the small lumen gives a steep gradient fast.

Remember it Two sides of the thylakoid

  • LoadsLumenwhere protons pile up and water is split
  • SpendsStromawhere ATP and reduced NADP are made, then spent by the Calvin cycle
Watch out NADP is reduced at photosystem I, not photosystem II; photosystem II splits water. Electrons go through II first: the numbers record the order of discovery.

On which side of the thylakoid membrane is NADP reduced, and why does that side make sense?

LUMENSTROMAenvelope1stroma2granum3thylakoid lumen4photosystem II5photosystem I7chain of carriers6NADP8ATP synthase9

Tap a part of the chloroplast or the membrane, or Tab to it and press Enter.

A chloroplast cut open, and one thylakoid membrane enlarged. Which side of the membrane does each part work on?
Light in, water split, protons pumped and ATP made. Switch the light off, or send the electrons round the cyclic path, and watch what stops.

C1.3.15 Carbon fixation by Rubisco

Fixing carbon, slowly

The light-independent reactions are a cycle in the stroma, the Calvin cycle, named after Melvin Calvin, who worked it out with radioactive carbon in algae. Its first step is carbon fixation. Carbon dioxide joins a five-carbon sugar already in the stroma, ribulose bisphosphate (RuBP). The six carbons split at once into two molecules of the three-carbon glycerate 3-phosphate (GP). The enzyme is Rubisco. So the substrates are RuBP and carbon dioxide, and the product is GP.

“Fixation” means turning carbon from a gas into part of an organic molecule: the carbon is now held. Adding carbon dioxide to a molecule is also called carboxylation, so fixation by Rubisco is the carboxylation of RuBP.

Rubisco is slow. Each active site fixes only about three carbon dioxide molecules a second, where catalase (C1.1) breaks down millions of hydrogen peroxide molecules a second. And it is not effective at low carbon dioxide concentrations: when carbon dioxide is scarce (on a hot day, with the stomata closed) it works far below its best. So the stroma needs a high concentration of Rubisco to fix carbon dioxide as fast as the light-dependent reactions supply ATP and reduced NADP. Rubisco is up to about half of the soluble protein in a leaf, and it is the most abundant enzyme on Earth.

  • Carbon fixation: carbon dioxide joins RuBP (5 carbons), which splits into two GP (3 carbons each).
  • The enzyme is Rubisco: slow, and poor at low carbon dioxide concentrations.
  • The stroma needs a high concentration of Rubisco for that reason.
Watch out Rubisco is an enzyme, not a product of the cycle, and it is not used up. It is abundant because it is slow, not because it is special in any other way.

A leaf cell could save a lot of protein by making less Rubisco. Why doesn’t it?

STROMARubiscoRuBP, 5 carbonscarbon dioxidetwo GP,3 carbons eachRubisco, one active site3 a secondcatalase, one active site830651millionsa secondso the stroma is packed with Rubisco
  1. RuBP, a five-carbon sugar, waits in Rubisco’s active site.
  2. Carbon dioxide joins it: carbon fixation.
  3. The six carbons split into two GP.
  4. Rubisco is slow, so a leaf makes a lot of it.
IIIlight: brightTHYLAKOIDSTROMACO2NORMAL AIRa charge: ATP + reduced NADPBACKLOGGLUCOSE78 of 100rising3RUBISCO 1glucose a second 0.2STROMACO2NORMAL AIRa charge: ATP + reduced NADPBACKLOGGLUCOSE46 of 100steady30RUBISCO 11glucose a second 1.7STROMACO2HOT DAY, STOMATA CLOSEDa charge: ATP + reduced NADPBACKLOGGLUCOSEslowing88 of 100rising12RUBISCO 11glucose a second 0.8The record00.511.5204812162024Number of RubiscoGlucose a secondExtra CO2Normal airHot daybright light, each point held steady
  1. One Rubisco cannot keep up.
  2. Eleven keep pace with bright light.
  3. With little carbon dioxide, each does less and fumbles more.
  4. More Rubisco helps until light is the limit.

C1.3.16 C1.3.17 Triose phosphate from GP, and RuBP regenerated

GP to TP, and RuBP made again

Reduced NADP and ATP from the light-dependent reactions turn GP into triose phosphate (TP), a three-carbon sugar, in the stroma. Reduced NADP gives the hydrogen (it reduces GP) and ATP gives the energy. NADP and ADP go back to the thylakoid. TP is the first sugar and the cycle’s product: some of it leaves to make glucose and everything else (chapter 14).

The rest has to remake RuBP, using more ATP. Five TP (fifteen carbons) are rearranged into three RuBP (fifteen carbons), so the cycle can fix carbon dioxide again. This is regeneration. You do not need the steps in between. Counting a round: three RuBP fix three carbon dioxide to give six GP; six GP give six TP; one TP leaves; five remake three RuBP. Three carbons in, three carbons out as one TP.

To make one glucose (six carbons, two TP), six carbon dioxide must be fixed, and five-sixths of all the TP made goes back to RuBP. Without regenerating RuBP, fixation would stop within moments. One turn of the cycle fixes one carbon dioxide, so six turns make one glucose. The figure runs three turns at a time (a “round”) only because three is the smallest number that gives a whole TP out.

Why a cycle? The molecule that accepts carbon dioxide is remade every turn, so a small stock of RuBP keeps fixing carbon as long as ATP and reduced NADP keep coming. The tally in the corner counts ATP and reduced NADP as they are used; it is there to show the cost, not to be learned.

  • GP is reduced to TP, using reduced NADP and ATP.
  • Five TP of every six made are remade into three RuBP, using ATP; one in six leaves.
  • Six turns of the cycle fix six carbon dioxide and make one glucose.

Remember it The Calvin cycle’s three stages

  • FreshFixRubisco joins carbon dioxide to RuBP, making GP
  • RollsReduceATP and reduced NADP turn GP into TP
  • RiseRegeneratefive TP in six remade into RuBP, using ATP
Watch out It is GP (glycerate 3-phosphate) that is reduced, to TP. “Glyceraldehyde 3-phosphate” is another name for a triose phosphate, so “the reduction of glyceraldehyde 3-phosphate” has the stages muddled.

Of every six TP the Calvin cycle makes, how many must be used to remake RuBP?

Calvin cycle,in the stromaFIXREDUCEREGENERATECO2 from the air3 RuBP6 GPRubisco6 ATP6 reduced NADPfrom the light-dependentreactionsADP and NADP go backout: to make glucoseand more (chapter 14)3 ATP5 TP become 3 RuBP3 RuBP6 CO2 fixed: 1 glucosecarbons in the cycle: 15 + 3ATP 0, reduced NADP 0carbons in the cycle: 18ATP 0, reduced NADP 0carbons in the cycle: 18ATP 6, reduced NADP 6in the cycle 15, out 3ATP 6, reduced NADP 6carbons in the cycle: 15ATP 9, reduced NADP 66 CO2 fixed in allone glucose made Calvin cycle,in the stromaFIXREDUCEREGENERATECO2 from the air3 RuBP6 GPRubisco6 ATP6 reducedNADPfrom the light-dependent reactionsADP and NADPgo backout: to make glucoseand more (chapter 14)3 ATP5 TP become 3 RuBP3 RuBPsix CO2 fixed,one glucosecarbons in the cycle: 15 + 3ATP 0, reduced NADP 0carbons in the cycle: 18ATP 0, reduced NADP 0carbons in the cycle: 18ATP 6, reduced NADP 6in the cycle 15, out 3ATP 6, reduced NADP 6carbons in the cycle: 15ATP 9, reduced NADP 66 CO2 fixed in allone glucose made
  1. Three RuBP wait for three carbon dioxide.
  2. Rubisco fixes them: six GP.
  3. Reduced NADP and ATP turn GP into TP.
  4. One TP in six leaves the cycle.
  5. Five TP are remade into three RuBP, using ATP.
  6. Six turns, six carbon dioxide: one glucose.

C1.3.18 Carbohydrates, amino acids and other compounds from the Calvin cycle

Every carbon came this way

Every carbon atom in every compound of a photosynthesising organism was fixed in the Calvin cycle. Its other carbon compounds are made by metabolic pathways that can be traced back to triose phosphate, or to another intermediate of the cycle. You do not need the details of the pathways.

Carbohydrates come first: TP makes glucose, and glucose makes sucrose (the sugar carried in the phloem), starch (the store) and cellulose (the cell walls). Lipids follow: TP makes glycerol and, through the acetyl groups of respiration, fatty acids, which join into triglycerides and, with phosphate, into phospholipids.

Amino acids need nitrogen as well as carbon. It comes from nitrate (or ammonium) taken up from the soil, and two amino acids need sulfur too. Nucleotides need nitrogen for their bases and phosphorus for their phosphate. These mineral nutrients come in through the roots by active transport (B2.1).

Fixation in the Calvin cycle is how carbon enters every food web: the carbon fixed in a leaf ends up in the plant’s own body, in whatever eats it, or back in the air through respiration. The carbon trail below follows one atom.

  • All the carbon in a plant’s compounds was fixed in the Calvin cycle.
  • Sugars, starch, cellulose, lipids, amino acids and nucleotides are made by pathways that start from TP.
  • Amino acids and nucleotides also need mineral nutrients: nitrate, and phosphate.
Watch out Plants do not take carbon from the soil. Every carbon atom came from carbon dioxide, in the air or dissolved in water, through the Calvin cycle.

A plant has plenty of light, water and carbon dioxide, but its soil has no nitrate. Which will it fail to make?

soilTP, from the Calvin cycleCarbohydratesglucosesucrosestarchcelluloseLipidsglycerolfatty acidstriglycerideAmino acidRSsulfur, in twoNO3​− nitrate,from the soilNucleotideAHPO4​3− phosphateNO3​− nitrateboth from the soil
  1. From TP: sugars, starch and cellulose.
  2. Lipids.
  3. Amino acids, with nitrogen from nitrate.
  4. Nucleotides, with nitrogen and phosphate.
One carbon atom from the air, fixed by Rubisco, into a sugar, then built into the plant, respired, or eaten. Choose where it goes next.

C1.3.19 Interdependence of the light-dependent and light-independent reactions

Each half needs the other

The light-dependent reactions in the thylakoids make ATP and reduced NADP. The light-independent reactions, the Calvin cycle in the stroma, use them and hand back ADP, phosphate and NADP. Each half needs what the other makes: that is their interdependence.

No light. The photosystems are not excited, so no ATP or reduced NADP is made. The Calvin cycle runs on for a few seconds on what is left, then stops.

No carbon dioxide. The Calvin cycle cannot fix carbon, so it stops using ATP and reduced NADP, and no NADP comes back. Once all the stroma’s NADP is reduced, photosystem I has nothing to pass its electrons to. The chain backs up, and photosystem II cannot pass its electrons on, so it stops, and so does photolysis.

So a leaf’s two halves run at the pace of the slower one, which links back to limiting factors (chapter 6). In bright light, carbon dioxide or Rubisco limits the rate; in dim light, the light-dependent reactions do. And a plant in the dark still respires. Everything in Unit 4 so far is on one map below, the metabolism map, where you can see both.

  • Light-dependent reactions make ATP and reduced NADP; the Calvin cycle uses them and returns ADP, phosphate and NADP.
  • No light: the Calvin cycle stops a few seconds later.
  • No carbon dioxide: NADP is not returned, so photosystem I fills, then the chain, then photosystem II stops.
Watch out “Light-independent” does not mean “happens in the dark”. The Calvin cycle needs the products of the light reactions, so in a leaf it runs only in the light.

A leaf in bright light is suddenly given no carbon dioxide. What happens to photosystem II?

THYLAKOIDCALVIN CYCLElight offwater inoxygen outwater inoxygen outIIIIIIIIIelectrons held: I, the chain, then IIATPreduced NADPADP + phosphateNADPATPreduced NADPADP + phosphateNADPATPreduced NADPADP + phosphateNADPRubiscofixes CO2​TP outRubiscofixes CO2​TP out stopsa few seconds laterRubiscofixes CO2​TP out stops

Choose a state, once you have made your prediction.

The thylakoid makes ATP and reduced NADP for the Calvin cycle, and the Calvin cycle hands back ADP, phosphate and NADP. Switch off the light, or the carbon dioxide, and watch what stops.
The light-dependent reactions and the Calvin cycle at work. Then switch off the light, or the carbon dioxide, and see what stops.
Glycolysis, the Krebs cycle and the Calvin cycle in one leaf cell. Follow a molecule to see where it is made and where it is used.

02Dry lab: Pondweed and the lamp

A sprig of pondweed in hydrogencarbonate solution gives off bubbles of oxygen as it photosynthesises. Move the lamp, change the carbon dioxide or the temperature, count the bubbles, then plan and write it up as an investigation with the coach beside you. Or float leaf discs instead.

Your questionHow does one limiting factor change the rate of photosynthesis? Start with the lamp: how does the rate change as the lamp moves away, and is it the distance or the light that matters?
What you can changeOne independent variable at a time: the distance of the lamp (with a light meter to read the light), the concentration of sodium hydrogencarbonate, the temperature of the water, or the colour of a filter. Everything else stays fixed unless you change it on purpose, and some of it changes when you are not looking.
What to recordBubbles counted in each of three minutes, after the sprig has settled, then the mean rate in bubbles per minute; or the time for half the leaf discs to float. Three trials at each value, a mean and a standard deviation, and a graph of the means with error bars. The coach under the bench helps you plan, process and evaluate.
room lights on- - - -light meter, lux0:00stopwatch0102030405060708090100cm from the sprigthe cut end, magnifiedThe settingsMethod: count the bubbles, three minutes a trialChange: distance from the lamp, 5 to 100 cmKept the same: hydrogencarbonate 1 %, bath 25 °C, white light, filament lamp, no heat shield, room lights onResultsDistance / cmTrialMinute 1Minute 2Minute 3Mean / bubbles min⁻¹Water / °C
Pondweed bubbles. A sprig of pondweed in sodium hydrogencarbonate solution, a lamp 20 cm away on a metre rule. Count the bubbles leaving the cut end in each of three minutes, once the sprig has settled.

IA coach

Write it up as an investigation

Your results from this dry lab can be written up the way an IB scientific investigation is: four criteria, each worth 6 marks. Tick each line as your write-up does it. The coach on the page checks these as you go; it never gives a mark.

1 Research design

A focused question set in its biology; your choices of what to measure, how, over what range and how often, explained rather than listed; what you kept the same and how; safety, ethics and the environment; a method someone else could follow and repeat.

  • My question names what I changed.
  • It gives the range I used, with units.
  • It names what I measured and how.
  • It names the organism or system.
  • My background explains, with the biology, why the two should be linked.
  • I cite my sources, and each reference can be traced.
  • If I give a hypothesis, it predicts and explains.
  • Every variable has its How, Why and Units.
  • For each thing kept the same, I say how I kept it so.
  • I list at least three things I kept the same.
  • I name the apparatus that set what I changed, and the instrument that measured.
  • I test enough values.
  • My values spread wide enough.
  • I run at least three trials at every value.
  • I run a control.
  • I explain why these values, this many and this often.
  • Someone else could repeat my method.
  • I deal with safety, ethics and the environment.

2 Data analysis

Raw data recorded clearly, with titles, units, uncertainties and the same decimal places down a column; what you saw as well as what you measured; processing that suits the question, shown with a worked example; the spread shown; a graph a reader can trust.

  • Each table has a numbered title that says what it shows.
  • Every heading has its quantity and its unit.
  • Every raw data heading has its uncertainty.
  • Each uncertainty is realistic for the instrument.
  • Each uncertainty has the same decimal places as its readings.
  • I record what I saw as well as what I measured.
  • I show one worked example of my processing, and it is right.
  • I say why I left out any trial.
  • My error bars show a spread my repeats can support.
  • My graph has a numbered title and labelled axes with units.
  • I say what the error bars show.
  • A straight line, if I draw one, has its R².
  • A statistical test, if I run one, has its hypotheses and suits the data.

3 Conclusion

Your question answered from the processed data, with numbers quoted and the spread taken into account; the biology that explains the pattern; a comparison with published work; no claim bigger than the data.

  • I answer my question in a sentence, naming both variables.
  • I quote my processed numbers.
  • I say how sure the spread lets me be.
  • I say whether my hypothesis is supported.
  • I explain the pattern with biology.
  • I compare my result with published work, and cite it.
  • I claim no more than my data show.

4 Evaluation

Weaknesses and limitations of this method (not slips in carrying it out), with evidence from your own data, the effect each had on the results, which mattered most and why, and a realistic improvement for each.

  • I give at least three weaknesses or limitations.
  • Every row is filled in.
  • No slips in carrying it out: weaknesses of the method itself.
  • Each improvement is specific: which instrument, how many, what changes.
  • Each effect says what it did to my data.
  • At least two rows point to evidence in my own data.
  • At least one limitation: what this experiment cannot tell me.
  • I say which mattered most, and why.
  • I deal with what stands out in my data.
  • My improvements improve this investigation, not a new one.

Variables

VariableHow?Why?Units
Independent: distance from the lamp
Dependent: rate of bubble production
Kept the same: the lamp (filament or LED)
Kept the same: concentration of sodium hydrogencarbonate
Kept the same: temperature of the water
Kept the same: colour of the light
Kept the same: the room lights
Kept the same: the sprig (the same sprig, or matched sprigs)
Kept the same: length of the sprig
Kept the same: volume of solution in the tube
Kept the same: time left to settle after each change

Evaluation

Weakness or limitationWhich?Evidence in my dataEffect on my resultsImprovement

Data generated with the pondweed dry lab, biologybybradford.com (a simulation). These checks catch what is missing. They cannot judge how good it is: that is what your teacher does.

Find out

  • How does the rate change with distance? Move the lamp from 5 to 100 cm: at least six distances, three trials at each, after the sprig has settled. Graph the rate against distance, then against 1 ÷ distance². Where is the graph a straight line, and where not?
  • Light is not the only thing changing. Read the thermometer before and after a run with the lamp 5 cm away, with and without the heat shield.
  • Carbon dioxide. Run hydrogencarbonate from 0 to 5 % with the lamp at 10 cm, then again at 40 cm. Where does each level off?
  • Temperature. Run the bath from 5 to 45 °C, lamp at 10 cm, 1 % hydrogencarbonate. Then cool a sprig you ran at 45 °C back to 25 °C and run it again.
  • Colour. Run white light and the four filters with the lamp at 10 cm, reading the light meter each time. Then improve your method so the comparison is fair. Comparing colours, the lamp may sit at a different distance for each filter: the table writes it down with each trial.
  • Leaf discs. Switch the method to leaf discs and run hydrogencarbonate at 0, 0.1, 0.2, 0.5 and 1 % with the lamp at 10 cm. Find the time for half the discs to float.

Record

  • Every run's settings: what you changed, and everything you kept the same.
  • Change one thing at a time, and let the sprig settle after each change before you count.
  • The bubbles in each of three minutes, or the gas bubble's two ends on the scale, or the discs floating each minute.
  • Three or more trials at each value, then a mean and its standard deviation.
  • Use the graph under the lab, or download the CSV and plot it yourself.
  • When you are done, choose one investigation and write it up with the IA coach under the bench. Improve your method, under the graph, opens better apparatus as you think of it.

With the lamp 80 cm away you count no bubbles at all. Has the sprig stopped photosynthesising?

Without the heat shield, your rates with the lamp close to the tube sit above the trend of the others. Why?

The rate plotted against 1 ÷ distance² is a straight line for distant lamps but bends over close up. Why?

Under the green filter the light meter reads more lux than under the red one, yet the sprig gives fewer bubbles. Why?

03Check

A fresh paper from the exam bank on this guide's topics each time: past-paper style questions, marked as you go, and saved to your Exam practice progress when you are signed in.

Exam practice

Exam questions on C1.3, marked

Start 15 marks of exam questionsYour exam practice

C1.3 revision mapC1.3 exam questionsC1.3 multiple choice quizC1.3 higher level quizBack: C1.2 cell respirationNext: D1.1 DNA replication

04Downloads

Take the guide with you, or into a classroom with no internet.

DOCXNote templateFor students to fill in alongside the guide: a page per chapter with cues, gaps for the key terms and a summary box. Edit it in Word or Google Docs (A4). 3.1 MB PDFNote template, to printThe same note template, ready to print (A4). 3.9 MB PDFRevision guideThis guide as a printed book: every chapter, every step of every figure, the key terms, the predictions with answers at the back, and a link to the Check. 12.1 MB HTMLThe guide, offlineOne file that opens in any browser with no internet: the figures, the animations and the dry lab all work. 2.0 MB

The whole IB Biology revision guide, every guide written so far in one PDF.

05Teacher resources

The guide as three one-hour lessons, and three more at higher level. Each has a plan to print (the timings, what to project and where to stop, the activities with what they need, what students get wrong) and slides to teach it from, in the same order, with the teacher's moves in the notes.

LessonCoversFocusChaptersLesson planSlides
1Light into sugar C1.3.1, C1.3.2, C1.3.3 and C1.3.560 min Where the energy and the atoms of glucose come from, why the oxygen is from water, and why leaves absorb red and blue light 1, 2, 4 Lesson planPDF 736 KB SlidesPPTX 5.4 MB
2Pigments and spectra C1.3.4 and C1.3.660 min Separating leaf pigments by chromatography, working out Rf, and comparing absorption and action spectra 3, 5 Lesson planPDF 686 KB SlidesPPTX 3.9 MB
3Limiting factors, and tomorrow’s air C1.3.7 and C1.3.860 min Light, carbon dioxide and temperature as limiting factors, how to vary each, and greenhouse against FACE experiments 6, 7, dry lab Lesson planPDF 704 KB SlidesPPTX 513 KB
4Photosystems and water HL C1.3.9, C1.3.10 and C1.3.1160 min Pigments in arrays round a reaction centre, why one pigment alone is useless, and photolysis at photosystem II and its consequences for Earth 8, 9 Lesson planPDF 705 KB SlidesPPTX 1.0 MB
5The thylakoid at work HL C1.3.12, C1.3.13 and C1.3.1460 min Chemiosmosis in the thylakoid, cyclic and non-cyclic photophosphorylation, NADP reduced at photosystem I, and where each step happens 10, 11 Lesson planPDF 681 KB SlidesPPTX 4.9 MB
6The Calvin cycle, and the whole system HL C1.3.15 to C1.3.1960 min Rubisco and carbon fixation, GP to TP, RuBP remade, every compound from the Calvin cycle, and why each half needs the other 12, 13, 14, 15 Lesson planPDF 811 KB SlidesPPTX 11.5 MB
PDFEvery lesson planAll six plans in one PDF, with this overview at the front. 1.6 MB KEYNote template, filled inThe class’s note template with every gap filled. 3.1 MB

The note template, the revision guide and the offline copy are in Downloads, for you and the class.

PRACTISE AND REVISE

Make it for your class, or set it

Build for your class

Already on the site for C1.3

Card sets on splycr

Open a set to host it as a class game, or make a copy to edit.

How this was made. The course structure, the activities and the teaching choices come from my own classroom, my presentations and my years of teaching IB and AP Biology. I use Claude, an AI, to help write and build the interactive guides, lesson plans, slides and practice questions, and to draw the diagrams and code the interactives. I direct the work and review it against the IB and AP specifications before it goes live.