IB DP Biology: Photosynthesis: pigments, limiting factors, light-dependent reactions and the Calvin cycle (DP Biology)

This study guide teaches IB Diploma Programme Biology topic C1.3 (Photosynthesis) from the start. It follows the IB Biology guide, first assessment 2025. Statements C1.3.1 to C1.3.8 are SL and HL. Statements C1.3.9 to C1.3.19 are additional higher level and are marked “HL only”.

Use it with the revision notes and the practice set. Course pages: IB DP Biology hub, printable checklist and free 10-minute diagnostics.

What this unit covers

Statement	What you must be able to do	Level
C1.3.1 to C1.3.3	Energy transformation, word equation, oxygen as a by-product from water	SL and HL
C1.3.4	Chromatography; Rf values	SL and HL
C1.3.5	Absorption of some wavelengths; absorption spectra	SL and HL
C1.3.6	Compare absorption and action spectra; plot an action spectrum	SL and HL
C1.3.7	Limiting factor experiments; hypotheses and variables	SL and HL
C1.3.8	Carbon dioxide enrichment: greenhouse and FACE	SL and HL
C1.3.9, C1.3.10	Photosystems and the advantage of the array	HL only
C1.3.11 to C1.3.14	Photolysis, chemiosmosis, NADP reduction in the thylakoid	HL only
C1.3.15 to C1.3.18	Rubisco, triose phosphate, RuBP regeneration, other compounds	HL only
C1.3.19	Interdependence of the two sets of reactions	HL only

Energy and the overall equation (C1.3.1 to C1.3.3)

Photosynthesis transforms light energy into chemical energy stored in carbon compounds. Most of the chemical energy supporting ecosystems comes from this.

The word equation is:

carbon dioxide + water → glucose + oxygen

Hydrogen from water is added to carbon dioxide, so carbon dioxide is reduced to glucose. Water is split, so the oxygen gas has water as its source. The balanced version, 6CO₂ + 12H₂O → C₆H₁₂O₆ + 6O₂ + 6H₂O, shows the oxygen gas coming from the twelve water molecules split.

Plants, algae and cyanobacteria all release oxygen as a by-product. If water labelled with ¹⁸O is supplied and the oxygen gas collected contains ¹⁸O, the oxygen came from water.

Pigment chromatography (C1.3.4)

A leaf extract contains several pigments. Chromatography separates them because each differs in solubility in the solvent and in attraction to the stationary phase (paper or a thin layer of adsorbent). Pigments that dissolve well and cling weakly travel far.

Method in steps:

1. Draw a pencil line near the bottom of the paper (pencil does not dissolve).
2. Apply a small, concentrated spot of extract on the line.
3. Stand the paper in shallow solvent, below the line.
4. Take it out near the top and mark where the solvent has reached straight away.
5. Measure to the centre of each spot from the line.

Rf is the pigment’s travel divided by the solvent front’s travel. It has no units and is below 1.

Worked example. The solvent front moves 8.5 cm. Four spots are found at 8.1 cm (orange-yellow), 5.9 cm (yellow), 4.6 cm (blue-green) and 3.2 cm (yellow-green).

Colour	Distance / cm	Rf	Likely pigment
Orange-yellow	8.1	8.1 ÷ 8.5 = 0.95	Carotene
Yellow	5.9	5.9 ÷ 8.5 = 0.69	Xanthophyll
Blue-green	4.6	4.6 ÷ 8.5 = 0.54	Chlorophyll a
Yellow-green	3.2	3.2 ÷ 8.5 = 0.38	Chlorophyll b

Rf values depend on the solvent and stationary phase, so compare with reference values from the same system as well as colour.

Absorption of light (C1.3.5)

Each wavelength of light carries a different amount of energy. A pigment absorbs a photon only if its energy matches the gap between two energy levels of one of its electrons, so only some wavelengths are absorbed. The rest are reflected or transmitted. Chlorophyll absorbs little green light, so leaves look green.

The excited electron holds the light’s energy. Passing excited electrons on to other molecules is how light energy becomes chemical energy.

An absorption spectrum shows how much light a pigment absorbs at each wavelength. Label the horizontal axis with wavelength in nanometres and with colours: violet and blue about 400 to 500 nm, green 500 to 570, yellow and orange 570 to 620, red 620 to 700. Chlorophylls absorb strongly in blue-violet and red. Carotenoids absorb mainly blue-violet and blue light.

Action spectra (C1.3.6)

An action spectrum plots the rate of photosynthesis against wavelength. The rate is found from oxygen production or carbon dioxide consumption.

	Absorption spectrum	Action spectrum
Measures	Light absorbed	Rate of photosynthesis
Usually made with	Extracted pigment	Whole leaf, alga or cells
Peaks	Blue-violet and red	Blue-violet and red
Green region	Low	Low, but often higher than the pigment alone suggests

They match closely because only absorbed light can drive photosynthesis. They differ because the action spectrum also reflects accessory pigments passing energy on.

Worked example. An alga suspension is lit with equal-intensity light of six wavelengths, and oxygen is collected for 15 minutes each.

Wavelength / nm	450	500	550	600	650	700
Oxygen / cm³ in 15 min	3.6	1.2	0.9	2.1	3.0	0.3
Rate / cm³ min⁻¹	0.24	0.080	0.060	0.14	0.20	0.020
Relative to highest, %	100	33	25	58	83	8

Rate = volume ÷ time, for example 3.6 ÷ 15 = 0.24. To plot the action spectrum, put wavelength on the horizontal axis and rate on the vertical axis. Peaks sit near 450 and 650 nm; the trough is near 550 nm. For carbon dioxide uptake, use the fall in concentration ÷ time. Net oxygen output understates photosynthesis if the plant respires.

Limiting factors and experimental technique (C1.3.7)

A limiting factor is the scarcest requirement, the one holding the rate below its potential. Raising it raises the rate; raising a factor that is not limiting does nothing. On a graph the rate rises, then levels off when another factor takes over.

Factor	How to vary it
Light intensity	Move a lamp; intensity is proportional to 1 ÷ distance²
Carbon dioxide	Dissolve different masses of sodium hydrogencarbonate in the water
Temperature	Water bath, with a thermometer; enzyme activity rises to an optimum, then enzymes denature

A common set-up uses an aquatic plant such as Elodea, counting bubbles or measuring gas volume, with repeats at each setting.

Variables. The independent variable is what you change. The dependent variable is what you measure (bubbles or gas volume per minute). Controlled variables are kept constant; a lamp’s heat is a hidden one, so place a water-filled tank between lamp and plant.

Worked example. A lamp is placed at 10, 20, 30, 40 and 50 cm. Relative intensity is 100 × (10 ÷ d)², giving 100, 25, 11, 6.3 and 4. Bubbles per minute are 44, 40, 29, 18 and 11. Between intensity 4 and 25 the rate rises steeply, so light is limiting. From 25 to 100 the rate barely changes (40 to 44), so something else, such as carbon dioxide or temperature, limits it.

Hypotheses and nature of science. A hypothesis is a provisional explanation that needs repeated testing. It can come from a theory, then be tested, or come from earlier observations. Example: “If carbon dioxide is limiting, more hydrogencarbonate will raise the rate.”

Carbon dioxide enrichment (C1.3.8)

Atmospheric carbon dioxide is rising, so ecologists test how plants will respond. Two designs are used:

• Enclosed greenhouse experiments. Plants grow in chambers where carbon dioxide, temperature and water are controlled. Control is easy, but the enclosure changes wind, light and soil conditions.
• FACE (free-air carbon dioxide enrichment). Pipes release carbon dioxide into open-air plots, with control plots at ambient concentration. Conditions are natural and whole ecosystems can be studied, but control is poorer.

Controlled variables are kept the same in all plots: species, soil type, plot size and watering.

Worked example (illustrative data). Mean above-ground dry mass was 1,240 g m⁻² in control plots and 1,455 g m⁻² in enriched plots.

Percentage change = (1,455 − 1,240) ÷ 1,240 × 100 = 17.3%. The photosynthetic rate rose from 14.2 to 18.0 µmol m⁻² s⁻¹, which is (18.0 − 14.2) ÷ 14.2 × 100 = 26.8%. A larger rise in rate than in biomass suggests other limits, so predictions need care.

Photosystems (C1.3.9 and C1.3.10, HL only)

A photosystem is an array of chlorophyll and accessory pigment molecules, always held in a membrane: in the thylakoids of chloroplasts and in cyanobacteria. A special chlorophyll at the centre is the reaction centre, the place an excited electron is emitted. Photosystem II and photosystem I are the two types.

Advantage of the array. Different pigments absorb different wavelengths, so together they capture more of the spectrum. Many pigment molecules catch photons and pass the energy to one reaction centre, which is supplied faster. A single pigment molecule could not perform any part of photosynthesis.

Light-dependent reactions (C1.3.11 to C1.3.14, HL only)

These take place in and across the thylakoid membrane.

1. Photolysis in photosystem II. Light excites electrons in the reaction centre, which are emitted. Water in the thylakoid space is split: 2H₂O → 4H⁺ + 4e⁻ + O₂. The electrons replace those lost from photosystem II, protons stay in the thylakoid space, and oxygen is a waste product. Its arrival had immense effects on organisms and geology.
2. Chemiosmosis. Emitted electrons pass along a chain of carriers. Their energy moves protons from the stroma into the space inside the thylakoid, building a proton gradient. The protons return through ATP synthase, which joins ADP and phosphate to make ATP.
3. Reduction of NADP by photosystem I. Light re-excites electrons in photosystem I. Two electrons and one hydrogen ion from the stroma reduce NADP: NADP⁺ + 2e⁻ + H⁺ → NADPH. Use one naming pair throughout: either NADP with reduced NADP, or NADP⁺ with NADPH.

In non-cyclic photophosphorylation, electrons come from photosystem II and end in NADPH, so ATP, NADPH and oxygen are all made. In cyclic photophosphorylation, electrons from photosystem I return to the chain, so only ATP is made.

The Calvin cycle (C1.3.15 to C1.3.18, HL only)

The light-independent reactions occur in the stroma.

1. Carbon fixation. Rubisco joins CO₂ to ribulose bisphosphate (RuBP, five carbons). The product is glycerate 3-phosphate (GP, three carbons). No enzyme on Earth is more abundant than Rubisco. It works slowly and is poor at low carbon dioxide concentration, so the stroma needs large amounts.
2. Reduction. GP becomes triose phosphate (TP), using energy from ATP and hydrogen from NADPH.
3. Regeneration. Five molecules of TP are converted to three of RuBP, using ATP, so the cycle continues.

Worked example: one glucose. Six turns fix six CO₂. Carbon check: 6 RuBP hold 30 carbons and 6 CO₂ add 6, so 36 carbons are shared among 12 GP. 12 GP gives 12 TP, using 12 ATP and 12 NADPH. Two TP leave to make one glucose. The other 10 TP regenerate 6 RuBP, using 6 ATP. So five-sixths (10 of 12) of the TP is recycled, and the cycle uses 18 ATP and 12 NADPH per glucose.

Other compounds. All carbon in a photosynthesising organism was fixed in the Calvin cycle. Carbohydrates, lipids and amino acids are made by pathways from a cycle intermediate such as TP. Amino acids also need mineral nutrients such as nitrate.

Interdependence (C1.3.19, HL only)

In darkness neither ATP nor reduced NADP is produced, so GP cannot be converted and RuBP is not regenerated. Without carbon dioxide, the Calvin cycle stops, reduced NADP is not used up, and NADP is not regenerated. With no NADP to accept electrons, the chain fills with electrons and photosystem II cannot pass its electrons on, so it stops.

Common errors

• Saying oxygen comes from carbon dioxide.
• Taking Rf distances from the paper edge instead of the start line.
• Putting photolysis in photosystem I.

Official syllabus

IB Diploma Programme Biology guide, first assessment 2025, published by the International Baccalaureate Organization. Topic C1.3 (Photosynthesis), statements C1.3.1 to C1.3.19; C1.3.9 to C1.3.19 are additional higher level.