Photosynthetic Pigments

Spec Mapping — OCR H420 Module 5.2.1 — Photosynthesis, content statements covering the structures and roles of photosynthetic pigments, the use of chromatography to separate pigments from a leaf, the calculation of R_f values, and the interpretation of absorption and action spectra (refer to the official OCR H420 specification document for exact wording).

Chloroplasts look green because of the photosynthetic pigments they contain — specialised molecules that absorb light energy at specific wavelengths. OCR specification module 5.2.1 and practical activity group 6 (chromatography) require you to know the main pigments, understand absorption and action spectra, and be able to use chromatography to separate pigments and calculate Rf values. This lesson links physical chemistry (absorption of photons) to biological function (exciting electrons in photosystems) and includes a required practical.

The relationship between absorption spectrum and action spectrum was made famous by the American biophysicist Robert Emerson (1957). His "red-drop" experiment (paraphrasing his findings) showed that photosynthesis efficiency dropped sharply as wavelength climbed above ~680 nm, but could be partially restored by simultaneously illuminating with shorter wavelengths. Emerson's "enhancement effect" was the first evidence that photosynthesis uses two photosystems acting in series, each absorbing different wavelengths and contributing different excitations. The result, paraphrasing Emerson's school of thought, anchored the Z-scheme architecture you will meet in the next lesson.

Key Definitions:

• Pigment — a coloured molecule that absorbs certain wavelengths of visible light and reflects or transmits others.
• Absorption spectrum — a graph showing the absorbance of different wavelengths of light by a pigment.
• Action spectrum — a graph showing the rate of photosynthesis at different wavelengths of light.
• Chromatography — a technique for separating mixtures of substances based on differences in solubility and affinity for a stationary phase.
• Rf value — the ratio of the distance travelled by a substance to the distance travelled by the solvent front.

Learning objectives — by the end of this lesson you should be able to:

• Name the four photosynthetic pigments of higher plants, classify them as primary or accessory, and state the wavelengths each absorbs.
• Distinguish an absorption spectrum from an action spectrum and explain why their close match is strong evidence that pigments drive photosynthesis (paraphrasing Emerson's enhancement effect).
• Describe and evaluate the chromatography required practical, calculate $R_f$Rf​ values, and explain separation in terms of pigment polarity and solvent affinity.
• Explain, in molecular terms, how a pigment converts an absorbed photon into an excited electron and how the antenna funnels energy to the reaction centre.

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The Physics of Light Absorption — Photons, Energy and Excited States

Before considering which pigments absorb which colours, it is worth being precise about what "absorbing light" means at the molecular scale — a point that separates the strongest OCR candidates from the rest.

Light is delivered in discrete packets (photons), and the energy carried by a single photon depends on its wavelength according to the Planck–Einstein relation:

$E = h f = \frac{hc}{\lambda}$E=hf=λhc​

where $h$h is the Planck constant ($6.63 \times 10^{-34}\,\text{J s}$6.63×10−34J s), $c$c is the speed of light ($3.00 \times 10^{8}\,\text{m s}^{-1}$3.00×108m s−1), $f$f is frequency and $\lambda$λ is wavelength. Because energy is inversely proportional to wavelength, a blue photon (~450 nm) carries more energy than a red photon (~680 nm):

$E_{\text{blue}} = \frac{(6.63 \times 10^{-34})(3.00 \times 10^{8})}{450 \times 10^{-9}} \approx 4.4 \times 10^{-19}\,\text{J}$Eblue​=450×10−9(6.63×10−34)(3.00×108)​≈4.4×10−19J

$E_{\text{red}} = \frac{(6.63 \times 10^{-34})(3.00 \times 10^{8})}{680 \times 10^{-9}} \approx 2.9 \times 10^{-19}\,\text{J}$Ered​=680×10−9(6.63×10−34)(3.00×108)​≈2.9×10−19J

So a blue photon delivers roughly 1.5× the energy of a red one. Yet plants do most of their useful photochemistry with red photons. Why? Because absorption of a photon promotes an electron from the ground state to an excited singlet state; if a higher-energy (blue) photon is absorbed, the extra energy above the lowest excited state is rapidly lost as heat (a process called internal conversion) before the electron can do any chemistry. In effect, a blue photon and a red photon both leave the pigment in the same lowest excited state — the excess energy of the blue photon is wasted. This is why the "quantum yield" of photosynthesis (O₂ evolved per photon absorbed) is roughly constant across the visible range even though photon energies vary.

An excited pigment has several competing fates: (1) photochemistry — donating the excited electron to an acceptor (the useful outcome, dominant at the reaction centre); (2) fluorescence — re-emitting a photon of slightly longer wavelength; (3) heat (non-radiative decay); (4) resonance energy transfer to a neighbouring pigment. In healthy antenna pigments, energy transfer to the reaction centre dominates. Under high-light stress, controlled dissipation as heat (non-photochemical quenching) is deliberately increased to protect the photosystems. Measuring chlorophyll fluorescence is now a standard, non-destructive way for plant physiologists to assess photosystem health — a technique routinely used in crop research and Oxbridge admissions discussions.

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Why Photosynthesis Needs Pigments

A photon of light only becomes useful biologically when it is absorbed by a pigment molecule. When absorbed, the photon transfers its energy to an electron in the pigment, raising it to a higher energy level ("excitation"). This high-energy electron is then harvested by the photosystem and passed down the electron transport chain.

Without pigments, chloroplasts would be transparent to visible light and no photosynthesis could occur. Different pigments absorb different wavelengths — together they allow plants to capture a broad range of the visible spectrum.

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The Main Photosynthetic Pigments

OCR expects you to know four main pigments found in higher plants. They fall into two groups: primary (chlorophyll a) and accessory (chlorophyll b and carotenoids).

Pigment	Colour	Absorbs	Role	Primary/Accessory
Chlorophyll a	Blue-green	Red (~670 nm) and blue-violet (~430 nm)	Direct involvement in the light reaction at the reaction centre of PSI and PSII	Primary
Chlorophyll b	Yellow-green	Red (~650 nm) and blue (~475 nm)	Harvests light and passes energy to chlorophyll a	Accessory
Carotene (β-carotene)	Orange	Blue-violet (~450 nm)	Harvests light energy; protects against photo-oxidative damage	Accessory
Xanthophyll	Yellow	Blue-violet (~450 nm)	Harvests light; also involved in photoprotection	Accessory

Chlorophyll a is essential — without it no photosynthesis can occur. Accessory pigments broaden the range of wavelengths captured and funnel energy to chlorophyll a in the reaction centre. Together, hundreds of pigment molecules plus a central chlorophyll a pair form a photosystem (a light-harvesting antenna complex with a reaction centre).

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Absorption and Action Spectra

An absorption spectrum tells you how much light of each wavelength a pigment absorbs. An action spectrum tells you how much photosynthesis occurs at each wavelength.

flowchart LR
    W[White light] --> P[Pigments]
    P -->|Absorb blue & red| E[Excited electrons]
    P -->|Reflect green| G[Green colour we see]
    E --> PS[Photosystem reaction centre]
    PS --> ETC[Electron transport chain]

• Both spectra peak in the red (~670 nm) and blue-violet (~430 nm) regions.
• Both show a trough in the green (~550 nm) region — this is why leaves look green: green light is poorly absorbed and instead reflected.
• The action spectrum closely matches the combined absorption spectrum of all the pigments. This match is strong evidence that the pigments are responsible for photosynthesis.
• The action spectrum is slightly higher in the green region than the chlorophyll a absorption spectrum alone — because accessory pigments (carotenoids, chlorophyll b) absorb some wavelengths chlorophyll a cannot.

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Why Plants Look Green

Plants reflect and transmit the wavelengths of light they do not absorb efficiently. Since chlorophylls absorb strongly in red and blue but weakly in green, green light is reflected into your eyes — hence leaves appear green. This sometimes surprises students: the green you see is the light the plant has "wasted", not the light it is using.

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Required Practical: Chromatography of Leaf Pigments

OCR practical activity group 11 requires you to separate the pigments in a leaf extract by paper or thin-layer chromatography (TLC) and calculate Rf values.

Method Summary

1. Grind a leaf (e.g. spinach, nettle) with a small amount of propanone (acetone) and sand to release the pigments.
2. Filter the extract and concentrate it by evaporation.
3. Draw a pencil origin line near the bottom of a strip of chromatography paper or silica TLC plate (~1 cm from the bottom).
4. Spot the pigment extract onto the origin line using a capillary tube. Allow to dry and respot several times to concentrate.
5. Place the strip in a beaker of solvent (e.g. 9:1 petroleum ether:propanone). The solvent level must be below the origin line.
6. Cover the beaker to prevent solvent evaporation.
7. Allow the solvent to run up the paper until near the top.
8. Mark the solvent front in pencil and allow the paper to dry.
9. Measure the distance from the origin to the centre of each pigment spot, and from the origin to the solvent front.

Calculating Rf

$R_f = \frac{\text{distance moved by pigment}}{\text{distance moved by solvent front}}$Rf​=distance moved by solvent frontdistance moved by pigment​

Rf values are always between 0 and 1, and they are characteristic of a particular pigment in a particular solvent system.

Typical Rf Values

Pigment	Colour of spot	Approximate Rf (petroleum ether:propanone)
Carotene	Orange-yellow	~0.95
Xanthophyll	Yellow	~0.70
Chlorophyll a	Blue-green	~0.60
Chlorophyll b	Yellow-green	~0.45

Rf values depend on the solvent system — if the solvent is changed, the values will change too. Always compare values from the same chromatography run.

Why Do Pigments Separate?

Each pigment has a different solubility in the solvent and a different affinity for the stationary phase (the paper or silica). Pigments that are more soluble in the solvent and less attracted to the stationary phase travel further (high Rf). Pigments that are less soluble and more attracted to the stationary phase travel less (low Rf). Carotene is non-polar, so it dissolves well in the non-polar solvent and moves near the top; chlorophyll b is the most polar, so it stays closer to the origin.

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Exam Tip

When drawing or interpreting chromatography, always remember to draw the origin line in pencil (ink would dissolve), mark the solvent front before the solvent evaporates, and measure to the centre of the spot, not the leading or trailing edge. A common OCR mark scheme point is that "Rf value has no units." If asked to identify a pigment from an Rf value, you can only do so if told the solvent system; the same pigment has different Rf values in different solvents.

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Common Exam Mistakes

• Confusing absorption and action spectra. Absorption = how much light absorbed by pigment; action = how much photosynthesis at each wavelength.
• Saying plants absorb green light. They do not — they reflect it, which is why they appear green.
• Drawing the origin line in ink. The ink would dissolve and ruin the chromatogram.
• Measuring to the top or bottom of a pigment spot. Always measure to the centre.
• Claiming Rf values have units. They are ratios and dimensionless.
• Saying chlorophyll a is the only pigment that does photosynthesis. Accessory pigments also capture light energy and pass it on — but only chlorophyll a at the reaction centre donates excited electrons to the ETC.
• Forgetting to link carotenoids to photoprotection. They also prevent photo-oxidative damage by quenching harmful excited states.

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Absorption Spectrum SVG