AQA A-level Biology: Photosynthesis (7402)

This guide teaches section 3.5.1 (Photosynthesis) of the AQA AS and A-level Biology specification (7401 and 7402), for first teaching 2015. Section 3.5 is A-level only, so none of this is examined at AS. It also covers required practicals 7 and 8. Use the revision notes for recall and the practice questions to test yourself. Course pages: AQA A-level Biology hub, printable checklist and free diagnostics.

What this guide covers

Specification point	You must be able to
3.5.1 light-dependent reaction	Link chlorophyll, photoionisation, the electron transfer chain, chemiosmosis and ATP synthase to the production of ATP and reduced NADP, and explain photolysis
3.5.1 light-independent reaction	Describe how carbon dioxide, RuBP, rubisco, GP, triose phosphate and the Calvin cycle produce simple sugars
3.5.1 limiting factors	Identify environmental factors that limit the rate of photosynthesis
3.5.1 agricultural data	Evaluate data on common agricultural practices that overcome limiting factors
Required practical 7	Use chromatography to investigate pigments from leaves
Required practical 8	Investigate a named factor and dehydrogenase activity in chloroplast extracts

The big picture

Photosynthesis transfers light energy to chemical energy stored in organic molecules. It has two linked stages in a chloroplast.

• The light-dependent reaction happens on the thylakoid membranes. It makes ATP and reduced NADP, and releases oxygen.
• The light-independent reaction happens in the stroma. It uses that ATP and reduced NADP to turn carbon dioxide into a simple sugar.

The specification also notes that the hydrolysis of ATP from the first stage provides the extra energy for the second. It needs no light directly but stops soon after the light goes off, because its supplies stop.

The light-dependent reaction

Photoionisation

Chlorophyll in the thylakoid membranes absorbs light. The energy raises electrons in chlorophyll to a higher energy level, and they leave the molecule. The chlorophyll has been ionised by light, which is why the process is called photoionisation.

The electron transfer chain

The electrons pass from carrier to carrier along a chain of proteins in the thylakoid membrane. Each transfer is a redox reaction and the electrons lose energy at each step. Some of that energy is used to move protons (H⁺) across the thylakoid membrane, from the stroma into the thylakoid space.

Chemiosmosis and ATP synthase

Pumping protons builds up a high concentration of H⁺ inside the thylakoid space. Because protons carry charge, the result is an electrochemical gradient across the membrane. The membrane is impermeable to H⁺, so protons can only return through channels in the enzyme ATP synthase. Their movement down the gradient drives the formation of ATP from ADP and inorganic phosphate. This explanation is the chemiosmotic theory.

A gradient of pH makes the idea concrete. Suppose the stroma is pH 8.0 and the thylakoid space is pH 5.0. Each pH unit is a tenfold change in H⁺ concentration, so the difference is 10³, a 1000-fold gradient. The gradient, not the pH value itself, stores the energy.

Reduced NADP

Electrons at the end of the chain are accepted by NADP, together with a proton from the stroma, giving reduced NADP. Some of the energy from the released electrons is therefore conserved in two products: ATP and reduced NADP.

Photolysis

Chlorophyll has lost electrons, so they must be replaced. They come from water, which is split in photolysis:

H₂O → 2H⁺ + 2e⁻ + ½O₂

Photolysis produces three things. The electrons replace those lost from chlorophyll. The protons add to the proton concentration inside the thylakoid space and are used with NADP. The oxygen diffuses out of the leaf or is used in respiration.

The light-independent reaction

Reduced NADP supplies hydrogen (reducing power) and ATP supplies energy. The cycle that uses them is the Calvin cycle.

1. Carbon fixation. Carbon dioxide combines with the five-carbon compound ribulose bisphosphate (RuBP). The enzyme rubisco catalyses this. The unstable product gives two molecules of glycerate 3-phosphate (GP).
2. Reduction. GP is reduced to triose phosphate (TP) using ATP and reduced NADP.
3. Regeneration. Most TP is used to regenerate RuBP, which also needs ATP. This closes the cycle.
4. Output. Some TP is converted to useful organic substances, such as glucose, other carbohydrates, lipids and amino acids.

Worked example 1: counting carbons

Show how three carbon dioxide molecules fixed in the cycle give one net triose phosphate.

• 3 CO₂ (3 carbons) + 3 RuBP (15 carbons) → 6 GP (18 carbons)
• 6 GP → 6 TP (18 carbons)
• 1 TP (3 carbons) leaves the cycle
• 5 TP (15 carbons) → 3 RuBP (15 carbons)

Carbon is balanced: 3 carbon atoms enter as CO₂ and 3 leave as one TP. The 15 carbon atoms in RuBP are recovered, so the cycle can continue. Two TP make a six-carbon sugar, so one glucose needs six turns.

Worked example 2: why GP and RuBP change

A culture of algae is in bright light with plenty of carbon dioxide, then the light is switched off.

• ATP and reduced NADP are no longer made, so GP cannot be reduced and its level rises.
• Less TP is made, so less RuBP is regenerated. Rubisco still fixes carbon dioxide while RuBP lasts, so RuBP falls.

If instead the carbon dioxide were removed in the light, RuBP could not be used, so RuBP would rise and GP would fall. Link each change to a reaction and you will be able to explain any graph of this kind.

Limiting factors

A limiting factor is the variable that is in shortest supply or furthest from its best value, so that changing it changes the rate while the others do not. The environmental factors to know are:

Factor	Why it limits	Typical graph
Light intensity	Fewer photons means less photoionisation, so less ATP and reduced NADP	Rises, then levels off
Carbon dioxide concentration	Rubisco has less substrate, so less GP is made	Rises, then levels off
Temperature	Enzyme-catalysed steps, including rubisco, speed up with heat and denature at high temperature	Rises to an optimum, then falls
Light wavelength	Chlorophyll and other pigments absorb some wavelengths more than others	Peaks in blue and red light

To identify the limiting factor, change one factor at a time. If increasing it raises the rate, it was limiting. If the rate does not change, another factor is limiting. On a plateau the factor on the x-axis is no longer limiting.

Worked example 3: reading a limiting-factor table

Treatment	Light	CO₂	Temperature	Relative rate
A	low	0.04%	25 °C	4
B	high	0.04%	25 °C	9
C	high	0.40%	25 °C	21
D	high	0.40%	15 °C	11

Comparing A with B changes only light, and the rate rises, so light limits A. Comparing B with C changes only carbon dioxide, so carbon dioxide limits B. Comparing C with D shows temperature affects the rate at 15 °C, which is a limiting factor in D.

Agricultural data

Growers in glasshouses change limiting factors on purpose: carbon dioxide enrichment, artificial lighting and heating. Each costs money, so compare the extra yield with the extra cost.

Worked example 4: evaluating a trial

A grower tests treatments in a 500 m² glasshouse. Tomatoes sell at £1.60 per kg.

Treatment	Yield (kg)	Extra cost (£)
Ambient conditions	3100	0
Plus carbon dioxide enrichment	3950	700
Plus carbon dioxide and extra light	4550	1050 more
Plus carbon dioxide, light and heating	4650	620 more

Percentage increase for carbon dioxide alone: (3950 − 3100) ÷ 3100 × 100 = 27.4%. The extra income is 850 × 1.60 = £1360, so the net gain is 1360 − 700 = £660.

Adding light raises income by 600 × 1.60 = £960 for £1050, a net loss of £90. Adding heat raises income by 100 × 1.60 = £160 for £620, a net loss of £460.

Evaluation: only carbon dioxide enrichment pays for itself in this trial. Light and heat raise yield but cost more than they earn. Note the limits: one trial, one crop, one season, and prices change.

Required practical 7: chromatography of pigments

Aim: separate pigments from leaves, such as shade-tolerant and shade-intolerant plants or leaves of different colours.

1. Grind leaf material with a small volume of a suitable solvent and filter or pipette off the extract.
2. Put a small, concentrated spot on a pencil origin line near the bottom of the paper or plate. Pencil is used because it does not dissolve and run.
3. Stand it in a shallow layer of solvent below the line, in a covered container. Remove it before the solvent reaches the top and mark the solvent front at once.
4. Measure from the origin to the solvent front and to the centre of each spot.

Pigments separate because they differ in solubility in the solvent and in how strongly they stick to the paper. The more soluble pigment travels further. The retention factor is:

Rf = distance moved by the pigment ÷ distance moved by the solvent front

Worked example 5: Rf values

The solvent front moved 7.8 cm. Spots were at 7.4, 5.5, 5.0 and 3.4 cm.

Rf = 7.4 ÷ 7.8 = 0.95; 5.5 ÷ 7.8 = 0.71; 5.0 ÷ 7.8 = 0.64; 3.4 ÷ 7.8 = 0.44.

Rf has no units and is always less than 1. Compare with reference values for the same solvent and paper to identify pigments. An extra or stronger spot in one extract shows that plant has more of that pigment. Safety: solvents are often flammable and harmful, so ventilate and keep flames away.

Required practical 8: dehydrogenase in chloroplast extracts

Dehydrogenase enzymes in the light-dependent reaction remove hydrogen and electrons and pass them to NADP. In the practical, the blue dye DCPIP takes the electrons instead, because it can act as an electron acceptor. It is reduced and turns from blue to colourless. A faster colour change means faster dehydrogenase activity.

Method outline:

1. Grind leaves in ice-cold, buffered, isotonic solution. Isotonic stops osmotic damage to chloroplasts, cold limits enzyme damage and buffer keeps the pH steady. Filter, then centrifuge to collect the chloroplasts.
2. Mix the extract with DCPIP in a tube. Vary one named factor, such as light intensity (distance from a lamp) or temperature.
3. Record the time to decolourise, or use a colorimeter to measure absorbance at intervals.

Controls: boiled extract, a tube without chloroplasts, and a tube kept in the dark (wrapped in foil) show that the colour change needs active chloroplast enzymes, and light.

Worked example 6: rate from absorbance

At 10 cm from the lamp, absorbance falls from 0.70 to 0.34 in 6.0 minutes. At 25 cm, it falls from 0.70 to 0.55 in 6.0 minutes.

Rate at 10 cm = (0.70 − 0.34) ÷ 6.0 = 0.060 per minute. Rate at 25 cm = (0.70 − 0.55) ÷ 6.0 = 0.025 per minute.

The rate is higher in brighter light. For a small lamp, light intensity is roughly proportional to 1 ÷ distance², so 25 cm gives about 0.16 of the intensity at 10 cm. The rate fell by far less than that, which suggests other factors, such as the amount of enzyme, were also limiting.

Common errors

• Writing that light-independent reactions happen in the dark. They need no light directly but depend on products from the light.
• Saying that oxygen comes from carbon dioxide. It comes from water in photolysis.
• Mixing up GP and TP. GP is reduced to TP.
• Saying ATP synthase pumps protons. The electron transfer chain pumps them; they flow back down the gradient through ATP synthase.
• Saying the x-axis factor still limits the rate on a plateau. It does not; another factor does.
• Giving Rf as a percentage or with units.

Official syllabus

AQA AS and A-level Biology (7401 and 7402), specification for first teaching 2015, published by AQA. Section 3.5.1 and required practicals 7 and 8.