The Light-Independent Reaction (Calvin Cycle) — AQA A-level Biology

SPEC 3.5.1 - ENERGY TRANSFERS

Photosynthesis: Light-Independent Reaction

The Calvin cycle: CO₂ fixation, RuBP, GP, triose phosphate, organic molecule synthesis and limiting factors

The Calvin Cycle: Overview

The light-independent reaction uses the ATP and reduced NADP produced by the light-dependent reaction to fix CO₂ into organic molecules. It does not directly require light — but it stops without the products of the light-dependent reaction.

Location

Stroma of the chloroplast

Contains: rubisco enzyme, RuBP, GP, TP and all Calvin cycle intermediates

Inputs & Outputs

Inputs: CO₂, ATP, reduced NADP

Outputs: Triose phosphate (TP) → organic molecules; ADP + Pᵢ; NADP (recycled to light-dependent reaction)

The Link to Lesson 5.01

ATP and reduced NADP from the light-dependent reaction are essential inputs to the Calvin cycle. If the light-dependent reaction stops — due to darkness, lack of water, or ATP synthase inhibition — the Calvin cycle rapidly slows and halts as these substrates are depleted.

Synoptic Link — Enzymes (1.05)

Rubisco is an enzyme — its rate is affected by substrate concentration (CO₂) and temperature. This is why temperature and CO₂ concentration are key limiting factors for the light-independent reaction specifically.

Key Definitions

Definition — RuBP (Ribulose Bisphosphate)

A 5-carbon compound found in the stroma that accepts CO₂ during the Calvin cycle. It is regenerated at the end of each cycle turn using ATP.

Definition — GP (Glycerate 3-Phosphate)

A 3-carbon compound — the first stable product of CO₂ fixation. Formed when CO₂ reacts with RuBP, catalysed by rubisco.

Definition — Triose Phosphate (TP)

A 3-carbon sugar phosphate produced by the reduction of GP using ATP and reduced NADP. Some is used to regenerate RuBP; some is used to synthesise organic molecules.

Definition — Rubisco

The enzyme (RuBP carboxylase) that catalyses the fixation of CO₂ onto RuBP to form two molecules of GP. It is the most abundant enzyme on Earth.

Calvin Cycle: Step by Step

1

CO₂ fixation: CO₂ (1C) + RuBP 5C → 2 × GP 3C — catalysed by rubisco. This is carbon fixation — inorganic CO₂ is incorporated into an organic molecule.

2

GP reduction: GP 3C is reduced to triose phosphate (TP) 3C using ATP (provides energy) and reduced NADP (provides hydrogen). Both come from the light-dependent reaction.

3

RuBP regeneration: Most TP (5/6) is used to regenerate RuBP 5C using ATP. This keeps the cycle running continuously.

4

Organic molecule synthesis: Remaining TP (1/6) is used to synthesise useful organic substances — glucose, fatty acids (for lipids), and (with nitrogen from nitrate ions) amino acids.

Examiner Alert — ATP roles

ATP is used in both GP reduction (step 2) AND RuBP regeneration (step 3). Reduced NADP is used only in GP reduction (step 2). Many students state ATP is only used in one step — both must be stated for full marks.

Calvin Cycle Diagram

Green = CO₂ fixation by rubisco. Black = GP reduction (requires ATP + reduced NADP) and RuBP regeneration (requires ATP only). Purple = TP used for organic molecule synthesis.

Carbon Accounting: Per 3 CO₂ Fixed

To make one net gain of TP (3C), three turns of the Calvin cycle must occur — fixing 3 CO₂. This is the minimum accounting unit.

MoleculeCarbon atomsNumberFate

CO₂ fixed1C each3 moleculesInput to cycle

RuBP used5C each3 moleculesAccepts CO₂

GP produced3C each6 moleculesReduced to TP

TP produced3C each6 moleculesSee below

TP → RuBP—5 moleculesRegenerate 3 RuBP (using ATP)

TP → organics3C1 moleculeNet gain: glucose, lipids etc.

ATP and reduced NADP usage

Per turn of the Calvin cycle, ATP is used in both GP reduction (step 2) and RuBP regeneration (step 3). Reduced NADP is used only in GP reduction (step 2). Both molecules come from the light-dependent reaction and are recycled (as ADP + Pᵢ and NADP) back to it — creating the interdependence between the two stages.

What Happens in Darkness?

A classic exam question asks you to predict what happens to GP, TP and RuBP when light is suddenly removed. Trace through the logic step by step.

1

No light → light-dependent reaction stops → no ATP and no reduced NADP produced

2

Without ATP and reduced NADP: GP cannot be reduced to TP → GP is still being produced (CO₂ + RuBP → GP via rubisco, as CO₂ is still present) but cannot be reduced → GP accumulates ↑

3

TP is no longer being produced → existing TP is used up → TP falls ↓

4

Without TP, RuBP cannot be regenerated (RuBP regeneration requires TP + ATP). RuBP continues to be used to fix CO₂ but is not replaced → RuBP falls ↓

5

Eventually: CO₂ fixation stops (no RuBP available) → GP also falls ↓ (no longer being made)

Examiner Alert — Address ALL THREE

When asked about darkness, always state what happens to GP, TP and RuBP separately, with a reason for each. Answering only one or two loses marks. Immediate changes: GP ↑, TP ↓, RuBP ↓.

What Happens When CO₂ Is Removed?

A variation on the classic question — here the light-dependent reaction still runs normally, but CO₂ is suddenly removed.

1

No CO₂ → CO₂ fixation stops → RuBP cannot react with CO₂ → RuBP accumulates ↑ (still being regenerated from TP using ATP, but not being consumed)

2

No GP being formed → existing GP depleted → GP falls ↓

3

GP needed to make TP → no GP → TP falls ↓

Comparison: Darkness vs No CO₂

ConditionGPTPRuBPDarkness↑ accumulates↓ falls↓ fallsNo CO₂↓ falls↓ falls↑ accumulates

Limiting Factors of Photosynthesis

A limiting factor is the factor that is present at the lowest level relative to the organism's needs — increasing it will increase the rate of photosynthesis.

FactorWhich stage limitedMechanism

Light intensityLight-dependentLess photoionisation → less ATP + reduced NADP → GP cannot be reduced → Calvin cycle slows

CO₂ concentrationCalvin cycleLess substrate for rubisco → less CO₂ fixation → less GP produced → less TP → less glucose

TemperatureCalvin cycle (mainly)Rubisco is an enzyme — low temperature reduces kinetic energy + enzyme-substrate collisions; above optimum, the enzyme denatures — active site changes shape and loses complementarity to substrate

Water availabilityLight-dependentLess substrate for photolysis → fewer replacement electrons → ETC slows → less ATP + reduced NADP

Examiner Alert — "Amount of" not accepted

AQA examiners specifically reject "amount of light" and "amount of CO₂" as answers for limiting factors. Always write "light intensity" and "CO₂ concentration" — these are the precise, accepted terms.

Limiting Factor Graphs

Understanding the shape of rate vs. factor graphs is essential for AO2 and AO3 questions.

Reading the plateau

A plateau on a rate vs. light intensity graph means light is no longer limiting — a different factor (CO₂ concentration or temperature) has become the limiting factor. Increasing light intensity further has no effect. Increasing the new limiting factor would raise the plateau.

Agricultural Applications of Limiting Factors

AQA specifically requires students to evaluate data relating to common agricultural practices used to overcome limiting factors. The three key methods:

Limiting factorAgricultural methodEffect on photosynthesis

CO₂ concentrationCO₂ enrichment of glasshouses (gas burners or CO₂ injection)Increases rubisco substrate → faster CO₂ fixation → more GP + TP → higher yield

Light intensityArtificial LED lighting in glasshouses; extending day lengthIncreases photoionisation → more ATP + reduced NADP → Calvin cycle runs faster

TemperatureHeated glasshousesIncreases kinetic energy → more enzyme-substrate collisions → faster rubisco activity (up to optimum)

Exam Technique — Evaluate, Don't Just Describe

When evaluating agricultural data, examiners expect you to: (1) identify which limiting factor is being overcome, (2) explain the mechanism, (3) discuss any trade-offs (e.g. cost of heating vs. yield gain). "More light increases photosynthesis" — 0 marks. "Increasing light intensity raises ATP and reduced NADP production in the light-dependent reaction, supplying more substrate for the Calvin cycle, increasing TP and hence glucose yield" — full marks.

Organic Molecules from Triose Phosphate

The 1/6 of triose phosphate not used for RuBP regeneration is the source of all organic molecules made by the plant.

From TP directly

Glucose — two TP molecules (3C + 3C) condense → glucose (6C); used for respiration, cellulose, starch

Glycerol — for lipid (triglyceride) synthesis

Fatty acids — for lipid synthesis

With additional elements

Amino acids — TP derivatives + nitrogen (from nitrate ions absorbed by roots) → amino acids → proteins

Key point — nitrogen source

Amino acids require nitrogen. Plants absorb nitrate ions (NO₃⁻) from the soil. Nitrogen from nitrate is incorporated into amino acids, which are then assembled into proteins. Nitrogen deficiency severely limits plant protein synthesis and growth.

DEEP Framework: Extended Answer

"Explain how a decrease in CO₂ concentration affects the rate of photosynthesis."

DEEP Answer Framework

DDefine: CO₂ concentration is a limiting factor for photosynthesis because it is the substrate for CO₂ fixation in the Calvin cycle, catalysed by rubisco.

EExplain mechanism: Lower [CO₂] → fewer CO₂ molecules available for rubisco → rate of CO₂ fixation (RuBP + CO₂ → GP) decreases → less GP produced → less GP available for reduction to TP → less TP for RuBP regeneration and organic molecule synthesis. RuBP accumulates (still regenerated using ATP from light-dependent reaction, but less CO₂ to react with). Glucose production falls.

EEvidence/example: Glasshouse experiments show that increasing CO₂ from 0.04% to 0.1% typically increases photosynthesis rate until another factor (light or temperature) becomes limiting.

PPractical/quantitative: Rate of O₂ production from Elodea is directly proportional to [CO₂] at low concentrations but plateaus when light intensity becomes limiting — demonstrating the principle of limiting factors.

Synoptic Links

Link to Enzymes (1.05)

Rubisco is the enzyme catalysing CO₂ fixation. Its rate is affected by substrate concentration (CO₂), temperature, and pH — exactly as covered in the enzymes lesson. Temperature and CO₂ concentration are limiting factors precisely because they affect rubisco activity.

Link to Light-Dependent Reaction (5.01)

ATP and reduced NADP from the light-dependent reaction are consumed in steps 2 and 3 of the Calvin cycle. ADP and NADP are recycled back — creating a tight interdependence between the two stages. Darkness affects the Calvin cycle indirectly, through loss of these substrates.

Link to Respiration (5.03–5.04)

Triose phosphate (TP) produced in the Calvin cycle is the same 3-carbon compound that appears in glycolysis. This connection explains how photosynthesis and respiration are linked — TP from the Calvin cycle feeds directly into the respiration pathway.

Link to Ecosystems (5.05)

The rate of the Calvin cycle determines gross primary production (GPP). Limiting factors explain why GPP varies with season, latitude, altitude and canopy cover — directly linking this lesson to ecology.

Practice Question

A student investigated the effect of light intensity on photosynthesis in Elodea. They measured the rate of O₂ production at three CO₂ concentrations (0.04%, 0.1% and 0.4%) across a range of light intensities. At low light intensity, all three CO₂ concentrations gave the same rate. At high light intensity, higher CO₂ concentrations gave higher rates, each reaching a different plateau.

(a) Explain why all three CO₂ concentrations give the same rate at low light intensity. [2 marks]

(b) Explain why the plateau rate is higher at 0.4% CO₂ than at 0.04% CO₂. [3 marks]

(c) Predict what would happen to the concentration of RuBP if, at the plateau for 0.04% CO₂, the student suddenly increased CO₂ concentration to 0.4%. Explain your answer. [3 marks]

(a) At low light intensity, light is the limiting factor for all three conditions. The light-dependent reaction produces limited ATP and reduced NADP regardless of CO₂ concentration — the Calvin cycle rate is restricted by insufficient ATP/reduced NADP to reduce GP, not by CO₂ availability. (2 marks: light is limiting; ATP/reduced NADP insufficient)

(b) At the plateau, light is no longer limiting — CO₂ concentration becomes the limiting factor. Higher [CO₂] provides more substrate for rubisco → faster CO₂ fixation → more GP produced → more GP reduced to TP → more TP available for organic molecule synthesis → higher rate of O₂ production. (3 marks: CO₂ limiting at plateau; more substrate for rubisco; more GP → more TP → higher rate)

(c) RuBP concentration would initially fall. At the plateau for 0.04% CO₂, RuBP was accumulating because CO₂ was limiting (rubisco had limited substrate). Suddenly increasing [CO₂] provides more substrate for rubisco → rate of CO₂ fixation increases → RuBP is consumed faster → RuBP concentration falls (until a new equilibrium is reached as the cycle speeds up). (3 marks: RuBP falls; more CO₂ = more rubisco activity; RuBP consumed faster)

Lesson Summary

Light-Independent Reaction (Calvin Cycle) — Key Points

Location: Stroma of the chloroplast

Step 1 — CO₂ fixation: CO₂ + RuBP (5C) → 2 × GP (3C), catalysed by rubisco

Step 2 — GP reduction: GP → TP using ATP + reduced NADP (both from light-dependent reaction)

Step 3 — RuBP regeneration: 5/6 TP → RuBP using ATP

Step 4 — Organic synthesis: 1/6 TP → glucose, lipids, amino acids

ATP is used in steps 2 and 3; reduced NADP only in step 2

Darkness: GP ↑, TP ↓, RuBP ↓ (no ATP/reduced NADP to reduce GP or regenerate RuBP)

No CO₂: GP ↓, TP ↓, RuBP ↑ (no CO₂ fixation; RuBP accumulates)

Limiting factors: light intensity, CO₂ concentration, temperature (affects rubisco)

Never Write

"Amount of light" or "amount of CO₂" → write light intensity and CO₂ concentration

"ATP is only used in GP reduction" → ATP used in both GP reduction and RuBP regeneration

"GP is oxidised to TP" → GP is reduced to TP (by reduced NADP)

"GP is glucose-3-phosphate" → GP is glycerate 3-phosphate