state that Calvin cycle intermediates are used to produce other molecules, limited to GP to produce some amino acids and TP to produce carbohydrates, lipids and amino acids

Photosynthesis – Energy Transfer Process (Cambridge A‑Level Biology 9700)

Learning Objective

State that Calvin‑cycle intermediates are used to produce other molecules, limited to glyceraldehyde‑3‑phosphate (GP) for some amino acids and triose‑phosphate (TP) for carbohydrates, lipids and additional amino acids.

1. Chloroplast Structure – The Site of Photosynthesis

• Envelope – outer and inner membranes; the inner membrane encloses the stroma.
• Stroma – fluid matrix containing Calvin‑cycle enzymes, chloroplast DNA, ribosomes and metabolites derived from the thylakoid system.
• Thylakoid system

  • Stacks of thylakoids form grana; unstacked thylakoids are called lamellae.
  • Thylakoid membrane houses Photosystem II, Photosystem I, the cytochrome b₆f complex, ATP synthase and the plastoquinone/plastocyanin electron carriers.
  • Thylakoid lumen contains the oxygen‑evolving complex that splits water (2 H₂O → 4 H⁺ + O₂ + 4 e⁻).

2. Pigments & Light Absorption

Quick activity – Interpreting an absorption spectrum

1. Examine the provided absorption curve (peak at ~460 nm, shoulder at ~660 nm).
2. Which pigment dominates the absorbance at 460 nm? Answer: β‑carotene / xanthophylls.
3. Predict which photosystem will receive the greatest excitation at 660 nm. Answer: Photosystem II (P680).

The action spectrum (rate of photosynthesis vs. wavelength) mirrors the absorption spectrum, but it also shows the relative contribution of PS I (peak ~700 nm) and PS II (peak ~680 nm). Linking the two demonstrates that chlorophyll a drives both photosystems, while accessory pigments funnel energy toward them.

3. Light‑Dependent Reactions – Production of ATP and NADPH

3.1 Non‑Cyclic (Linear) Electron Flow

H₂O  →  PSII (P680*) →  H₂O‑splitting (O₂ + 4e⁻ + 4H⁺)
e⁻ →  Plastoquinone (PQ) →  Cyt b₆f →  Plastocyanin (PC) →  PSI (P700*)
e⁻ →  Ferredoxin (Fd) →  NADP⁺ reductase →  NADPH
Proton gradient (ΔpH) →  ATP synthase →  ATP

• Water is split by the oxygen‑evolving complex, providing electrons and releasing O₂.
• For each 3 CO₂ fixed (one turn of the Calvin cycle) the light‑dependent reactions supply 9 ATP and 6 NADPH.

3.2 Cyclic Electron Flow (around PSI)

Fd (reduced) → Cyt b₆f → PC → PSI → Fd

• Electrons return to the cytochrome b₆f complex instead of reducing NADP⁺.
• Only ATP is generated (no NADPH, no O₂). This supplements ATP when the Calvin cycle’s ATP demand exceeds the supply from linear flow.

3.3 Summary of Products (per 3 CO₂)

4. Calvin Cycle (Light‑Independent Reactions)

4.1 Overall Equation (per 3 CO₂)

3 CO₂ + 9 ATP + 6 NADPH + 5 H₂O → Glyceraldehyde‑3‑phosphate (GP) + 9 ADP + 8 P_i + 6 NADP⁺ + 3 H⁺

4.2 Three Phases

1. Carbon fixation – CO₂ + ribulose‑1,5‑bisphosphate (RuBP, 5‑C) → 2 × 3‑phosphoglycerate (3‑PGA, 3‑C).
2. Reduction – 3‑PGA + ATP → 1,3‑bisphosphoglycerate; + NADPH → glyceraldehyde‑3‑phosphate (GP, also called G3P).
3. Regeneration – 5 GP molecules are rearranged (using ATP) to regenerate 3 RuBP, allowing the cycle to continue.

4.3 Key Intermediates

• Glyceraldehyde‑3‑phosphate (GP, G3P) – the direct product of the reduction phase.
• Triose phosphate (TP) – the combined pool of GP and dihydroxyacetone phosphate (DHAP); DHAP ⇌ GP via triose‑phosphate isomerase.

5. Fate of Calvin‑Cycle Intermediates

5.1 Glyceraldehyde‑3‑Phosphate (GP) – Limited Amino‑Acid Synthesis

Only a small proportion of GP leaves the cycle. The principal biosynthetic routes are:

1. Serine (phosphorylated pathway)

   GP → 3‑phosphoglycerate → 3‑phosphohydroxypyruvate → phosphoserine → serine

   (Key enzymes: phosphoglycerate dehydrogenase, phosphoserine aminotransferase, phosphoserine phosphatase)

2. Cysteine

   Serine + sulfide (S²⁻) → cysteine

   (Key enzyme: O‑acetylserine (thiol)‑lyase)

5.2 Triose Phosphate (TP) – Carbon Skeleton for Major Biosynthetic Pathways

1. Carbohydrate synthesis

   • Starch (chloroplast): TP → ADP‑glucose (via ADP‑glucose pyrophosphorylase) → polymerised into starch.
   • Sucrose (cytosol): 2 TP → sucrose‑6‑phosphate (via sucrose‑phosphate synthase) → sucrose (via sucrose‑phosphate phosphatase).

2. Lipid synthesis

   • TP → pyruvate (glycolysis) → acetyl‑CoA (pyruvate dehydrogenase complex).
   • Acetyl‑CoA enters the fatty‑acid synthase cycle → long‑chain fatty acids → triacylglycerols (oil bodies).

3. Additional amino‑acid synthesis

   • Alanine: pyruvate + glutamate ⇌ alanine + α‑ketoglutarate (alanine aminotransferase).
   • Glycine: serine (derived from GP) + tetrahydrofolate ⇌ glycine + 5,10‑methylenetetrahydrofolate (serine hydroxymethyltransferase).
   • Branched‑chain amino acids (valine, leucine, isoleucine) and others ultimately derive carbon skeletons from pyruvate or oxaloacetate, both generated from TP.

5.3 Summary Table – From Calvin‑Cycle Intermediates to End Products

6. Integrated View – Linking Light‑Dependent and Light‑Independent Stages

• Light‑dependent reactions supply the ATP and NADPH required for the reduction phase of the Calvin cycle.
• CO₂ fixation creates GP, the gateway to both primary carbohydrate storage (starch, sucrose) and the limited synthesis of serine and cysteine.
• TP provides the carbon backbone for the majority of plant biosynthesis (lipids, bulk carbohydrates, a wide range of amino acids).
• Because only a small proportion of GP/TP leaves the cycle, the plant can regulate growth, storage and stress responses by adjusting flux through these branching pathways.

7. Investigation of Limiting Factors (Syllabus 13.2)

Goal: Determine which environmental factor (light intensity, CO₂ concentration, temperature, or water availability) limits the rate of photosynthesis in a given plant.

Suggested experimental design

1. Choose a single factor to vary while keeping the other three constant.
2. Use identical leaf discs (same species, similar size) for each treatment.
3. Measure O₂ evolution for a fixed period (e.g., 5 min) using a gas‑collection syringe.
4. Plot rate (mL O₂ min⁻¹) against the variable. The plateau or peak indicates the point at which the tested factor ceases to be limiting.
5. Repeat for the remaining three factors to identify the overall limiting factor under the chosen experimental conditions.

8. Key Points to Remember

• The chloroplast’s internal architecture (envelope, stroma, grana, lamellae) underpins the two photosynthetic phases.
• Chlorophyll a is the primary photochemical pigment; chlorophyll b and carotenoids extend the usable spectrum and protect against excess light.
• Non‑cyclic electron flow produces both ATP and NADPH and releases O₂ via the oxygen‑evolving complex; cyclic flow supplies extra ATP when needed.
• The Calvin cycle fixes CO₂ into GP; most GP is recycled to RuBP, but a limited amount is diverted to serine and cysteine synthesis.
• TP (GP + DHAP) is the hub for synthesis of starch, sucrose, fatty acids, triacylglycerols and a broader set of amino acids (alanine, glycine, branched‑chain AAs, etc.).
• All downstream biosynthetic routes depend on the ATP and NADPH generated in the light‑dependent reactions, illustrating the tight coupling of the two stages.
• Experimental investigation of limiting factors (light, CO₂, temperature, water) is a core skill for understanding how environmental conditions control photosynthetic rate.