state that within a chloroplast, the thylakoids (thylakoid membranes and thylakoid spaces), which occur in stacks called grana, are the site of the light-dependent stage and the stroma is the site of the light-independent stage

Photosynthesis – An Energy Transfer Process

Learning Objective

State that within a chloroplast the thylakoids (thylakoid membranes and thylakoid lumen), which are organised into stacks called grana, are the site of the light‑dependent reactions, whereas the stroma is the site of the light‑independent (Calvin‑Benson) reactions.

1. Overall Equation

\[

6\;\text{CO}2 + 6\;\text{H}2\text{O}

\;\xrightarrow{\text{light}}\;

\text{C}6\text{H}{12}\text{O}6 + 6\;\text{O}2

\]

2. Chloroplast Structure (Syllabus 13.1)

• Outer membrane – porous to small molecules; encloses the organelle and allows diffusion of gases and ions.
• Inner membrane – less permeable; contains transport proteins that regulate entry of larger metabolites (e.g., ADP, Pi) into the stroma.
• Stroma – aqueous matrix surrounding the thylakoid system; contains the enzymes of the Calvin‑Benson cycle and the chloroplast DNA.
• Thylakoid system

  • Thylakoid membranes – embed chlorophyll a, accessory pigments and the protein complexes of the electron‑transport chain.
  • Thylakoid lumen (space) – becomes acidic during the light‑dependent reactions; the H⁺ gradient across the membrane drives ATP synthesis (chemiosmosis).
  • Grana – stacks of flattened thylakoids; the principal site of light capture and electron transport.
  • Lamellae (inter‑granal thylakoids) – unstacked thylakoids that connect individual grana, allowing ATP and NADPH to diffuse throughout the chloroplast.

3. Photosynthetic Pigments & Their Roles (Syllabus 13.1)

The action spectrum of a plant mirrors the combined absorption spectra of these pigments – wavelengths that are strongly absorbed (e.g., around 430 nm and 660 nm) drive the highest rates of photosynthesis.

4. Practical: Paper Chromatography of Leaf Pigments (Syllabus 13.1)

5. Light‑Dependent Reactions (Thylakoid Membranes & Grana)

These reactions occur in the thylakoid membranes of the grana and require light to drive electron flow, proton pumping and ATP synthesis.

5.1. Photon‑budget (balanced) equation

For one complete turn of non‑cyclic photophosphorylation (using 8 photons, 4 absorbed by PSII and 4 by PSI):

\[

8\;\text{photons} + 2\;\text{H}_2\text{O}

\;\longrightarrow\;

\text{O}2 + 4\;\text{H}^+{\text{lumen}} + 4\;e^- + 4\;\text{ATP} + 2\;\text{NADPH}

\]

5.2. Non‑Cyclic (Z‑Scheme) Photophosphorylation

• Excitation – Light excites chlorophyll a in Photosystem II (PSII). Energy is transferred from accessory pigments to chlorophyll a.
• Water splitting (OEC) – The oxygen‑evolving complex supplies electrons:

  \[

  2\;\text{H}2\text{O} \;\rightarrow\; 4\;\text{H}^+{\text{lumen}} + 4\;e^- + \text{O}_2

  \]

• Electron transport chain (all embedded in the thylakoid membrane):

  PSII → Plastoquinone (PQ) → Cytochrome b₆f → Plastocyanin (PC) → PSI

• Proton pumping – At the cytochrome b₆f complex, electrons drive the translocation of additional H⁺ from the stroma into the lumen, increasing lumen acidity.
• ATP synthesis – The H⁺ gradient powers ATP synthase; H⁺ flow back into the stroma yields ATP (photophosphorylation).
• NADPH formation – Excited electrons from PSI reduce NADP⁺ via ferredoxin (Fd) and ferredoxin‑NADP⁺ reductase (FNR):

  \[

  \text{NADP}^+ + 2\;e^- + \text{H}^+_{\text{stroma}} \rightarrow \text{NADPH}

  \]

• Outputs – O₂ (released to the atmosphere), ATP and NADPH (used in the stroma).

5.3. Cyclic Photophosphorylation (PSI only)

• Only PSI is active; electrons from ferredoxin are routed back to the cytochrome b₆f complex.
• No water splitting – therefore no O₂ is produced.
• The cyclic flow generates additional H⁺ pumping, giving extra ATP without producing NADPH.

5.4. Role of the Thylakoid Lumen

The lumen’s acidity (pH ≈ 5) is the direct result of water splitting and proton pumping. This gradient is the energy source for ATP synthase, linking the structural description of the thylakoid to the chemiosmotic mechanism required by the syllabus.

5.5. Electron‑Transport Chain Diagram (placeholder)

6. Light‑Independent Reactions – Calvin‑Benson Cycle (Stroma)

The stroma hosts the three‑phase Calvin‑Benson cycle, using ATP and NADPH produced in the thylakoids to fix CO₂ into carbohydrate.

6.1. Overall balanced equation (per 3 CO₂)

\[

3\;\text{CO}2 + 9\;\text{ATP} + 6\;\text{NADPH} + 6\;\text{H}2\text{O}

\;\longrightarrow\;

\text{G3P} + 9\;\text{ADP} + 8\;\text{Pi} + 6\;\text{NADP}^+ + 3\;\text{H}2\text{O}

\]

6.2. Cycle steps

1. Carbon fixation – 3 CO₂ + 3 RuBP → 6 3‑phosphoglycerate (3‑PGA).
2. Reduction phase – 6 3‑PGA + 6 ATP + 6 NADPH → 6 glyceraldehyde‑3‑phosphate (G3P) + 6 ADP + 6 Pᵢ + 6 NADP⁺.
3. Regeneration of RuBP – 5 G3P are rearranged, using 3 ATP, to regenerate 3 RuBP, allowing the cycle to continue.
4. Carbohydrate formation – 2 G3P exit the cycle; two molecules combine (via gluconeogenesis) to give one molecule of glucose (or other carbohydrates).

7. Summary Table – Location, Main Inputs & Main Outputs

8. Key Points to Remember (Syllabus 13.2)

1. The thylakoid membranes of the grana are the exclusive site where light energy is captured and converted into chemical energy (ATP + NADPH).
2. Chlorophyll a is the reaction‑centre pigment; accessory pigments (chlorophyll b, carotene, xanthophyll) broaden the range of absorbed wavelengths and funnel the excitation energy to chlorophyll a.
3. The thylakoid lumen becomes acidic as a result of water splitting and proton pumping; this H⁺ gradient drives ATP synthesis (chemiosmosis).
4. Lamellae interconnect grana, ensuring that ATP and NADPH can diffuse from the sites of production to the stroma where the Calvin‑Benson cycle operates.
5. Non‑cyclic photophosphorylation produces both ATP and NADPH and releases O₂; cyclic photophosphorylation produces ATP only and is used when the ATP demand exceeds that supplied by the Z‑scheme.
6. The Calvin‑Benson cycle uses ATP and NADPH to fix CO₂ into G3P, which can be converted into glucose or other carbohydrates.
7. Energy flow in photosynthesis: photons → excited electrons → H⁺ gradient → ATP + NADPH → carbon fixation → carbohydrate.
8. Chromatography of leaf pigments provides experimental evidence for the presence of several pigments with distinct Rf values and absorption maxima, linking the action spectrum to pigment composition.