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Biology 230 - Molecules and Cells


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  • carbon fixation cycle (Calvin cycle)
  • CF0 subunit
  • CF1 subunit
  • chlorophyll
  • cyclic photophosphorylation
  • cytochrome b6-f complex
  • ferredoxin (Fd)
  • granum (pl. grana)
  • nicotinamide adenine dinucleotide phosphate (NADP+)
  • linear photophosphorylation
  • photophosphorylation
  • photosystem
  • plastocyanin (PC)
  • plastoquinone (Q)
  • reaction center
  • ribulose 1,5-biphosphate
  • stroma
  • thylakoid membrane

Introduction and Goals

This tutorial will describe the mechanisms involved in photosynthesis. Photosynthesis occurs in the chloroplasts, where the energy derived from sunlight is used to excite electrons that are subsequently donated to a protein-mediated electron transport system analogous to the respiratory chain in the mitochondria. These electrons are finally donated to a reduced electron carrier. As electrons move through the transport chain, a hydrogen electrochemical gradient is generated and it drives the synthesis of ATP by ATP synthase. The ATP and reduced electron carriers generated from photosynthesis are used to convert CO2 into organic carbon in the form of sugars and carbohydrates.

By the end of this tutorial you should understand:

  • The features of a chloroplast
  • The role of chlorophyll in the light-gathering complexes
  • The mechanisms of the light-dependent reactions of photosynthesis, including the electron carrier NADP and water
  • How the energy of the light-dependent reactions is used to convert carbon dioxide into sugars

Photosynthesis Occurs In the Chloroplasts

Figure 1.  The structure of a chloroplast. A chloroplast has three distinct membranes: an outer membrane, an inner membrane and a thylakoid membrane. Stacks of disc-shaped invaginations of the thylakoid membrane are referred to as grana (singular: granum). The space surrounded by the inner membrane is referred to as the stroma. Photosynthesis occurs in the thylakoid membrane.

Photosynthesis is the conversion of the energy from sunlight into the chemical bonds of organic compounds synthesized from atmospheric CO2. There are two distinct pathways of reactions in photosynthesis: the light-dependent reactions and the light-independent reactions. In the light-dependent reactions, also referred to as photophosphorylation, the energy of light is used to excite electrons that are transported through an electron transport chain analogous to the respiratory chain in the mitochondria. Chemiosmotic coupling links light-dependent electron transport and ATP synthesis with the electrons eventually donated to the high-energy molecule NADP. In addition, water is split, thus releasing oxygen. The light-independent reactions, also referred to as the carbon fixation cycle, use the energy of ATP and NADPH produced in the light reactions to convert CO2 into 5-carbon sugars. Both the light and dark reactions of photosynthesis occur in chloroplasts (illustrated in Figure 1). The chloroplast has an inner and outer membrane, separated by an intermembrane space, and the inner membrane surrounds a space termed the stroma (analogous to the matrix in mitochondria). A third membrane in the stroma, the thylakoid membrane, is unique to chloroplasts. It appears as stacks of disc-shaped invaginations that are referred to as grana. The light-gathering complexes, the electron transport chain and the ATP synthase of photosynthesis are all located in the thylakoid membrane. Like mitochondria, chloroplasts have their own genome. 

Chlorophyll absorbs light and transfers the energy to excited electrons

Figure 2.  Photosystems and the structure of chlorophyll. The light-gathering complexes, photosystems, are embedded in the thylakoid membrane of the chloroplast. A photosysytem (illustrated right) is composed of many molecules of pigments, mostly chlorophylls (shown in green), however, others such as carotenoids (shown in orange) are also present. The structure of chlorophyll is illustrated in the box on the lower left. Chlorophyll absorbs light with wavelengths of 450 nm, whereas carotenoids absorb light with wavelengths of 500 nm. When light is absorbed, electrons in chlorophyll (and the other pigments) are excited. As the electrons return to their ground energy state, the free energy released is funneled into a reaction center that contains special chlorophyll molecules (either P680 and P700) and it is used to excite these molecules. Once excited, these chlorophyll molecules can donate their electrons to the electron transport chain in the thylakoid membrane.

The two photosystems of the light-dependent reactions of photosynthesis are comprised of hundreds of molecules of chlorophyll. These light-absorbing molecules (see Figure 2) are embedded in the thylakoid membrane. A chlorophyll molecule absorbs photons of mostly red light (~ 450 nm), which excite electrons in the molecule to a higher energy level. Within a photosystem (illustrated inFigure 2), many chlorophyll molecules (and other pigment molecules) absorb light, and the energy of the excited electrons is passed from one molecule to another, funneling the energy into a reaction center that contains a special pair of chlorophyll molecules (P680 and P700). In the reaction center, the electrons of P680 and P700 are excited and then carried through an electron transport chain analogous to the respiratory chain in mitochondria.

Linear Photophosphorylation

Linear Photophosphorylation and ATP Synthesis In the Chloroplasts

Figure 3.  Linear photophosphorylation: electron transport and ATP synthesis.The respiratory chain is composed of three large protein complexes fixed in the membrane (colored green) and two mobile electron carriers (colored black). Light absorbed in photosystem II (PSII) excites the electrons of P680, which are donated to the mobile molecule plastoquinone (Q). The electron-depleted P680 chlorophylls are restored by the splitting of water, which liberates oxygen and donates electrons to P680. From Q, the electrons are donated to the cytochrome b6-f complex. In PSI, the electrons of the P700 chlorophylls are excited and donated to the protein ferredoxin (Fd). The electrons are then donated to Fd NADP reductase (FNR), which catalyzes the reduction of NADP+. The electron-depeleted P700 chlorophylls in PSI are restored by the electrons that are donated from the cytochrome b6-f complex via the small, mobile protein plastocyanin (PC). The hydrogen electrochemical gradient is generated by the proton pumping of the cytochrome b6-f complex, the release of protons into the thylakoid lumen by PSII, and the depletion of the protons from the stroma by Fd NADP reductase (FNR). This gradient drives protons back across the inner membrane through the ATP synthase (shown in gray) that catalyzes the synthesis of ATP from ADP and inorganic phosphate (Pi).

Electron transport in the thylakoid membrane of a chloroplast (illustrated schematically in Figure 3) involves two distinct, but linked, photosystems, and is referred to as linear photophosphorylation. Electrons are excited in both photosystems and donated to an ETC that links the two photosystems. Light energy is absorbed by chlorophyll (i.e. P680) in photosystem II (PSII), and the excited electrons are donated to plastoquinone (Q) (which is similar to CoQ in the respiratory chain of mitochondria). The electron deficit in chlorophyll P680 is filled by the electrons derived from splitting two molecules of water, which releases four electrons, protons and free oxygen. A component of PSII, a protein complex associated with manganese ions, catalyzes the splitting of water. The chlorophyll then returns to its low-energy state, ready to be activated once more. The excited electrons donated to the ETC travel from Q to the cytochrome b6-f complex, and subsequently, to plastocyanin (PC)(a small, copper-containing protein). The chlorophyll (i.e. P700) in photosystem I (PSI) also absorbs light, and the excited electrons are donated to ferredoxin (a small, iron/sulfur-containing protein). The electron deficit of PSI is filled by the electrons donated by Pc, which originated from PSII, thereby linking the two photosystems. To complete electron transport in the thylakoid membrane, the electrons from ferredoxin are finally donated to nicotinamide adenine dinucleotide phosphate (NADP+) in a reaction catalyzed by ferredoxin-NADP reductase to generate the high-energy molecule NADPH. Overall, the photoactivated electrons donated from PSII and PSI travel through an ETC and are ultimately donated to and reduce NADP+. In addition, a hydrogen gradient is generated across the thylakoid membrane, which is used to generate ATP via the ATP synthase. The gradient is generated in three places during electron transport: protons are moved from the stroma to the lumen of the thylakoid by PSII; the cytochrome b6-f complex pumps protons into the thylakoid lumen; and the reduction of NAD+ to NADPH + H+ depletes the free protons in the stroma, resulting in a higher concentration of protons in the lumen of the thylakoid than in the stroma. The hydrogen ions will flow from the thylakoid lumen into the stroma (down the electrochemical gradient), through the ATP synthase complex, and catalyze the synthesis of ATP in a fashion analogous to the ATP synthase found in mitochondria (described in the Oxidative Phosphorylation tutorial and illustrated in Figure 4).

Cyclic Photophosphorylation

Cyclic photophosphorylation is an alternative mechanism of electron transport in the thylakoid membrane, and it uses only PSI. This electron transport chain is cyclic: electrons in PSI are photoactivated and donated to ferredoxin; they are then transferred to the cytochrome b6-f complex (instead of Fd NADP reductase); and finally, they travel back to PSI via PC. This electron transport chain generates a hydrogen electrochemical gradient; therefore, ATP synthesis occurs. Unlike linear photophosphorylation, cyclic photophosphorylation does not generate NADPH or liberate oxygen. Chloroplasts use both linear and cyclic photophosphorylation to alter the relative levels of NADPH and ATP.

ATP Synthesis In Photophosphorylation

Figure 4.  Electron transport and ATP synthesis. A comparison of electron transport and ATP synthesis in a mitochondrion and a chloroplast.

ATP synthesis in chloroplasts is analogous to ATP synthesis in mitochondria; that is, electron transport is linked to ATP synthesis through chemiosmotic coupling (see Figure 4). Electron transport, for both linear and cyclic photophosphorylation, generates a hydrogen gradient across the thylakoid membrane. The lumen of the thylakoid is pH 4.5, whereas the stroma is pH 8.0. As a result of this gradient, hydrogen ions will flow through the ATP synthase from the lumen of the thylakoid into the stroma. The ATP synthase in the thylakoid membrane is composed of two subunits: CF0 subunit and CF1 subunit. Protons flow through CF0 and cause it to rotate. This rotation induces conformational changes in the stationary CF1 subunit that catalyzes ATP synthesis. The structure and mechanism of a chloroplast's ATP synthase is similar to that of the mitochondrial ATP synthase (described in detail in the previous tutorial).

The chemiosmotic coupling of electron transport and ATP synthesis is analogous in mitochondria and chloroplasts. In both cases, the electron transport chain generates a hydrogen electrochemical gradient across the inner membrane of the mitochondria or the thylakoid membrane of the chloroplast. The ATP synthase (composed of F0 and F1 subunits in the mitochondria, and CF0 and CF1 subunits in the chloroplasts) uses the hydrogen electrochemical gradient to drive ATP synthesis. As the protons move through the F0 and CF0 subunits, these subunits rotate and induce conformational changes in the F1 and CF1 subunits, respectively, to activate ATP synthesis.

Carbon Fixation

The Light-Independent Reactions of Photosynthesis: Carbon Fixation

Figure 5.  The carbon fixation cycle (Calvin cycle).The carbon fixation cycle has three phases: phase I is carbon fixation (each molecule of ribulose 1,5-biphosphate + CO2 -> 2 molecules of 3-phosphoglycerate); phase II is reduction (each molecule of 3-phosphoglycerate + ATP + NADPH -> glyceraldehyde 3-phosphate + ADP + Pi + NADP+); and phase III is regeneration of ribulose 1,5-biphosphate (5 molecules of glyceraldehyde 3-phosphate + 3ATP -> 3 molecules of ribulose 1,5-biphosphate + 3ADP + 3Pi.) For each molecule of CO2 fixed, 3 ATPs and 2 NADPHs are consumed.

The high-energy molecules ATP and NADPH, synthesized in the light-dependent reactions of photosynthesis, are used to synthesize carbohydrates from carbon dioxide - hence the term carbon fixation. The carbon fixation cycle, also called the Calvin cycle, is a 3-phase cycle that occurs in the stroma and that converts CO2 into carbohydrates using the energy of ATP and the oxidation of NADPH (illustrated in Figure 5). The first phase of the cycle is carbon fixation, the combination of CO2 and ribulose 1,5-biphosphate(a 5-carbon sugar), resulting in two molecules of 3-phosphoglycerate (a 3-carbon sugar). The second phase is the reduction of 3-phosphoglycerate to glyceraldehyde 3-phosphate, which you may recall is essentially steps #6 and #7 of glycolysis in reverse (see tutorial entitled Glycolysis, Fermentation and the Citric Acid Cycle). This phase requires ATP hydrolysis and NADPH oxidation. The final phase of the cycle is ribulose 1,5-biphosphate regeneration. Some glyceraldehyde 3-phosphates are used to make common simple sugars or are stored as starch. The remainder of the glyceraldehyde 3-phosphates are used as intermediates in the carbon fixation cycle, ultimately regenerating ribulose 1,6-biphosphate. This phase also requires ATP. For each molecule of CO2 that is fixed, 3 ATPs and 2 NADPHs are consumed. 


Photosynthesis is the process of converting the energy of light into the energy of chemical bonds. This occurs in the chloroplasts of cells, specifically, in the thylakoid membranes. In photophosphorylation, or the light-dependent reactions, light is absorbed by chlorophyll and other pigment molecules. Light's energy is used to excite a pair of electrons in specialized chlorophyll molecules (P680 and P700) in the photosystems (PS). These electrons are donated to an electron transport chain embedded in the thylakoid membrane, which consists of large protein complexes and small, mobile electron carriers. In linear photophosphorylation, both photosystems I and II are used. The electrons that were excited and donated by PSII are replenished by a protein-mediated reaction that splits water to release electrons, protons and free oxygen. Eventually the electrons are donated to NADP+, which is reduced to NADPH. In cyclic photophosphorylation, only PSI is used and the excited electrons from P700 are donated to the electron transport chain and eventually returned to P700. In this case, no NADPH is generated and no oxygen is liberated. In both linear and cyclic photophosphorylation, ATP is generated from ADP + Pi. As electrons move through the electron transport chain, hydrogen ions are moved across the thylakoid membrane and they accumulate in the thylakoid lumen where they generate a hydrogen electrochemical gradient. This gradient drives the hydrogen ions back across the membrane through the ATP synthase, thereby driving the synthesis of ATP in a fashion analogous to the synthesis of ATP in the mitochondria. The products of linear photophosphorylation, ATP and NADPH, are used in the light-independent reactions of photosynthesis (also termed the carbon fixation cycle or the Calvin cycle). This cycle uses ATP and NADPH to convert CO2 into simple sugars. It has three phases: carbon fixation (the addition of CO2to ribulose 1,5-biphosphate); reduction of sugars to glyceraldehyde 3-phosphate (requiring NADPH and ATP); and regeneration of ribulose 1,5-biphosphate (requiring ATP).