Linear electron flow in chloroplasts involves PSII and PSI in an obligate series in which electrons are transferred from H₂O to NADP⁺ (see Figure 12-44). The process begins with absorption of a photon by PSII, causing an electron to move from a P₆₈₀ chlorophyll a to an acceptor plastoquinone (Q_B) on the stromal surface. The resulting oxidized P₆₈₀⁺ strips one electron from the relatively unwilling donor H₂O, forming an intermediate in O₂ formation, as we shall see shortly, and a proton, which remains in the thylakoid lumen and contributes to the proton-motive force. After P₆₈₀ absorbs a second photon, the semiquinone Q^•– accepts a second electron and picks up two protons from the stromal space, generating QH₂. After diffusing in the membrane, QH₂ binds to the Q_o site on a cytochrome bf complex that is analogous to the bacterial cytochrome bc₁ complex and to the mitochondrial complex III. As in those systems, a Q cycle (see Figure 12-24) operates, thereby increasing the proton-motive force generated by electron transport. After the cytochrome bf complex accepts electrons from QH₂, it transfers them, one at a time, to the Cu²⁺ form of the soluble electron carrier plastocyanin (analogous to cytochrome c), reducing it to the Cu¹⁺ form. Reduced plastocyanin then diffuses in the thylakoid lumen, carrying the electron to PSI.

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Absorption of a photon by PSI leads to removal of an electron from the reaction-center chlorophyll a, P₇₀₀ (see Figure 12-44). The resulting oxidized P₇₀₀⁺ is reduced by an electron from plastocyanin that originated in PSII. Again, this process is analogous to the electron-transport chain in mitochondria (see Figure 12-22). The electron taken up at the luminal surface by the P₇₀₀ and energized by photon absorption moves within PSI via several carriers to the stromal surface of the thylakoid membrane, where it is accepted by ferredoxin, an iron-sulfur (Fe-S) protein. In linear electron flow, electrons excited in PSI are transferred from ferredoxin via the enzyme ferredoxin-NADP⁺ reductase (FNR). This enzyme uses the prosthetic group FAD as an electron carrier to reduce NADP⁺, forming, together with one proton picked up from the stroma, the reduced molecule NADPH. The linear electron flow pathway is now completed.

F₀F₁ complexes in the thylakoid membrane use the proton-motive force generated during linear electron flow to synthesize ATP on the stromal side of the membrane. Thus this pathway exploits the energy from multiple photons absorbed by both PSII and PSI and their antennas to generate both NADPH and ATP in the stroma of the chloroplast, where they are used for CO₂ fixation.