20.1: Light Absorption in Photosynthesis - An Overview

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Learning Goals 

(Learning goals written by Claude, Sonnet 4.6, Anthropic)

Thermodynamic Requirements and Physical Basis of Photosynthesis

• State the three thermodynamic requirements for photosynthesis — generation of an oxidizing agent stronger than O₂, production of NADPH as a reductant for biosynthesis, and generation of ATP — and explain why the light reactions must produce all three before the dark reactions can fix CO₂ into carbohydrates.
• Explain how chlorophyll's excited state enables the charge separation at the reaction center, tracing the sequence from photon absorption through resonance energy (exciton) transfer among antenna chlorophylls, to the unique lower excited-state energy of the reaction center chlorophyll (P680), to the electron transfer event that generates the radical cation P680·⁺ and radical anion pheophytin·⁻, explaining why this constitutes a charge separation rather than a simple energy transfer.

Architecture of the PSII-LHCII Supercomplex

• Describe the hierarchical organization of the PSII-LHCII supercomplex — including the PSII core (D1/D2 reaction center subunits, CP43/CP47 inner antennae, and OEC peripheral proteins), the minor antennae proteins (CP29, CP26, CP24), and the major LHCII trimers (strongly bound S-type, moderately bound M-type) — and explain how the C₂S₂M₂ stoichiometry relates to the dimeric supercomplex seen under standard light conditions.
• Describe the structure of the LHCII light-harvesting protein — including its three transmembrane α-helices and the binding of eight chlorophyll a, six chlorophyll b, and four carotenoid molecules per monomer — and explain how the overlapping absorption spectra of these pigments with the solar spectrum maximize photon capture across the visible range.
• Explain the role of the four reaction center chlorophylls (PD1, PD2, ChlD1, ChlD2) in P680 photoexcitation, describing how quantum mechanical delocalization distributes the excited state and positive charge (with ~80% on PD1), and trace the first electron transfer steps from P680·⁺ through Tyr161 (Yz) toward the oxygen-evolving complex.

Regulation and Photoprotection of PSII

• Describe how the PSII-LHCII supercomplex is regulated in response to light intensity — including changes in LHCII stoichiometry (C₂S₂M₂ at low light, C₂S₂ at high light), post-translational phosphorylation by Stn7 (peripheral LHCII proteins) and Stn8 (core proteins D1, D2, CP43, PsbH), and the role of N-terminal acetylation in grana stacking — and explain the state 1–state 2 transitions driven by LHCII migration between PSII and PSI in response to wavelength changes.
• Explain the photoprotection mechanisms that prevent excessive light absorption from damaging the photosynthetic apparatus, including thermal energy dissipation sensed by PsbS and mediated by xanthophylls/zeaxanthin, carotenoid-mediated quenching of excited-state chlorophyll before it generates singlet oxygen, and carotenoid/vitamin E scavenging of ROS — and connect the production of plant antioxidants to their protective roles in human health against cancer, cardiovascular disease, and inflammatory conditions.

Introduction

We have seen how we can transduce the chemical potential energy stored in carbohydrates into the chemical potential energy of ATP. This occurs by coupling the energy released during the thermodynamically favored oxidation of carbon molecules via intermediates (a high-energy mixed anhydride in glycolysis or a proton gradient in aerobic metabolism) to the thermodynamically uphill synthesis of ATP. There is a situation that occurs when we wish to reverse the entire process:

\[\ce{CO2 + H2O → carbohydrate + O2} \nonumber \]

This process is photosynthesis, which occurs in plants, certain photosynthetic bacteria, and algae. Given that this process must, by nature, be an uphill thermodynamic battle, let us consider the major requirements that must be in place for it to occur:

• A strong oxidizing agent must be formed to oxidize water to dioxygen. We know that redox reactions occur in the direction of a stronger to a weaker oxidizing agent (just as acid/base reactions are thermodynamically favored in the direction of a stronger to a weaker acid). Somehow, we must generate a stronger oxidizing agent than product dioxygen, which often has the most positive standard reduction potential in common tables.
• Plants must have high concentrations of a reducing agent for the reductive biosynthesis of glucose from CO₂. NADPH is the reducing agent used for most biosynthetic reactions in nature, which differs from NADH only by adding a phosphate to the ribose ring. This phosphate differentiates the pool of nucleotides in the cells used for reductive biosynthesis (NADPH/NADP⁺) from those used for oxidative catabolism (NADH/NAD⁺)
• Ultimately, plants require a plentiful source of ATP, which is essential for reductive biosynthesis.

The light reaction of photosynthesis produces three molecules: O₂, NADPH, and ATP. We will explore the light reaction in the next few sections of this chapter. The dark reaction, which, as the name implies, can occur in the dark, involves the actual fixation of carbon dioxide into carbohydrates using the ATP and NADPH produced in the light reaction.

The energy to power the light reactions comes directly from sunlight. Clue two is that plants have an organelle that animal cells don't - the chloroplast. Its structure is similar to that of mitochondria, with an outer membrane, an intermembrane space, and an inner membrane. In addition, it has a series of stacked, interconnected compartments called thylakoids, bounded by a thylakoid membrane that surrounds a lumen. A schematic is shown in Figure \(\PageIndex{1}\) below.

Figure \(\PageIndex{1}\): The chloroplast. chloroplast: https://commons.wikimedia.org/wiki/F...roplast-en.svg. Creative Commons Attribution-Share Alike 4.0

Stacks of thylakoids are called grana. Each thylakoid represents one granum. The thylakoids are where the light reactions occur. In contrast, the stroma contains the enzymes for the dark reactions of photosynthesis.

The enzyme complexes involved in the light reaction are aligned in the thylakoid membrane just as the membrane complexes involved in mitochondrial electron transport/oxidative phosphorylation were aligned in the mitochondrial inner membrane. That process uses Complex I, Complex III, Complex II (succinate dehydrogenase), and Complex IV to transfer electrons from NADH and FADH₂ to increasingly potent oxidizing agents (ubiquinone, cytochrome C), ending with dioxygen. The energy released during this thermodynamically favored process was captured by forming a proton gradient, which was then collapsed through the F₀F₁ATPase to drive ATP synthesis.

For the light reaction, three complexes, the Light Harvesting ComplexII -Photosystem II (also called the LHC-PSII supercomplex), cytochrome b₆f, and the light-harvesting complex Photosystem I (called the LHC-PSII supercomplex) are used to carry out the light reactions of photosynthesis. These include the photooxidation of water to produce O₂ and the transfer of the lost electrons through a series of mobile electron carriers (plastoquinone and plastocyanin) to a terminal acceptor, NADP⁺, to form the reducing agent NADPH needed for carbohydrate synthesis in the dark reaction. The energy released during the electron transfer process is likewise captured in a proton gradient as protons are moved from the chloroplast stroma to the thylakoid lumen. The collapse of the resulting proton gradient powers ATP synthesis. These reactions are shown in Figure \(\PageIndex{2}\).

Figure \(\PageIndex{2}\): Light reaction of photosynthesis. The boxed numbers represent Enzyme Commission Number. Original KEGG Map with embedded links. (reprinted with permission from Kanehisa Laboratories and the KEGG project: www.kegg.org )

In this section, we will explore light absorption by the light-harvesting complex (LHCII) of the LHC-PSII supercomplex. Before we get into too much detail, let's start with a simplified review of light absorption in the LHCII.

Absorption of Light

Plants have many pigments (chlorophylls, phycoerthryins, carotenoids, etc.) whose absorption spectra overlap that of the solar spectra. The primary pigment, chlorophyll, has a protoporphyrin IX ring (the same as in heme groups) with Mg²⁺ at its center, instead of Fe²⁺. When the chlorophyll absorbs light, the excited electrons must eventually relax to their ground state. It can do this by either radiative or nonradiative processes. In radiative decay, a lower-energy photon is emitted after a loss of vibrational energy.  Photon emission occurs via fluorescence or phosphorescence. In nonradiative decay, the energy of an excited electron can be transferred to another similar molecule (in this case, other chlorophyll molecules) in a process that excites the electron in the second molecule to the same excited state. It is as if a photon is released by the first excited molecule, which is then absorbed by an electron in a second molecule, exciting it to the same excited state. However, no photon is involved in the energy transfer. In this fashion, energy is transferred from one chlorophyll to another. This type of energy transfer is called resonance energy transfer or exciton transfer, as shown in Figure \(\PageIndex{3}\).

Figure \(\PageIndex{3}\): Resonance Energy (Exciton) Transfer

Due to its unique environment, one type of chlorophyll exhibits slightly different characteristics. The energy level of the first excited state in the chlorophyll reaction center is lower than in the rest of the chlorophyll molecules, in much the same way that pKa values of amino acid side chains differ with the local and solvent environment and the standard reduction potential of FAD molecules that are tightly bound to enzymes differ due to the different environment of bound FAD/FADH₂.

Instead of a radiationless energy transfer to this special chlorophyll, an electron from the excited-state chlorophyll is transferred, which, by definition, is a redox reaction. The electron donor (the excited chlorophyll) loses an electron (an oxidation reaction) as the recipient molecule gains one (a reduction). This charge (electron) transfer reaction produces charge separation in the formation of a positively charged chlorophyll (now an oxidizing agent) and a negatively charged chlorophyll (now a reducing agent). The chlorophylls directly involved in this final process are collectively referred to as the reaction center. This process is shown in Figure \(\PageIndex{4}\) below.

Figure \(\PageIndex{4}\): Reaction Center

The reaction center chlorophylls absorb light at 680 nm; therefore, they are sometimes labeled P680. Four unique chlorophylls (PD1, PD2, ChlD1, and ChlD) are the main players in the reaction center. Both sets of labels are shown in the figure above.

Figure \(\PageIndex{5}\) shows a cartoon of the absorption of photons and subsequent handoff of energy to "antenna" chlorophylls leading to photoexcitation of the reaction center and subsequent transfer of an electron to the special chlorophyll, which has a lower first excited state energy. This molecule is named pheophytin A. It is identical to chlorophyll A but lacks the central Mg²⁺ ion.

Figure \(\PageIndex{5}\): Photoexcitation and electron transfer of chlorophylls

Photosystems I and II contain many chlorophyll molecules that act as antennas, transferring energy to the reaction centers. The "antenna" proteins involved in photon adsorption and energy transfer in Photosystems I and II are shown in Figure \(\PageIndex{6}\) below. Note that the D1, D2, cp47, and cp43 protein subunits in the figure below are also shown in the figure above. The D1 and D2 subunits contain the reaction center chlorophylls.

Figure \(\PageIndex{6}\): Antennae Proteins (reprinted with permission from Kanehisa Laboratories and the KEGG project: www.kegg.org )

The different chlorophylls have absorption spectra that overlap reasonably well with the solar spectrum, as illustrated in Figure \(\PageIndex{7}\).

Figure \(\PageIndex{7}\): Solar spectrum and absorption profiles of chlorophyll and bacteriochlorophyll pigments. Cardona T, Shao S, Nixon PJ. Enhancing photosynthesis in plants: the light reactions. Essays Biochem. 2018;62(1):85-94. Published 2018 Apr 13. doi:10.1042/EBC20170015Creative Commons Attribution License 4.0 (CC BY).

The black lines represent the solar flux spectrum (photons per square meter per wavelength) from 300 to 1200 nm. The yellow line represents the photon energy (E = hc/λ) at each wavelength. The absorbance spectra of the chlorophyll species are normalized to the same maximal value.

Suppose you use the energy required to produce glucose from CO₂ and H₂O as a standard. In that case, approximately 95% of the incoming solar energy is wasted because not all incident photons have the correct wavelength. Waste also occurs due to reflectance and heat generation.

The Light Harvesting Complex (LHCII) - Photosystem II (PS II) Supercomplex

Now, let's look more at the chloroplast thylakoid membrane complex that interacts with light and results in water oxidation to form O_2. The first structure is called the Light-Harvesting Complex II (LHCII)-Photosystem II (PSII) Supercomplex. It is a super complex (a pun) to understand. The supercomplex has a PSII core complex interacting with a variable number of light-harvesting complex IIs (LHCIIs) complexes. Sometimes, the entire supercomplex is more simply referred to as Photosystem II. The supercomplex consists of

• a PSII core C with a Mn₄CaO₅ cluster called the oxygen-evolving complex (OEC or OEX) that oxidizes water to O₂;
• peripheral antennae complexes M and S, also called light-harvesting complexes II (LCHIIs)

The core part of the Photosystem II supercomplex contains the key to the existence of aerobic organisms, as it produces the dioxygen in our atmosphere. Its chemistry is phenomenal. Many seek to modify it to produce, instead of H₂​​​​​​, a green energy source. In the next section, we will explore the mechanisms for water oxidation to O₂ by a PSII-bound inorganic Mn₄CaO₅ cluster, the oxygen-evolving complex (OEC). Let's first look at PSII in light of the discussion above. Where are all the chlorophylls? The mystical "reaction center"?

The PSII Core Complex (within the supercomplex) has over 20 subunits. These include:

• reaction center subunits D1 and D2
• inner antennae subunits CP43, CP47
• many other small protein subunits
• peripheral subunits that project into the lumen that interact with the OEC

The peripheral antennae complexes (light-harvesting complexes - LHCIIs M and S - consist of proteins encoded by six different Lhcb genes (1-6).

• Lhcb1-3 monomers form trimeric (homo- or hetero) LHCIIs (Lhcb1-3). An example is (Lhcb3)₃. That trimer is often referred to as the M-LHCII. There are also S-form, L-form, and N-form trimers. S is strongly associated with the reaction center; M, moderate; and L, loose.
• Lhcb4-6 are the minor components and consist of the monomeric proteins CP29, CP26, and CP24, respectively.

Light-harvesting complex proteins

Each Lhc apoprotein consists of 3 alpha-helices and binds eight chlorophyll a, six chlorophyll b, and four carotenoid molecules. Figure \(\PageIndex{8}\) shows an interactive iCn3D model of the monomeric pea chlorophyll a-b binding protein AB80 (LHCII type I CAB-AB80) (2BHW)

Figure \(\PageIndex{8}\): Monomeric pea chlorophyll a-b binding protein AB80 (LHCII type I CAB-AB80) (2BHW). (Copyright; author via source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...QtEEWeQ5Y9n2i8

The color scheme is as follows:

• protein - secondary structure colors
• Chlorophyll a - Green
• Chlorophyll b - yellow
• carotenoids - cyan

Now, let's look at a trimeric form of the same protein. of LHCII, the chlorophyll-binding protein, from PSII. It's also called LHCII type I CAB-AB80. We showed the role of the LHCII trimer in the figures above. The subunits absorb light during the light reaction.  The energy is sent through resonance energy transfer to reaction centers in PSII and PSI. Figure \(\PageIndex{9}\) shows an interactive iCn3D model of the trimeric Light Harvesting Complex (LHC_II) from pea photosystem II (2bhw).

Figure \(\PageIndex{9}\): Light Harvesting Complex (LHC_II) from pea photosystem II (2bhw). (Copyright; author via source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...BK6WvzrxABPDh6

The protein is shown in gray. To simplify the model, chlorophyll A molecules are shown in magenta, and chlorophyll B isomeric variants are shown in green. Note the large number of chlorophylls (42) in the LHCII complex, which differentiates it from most protein complexes, which might have just a few ligands bound.

Photosynthetic bacteria and plants have a wide range of molecules that interact with visible light. The main one in PS II is chlorophyll a, whose structure is shown in Figure \(\PageIndex{10}\ below, along with the variant, chlorophyll b. Remember that pheophytin A is identical to chlorophyll A but lacks the central Mg²⁺ ion.

Figure \(\PageIndex{10}\): Chlorophyll a and b

Photosystem II (PS II) Supercomplex Structures

The most common version of the supercomplex is a dimer. A simplified cartoon of the monomeric version of the PSII-LHCII supercomplex is shown in Figure \(\PageIndex{11}\). The PSII core is shown in the blue rectangle. The CP29, CP26, and CP24 in the peripheral antennae complexes (light-harvesting complexes - LCHIIs) are shown outside the blue-outlined rectangle. They surround the PSII core.

Figure \(\PageIndex{11}\): Cartoon of the monomeric PSII-LHCII supercomplex structure of the PSII-LHCII supercomplex from Pisumsativum

• The PSII core C (outlined in the blue box) contains two reaction center subunits, D1 and D2, and two inner antennae subunits, CP43 and CP47. The core also contains extrinsic subunits (pink) surrounding the OEC (red spacefill)
• A Strongly bound LHCIIs protein, S -LHCII, left (maroon rectangle), interacting with CP26. The S-LHCii complex is a trimer of individual Lhcb monomers.
• A Moderately bound LHCIIs protein complex, M-LHCII, right (lighter blue rectangle), interacting with the CP24/CP29 dimer. The M-LHCII complex is a trimer of 3 lcbh-3 subunits (Lcbh3)₃.

There can be a variable number of LHCIIs in the complex. The predominant form of the supercomplex is the C₂S₂M₂ complex. There are also many other proteins in the supercomplex that are not shown in Figure 11. A cartoon showing the top-down view of the actual supercomplex dimer, C₂S₂M₂, is shown in Figure \(\PageIndex{12}\).

Figure \(\PageIndex{12}\): Top town view of the PSII-LHCII supercomplex dimeric complex.

You could imagine forming the dimer by spinning the CSM monomer 180° and then reproducing it there.

Figure \(\PageIndex{13}\) shows an interactive iCn3D model of the full C2S2M2-type PSII-LHCII supercomplex from Pisum sativum (5XNL). (long load time)

Figure \(\PageIndex{13}\): C2S2M2-type PSII-LHCII supercomplex from Pisum sativum (5XNL). (Copyright; author via source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...F4WFfHoevxaVV8 (long load time)

Only a single CSM monomer of the C2S2M2 dimeric supercomplex is colored. The colors match those in Figures 8 and 9. The molecules shown in gray sticks that outline a bilayer include chlorophyll Bs (98 of them), chlorophyll As (216), and carotene or its derivatives (88) as well. The different proteins in the supercomplex are colored, as shown below.

• CP47 Rx Center (inner antenna protein) Dark Blue
• CP43 Rx Center (inner antenna protein) - Purple
• D1: green
• D2: yellow
• OEC: spacefill Red
• O, P, Q - OEC peripheral: Light pink
• CP24 (peripheral antenna protein): yellow
• CP29 (peripheral antenna protein): orange
• CP26: Light blue
• LHCIIs (S and M) - not shown
• membrane bilayers - cyan spheres

(A quick load version of the C2S2M2-type PSII-LHCII supercomplex with different coloring than above)

PSII Supercomplex Regulation

Plants have evolved a strong ability to absorb light across the entire visible spectrum. Can they absorb too much energy? The answer is yes, so plants have developed many ways to protect themselves. IF too much light is absorbed, the pH gradient developed across the thylakoid membranes becomes greater. This is sensed by a protein, PsbS, and through subsequent conformational changes transmitted through the light-harvesting antennae, the excess light energy is dissipated as thermal energy. Mutants lacking PsbS showed reduced seed yield, indicating they were less adaptable under stress conditions (e.g., rapidly fluctuating light levels). Molecules called xanthophylls and other carotenoids, such as zeaxanthin, are also important in excess energy dissipation. These molecules appear to cause excited chlorophyll (a singlet-like excited-state dioxygen) to deexcite. Without the xanthophylls, the excited-state chlorophyll could deexcite by transferring energy to ground-state triplet dioxygen, promoting it to the singlet, reactive state, which could also be converted to superoxide through electron acquisition. These reactive oxygen species (ROS) can cause oxidative damage to proteins, lipids, and nucleic acids, alter gene transcription, and even trigger programmed cell death. Carotenoids can also act as ROS scavengers. Hence, both heat dissipation and the inhibition of ROS formation (by molecules such as vitamin E) are mechanisms of defense against excessive solar energy.

Given that both plants and animals must protect themselves from ROS, plant-derived antioxidant molecules protect humans from diseases such as cancer, cardiovascular disease, and general inflammatory diseases, all of which have been shown to involve oxidative damage to biological molecules. Humans, who can't synthesize the variety and amounts of antioxidants found in plants, are healthier when they consume large amounts of plant products. These phytomolecules also possess other properties, including regulating gene transcription, which can significantly impact disease propensity.

Plants have to respond to different qualities and quantities of light. When light levels are low, they strive to maximize light capture. Too much light can damage a plant, so plants have evolved molecular adaptations to prevent it. Part of the regulation occurs in the supercomplex's stoichiometry by altering the composition of the antenna proteins (the LHCs). The most abundant components of the complex are C₂S₂M₂ and C₂S₂M. C₂S and C₂S₂ increase as an adaptation to higher light levels.

Light levels can also promote the association of grana membranes mediated by interactions between a PSII-LHCII supercomplex (PSII-LHCIIsc) on one thylakoid membrane and a PSII-LHCIIsc on an adjacent thylakoid membrane, forming a large PSII-LHCIIsc dimer. The structure and properties of paired PSII-LHCIIsc are illustrated in Figure \(\PageIndex{14}\).

Figure \(\PageIndex{14}\): Light-driven modulation of paired PSII–LHCIIsc. Heterogeneous mixtures of PSII–LHCIIsc from pea plants grown at different light intensities (L, low; C, moderate used as control; H, high) were isolated and analyzed. Albanese et al. Nature Communications | (2020) 11:1361 | https://doi.org/10.1038/s41467-020-15184-1. Creative Commons Attribution 4.0 International License. http://creativecommons.org/ licenses/by/4.0/.

The figure also shows the variation in the PSII–LHCIIsc with light intensity. At low light, C₂M₂S₂ prevails, while at high light intensity, C₂S₂ is most abundant. The system regulates activity by increasing LHCII abundance under low light and decreasing it under high light.

Figure 1 shows the stacking of individual grana in the chloroplasts. Stacking is maintained across various light levels and is mediated by loops of LHCII trimers exposed to the stroma, as well as by Lhcb4 subunits on adjacent membranes. The stromal surfaces are flat and tightly stacked in grana. Stacking is a dynamic process that depends on cross-membrane interactions and the reorganization of the PSII-LHCIIsc.

The PSII–LHCIIsc is regulated by light-dependent post-translational phosphorylation, particularly of LHCII, as well as by acetylation, which further regulates energy distribution. In plants, the core proteins CP43, D1, and D2, and PsbH are phosphorylated by the kinase Stn8. Stn7 phosphorylates the peripheral antenna proteins of LHCII. Phosphorylation of PSII is not seen in cyanobacteria and red algae. Higher light levels promote greater core protein phosphorylation. Stn7 appears to be inhibited at high light levels. Figure \(\PageIndex{15}\) shows putative Stn8 phosphorylation sites in the PSII -LHCIIsc

Figure \(\PageIndex{15}\): Phosphorylation map of the C2S2M2 supercomplex as catalyzed by the Stn8 kinase. Puthiyaveetil Sujith and Kirchhoff Helmut, Frontiers in Plant Science, 4 ,2013. https://www.frontiersin.org/article/...pls.2013.00459. DOI=10.3389/fpls.2013.00459. Creative Commons Attribution License (CC BY)

The structure is a model pieced together from multiple pdb files. It shows the approximate positions of the phosphorylation sites of D1, D2, CP43, PsbH, and CP29.

Most free N-terminal loops in LHCII can be phosphorylated. Both phosphorylation and lysine acetylation on Lhcb2 N-terminal loops help regulate the redistribution of LHCII from PSII (in grana stacks) to PSI (in single-layered thylakoid regions). Grana stacking by N-terminal loop association between facing PSII–LHCIIsc and their N-terminal acetylation appears to strengthen grana stacking.

How does PSII respond when the wavelength (not the intensity) of light is changed? For this, we must briefly discuss photosystem I (PSI), which we will explore in more detail in Chapter 20.3. Both PSII and PSI work together to transduce light into chemical energy, so you would expect that their activities are regulated in a linked fashion. They also have different absorbance spectra characteristics, with PSI absorbing more in the red region. If the effective absorbance (normalized for concentrations and LHCIIs) were the same, you would predict that the effective absorbance ratio over a broad wavelength range for the two photosystems, PSI/(PSI+PSII) would be 0.5. This is approximately the case across the entire spectral range, except for the 670-730 nm range, where the ratio is close to 1, indicating that PSI absorbance and activity are skewed toward the red end of the spectrum. Changes in light characteristics (i.e., wavelength) would then affect each photosystem differently and could cause imbalances in their activities and states, leading to a restorative balance. When exposed to far-red light, the systems move to state I. The major mobile antenna proteins (LHCIIs) move to PSII to restore a "photoabsorption" balance in this state. When exposed to light depleted at the high end of the visible spectrum, the system transitions to state II, in which mobile LHCIIs migrate to PSI. What an interesting reciprocal way to balance activity, even if it is hard to conceptualize regulation involving the movement of membrane proteins. Of course, such movement is often seen in the clustering of ligand-bound membrane receptors.

As mentioned above, the location and, hence, movement of the LHCII are regulated by phosphorylation by LHCII kinase. We'll explore that more in Chapter 20.3, when we discuss PSI in more detail.

A closer view of the reaction center and its local environment

Let's look at the structure of a simpler PSII complex from Thermostichus vulcanus (3WU2). It has 70 chlorophyll a molecules, four special chlorophylls, four pheophytin As (PHOs), 20 beta-carotenes, four plastoquinol-9s (PL9s), four hemes, and two caroten-3-ols. Figure \(\PageIndex{16}\) shows the arrangement of chlorophyll molecules in the CP47 and CP44 (not CP43, as shown in several of the above diagrams) antennae subunits of PSII from T. vulcanus (3WU2).

.

Figure \(\PageIndex{16}\): Reaction Center with special chlorophylls sandwiched between antennae subunits

• CP44 is the Photosystem II CP44 reaction center protein, psbC gene, Photosystem II 44 kDa reaction center protein;
• CP47 is the Photosystem II CP47 reaction center protein, psbB gene; Photosystem II CP47 chlorophyll apoprotein

Sandwiched in between them is the reaction center containing the four special chlorophylls, the inorganic metal cluster called the oxygen-evolving complex (OEC or OEX), and a key amino acid near the OEC, Tyr 161 (pdb 3ARC).

Two special chlorophylls, ChlD₁ and ChlD₂, accompanied by partner chlorophylls, P_D1 and P_D2, which are coplanar with each other, are found near the OEC and are the key chlorophylls in the reaction center that convert the OEC into a powerful enough oxidant to oxidize H₂O.

A special reaction center chlorophyll/pheophytin absorbs a photon of light at 680 nm, so the species that absorbs the photon is labeled P680. On absorption, it forms the excited state, P680*. This transfers the excited-state electron to pheophytin, which forms a pheophytin radical anion, while the electron donor P680* becomes P680^.+, a radical cation. The radical cation, an unstable species, can oxidize another molecule to regain stability, and in a series of addition-linked oxidation steps, water is oxidized (O in water has an oxidation state of 2-) to O2 (in which each oxygen has an oxidation state of 0). This process occurs through the oxygen-evolving complex, which we will examine in the next section.

Which of the chlorophyll molecules absorbs the light (i.e, which is P680)? The answer is probably all four chlorophylls in the reaction center, P_D1, P_D2, Chl_D1, and Chl_D2, through a delocalization of the excited electron, which would be described by a wave function for the combined chlorophylls. When donating the electron from P680*, the positive charge, which can also be described as a "hole" (similar to transistors), becomes delocalized. Quantum mechanical calculations show a coupling between P_D1 and P_D2, such that 80% of the positive charge and radical character is situated on P_D1 and 20% is on P_D2.)

Figure \(\PageIndex{17}\) shows the four chlorophylls in the reaction center of T. Vulcanus. P_D1 appears closest to the OC.

Figure \(\PageIndex{17}\): Closeup of the reaction center chlorophylls and OEC

Figure \(\PageIndex{18}\) shows an interactive iCn3D model of the key chlorophylls and OEC of photosystem II from Thermostichus vulcanus (3WU2)

Figure \(\PageIndex{18}\): Key chlorophylls and OEC of photosystem II from Thermostichus vulcanus (3WU2). (Copyright; author via source). Click the image for a popup or use this external link: https://structure.ncbi.nlm.nih.gov/i...qYxWN5sKcquGK7

In any enzymatically catalyzed reaction mechanism, the enzyme must return to the beginning state, and a path for electron flow must be apparent. How does the radical cation P680^.+ return to the ground state? As we will see in the next section, it "grabs" an electron from the nearby Y161 (also known as YZ), forming a radical cation, Y^.+. This returns to the ground state by capturing an electron from the OEC, which ultimately grabs one from water. This process repeats four times to remove the four electrons from two waters needed to form dioxygen.

Figure \(\PageIndex{19}\) shows the first step in the process of reforming P680 and the formation of the Y161 radical cation.

Figure \(\PageIndex{19}\): First step in the process of reforming P680 and formation of the Y161 radical cation.

A different process removes electrons from the radical anion, P680^.-. This is passed to a series of other electron acceptors/carriers as part of the Z scheme of the light reaction in photosynthesis. The electron is ultimately passed on to NADP⁺ to form NADPH, which is used in the reductive biosynthesis of carbohydrates.

Light is also absorbed in photosystem I, which does not form O₂. Rather, it receives electrons from a mobile electron carrier and transfers them to NADP⁺, forming NADPH, a reducing agent required for the reductive biosynthesis of carbohydrates. It also helps generate a proton gradient, which drives ATP synthesis.

With this background, we can now explore in greater detail the key reactions that enable the evolution of aerobic organisms.

Summary

(Summary written by Claude, Sonnet 4.6, Anthropic)

This chapter introduces the light reactions of photosynthesis, describing the thermodynamic requirements of the process, the molecular architecture of the PSII-LHCII supercomplex, the mechanism of light-driven charge separation at the reaction center, and the regulatory and photoprotective mechanisms that allow plants to adapt to varying light conditions.

Photosynthesis is thermodynamically demanding: it requires reversal of the spontaneous oxidation of carbohydrates by dioxygen. Three chemical products of the light reaction are essential before the dark reactions can fix CO₂: molecular oxygen (O₂) released from water oxidation, NADPH as the reductant for carbohydrate biosynthesis (distinct from the catabolic NADH pool by a single phosphate on the ribose ring), and ATP. The organelle where this occurs is the chloroplast, which shares the dual-membrane architecture of mitochondria but adds an additional membrane system — stacked, interconnected thylakoids surrounded by a lumen — embedded in the stroma. The light reactions occur in the thylakoid membrane, while the dark reactions (carbon fixation) occur in the stroma. The three major light-reaction complexes — the LHC-PSII supercomplex, cytochrome b₆f, and Photosystem I — are structurally and functionally analogous to the electron transport complexes of mitochondria, including the generation of a proton gradient across the thylakoid membrane to drive ATP synthesis by a chloroplast F₁F_o ATP synthase.

The fundamental energy transduction event of the light reactions is the absorption of photons by pigment molecules (chlorophylls, carotenoids, phycobiliproteins) and the transfer of that energy to the photochemical reaction center. Chlorophyll a and b — porphyrin-ring pigments with Mg²⁺ at their centers rather than the Fe²⁺ of heme — absorb light in the blue (~430 nm) and red (~680 nm) regions of the visible spectrum, while carotenoids absorb in the blue-green region, together providing broad coverage of the solar spectrum. When a chlorophyll absorbs a photon, its electron is promoted to an excited state. This excitation energy migrates through the antenna system by resonance energy transfer (exciton transfer), a radiationless process in which the excited electron in one chlorophyll induces excitation of an adjacent chlorophyll without an actual photon being emitted or absorbed. The energy is funneled directionally toward the reaction center chlorophylls because the reaction center contains a special chlorophyll — labeled P680 for its 680-nm absorption — whose lowest excited state is slightly lower in energy than that of the surrounding antenna chlorophylls, trapping the excitation energy. This lowered excited-state energy in the reaction center, analogous to how the protein environment shifts the pKa of amino acid side chains or the E°′ of enzyme-bound FAD, is a subtle but critical quantum-mechanical adaptation.

The PSII-LHCII supercomplex is an elaborate multi-megadalton assembly. Its PSII core contains the D1 and D2 reaction center subunits (which harbor the four reaction center chlorophylls PD1, PD2, ChlD1, and ChlD2, along with pheophytin A — chlorophyll a lacking its central Mg²⁺), the inner antenna proteins CP43 and CP47 (which together bind ~70 chlorophyll a molecules in the T. vulcanus structure), and peripheral subunits surrounding the oxygen-evolving complex (OEC), the inorganic Mn₄CaO₅ cluster that catalyzes water oxidation. Surrounding the core are the minor antenna proteins CP29, CP26, and CP24, and the major LHCII trimers in strongly bound (S) and moderately bound (M) forms. Each LHCII monomer binds eight chlorophyll a, six chlorophyll b, and four carotenoids within a three-helix integral membrane protein, making the LHCIIs among the most pigment-dense proteins known. The predominant supercomplex form — C₂S₂M₂ — is a dimer of monomeric CSM units and is the standard organization under moderate light conditions.

Photoexcitation at P680 generates a charge-separated state: the excited electron is transferred from P680* to the adjacent pheophytin A, generating P680·⁺ (a radical cation, now a powerful oxidizing agent) and pheophytin·⁻ (a radical anion, a reducing agent). Quantum mechanical calculations indicate that the positive charge is delocalized across all four reaction-center chlorophylls, with approximately 80% on PD1 and 20% on PD2. The radical cation P680·⁺ is the strongest biological oxidizing agent known, with a standard reduction potential of approximately +1.2 V — more positive than that of O₂ itself (+0.82 V) — enabling the thermodynamically unfavorable oxidation of water. P680·⁺ is rapidly re-reduced by abstracting an electron from the adjacent tyrosine residue Tyr161 (Yz), forming a tyrosyl radical (Yz·⁺) that in turn extracts electrons from the OEC, which ultimately oxidizes water. The electron from pheophytin·⁻ is passed forward through a series of quinone acceptors (plastoquinone A and B) to the cytochrome b₆f complex, and eventually to Photosystem I, where it reduces NADP⁺ to NADPH.

Regulation of PSII is multilayered. In response to light intensity, the composition of the supercomplex changes: C₂S₂M₂ predominates at moderate light, C₂S₂M₂ and C₂S₂M at intermediate intensities, and C₂S₂ and C₂S at high light. This alters the effective antenna size, reducing photon capture at high light levels. Post-translational phosphorylation plays a central regulatory role: kinase Stn8 phosphorylates core subunits D1, D2, CP43, and PsbH at higher light levels, while Stn7 phosphorylates the peripheral LHCII proteins and is inhibited at high light. State transitions — movements of LHCII trimers between PSII (state 1, at far-red light) and PSI (state 2, at red-depleted light) — balance activity between the two photosystems in response to wavelength changes, a process regulated by Stn7-mediated phosphorylation and N-terminal acetylation of Lhcb2. Grana stacking itself is a regulated process, stabilized by interactions between N-terminal loops of LHCII trimers on adjacent thylakoid membranes.

Photoprotection is equally important: when light absorption exceeds the capacity for productive photochemistry, the resulting excess excitation energy can sensitize ground-state triplet O₂ to its reactive singlet form, generating reactive oxygen species that damage proteins, lipids, and nucleic acids, and induce cell death. Plants counter this through several mechanisms: PsbS senses the increased thylakoid ΔpH and triggers conformational changes in the antenna system that dissipate excess energy as heat; xanthophylls (especially zeaxanthin) and other carotenoids quench excited-state chlorophylls before they can sensitize oxygen; and carotenoids (along with vitamin E) scavenge ROS already produced. These plant antioxidant systems, producing diverse phytochemicals, provide humans who consume plant-rich diets with exogenous protection against the oxidative damage that underlies cancer, cardiovascular disease, and chronic inflammatory conditions.