A light-harvesting system that relied only on the chlorophyll a molecules of the special pair would be rather inefficient for two reasons. First, chlorophyll a molecules absorb light only at specific wavelengths (Figure 19.6). A large gap is present in the middle of the visible region between approximately 450 and 650 nm. This gap falls right at the peak of the solar spectrum, and so failure to collect this light would constitute a considerable lost opportunity. Second, even on a cloudless day, many photons that can be absorbed by chlorophyll a pass through the chloroplast without being absorbed, because the density of chlorophyll a molecules in a reaction center is not very great. Accessory pigments, both additional chlorophylls and other classes of molecules, are closely associated with reaction centers. These pigments absorb light and funnel the energy to the reaction center for conversion into chemical forms. Accessory pigments prevent the reaction center from sitting idle.

Chlorophyll b and carotenoids are important accessory pigments that funnel energy to the reaction center. Chlorophyll b differs from chlorophyll a in having a formyl group in place of a methyl group. This small difference shifts its two major absorption peaks toward the center of the visible region. In particular, chlorophyll b efficiently absorbs light with wavelengths between 450 and 500 nm (Figure 19.27).

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Carotenoids are extended polyenes that absorb light between 400 and 500 nm. The carotenoids are responsible for most of the yellow and red colors of fruits and flowers, and they provide the brilliance of fall, when the chlorophyll molecules degrade, revealing the carotenoids. Tomatoes are especially rich in lycopene, which accounts for their red color, whereas carrots and pumpkins have abundant β-carotene, accounting for their orange color.

In addition to their role in transferring energy to reaction centers, the carotenoids serve a safeguarding function. Carotenoids suppress damaging photochemical reactions, particularly those including oxygen, that can be induced by bright sunlight. This protection may be especially important in the fall, when the primary pigment chlorophyll is being degraded and thus not able to absorb light energy. Plants lacking carotenoids are quickly killed on exposure to light and oxygen.

How is energy funneled from accessory pigments to a reaction center? The absorption of a photon does not always lead to electron excitation and transfer. More commonly, excitation energy is transferred from one molecule to a nearby molecule through electromagnetic interactions through space (Figure 19.28). The rate of this process, called resonance energy transfer, depends strongly on the distance between the energy-donor and the energy-acceptor molecules; an increase in the distance between the donor and the acceptor by a factor of 2 typically results in a decrease in the energy-transfer rate by a factor of 2⁶ = 64. For reasons of conservation of energy, energy transfer must be from a donor in the excited state to an acceptor of equal or lower energy. The excited state of the special pair of chlorophyll molecules is lower in energy than that of single chlorophyll molecules, allowing reaction centers to trap the energy transferred from other molecules.

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What is the structural relationship between the accessory pigment and the reaction center? The accessory pigments are arranged in numerous light-harvesting complexes that completely surround the reaction center (Figure 19.29). The 26-kDa subunit of light-harvesting complex II (LHC-II) is the most abundant membrane protein in chloroplasts. This subunit binds seven chlorophyll a molecules, six chlorophyll b molecules, and two carotenoid molecules. Similar light-harvesting assemblies exist in photosynthetic bacteria (Figure 19.30).

The intricacy of photosynthesis, seen already in the elaborate interplay of complex components, extends even to the placement of the components in the thylakoid membranes. Thylakoid membranes of most plants are differentiated into stacked (appressed) and unstacked (nonappressed) regions (Figures 19.2 and 19.3). Stacking increases the amount of thylakoid membrane in a given chloroplast volume. Both regions surround a common internal thylakoid space, but only unstacked regions make direct contact with the chloroplast stroma. Stacked and unstacked regions differ in the nature of their photosynthetic assemblies (Figure 19.31). Photosystem I and ATP synthase are located almost exclusively in unstacked regions, whereas photosystem II is present mostly in stacked regions. The cytochrome bf complex is found in both regions. Plastoquinone and plastocyanin are the mobile carriers of electrons between assemblies located in different regions of the thylakoid membrane. A common internal thylakoid space enables protons liberated by photosystem II in stacked membranes to be utilized by ATP synthase molecules that are located far away in unstacked membranes.

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What is the functional significance of this lateral differentiation of the thylakoid membrane system? The positioning of photosystem I in the unstacked membranes also gives it direct access to the stroma for the reduction of NADP⁺. ATP synthase is also located in the unstacked region to provide space for its large CF₁ globule and to give access to ADP. In contrast, the tight quarters of the appressed region pose no problem for photosystem II, which interacts with a small polar electron donor (H₂O) and a highly lipid soluble electron carrier (plastoquinone).

Many commercial herbicides kill weeds by interfering with the action of photosystem II or photosystem I. Inhibitors of photosystem II block electron flow, whereas inhibitors of photosystem I divert electrons from the terminal part of this photosystem. Photosystem II inhibitors include urea derivatives such as diuron and triazine derivatives such as atrazine. These chemicals bind to the Q_B site of the D1 subunit of photosystem II and block the formation of plastoquinol (QH₂).

Paraquat (1,1′-dimethyl-4-4′-bipyridinium) is an inhibitor of photosystem I. Paraquat, a dication, can accept electrons from photosystem I to become a radical. This radical reacts with O₂ to produce reactive oxygen species such as superoxide (O₂⁻) and hydroxyl radical (OH•). Such reactive oxygen species react with many biomolecules, including double bonds in membrane lipids, damaging the membrane.