As noted above, rubisco catalyzes the incorporation of CO₂ into ribulose 1,5-bisphosphate as part of photosynthesis. It can catalyze a second, distinct, and competing reaction with the same substrate—ribulose 1,5-bisphosphate—but with O₂ in place of CO₂ as a second substrate, in a process known as photorespiration (Figure 12-49). The products of this second reaction are one molecule of 3-phosphoglycerate and one molecule of the two-carbon compound phosphoglycolate. The carbon-fixing reaction is favored when the ambient CO₂ concentration is relatively high, whereas photorespiration is favored when CO₂ is low and O₂ is relatively high. Photorespiration takes place in light, consumes O₂, and converts ribulose 1,5-bisphosphate in part to CO₂. As Figure 12-49 shows, photorespiration is wasteful to the energy economy of the plant: it consumes ATP and O₂, and it generates CO₂ without fixing carbon. Indeed, when CO₂ is low and O₂ is high, much of the CO₂ fixed by the Calvin cycle is lost as the result of photorespiration. This surprising, wasteful alternative reaction catalyzed by rubisco may be a consequence of the inherent difficulty the enzyme has in specifically binding the relatively featureless CO₂ molecule and of the ability of both CO₂ and O₂ to react and form distinct products with the same initial enzyme/ribulose 1,5-bisphosphate intermediate.

Excessive photorespiration could become a problem for plants in a hot, dry environment because they must keep the gas-exchange pores (stomata) in their leaves closed much of the time to prevent excessive loss of moisture. As a consequence, the CO₂ level inside the leaf can fall below the K_m of rubisco for CO₂. Under these conditions, the rate of photosynthesis is slowed, photorespiration is greatly favored, and the plant might be in danger of fixing inadequate amounts of CO₂. Corn, sugarcane, crabgrass, and other plants that can grow in hot, dry environments have evolved a way to avoid this problem by using a two-step pathway of CO₂ fixation in which a CO₂-hoarding step precedes the Calvin cycle. This pathway has been named the C₄ pathway because [¹⁴C]CO₂ labeling showed that the first radioactive molecules formed during photosynthesis in this pathway are four-carbon compounds, such as oxaloacetate and malate, rather than the three-carbon molecules that initiate the Calvin cycle (C₃ pathway).

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The C₄ pathway involves two types of cells: mesophyll cells, which are adjacent to the air spaces in the leaf interior, and bundle sheath cells, which surround the vascular tissue and are sequestered away from the high oxygen levels to which mesophyll cells are exposed (Figure 12-50a). In the mesophyll cells of C₄ plants, phosphoenolpyruvate, a three-carbon molecule derived from pyruvate, reacts with CO₂ to generate oxaloacetate, a four-carbon compound (Figure 12-50b). The enzyme that catalyzes this reaction, phosphoenolpyruvate carboxylase, is found almost exclusively in C₄ plants and, unlike rubisco, is insensitive to O₂. The overall reaction that forms oxaloacetate from pyruvate involves the hydrolysis of one ATP and has a negative ΔG. Therefore, CO₂ fixation will proceed even when the CO₂ concentration is low. The oxaloacetate formed in the mesophyll cells is reduced to malate, which is transferred by a special transporter to the bundle sheath cells, where the CO₂ is released by decarboxylation and enters the Calvin cycle (see Figure 12-50b).

Because of the transport of CO₂ from mesophyll cells, the CO₂ concentration in the bundle sheath cells of C₄ plants is much higher than it is in the normal atmosphere. Bundle sheath cells are also unusual in that they lack PSII and carry out only cyclic electron flow catalyzed by PSI, so no O₂ is evolved. The high CO₂ and reduced O₂ concentrations in the bundle sheath cells favor the fixation of CO₂ by rubisco to form 3-phosphoglycerate and suppress photorespiration.

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In contrast, the high O₂ concentration in the atmosphere favors photorespiration in the mesophyll cells of C₃ plants (pathway 2 in Figure 12-49); as a result, as much as 50 percent of the carbon fixed by rubisco may be reoxidized to CO₂ in C₃ plants. C₄ plants are superior to C₃ plants in their ability to use the available CO₂ because the C₄ enzyme phosphoenolpyruvate carboxylase has a higher affinity for CO₂ than does rubisco. However, one ATP is converted to one AMP in the cyclical C₄ process (to generate phosphoenolpyruvate from pyruvate); thus the overall efficiency of the photosynthetic production of sugars from NADPH and ATP is lower than it is in C₃ plants, which use only the Calvin cycle for CO₂ fixation. Nonetheless, the net rates of photosynthesis for C₄ grasses, such as corn or sugarcane, can be two to three times the rates for otherwise similar C₃ grasses, such as wheat, rice, or oats, owing to the elimination of losses from photorespiration.

Of the two carbohydrate products of photosynthesis, starch remains in the mesophyll cells of C₃ plants and in the bundle sheath cells of C₄ plants. In these cells, starch is subjected to glycolysis, mainly in the dark, forming ATP, NADH, and small molecules that are used as building blocks for the synthesis of amino acids, lipids, and other cellular constituents. Sucrose, in contrast, is exported from the photosynthetic cells and transported throughout the plant.