As its full name indicates, rubisco (ribulose bisphosphate carboxylase/oxygenase) is an oxygenase as well as a carboxylase—it can add O₂ or CO₂, respectively, to the acceptor molecule RuBP:

Think about the concentrations of O₂ and CO₂ in the typical air that you breathe. The concentration of CO₂ in Earth’s atmosphere is about 400 ppm, or 0.04%. The concentration of O₂ in the air is about 20%. You would think that if there were an “even competition” between CO₂ and O₂ for rubisco that the latter, with its higher concentration, would be favored. But such is not the case. It turns out that the affinity (binding) of rubisco for CO₂ is much stronger than it is for O₂, so in normal air inside a leaf, CO₂ fixation is favored even though the concentration of CO₂ in the air is far lower than that of O₂. It is when there is an even higher concentration of O₂ in the leaf relative to outside that O₂ competes with the CO₂, and rubisco combines RuBP with O₂ rather than with CO₂. This oxygenase activity reduces the overall amount of CO₂ that can be converted into carbohydrates, and may play a role in limiting plant growth.

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Under what conditions inside the leaf does the air have higher O₂ and lower CO₂, favoring the oxygenase activity? On a hot, dry day, small pores in the leaf surface called stomata close to prevent water from evaporating from the leaf (see Figure 10.1). But stomata closure also prevents gases from entering and leaving the leaf. If stomata are closed, the CO₂ concentration in the leaf falls as CO₂ is used up in photosynthetic reactions, and the O₂ concentration rises because of these same reactions where water is used to form O₂ (see Investigating Life: What Is the Chemistry of Photosynthesis, and How Will Increasing CO₂ in the Atmosphere Affect It?). As the ratio of CO₂ to O₂ falls, the oxygenase activity of rubisco is favored.

The consequences of oxygenase activity and lower carboxylase activity are significant. When O₂ is added to RuBP, one of the products is a two-carbon compound, phosphoglycolate:

RuBP + O₂ → phosphoglycolate + 3-phosphoglycerate (3PG)      (10.11)

The 3PG formed by rubisco’s oxygenase activity enters the Calvin cycle, but the phosphoglycolate does not. Plants have evolved a metabolic pathway that can partially recover the carbon in phosphoglycolate. The phosphoglycolate is hydrolyzed to glycolate, which diffuses into peroxisomes (Figure 10.14). There, a series of reactions converts it into the amino acid glycine:

Glycolate + O₂ → glycine                                             (10.12)

The glycine then diffuses into a mitochondrion, where two glycine molecules are converted in a series of reactions into the amino acid serine, releasing CO₂:

2 Glycine → serine + CO₂                                          (10.13)

The serine moves into the peroxisome, where it is converted to glycerate. The glycerate then moves into the chloroplast, where it is phosphorylated to make 3PG, which enters the Calvin cycle. Note that it takes two phosphoglycolate molecules from Equation 10.11 to produce the two glycines used in Equation 10.13. So overall:

2 Phosphoglycolate (4 carbons) + O₂ → 3PG (3 carbons) + CO₂     (10.14)

This pathway thus reclaims 75 percent of the carbons from phosphoglycolate for the Calvin cycle. In other words, the reaction of RuBP with O₂ instead of CO₂ reduces the net carbon fixed by the Calvin cycle by 25 percent. The pathway is called photorespiration because it consumes O₂ and releases CO₂ and because it occurs only in the light (mediated by the same enzyme activation processes that we mentioned above with regard to the Calvin cycle).