The enzyme responsible for incorporating atmospheric CO2 in the reactions of photosynthesis is called Rubisco, an ancient, large, multi-subunit enzyme with a major apparent weakness. In addition to incorporating CO2, Rubisco can also bind O2 and perform an oxygenation reaction with the substrate ribulose bis-phosphate. The results of this oxygenation reaction are one molecule of phopshoglycerate and one molecule of a 2-carbon product called phosphoglycolate. While the PGA can enter the reduction pathway in the chloroplast, the phosphoglycolate cannot and instead enters a recovery pathway spread across two other organelles, the peroxisome and mitochondria. The oxygenation reaction together with the various recovery steps are known as the photorespiratory pathway and represent a significant energetic cost to the plant.

There are probably many explanations for the existence of this costly pathway, beginning with a consideration of the conditions under which Rubisco evolved. Photosynthetic carbon reduction probably began over 1 billion years ago, and is itself thought to have been responsible for the formation of most of the O2 in the atmosphere. In other words, in the earliest cases, there was little to no competition between CO2 and O2 for the active site of Rubisco. So the simplest explanation for why oxygenation happens is that there was not a selective pressure to discriminate between these two substrates. Another explanation is that, given the integration of the recovery pathway with various metabolic pathways such as amino acid biosynthesis, it represents a source of inputs to these pathways. A third explanation is that photorespiration is a strategy for the plant to cope with excess light energy under conditions in which CO2 is limiting. Such conditions arise when the plant is water-stressed and closes stomata to conserve water, which results in a build-up of O2 and draw-down of CO2. Evidence for photorespiration as an important energy-shunting pathway comes from experiments in which mutants for various steps in the recovery pathway were isolated and grown under various conditions. Mutants grow normally under low-light conditions, but when challenged with light levels similar to full sun the mutants show symptoms consistent with damage due to photoinhibition.