Because the decarboxylation reactions are bypassed, the two carbons lost during each turn of the citric acid cycle are retained in the glyoxylate cycle. In fact, the glyoxylate cycle results in the net synthesis of oxaloacetate, a four-carbon molecule, because each turn of the cycle incorporates two molecules of acetyl-CoA. The oxaloacetate can then can be used for other purposes, such as gluconeogenesis. Animal cells can use oxaloacetate from the citric acid cycle for gluconeogenesis too, but there is no net synthesis of glucose from acetyl-CoA because for every carbon introduced via acetyl-CoA, one is lost via CO2.

The glyoxylate cycle also allows many microorganisms (i.e., many bacteria, fungi, protozoans, and algae) to metabolize two-carbon substrates such as acetate. E. coli can be grown in a medium that provides acetate as the sole carbon source. E. coli synthesize acetyl-CoA, then uses it for energy production (via the citric acid cycle) and for synthesis of gluconeogenic precursors (via the glyoxylate cycle).

Reaction Summary of the Glyoxylate Cycle:

1. Acetyl-CoA + Oxaloacetate + H2O <=> Citrate + CoASH + H⁺  (catalyzed by Citrate Synthase, = -32.2 kJ/mol)

2. Citrate <=> cis-Aconitate + H2O <=> Isocitrate (catalyzed by Aconitase, = +6.3 kJ/mol)

3. Isocitrate <=> Succinate + Glyoxylate (catalyzed by Isocitrate Lyase)

4. Glyoxylate + Acetyl-CoA <=> L-Malate + CoASH + H⁺  (catalyzed by Malate Synthase

5.. Succinate + FAD (enzyme bound) <=> Fumarate + FADH2 (enzyme bound) (catalyzed by Succinate Dehydrogenase, = 0)

6. Fumarate + H2O <=> L-Malate (catalyzed by Fumarate Hydratase, = -3.8 kJ/mol)

7. L-Malate + NAD⁺ <=> Oxaloacetate + NADH + H⁺  (catalyzed by Malate Dehydrogenase, = +29.7 kJ/mol)