Citric acid cycle and lipid metabolism part a. Glucose is broken down in phase: first phase is glycolysis occurs in cytosol (from glucose to two 3 carbon pyruvates) Net output of glycolysis is two nadh and two atp molecules: oxidation of pyruvate occurs in mitochondrion catalyzed by pdh, acetyl-coa is then broken down via. citric acid cycle in mitochondrion. Break down to co2, three nadh, one fadh2, one gtp: reducing equivalents go down to the electron transport chain (etc) Outer mitochondrial matrix is highly permeable with channels that span the membrane porins allow small compounds to pass through. Inner mitochondrial matrix is relatively impermeable, only allowing water and co2, and larger or charged molecules will cross with specific transport proteins: allows ion gradient to be. One of the enzymes in the citric part of protein complex ii of the is embedded in the inner membrane established acid cycle is.