matrix

Meaning: The mitochondrial matrix is the compartment enclosed by the inner mitochondrial membrane. It holds the pyruvate dehydrogenase complex, the citric acid cycle enzymes (succinate dehydrogenase is the exception, built into the inner membrane as Complex II), fatty acid β-oxidation enzymes, mitochondrial DNA, and ribosomes. NADH and FADH₂ made here feed the electron transport chain. Complexes I, III and IV pump H⁺ out of the matrix into the intermembrane space, so the matrix has a lower [H⁺] and a higher pH. ATP synthase lets H⁺ flow back in, driving ATP synthesis. In cell biology, matrix can also mean the extracellular matrix.

On the MCAT: Expect location questions (glycolysis in the cytosol; pyruvate oxidation and the citric acid cycle in the matrix) and gradient questions. An uncoupler lets H⁺ leak into the matrix and dissipates the gradient. An electron transport chain inhibitor stops the pumping, so the gradient falls.

Common confusion: Students put the high [H⁺] in the matrix. The proton buildup is in the intermembrane space, and the matrix is the more alkaline side. The electron transport chain itself sits in the inner membrane, not free in the matrix.