Cristae membranes are studded on the matrix side with small round protein complexes known as F1 particles, the site of proton-gradient driven ATP synthesis.

This phenomenon can be explained by the endosymbiont hypothesis of the origin of mitochondria as prokaryotes internalized by a eukaryotic host cell.

In pig heart mitochondria, phosphatidylethanolamine makes up the majority of the inner mitochondrial membrane at 37.0% of the phospholipid composition.

[8] It is much less permeable to ions and small molecules than the outer membrane, creating compartments by separating the matrix from the cytosolic environment.

There are several antiport systems embedded in the inner membrane, allowing exchange of anions between the cytosol and the mitochondrial matrix.