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ATP synthase is a ubiquitous enzyme that is located in the inner membranes of mitochondria, thylakoid membranes of chloroplasts, or the plasma membranes of bacteria.
Located within the thylakoid membrane and the inner mitochondrial membrane, ATP synthase consists of two regions. 1  the FO portion embedded within the membrane.  the F1 portion of the ATP synthase is outside the membrane, but inside the matrix of the mitochondria.