The structure of mitochondria plays a crucial role in maximizing ATP production during cellular respiration. Mitochondria have a double-membrane structure, consisting of an outer membrane and a highly folded inner membrane. The inner membrane forms folds called cristae, which greatly increase the surface area for chemical reactions. This is where the electron transport chain (ETC) and ATP synthase are located. The space between the inner and outer membranes, known as the intermembrane space, is crucial for establishing the proton gradient during the ETC. Protons are pumped into this space by the ETC, creating a concentration gradient. ATP synthase, embedded in the inner membrane, uses the energy from this gradient as protons flow back into the mitochondrial matrix to synthesize ATP from ADP and inorganic phosphate. The matrix itself contains enzymes for the Krebs cycle and other reactions involved in energy production. This compartmentalization and structural organization are key to the efficient production of ATP in mitochondria.

NAD+ (Nicotinamide Adenine Dinucleotide) and FAD (Flavin Adenine Dinucleotide) are essential coenzymes in cellular respiration, acting as electron carriers. During glycolysis and the Krebs cycle, various enzymes catalyze reactions where electrons are removed from organic molecules, such as glucose. These electrons are initially transferred to NAD+, reducing it to NADH, and to FAD, reducing it to FADH2. These reduced coenzymes then carry the electrons to the electron transport chain in the mitochondria. Here, NADH and FADH2 donate their electrons to the chain, which are passed along a series of proteins and other molecules. This electron transfer facilitates the pumping of protons across the mitochondrial inner membrane, creating the proton gradient necessary for ATP synthesis. After releasing their electrons, NAD+ and FAD are regenerated and can be reused in earlier stages of cellular respiration, making them critical in the continual flow of electrons and the efficient production of ATP.

The proton gradient in the mitochondria is central to ATP synthesis, a process known as chemiosmosis. This gradient is established by the electron transport chain (ETC) located in the mitochondrial inner membrane. As electrons move through the ETC, the energy released is used to pump protons (H+) from the mitochondrial matrix into the intermembrane space. This creates a high concentration of protons in the intermembrane space and a low concentration in the matrix, resulting in a proton gradient and an electrochemical potential across the membrane. ATP synthase, an enzyme also located in the inner membrane, uses this gradient for ATP synthesis. As protons flow back into the matrix through ATP synthase, due to the concentration gradient, the enzyme catalyzes the synthesis of ATP from ADP and inorganic phosphate. The movement of protons through ATP synthase provides the necessary energy for the enzymatic addition of a phosphate group to ADP, thus generating ATP.

The fate of pyruvate, the end product of glycolysis, is a key factor that differentiates cellular respiration from fermentation and significantly affects ATP production. In cellular respiration, when oxygen is available, pyruvate is transported into the mitochondria. Here, it undergoes oxidative decarboxylation by the enzyme complex pyruvate dehydrogenase to form acetyl-CoA. This acetyl-CoA enters the Krebs cycle, leading to further production of NADH and FADH2, which drive ATP synthesis via the electron transport chain.

In contrast, during fermentation, which occurs in the absence of oxygen, pyruvate remains in the cytoplasm and undergoes different pathways depending on the organism. In lactic acid fermentation, pyruvate is reduced to lactate, regenerating NAD+ for glycolysis. In alcoholic fermentation, pyruvate is converted into ethanol and carbon dioxide, also regenerating NAD+. Since fermentation does not involve the Krebs cycle or the electron transport chain, the ATP yield is limited to the 2 ATP molecules produced during glycolysis, compared to the up to 38 ATP molecules produced during cellular respiration.

Some cells prefer fermentation over cellular respiration even in the presence of oxygen due to various factors such as the rate of ATP production, the specific needs of the cell, or environmental conditions. For example, yeast cells undergo alcoholic fermentation even in aerobic conditions, a phenomenon known as the Crabtree effect. This is because fermentation can occur at a faster rate than aerobic respiration, allowing for rapid ATP production and growth when glucose is abundant. In muscle cells, during intense exercise, the demand for ATP can exceed the rate at which oxygen can be supplied to the mitochondria. In such scenarios, muscle cells switch to lactic acid fermentation to rapidly produce ATP, despite the presence of oxygen. Additionally, some cells may lack sufficient mitochondria or enzymes necessary for efficient cellular respiration. In these cases, fermentation provides a simpler and more feasible way to generate ATP. This preference for fermentation, despite its lower efficiency compared to cellular respiration, is an adaptive strategy for certain cells under specific conditions.