Magnesium Protects the Mitochondria. Magnesium and bicarbonate given together work to combat the drop in energy within the mitochondria during constant bombardment from toxins. First, magnesium bicarbonate protects the natural organic and inorganic phosphate buffers in the cytoplasm of cells. Second, magnesium bicarbonate neutralizes the acid produced as a result of metabolic processes and ATP hydrolysis. This allows more ATP to be hydrolyzed, or more energy to be made. Magnesium bicarbonate buffers the mitochondria in body cells from excess acid concentrations, which improves mitochondrial function and increases ATP.