A method for determining the subcellular metabolite levels in spinach protoplasts is described. The protoplasts are disrupted by centrifugation through a nylon net, releasing intact chloroplasts which pass through a layer of silicone oil into perchloric acid while the remaining cytoplasmic components remain over the oil and are simultaneously quenched as acid is centrifuged into them. Cross-contamination is measured and corrected for using ribulose 1,5-bisphosphate as a chloroplastic marker and phosphoenolpyruvate carboxylase as a cytoplasmic marker. A method for separation of intact protoplasts from the medium by silicone oil centrifugation is described, which allows a correction to be made for the effect of free chloroplasts and broken protoplasts. Methods for inhibiting chloroplast photosynthesis, without inhibiting protoplasts, are presented. It is demonstrated that ribulose 1,5-bisphosphate, ATP, ADP, AMP, inorganic phosphate, hexose phosphate, triose phosphate, fructose 1,6-bisphosphate, and 3-phosphoglycerate can be reliably recovered in the subcellular fractions isolated from protoplasts, and measured by enzymic substrate analysis.give reliable measurements of the subcellular metabolite levels. The method has been specifically developed for the enzymic analysis of the subcellular levels of metabolites in unlabeled extracts but can obviously be extended to, and used in conjunction with, radioactive analysis techniques.A method for subcellular metabolite analysis must meet the following criteria. (a) The cellular compartments must be separated into fractions with acceptably low levels of cross-contamination. The extent of cross-contamination must be determined and corrected for by the use of suitable markers. (b) Separation and quenching of the fractions must be rapid enough to prevent any significant changes in the metabolite levels during, or as a result of, the fractionation procedures. (c) Protoplast preparations inevitably contain some free chloroplasts. The activity of these chloroplasts must be inhibited, without altering protoplast metabolism. The end products of chloroplast photosynthesis which accumulate in the medium are triose-P and, to a lower extent, 3-P-glycerate (2, 13). These are relatively small, rapidly turning Isolated intact chloroplasts are widely used to investigate photosynthesis. However the isolation of chloroplasts can produce changes in their metabolism. Interactions with the cytoplasm and other organelles are lost, and changes in the rates of transport of metabolites across the bounding envelope membrane are to be expected. Moreover, important processes which occur in the cytoplasm and other organelles cannot be studied; these include sucrose synthesis, interactions with respiration, photorespiration, and aspects of nitrogen metabolism and lipid metabolism. On the other hand, isolated cells (15) or protoplasts (4) provide an easily manipulable whole cell system but pose the problem of resolving the internal compartmental organization.When protoplasts are forced through...