Tuesday, July 17, 2007
The Calvin Cycle: Regeneration
Nobody took me up on the offer to become an intelligent designer. The goal was to figure out a way of converting the five products of the Rubisco reaction into three new substrate molecules [The Calvin Cycle]. The five products are three carbon (3C) compounds and the three new substrate molecules are five carbon (5C) compounds. Here's how it's done ...
Two 3C molecules are joined to make one six carbon (6C) compound (fructose). Then two of the carbon atoms from fructose are transferred to another 3C molecule to make the first of the five carbon products (red, ribulose). This leaves a 4C molecule that is joined to another one of the 3C molecules to produce a seven carbon (7C) sugar called sedoheptulose. Two carbon are transferred from sedoheptulose to the last 3C molecule to produce a second 5C molecule. This leaves the third and last 5C molecule.
Of course there's a lot of fiddling in the pathway to get the molecules into the right form for these reactions. Here's the complete Calvin Cycle in all its glory. Click on it to see a bigger picture.
You can simplify the pathway a great deal by writing it like this ...
This shows you that, in spite of the complexity, the overall pathway takes three molecules of carbon dioxide and converts it to one molecule of glyceraldehyde 3-phosphate. That's the purpose of the Calvin Cycle, it fixes carbon.
The pathway is expensive. It uses two types of energy currency, ATP and NADPH, but these are produced in abundance by photosynthesis. It's a fair bet that this particular reaction is the ultimate source of 99% of the carbon atoms in your food.
There's a neat trick we can do with this reaction. We can use it to estimate the cost of synthesizing acetyl CoA—the substrate for the citric acid cycle and the product of the pyruvate dehydrogenase reaction. The pathway from glyceraldehyde 3- phosphate to acetyl CoA is coupled to the synthesis of two molecules of NADH and two molecules of ATP. If we subtract these from the cost of making glyceraldehyde 3-phosphate then the total cost of synthesizing acetyl CoA from CO2 is 7 ATP + 4 NAD(P)H. This can be expressed as 17 ATP equivalents since each NADH is equivalent to 2.5 ATP.
Since the net gain from complete oxidation of acetyl CoA by the citric acid cycle is 10 ATP equivalents, the biosynthesis pathway is more expensive than the energy gained from catabolism. In this case, the "efficiency" of acetyl CoA oxidation is only about 60% (10/17 = 59%) but this value is misleading since it is actually the biosynthesis pathway (costing 17 ATP equivalents) that is complex and inefficient.