PhotoSYNTHESIS

I’ve decided to do this in two parts…a somewhat watered down version, similar to what the book does and then a separate part that gets into more detail. You can read the detail or not. It’s up to you. You won’t be tested on it.

Basic. There are three phases.


  1. Carbon Fixation: The starting molecule is Ribulose 1-5 bisphosphate, a 5-carbon sugar derivative with a phosphate on each end. CO2 is pulled from the air and attached to one end, creating a very unstable 6-carbon molecule that breaks almost immediately in to two 3-carbon molecules called 3 phosphogycerate. If you’re counting Carbons, you started with 5, added 1 CO2 to get 6, then broke that into two 3-carbon molecules.
  2. Reduction: This molecule may be used for some biosynthetic pathways. However, to be really useful, it needs to be reduced from the carboxyl (COO-) form to the aldehyde form (C=O). This goes in two steps involving first ATP, then reduction with NADPH. This yields the very useful glyceraldehyde 3-phosphate (G3P). Do you remember that one from glycolysis?
  3. Regeneration: For it to be a “cycle,” the starting material Ribulose, 1-5 bisphosphate has to be regenerated. This is actually has several steps and if you don’t look a little at the details, the math doesn’t seem to work. For that reason, I’ll do a little detail here. What happens is the first two steps are run 3 times, (requiring 3 Ribulose 1-5 bisphosphate molecules), which gets you 6 G3P. One of those can be syphoned off to use for other things such as glucose synthesis. The remaining 5 G3P are rearranged through several enzymatic steps to get you back your 3 Ribulose 1-5 bisphosphate. (Five 3-carbon molecules get you three 5-carbon molecules…15 carbons in each case)
So, running the Calvin cycle 3 times gets you a net gain of one G3P. Run it 3 more times and you can use two of those to make a glucose. That takes more ATP and is essentially the reverse of the first few steps of glycolysis. It takes a total of 6 times round the cycle to make a single glucose.



Detail


  1. We start with Ribulose 1-5 bisphosphate (that means 2 phosphates, one on each end of the molecule at positions 1 and 5). Note that ribulose is a ketose, with a carbonyl at position 2. I believe the attack of the CO2 is at position 4, one from the right end.
  2. RuBP-2D-skeletal
  3. The intermediate, 3-keto-2-carboxyarabinitol-1,5-bisphosphate, is immediately broken into two 3-phosphoglycerates. These have a phosphate on position 3, a carboxyl group (acid) at position 1. Note that here they are assumed to be deprotonated, as they would be at normal pH.rubismech
  4. Phosphoglycerate can itself be used as starting material for many biosynthetic pathways. Some molecules may get syphoned off for other uses.
  5. ATP is used to add a phosphate to the other end (carbon 1) of 3-phosphoglycerate, yielding 1,3 bisphosphoglycerate (you need two ATP because you have two 3-PG). Note that the carboxyl end (left side) now goes COOPO3-. In ATP hydrolysis, ADP would be left with the extra oxygen and the Pi picks up its fourth O from water. Here, the transferred Phosphate the fourth Oxygen from the carboxyl.
    BIPGLYC
  6. NADPH is a reducing agent...that is, it is oxidized easily. Note that if you now remove the Pi, the oxygen that was the end of the carboxyl is removed, leaving just the carbonyl. So, it’s now an aldehyde (terminal carbonyl) and is Glyceraldehyde 3-phosphate. (you know, G3P from the song). It can be used in biosynthetic pathways too. The H from NADPH is now at the end of the molecule, where the O used to be.
  7. Once you build up enough G3P, you can syphon one off for Glucose synthesis (note that this particular version of the cycle implies that it’s the 3 phosphoglycerate that is syphoned off. This is a bit of a controversy...and may just be a point of view. Let’s stick with the G3P as being the main intermediate used to build glucose.
  8. I’m not going to go into any more detail on the regeneration process than I did above in phase 3.