We haven't gotten to the Calvin Cycle yet (the "synthesis" part, below).
Remember to read the Entry in LabArchives about the photosynthesis lab.


Plants are examples of “Autotrophs,” or, organisms that can support themselves and don’t need to eat other things (we are “heterotrophs;” we do eat other things). In particular, plants are “photoautotrophs,” supporting themselves with light.
This is the basic scheme we have been following. Photosynthesis can be broken into two parts, the “photo” part (light reactions” and the “Synthesis part” (Calvin Cycle). The light reactions take place in the thylakoid membrane and produce two main things: ATP and NADPH (It’s just like NADH, except it has an extra phosphate on the ribose…at the 2' position, if you care). The processes that result look like the ones we learned about in respiration (except, backward). The ATP synthase works the same way as it does in respiration.
The ATP and reduced nucleotide cofactor (NADPH) are used in the synthesis part (Calvin Cycle) to pull CO
2 out of the air and synthesize carbohydrates. In the process, the oxidized NADP+ and ADP are produced…and fed back into the light reactions.

Light Reactions

The general idea is that photons of light hit electrons, exciting them to a higher energy level. Instead of “falling” back down and emitting light, the high energy electrons are passed to other molecules, reducing them, and the electrons are passed down an electron transport chain of proteins or smaller molecules that are reduced, then oxidized by the next player in the chain. The actual electron transport system is simpler in the chloroplast than in the mitochondrion. However, it includes two separate places where electrons are excited by light.
Just like in respiration, electron transport moves protons across the membrane and those drive the ATP synthase. The first recipient in the chain is called “Plastoquinone” and it looks like this:
(That structure in the brackets is repeated 9 times). (The protein complex that gets the electrons next is called “cytochrome b6f”).You don’t have to know what all of them are.
There are two different photosystems (called
PSI and PSII) that can work together. PSI can also work on its own. Each has their own chlorophyl. In a pattern known as the “Z scheme,” electrons starting in PSII get passed though electron transport to PSI, where light excites it. Another electron RedOx reaction can pass two electrons onto NADP+, generating NADPH, the reduced form. This will be passed to the “synthesis” part, or Calvin Cycle. The Z scheme looks like this:Thylakoid_membrane

Some key points:
  1. In the Z scheme, or "linear electron flow," PSII is excited “first,” (there are many reaction centers all being hit more or less simultaneously. It’s just that to see the “scheme,” we have to imagine things happening in sequence).
  2. Electrons leave PSII, passed to Plastoquinone (PQ). They are replaced by electrons taken from oxygen in water (a rare case of oxygen being oxidized). This generates O2, which is good for us.
  3. At some point PSI also gets hit by a photon of the right energy. That electron is can be passed directly to an iron-containing protein called “Ferrodoxin” and eventually used to reduce NADP. The electrons are replaced by electrons coming down the from the PSII system.
  4. The Z scheme is also called “linear flow” of electrons because they appear to start at one place (PSII) and pass down the chain, eventually leaving the system.
  5. Photosystem 1 (PSI) can work on its own without PSII. In that case the electrons excited from PSI get passed down the chain to Cytochrome b6f and passed back into a PSII reaction center. When this happens: Oxygen is NOT released and NADPH is not made. In some organisms, the electrons can be taken from some other source and NADPH can be made, but, oxygen is not produced.
  6. From an evolutionary point of view, PSI appears to be older. If that’s the case, photosynthesis was going on for a long time without oxygen being produced.

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.

PhotoSYNTHESISBasic. There are three phases to the synthesis part.

  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.


Below I describe the process in more detail. You would never be held accountable for this. But, I thought some of you might like to read it.
  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. The enzyme phosphoglycerate kinase (which you may remember from glycolysis) uses ATP 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 gets its fourth Oxygen from the carboxyl.
  6. Recall that 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. This is carried out by an enzyme just like the one we see in glycolysis, Glyceraldehyde phosphate dehydrogenenase…just in the opposite direction.
  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. Just know that it is a multi-step pathway.