How does photosynthesis work? (part 2): Light and dark reactions and the Calvin cycle

The basic reaction of water + CO2  (catalyze with sunlight) ------> H2O + O2 is explained in more depth below, mostly because I get sick of the 'add CO2 and water and sunlight and.... magic happens!' explanation ;)
Photosynthesis is a rather complicated process, and I'll try to keep this simple.

Within a leaf there are cells that specialise and become functionally different from each other. As previously discussed, in leaves one of the major cell types are known as mesophyll, and this again differentiates into 2 types with different functions.
However it's not just plant tissues that specialise, they do it at the cellular level too, and even the sub-cellular level! (I told you it gets complicated).
Within the cells that make up mesophyll tissue, there are organelles that are called chloroplasts (these are what make leaves appear green). This is where the photosynthetic process actually happens.

So the mechanisms of photosynthesis are best discussed if you split them along the conventional lines and talk about them in two parts. The first part is known as the 'Light reactions' as it takes place in direct sunlight, and the second part is the 'Dark reactions' which do not need direct sunlight (although they usually take place during the day).

Light reactions occur in the membrane of the chloroplasts (which remember are within the plant cells). When light is available, it causes a chain reaction that converts chemicals in the chloroplast to ATP (adenosine triphosphate) and NADPH (Nicotinamide adenine dinucleotide phosphate), two molecules that are basically the universal fuels of cells. The ATP acts to move energy to where it's needed, and the NADPH allows phosphorous and more importantly Hydrogen ions to move to where they're needed for photosynthetic reactions.
So once these molecules are generated in light reactions the ATP and NADPH can be used to make sugars in the Dark reactions.

The Dark reactions are where the carbon dioxide is converted into sugars by the plant, in a process known as the Calvin cycle (because it was discovered by Melvin Calvin, James Bassham, and Andrew Benson). For a diagram of this cycle, use your favourite search engine - wikipedia is more than a little complex for this one. Or for a written explanation, keep reading below ;)
So the ATP and NADPH generated in the Light reactions are essential to the turning of this cycle, which is a rather complicated piece of molecular-energy transfer. It occurs in 3 stages, known as Carbon fixation, Reduction and Regeneration.

In Carbon fixation, CO2 is incorporated into a 5-carbon sugar, called ribulose biphosphate, via the enzyme Ribulose-1,5-bisphosphate carboxylase oxygenase (aka Rubisco). Rubsico is an important enzyme, not only as it allows CO2 to be captured and converted into a sugar, but also as it has an affinity to Oxygen, which can cause problems with something called photorespiration (I'll discuss why photorespiration is a problem and how plants deal with it in the next post). So at this point if the Rubisco has fixed CO2 as it should (and not O2), the sugar has 6 Carbon units in it. However this is only an intermediate product and it is then split into two 3-carbon sugars.

The next stage, Reduction, uses the ATP and NADPH from the light reactions to alter the structure of the 3-carbon sugars (this is where the chemistry will take over this post, so I'm keeping it simple here!) and turns them into the precursor to glucose. This can then be used to generate the 6-carbon sugars for the plant. The remaining 3-C sugars continue within the cycle, and enters the next stage, Regeneration. For this, more ATP is used to convert the 3-C sugar from this pool back into the original 5-C sugar that is used to capture the CO2, and the cycle can begin again.

So in summary, while a complicated process, each turn of the Calvin cycle will actually only capture just a single additional Carbon, so for a 6-C glucose molecule to be generated it will require 6 turns of the cycle. This involves 12 photons hitting the chloroplasts and generating 18 ATP and 12 NADPH molecules in the light reactions, which can then be used for 6 turns of the Calvin cycle in the Dark reactions to fix 6 CO2 molecules to end up with a single 6-Carbon sugar. In a nutshell, the light reactions provide the energy required for the dark reactions to fix carbon, and this is how basic C3 photosynthesis works (so called C3 as it's based on 3-Carbon sugars).

However some plants run into trouble with maintaining water balance, or with excessive light or temperatures. As such they've evolved to cope with this by photosynthesising in a different way. There are 2 main alternatives to C3 photosynthesis: C4 or CAM photosythesis, and I'll discuss these (along with photorespiration) in the next post...