This past week, we have begun to explore Photosynthesis, the process that plants use to make energy so that they can live long and prosper. Photosynthesis is well known to be the energy generator that it is, but we have been learning the specifics of how it makes energy. First off, photosynthesis is comprised of two main sections. There are the light reactions, or the light dependent reactions, and there are the dark reactions, or the light independent reactions. We also must recognize where photosynthesis is taking place. If you recall the anatomy of a plant cell, you will remember that plants have these things called chloroplasts which are located inside the cell. Now if we zoom in to the chloroplast, we will find some stacks of objects that look like pancakes. These are thylakoids, and when several are stacked together they form a granum. These grana are located inside the stroma, which is effectively the cytosol of the chloroplast. The first part of photosynthesis, or the light dependent reactions, occur inside the membrane of a thylakoid. Inside that membrane, there are sets of two photosystems, PSI and PSII as well as many ATP synthase. In the photosystems, there are pigments that are waiting to be excited by some force of energy. This energy is supplied by photons from some light source. As the photon first hits PSII, it excites a pigment that then releases an electron. This electron moves to the top of PSII and then begins its descent whil it moves across the membrane. As it is moving down, it releases energy that is used in active transport to pump protons across the membrane into the thylakoid lumen, which is the area inside of the thylakoid. At the end of this electrons journey, it will reach PSI, but first we need to know why. While this electron was making its journey through the fire and flames and voer the mountains and through the hills, photons hit PSI and excited an electron from a pigment there. This electron went up, as the first one did, but instead of going down it is metaphorically adopted by an NADP+ molecule, form NADPH and will be used later in photosynthesis. Now we are left with a gaping void where an electron should be in PSI, and this is where the first electron we talked about comes in to play. This electron replaces the empty seat that the PSI electron left and will soon be adopted by an NADP+ molecule after some photons energize it. Now, you may recall the protons that I mentioned getting pumped across the membrane into the thylakoid lumen, and now we see them come in to play. If you happened to listen to my cellular respiration rendition of "Baby" by Justin Bieber, then this part of photosyntehsis should slap you in the face with dejá vu. As you may recall, I sang the words, "Just take some protons, pump them across, make it acidic, for chemiosmosis, H+ ions through the ATP synthase." Well this essentially happens in this stage of photosynthesis. The H+ ions, or protons, that were pumped across are sent through the ATP synthase via chemiosmosis and generate a phosphate that can be metaphorically adopted by an ADP molecule and make ATP, which will be used to power later reactions in photosynthesis. Now only one part of this stage of photosynthesis is left, and we must answer the question, "Where did the electron that was used in PSII come from?" Well, you and your seven year old brother might know that plants must be watered, but now you will learn why. This electron is supplied through the oxidation of water. First I will explain this metaphorically, and then I will explain it scientifically. So let's say that the water molecule family is walking down the street. Mrs. Hydrogen, Mr. Hydrogen, and their child Oxygen. While they are taking a stroll in the park, big bad Thug Doctor PSII steps out of the bushes and kidnaps the baby Oxygen. Then Thug Doctor removes baby Oxygen's heart and has it placed in him surgically to stop suffering from heart failure. Check out my Sketch Fu about this metaphor. 
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Now, done with the forced metaphor, we will look at it scientifically. A water molecule approaches the ATP synthase and oxidized. An electron is taken from the water molecule and replaces the lack of one in PSII. The H+ ions from the water molecule are involved in chemiosmosis and oxygen is released into the world as waste. Now my metaphor makes perfect sense, right? So that sums up the light dependent reactions of photsynthesis, but let's take some time to review the inputs and outputs of these reactions. The inputs needed are water and photons, and the outputs are oxygen, NADPH, and ATP. The oxygen is released as waste, and the NADPH and the ATP will be used in the light independent reactions.
So now you are probably asking, "When are you going to tell me about the light independent reactions?" So let's begin. The light independent reactions occur in the stroma as opposed to the lumen, and these reactions do not directly require light. The name of this stage is the Calvin Cycle, and it requires the inputs ATP, NADPH, and CO2. Let's say that 3CO2 enter the cycle (I will explain the numbering later) and immediately the carbons are separated from the oxygens and the oxygens are released. The three carbons, thanks to an enzyme called RuBiSco, these 3 carbons bond with three preexisting 5 carbon molecules and form three 6 carbon molecules. However, these 6 carbon molecules are extremely unstable and almost as sooon as they are formed they are split into two 3 carbon molecules each. So now we have six 3 carbon molecules. These molecules are then rearranged as ATP and NADPH phosphorylize them until they become PGAL or G3P, a three carbon molecule that can be used to make glucose. However, out of the six PGAL that we have five must continue moving along the cycle. These five are phosphorylized by ATP once more and rearranged until they form the original 5 carbon compound that we joined with in the first place. But what happened to the one PGAL we kept? Well, that PGAL can be used to make glucose or other sugars and, if it becomes glucose, it could be used in cellular respiration. Now here is the catch. While I said that 3 go through in one cycle, only one carbon can enter at a time. However, the carbons kind of go separately almost simultaneously, and this allows them to bond and make one whole PGAL. After the Calvin Cycle, (for 3 carbons) your outputs are 9ADP, 6NADP+, and 1PGAL.
Image from: http://biomassauthority.com/archives/why-is-biomass-better-than-fossil-fuels.html
