Photosynthesis
... light reactions are 1) the absorption of energy, 2) the excitation of electrons, and 3) the formation of ATP and NAPDH using energy made available by the cascading of energized electrons down electron transport chains. To help the electrons become excited, the plants uses certain components of visible light. Light-absorbing molecules, called pigments, absorb mainly blue-violet and red-orange wavelengths. The green wavelengths are reflected, and this is what we are able to see. Light absorbed by chlorophyll in the thylakoid membranes is used to makes ATP from ADP and phosphate. It is also used to drive a transfer of electrons from water to NADP+ that carries a hydrogen into cellular respiration. Enzymes reduce NADP+ to NADPH by adding a pair of light excited electrons along with an H+ ion. As the reduction is happening, water is split (oxidized) giving off oxygen. Sugar (glucose) is not made until the Calvin Cycle, the second stage of photosynthesis. Photosystems are arrangements of chlorophyll and other pigments packed into thylakoids. Eukaryotes have Photosystem I and Photosystem II. Photosystem I uses chlorophyll a, referred to as P700. Photosystem II uses a form of chlorophyll a known as P680. The number refer to the length of the wave (wavelengths). The longer the wavelength of visible light, the more red the color. The shorter the wavelength of visible light, the more violet the color. Different pigments, as mentioned in the previous paragraph, absorb different wavelengths. Chlorophyll a participates directly in the light reactions and absorbs mainly blue-violet and red lights. Chlorophyll b absorbs mainly blue and orange light and reflects yellow-green light. Carotenoids, held in the chloroplasts, do not participate directly in light reactions however, they broaden the range of light that a plant can use. These pigments convey the light energy they absorb to chlorophyll a, which then puts the energy to work in the light reactions. Chlorophyll a, chlorophyll b, and the carotenoid pigments are clustered in the thylakoid membrane of each chloroplast. One of the chlorophyll a molecules donates excited electrons to the primary acceptor, triggering light reactions. This makes up the reaction center of the pigment. The reaction center functions as a light-gathering antenna that absorbs photons and passes the energy from molecule to molecule until it reaches the reaction center. The antenna molecules, reaction center, and the primary electron acceptor is what makes up the two photosystems. Chemiosmosis is the second step in photosynthesis. Chemiosmosis produces ATP by substrate-level phosphorylation. This takes place within the thylakoid membrane of a chloroplast. Excited electrons pass along a series of electron carriers within a membrane, as redox reactions occur. This is when the energy given up from electrons is used to make ATP. Specifically, some of the electron carriers use energy released from the electrons to actively transport H+ ions from one side of a membrane to the other. They move across the thylakoid membrane from the stroma into the thylakoid compartment. A concentration gradient (more protons on one side of membrane, more electrons on the other) is created. ATP synthase, a protein, allows the protons to diffuse back into the stroma from the compartment. The energy of the gradient drives H+ ions back across, and energy is released in the process. ATP synthase uses this energy to create ATP from the ADP and the phosphate in the two active sites of the synthase. Unlike cellular respiration, oxygen is not the final electron acceptor, in this process it is NADP+. Rather than being consumed, oxygen is produced when water is split. Dark reactions occur when products of the light reaction are used to from C-C covalent bonds of carbohydrates. These reactions can usually occur in the dark, if the energy carriers from the light process are present. Dark reactions take place in the stroma of the chloroplast. Dark reactions produce the sugar (glucose) from carbon dioxide using the NADPH produced by the light reactions. Carbon dioxide is captured by the chemical ribulose biphosphate (RuBP). Six molecules of carbon dioxide enter the next stage of photosynthesis, which is the Calvin cycle. This eventually produces one glucose molecule. The first stable product of the cycle is phosphoglycerate (PGA). The energy from ATP and NADPH carriers, generated from the two photosystems, is used to attach phosphates to PGA. Eventually there are twelve molecules of glyceraldehydes phosphate, two of which are removed to make a glucose molecule. The next stage of photosynthesis is the Calvin cycle. There are three main phases to this cycle. In the first phase, carbon dioxide enters the stroma of the chloroplast through the stomata of the leaves. Rubisco catalyzes the bonding of carbon dioxide to RuBP to create an unstable 6-carbon molecule that instantly splits into two 3-carbon molecules of 3-PG. In phase two, ATP phosphorylates each 3-PG molecule and creates one 3-bisphosphoglycerate. This results in the loss of a phosphate group from ATP making ADP. NADPH reduces one 3-bisphosphoglycerate which then causes the phosphate group to break off once again. The molecule then picks up a proton from the medium to become glyceraldehydes-3-ph...