Adenosine triphosphate. An adenine molecule, or a nucleotide, attached to three linearly connected phosphate groups (–H2PO4R, where R is a functional group). The breaking of chemical bonds between the 2nd and 3rd phosphate groups provides most of the chemical energy used by a cell. Most of the ATP in a cell is made in the mitochondria, the cell's powerhouse. ATP is a coenzyme (the -ase in the name gives it away) and a strong reducing agent, or electron donor, that acts as the principal energy carrier in the cell. Donating the terminal phosphate group, or the phosphate group on the end, from ATP causes the release of a large amount of energy. ATP basically shuffles energy around to support metabolism and a bunch of super important cellular processes, like photosynthesis.
Autotroph
An organism that can use light energy and the photosynthetic process to produce organic food (read: containing carbon and hydrogen) from inorganic molecules.
Calvin Cycle
A series of reactions that occur during photosynthesis in the inner area, or stroma, of chloroplasts, aka the photosynthetic organelle in plants. The Calvin cycle is part of the light-independent reactions of photosynthesis. During the Calvin cycle, carbon dioxide (CO2) is "fixed" using energy in the form of adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH), which are generated in the first stage of photosynthesis, called the light-dependent reactions. During the Calvin cycle, the carbon in CO2 is fixed to the 5-carbon molecule ribulose biphosphate (RuBP). The resulting 6-carbon product is quickly broken down to phosphoglycerate (PGA). The rest of the cycle works to rebuild RuBP from PGA while at the same time removing a 3-carbon sugar called glyceraldehyde-3-phosphate, or G3P. G3P can be used to make carbohydrates such as starch. The whole point of the Calvin cycle is to fixate carbon.
Carbohydrate
A biological molecule that has the elements carbon (C), hydrogen (H), and oxygen (O) in a ratio of 1:2:1. Carbs provide energy to cells, can be used for energy storage, and provide structural support. Carbohydrate is not synonymous with the word sugar, however. Carbohydrates can be in the form of sugars, starches, and fibers. In photosynthesis, light energy from the Sun is used to build carbohydrates.
Chlorophyll
A magical green pigment that absorbs light and is found in all plants, algae, and cyanobacteria. Photosynthesis cannot happen without chlorophyll.
Chloroplast
The organelle, or "mini organ," in plant cells and a few other eukaryotic cells that carries out photosynthesis, or the conversion of sunlight into food. Chloroplasts contain chlorophyll, the magical green pigment (see above). The chloroplast is believed to have originated from an earlier version of a eukaryotic cell that decided to house a photosynthetic bacterial cell through the process of endosymbiosis (see definition). The chloroplast is surrounded by outer and inner membranes and contains membrane-bound structures called thylakoids.
Electron Transport Chain
A specific process used in the light-dependent reactions of photosynthesis. During the electron transport chain, electrons are repeatedly transferred from a high-energy electron donor (nicotinamide adenine dinucleotide phosphate, or NADPH), to an electron acceptor, such as O2. This process is coupled to the transfer of H+ ions, or protons, across a membrane. Essentially, the transfer of electrons across the thylakoid membrane in the chloroplast drives a proton gradient that is used to produce chemical energy in the form of adenosine triphosphate (ATP).
Electron
A negatively charged (-1) subatomic particle. An electron is part of an atom.
Endosymbiosis
The theory that explains how mitochondria and chloroplasts became organelles of other cells. Endosymbiosis is the condition of living within the body or cells of another organism. There is evidence that, millions of years ago, the ancestors of mitochondria and chloroplasts, two organelles ("mini organs") were actually prokaryotic organisms that entered into endosymbiotic relationships with eukaryotic cells. We are supposing that they liked each other just a little too much.
H+
Hydrogen ion, otherwise known as a proton. The atomic number of hydrogen is 1, meaning that it has only one proton in its nucleus. A positively charged hydrogen atom (H+) has lost its only electron and is an ion, meaning that its one proton in its nucleus gives it a positive charge of +1. Hydrogen does not have neutrons unless it is an isotope, so an H+ ion consists of only one proton. For this reason, the terms proton and H+ are used interchangeably most of the time in biology. Tsk, tsk…lazy biologists.
Heterotroph
An organism that consumes organic matter created by autotrophs. Autotrophs produce organic compounds from inorganic molecules using either photosynthesis or chemosynthesis (read: chemical reactions using inorganic molecules). Heterotrophs cannot fix carbon and only use organic carbon to grow. Heterotrophs cannot make their own organic compounds like plants can. We saw that light bulb go on in your head; don't try to hide it. Yes, humans, and 95% of all other organisms, are heterotrophic.
Light Reactions, Or Light-dependent Reactions
The first stage of photosynthesis, where light energy from the Sun is captured, and with a little help from our good buddy, water (H2O), changed into chemical energy in the forms of ATP and NADPH. The light-dependent reactions take place in the thylakoid membrane of the chloroplast in plants. They comprise two photosystems, named Photosystem I and Photosystem II.
Light-independent Reactions, Or Dark Reactions
The second stage of photosynthesis, where carbohydrates from carbon dioxide, or CO2, are produced using the energy forms (ATP and NADPH) generated in the first stage of photosynthesis, aka the light-dependent reactions. The light-independent reactions occur in the stroma of the chloroplast in plants.
Lumen
The inner membrane space of a chloroplast. The lumen is also called the thylakoid lumen. Protons are pumped into the lumen during the light-dependent reactions of photosynthesis.
NADPH
Nicotinamide adenine dinucleotide phosphate, which is a strong reducing agent, or electron donor, as well as a coenzyme. NADP+ is the common notation for the nonreduced form, and NADPH is the name once it has been reduced, or gained an electron. NADPH acts as a carrier of electrons and is used extensively in the synthesis of biological molecules.
Oxidized
A state of a molecule once it has lost an electron.
Oxidizing Agent
A molecule that accepts electrons and oxidizes the molecule that it accepts electrons from.
Photorespiration
The process where ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCo), an enzyme, catalyzes the attachment of oxygen (O2) to the 5-carbon ribulose-1,5-bisphosphate (RuBP) in the stomata of plant leaves. The end products are phosphoglycerate (PGA) and carbon dioxide (CO2). Photorespiration is thought to reduce the efficiency of photosynthesis in some plants but is still actively being studied. We'll keep you posted.
Photosynthesis
What this whole unit is about. Obviously. The process by which carbon dioxide (CO2) from the atmosphere is converted, or "fixed," into organic compounds (those containing carbon and hydrogen) using the energy from the Sun’s light. The byproduct of this process is oxygen (O2).
Proton Gradient
The movement of protons from the lumen to the stroma, or from high to low concentration, in chloroplasts. The proton gradient is exploited to generate ATP and NADPH.
Reduced
The state of a molecule that has gained electrons.
Reducing Agent
A molecule that can donate electrons. A reducing agent reduces the molecule that it donates electrons to.
RuBisCo
Ribulose-1,5-bisphosphate carboxylase oxygenase, or the enzyme used in the light-independent reactions to fix carbon dioxide (CO2) to the 5-carbon ribulose-1,5-bisphosphate (RuBP).
Stoma, Or Stomate (plural stomata)
The opening(s) or pore(s) in a leaf that allow the passing of gases into and out of the leaf.
Stroma
The inner area of a chloroplast where the light-independent reactions occur. The stroma is the water-based, fluid-filled area of the chloroplast.
Thylakoid
A membrane-bound compartment inside of the chloroplast where the light-dependent reactions of photosynthesis occur.
Visible Light Spectrum
The range of wavelengths of the electromagnetic spectrum that is visible to the human eye. These wavelengths of light are used by plants for photosynthesis.