Energy Flow and Enzymes Terms
Get down with the lingo
Activation EnergyAn energy barrier that must be overcome in order for a reaction to occur. Activation energies can be thought of as substantially sized chemical hurdles.
Active SiteThe special binding site on an enzyme (usually, a kind of protein; see definition) where the substrate (usually, a molecule of some sort; see definition) binds. After binding, a chemical reaction takes place.
Anabolic PathwayA metabolic pathway, or a series of chemical reactions, in a cell that produces complicated biological molecules from simpler biological building blocks. Anabolic pathways require energy to occur. The processes that produce starch and glucose are examples of anabolic pathways.
ATPAdenosine triphosphate. An adenine molecule, or a nucleotide, attached to three linearly connected phosphate groups (–H2PO4R, depending on pH, 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.
Catabolic PathwayA metabolic pathway, or a series of chemical reactions, in a cell that causes the breakdown of larger biological molecules into smaller biological building blocks. Catabolic pathways have two major functions: i) to produce smaller building blocks that can be used to make other biological molecules, and ii) to generate energy to fuel anabolic pathways.
CatalystA molecule that changes the rate of a chemical reaction. Catalysts can either raise or lower the activation energy, or energy barrier (see definition), of a reaction, causing an increase or decrease in the rate of a reaction. Importantly, catalysts are not used during reactions, a feature tjat allows them to continue catalyzing other reactions. Enzymes, usually proteins, are catalysts that always increase the rates of chemical reactions in a biological cell. You might even call them biocatalysts. Catalysis, or biocatalysis, is the name given to these reactions.
ChaperoneA protein that helps other proteins and biological structures fold, unfold, assemble, or disassemble. Chaperones guide these molecules into their lowest energy configurations (read: optimized protein shape). Chaperones make sure that proteins fold into a shape that is functional, rather than a shape that makes a useless blob.
DiffusionThe random "walking" of molecules from an environment with a higher concentration of molecules to an environment with a lower concentration of molecules. This "walking" is actually more like flopping about and jittering around, but the analogy still works. Basically, molecules try to spread out and use the space available to them.
Closed SystemA contained space that can exchange energy, but not matter, with its surrounding environment.
CoenzymeA small molecule that binds to enzymes and assists in their catalysis, a process that increases the rates of chemical reactions in a cell.
EndergonicA reaction that is thermodynamically unfavored and will therefore only occur spontaneously if linked to an exergonic reaction (see definition). Otherwise, these reactions are not spontaneous. Endergonic reactions have a positive ∆G, or free energy (see definition). Endergonic reactions absorb energy from their surroundings; therefore, energy needs to be put into them. Photosynthesis is an example of an endergonic reaction.
EnergyA measurable quantity that a particular object 'has' because of its ability to do work or generate heat. Energy is not directly observed and is usually measured as the ability of a physical system to do 'work' on another physical system. Remember, it's that thing that cannot be created or destroyed. Talk about high maintenance.
EnthalpyA measurable quantity with the handy dandy nickname of ΔH; for biological purposes, enthalpy can be thought of as the total amount of energy in a system. If a system gains heat from a chemical reaction, ΔH will be positive. Alternatively, if heat is lost from a system, ΔH will be negative.
EntropyA measurable quantity, often noted as ΔS for kicks, that represents the disorder in a system or surroundings. More technically, knowing the entropy of a system can help us determine the energy available for work in a process. That's right, Nature makes all of her randomness available for good use.
EnzymeA biological molecule, often a protein, that increases, or catalyzes, the rate of a chemical reaction by lowering the activation energy, or energy threshold, of that reaction. RNA molecules, or nucleic acids, are thought to be some of the "oldest" enzymes around.
EquilibriumA condition met when the free energy, ∆G, equals zero, meaning that there is no net energy change going into or out of a system. A reaction is said to be at equilibrium when both the forward and backward reaction rates are equal. When a reaction rate is "equal," the amount of reactants used to make the product is the same as the amount of reactants produced from the product. Much like two kids on a seesaw at a standstill. At equilibrium, there is no change in the amount of product or reactant.
ExergonicA reaction that is thermodynamically favored and will occur spontaneously. Remember we said that endergonic reactions are not spontaneous unless they join with exergonic reactions. A bit like how you bust out of your introverted shell and don a miniskirt (or super fly button-down) when your outgoing cheerleader friend takes you out on Saturday night. Exergonic reactions have a negative ∆G and release energy in the form of work. Note: Knowing that a reaction is exergonic does not tell you how fast the reaction will proceed.
Free EnergyA quantity that goes by the nickname of ΔG. Free energy is the amount of useful energy that can be extracted from a reaction to do work. More importantly, though, ΔG is used to predict whether a reaction will proceed spontaneously or not. Reactions that have a negative ΔG will occur spontaneously, like exergonic reactions. Alternatively, reactions that have a positive ΔG will only occur spontaneously if they are coupled to a reaction with a negative ΔG, such that the total ΔG of both reactions is negative—like endergonic reactions.
Gibbs EquationThe equation written out as ΔH = ΔG +TΔS, which we can rewrite as: ∆G = ΔH -TΔS (see definitions for enthalpy and entropy). Good old Gibbs, not to be mistaken for a member of The Bee Gees. The Gibbs equation says that the amount of useful energy, ΔG, that can be extracted from a reaction equals the total energy change, ΔH, minus the energy that cannot do work because it increases the disorder of the system, TΔS. Solving for ΔG is important because ΔG tells us whether a reaction will occur spontaneously or not.
Kinetic EnergyThe energy that an object has because of its motion. If you catch a fly ball in baseball and get ready to throw, the fly ball has kinetic energy, and the ball in your hand has potential energy.
Open SystemA designated area where matter, energy, and entropy pass freely between the system and its outside environment.
OxidationThe chemical reaction by which electrons are transferred from one atom, molecule, or ion to another, changing its oxidation number and oxidation state. Oxidation specifically refers to the loss of an electron by a molecule, atom, or ion, which increases its oxidation state.
PhotosynthesisThe chemical process by which carbon dioxide, or CO2, from the atmosphere is converted or ‘fixed’ into organic compounds, mainly sugars, using the energy from the sun’s light. Photosynthesis occurs in plants, algae, and certain types of bacteria.
Potential EnergyEnergy that an object has because of its position. A rock sitting on a top of a hill has potential energy. If the rock is pushed over the edge, this energy is converted to kinetic energy.
ProductA molecule that is produced in a chemical reaction. Products are generated by reactants.
ReactantA molecule that is used in a chemical reaction to generate product(s).
ReductionThe chemical reaction where an electron is added to an atom, molecule, or ion. Since the atom, molecule, or ion gained an electron, its oxidation state or oxidation number decreases.
RespirationA set of chemical reactions that occur in the cell where atmospheric oxygen, or O2, is broken down into organic molecules, or molecules that contain carbon and hydrogen. Carbon dioxide, or CO2, and water, H2O, are produced as waste during respiration. Except that water is not waste; it is kind of important for staying alive.
SubstrateA molecule that is bound to and worked on by an enzyme (see definition), usually a protein, to lower the activation energy of a chemical reaction that occurs in a cell.
SystemA designated area that we select for study. Systems are defined regions of space and content.
The First Law Of ThermodynamicsA law that states that energy can be transferred from one form to another, but can never be created or destroyed.
The Second Law Of ThermodynamicsThe most fundamental law of physics that states that the amount of disorder in the universe is always increasing. This law is the best existing explanation of Nature's irreversible behavior (male pattern baldness, for instance).
ThermodynamicsThe study of energy conversion from heat to work. Fun words you will see while studying thermodynamics include heat, work, temperature, volume, pressure, and system.
Transition StateA particular arrangement, often called a conformation, that a protein adopts while it is folding and on its way to finding its lowest energy configuration. Proteins are pretty lazy in that they are always looking for the lowest energy state.
WorkThe effort, in the form of energy, transferred from one system to another. In thermodynamics, work is done by a system on the surroundings if energy has been transferred to that object. If a first object transfers energy to a second object, the first object is said to have done work on the second object.
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