Activation Energy: an initial input of energy in a ”chemical reaction” that allows the “molecules” to get close enough to cause a rearrangement of “bonds.” (Brooker, G-1) Needed for molecules to achieve a “transition state.” The activation energy required to achieve the transition state is a barrier to the formation of "products." One way that “enzymes” lower the activation energy is by straining (‘stretching’) the “reactants” so that less energy is required to attain the transition state. (Brooker, 129)

Adenosine Diphosphate (ADP): "nucleotide" containing two "phosphate groups" at the 5'-position that is converted to "ATP" for energy for storage. (UMLS) Product of the breakdown of ATP. In the reaction, the “free energy” released is -7.3 kcal/mole. (Brooker, 127) Nucleotide made of "adenosine" linked to two phosphate groups in series, important in all living cells in energy transfer reactions, where it is converted to ATP (e.g. during “oxidative phosphorylation” and “photosynthesis”) or formed from the “hydrolysis” of ATP. (Lawrence)

Adenosine Triphosphate (ATP): the main type of fuel a cell can burn. Created by “mitochondria” from “glucose,” as glucose is absorbed into a cell. (Ratey, 71) All cells metabolize glucose to generate ATP. (Norman, 6/23/09) A substance present in all living cells that provides energy for many metabolic processes and is involved in making RNA. A nucleotide that is a common energy source of all cells. (Brooker, G-1) The primary energy-containing molecule used in biological systems. (Edvotek, 6) An important molecule, found in all living cells, which is involved in the transfer of energy. A molecule of ATP is made up from a molecule of adenine joined to the five-carbon sugar, “ribose” and to three “phosphate groups." When ATP is broken down, the third phosphate group is lost and a considerable amount of energy is released. The reverse reaction can also take place. ADP can join with a phosphate group to produce ATP. In this case, energy is required. Most of the ATP within a cell is produced using energy released during the process of “respiration.” (Indge, 23-24)

Chemiosmosis: a process for making ATP in which energy… is used to make ATP from ADP. (Brooker, G-7) A mechanism by which energy derived from “aerobic respiration” or from sunlight can be used to power ATP synthesis. (Lawrence)

Degeneration: having a simpler or lower degree of activity. (Oxford) The process of declining from a higher to a lower level of effective power or vitality or essential quality. (NCIt) Breakdown in structure. Change to a less specialized or functionally less active form. Evolutionary change resulting in change from a complex to a simpler form. (Lawrence) Adjective - ‘degenerate.’

Electrochemistry: the branch of science that deals with the relation between electrical and chemical “phenomena” and the interconversion of these forms of energy. (Oxford) Adjective - ‘electrochemical.’

Electron Carriers: any of the proteins and other molecules that transport electrons in an “electron transport chain.” (Lawrence) These act like a ‘shuttle craft’ taking an electron from somebody and giving it to somebody else. (Norman, 6/23/09) Also referred to as 'electron carrier.”

NADH: an energy carrier. (Brooker, 139)

NADPH: nicotinamide adenine dinucleotide phosphate. An energy carrier. Its structure differs from NADH by the presence of an additional phosphate group. In the 'Calvin cycle,' atmospheric carbon dioxide is incorporated into organic molecules, some of which are converted to carbohydrates. (Brooker, 153)

Electron Transport Chain: a group of protein complexes and small “organic” molecules embedded in the inner 'mitochondrial' “membrane.” These components are referred to as an electron transport chain because the components can accept and donate electrons to each other in a linear manner. (Brooker, 138) The energy released during electron transport is used to pump protons across the membrane. (Lawrence) A cluster of protein complexes that reside in the inner membrane of the "mitochondria." In the final step of energy production, “protons” generated by the electron transport chain flow through a pump known as ”ATP synthase,” driving the production of ATP. (Edvotek, 6) Also referred to as ‘electron transfer chain.’

Energy: the ability to do work. (Norman, 6/11/09) The capacity of a physical system to do work. (NCIt) The ability to promote change. (Brooker, 126) The amount of work used to perform a task or stored for future use. Energy is “power” exerted over time. Typically measured in “kWh.” (BHO, 2) Energy can produce “light,” “heat,” “motion,” sound, and growth. (Hall, 9/19/09)

Enthalpy: the total energy. (Brooker, 127) A unit used to express a quantity associated with a thermodynamic system, defined as the internal energy of a system plus the product of the pressure and volume of the system, calculated from an accepted temperature base. (NCIt) Describes the energy lost as heat to the environment in a... chemical reaction, or (from) a living organism. (Lawrence)

Entropy: a measure of the disorder that cannot be harnessed to do work. (Brooker, 127) Describes the disorder or randomness of a system. (Lawrence) The measure of that part of the heat or energy of a system which is not available to perform work. (MeSH)

Free Energy: a thermodynamic term used to describe the energy that may be extracted from a system at constant temperature and pressure. (NCIt) The amount of available energy that can be used to do work. (Brooker, 127) Also referred to as ‘usable energy.’

Kinetic Energy: energy employed in producing or changing motion. (Lawrence) The energy of motion. Forms include "chemical," "electric," "mechanical," "radiant," and sound.  (Norman, 6/11/09) Transitional energy. Energy changing form. (Olwell, 2/1/10) The energy possessed by a mass, by reason of its motion. (Chapple, 141)

Potential Energy: stored energy. (Norman, 6/11/09) The energy stored in a system by reason of its position or its condition. (Chapple, 186) In biological systems energy is stored in the structure of molecules and is released through "metabolism." (NCIt)

Energy Balance: in biology, the state at which the number of calories eaten equals the number of calories used. Energy balance is affected by physical activity, body size, amount of body fat and muscle, and genetics. (NCIt) Also referred to as 'energy budget.'

Energy Intermediates: molecules directly used to drive “endergonic reactions” in cells. When cells break “bonds” in organic molecules such as “carbohydrates” and proteins, they do not directly use the energy that is released in this process. Instead, the released energy is stored in energy intermediates. (Brooker, 130-131)

FADH2: fatty acid hydroxylase 2. NADH and FADH2 are oxidized (during "oxidative phosphorylation") due to the removal of electrons. (Brooker, 138)

NAD+: nicotinamide adenine dinucleotide; a dinucleotide that functions as an energy intermediate molecule. It combines with two electrons and H+ to form NADH. (Brooker, G-24)

NADP+: nicotinamide adenine dinucleotide phosphate; a dinucleotide that functions as an energy intermediate molecule in 'chloroplasts.' It combines with two electrons and H+ to form NADPH. (Brooker, G-24)

Phosphorylation: the transfer of a 'phosphate group' from "ATP" to another molecule. (Oxford) A process in which a phosphate group is added to a molecule, such as a sugar or a protein. (NCIt) The phosphorylation of proteins at specific "amino acids" by protein "kinases" is a widespread means of rapidly altering a protein's activity in response to "intracellular" or "extracellular" signals. (Lawrence)

Oxidative Phosphorylation: a process during which NADH and FADH2 are oxidized to make more ATP via the “phosphorylation” of ADP. (Brooker, G-27) The formation of ATP from ADP as the result of aerobic respiration. (Lawrence)

Substrate-Level Phosphorylation: a method of “synthesizing” ATP that occurs when an enzyme directly transfers a phosphate from one molecule to a different molecule. (Brooker, G-36) Formation of ... ATP by transfer of phosphate from a metabolic "substrate" directly with no respiratory chain involvement. (Lawrence)

Thermodynamics: the study of energy interconversions. (Brooker, 126) The branch of physics concerned with the conversion of different forms of energy. (NCIt) Describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (MeSH)

First Law of Thermodynamics: energy cannot be created or destroyed. (Brooker, 126) Any increase in the internal energy of a system is the sum of the heat flowing into the system and the work done on the system. (Chapple, 252) Also referred to as the ‘law of conservation of energy.’

Second law of Thermodynamics: the transfer of energy or the transformation of energy from one form to another increases the entropy or degree of disorder of a system. (Brooker, 126)