Chemical Reactions: reactions that occur when one or more substances are changed into other substances. This can happen when two or more “elements” or “compounds” combine with each other…, when one compound breaks down into two or more “molecules,” or when “electrons” are added to or taken away from an atom. (Brooker, 32)

Chemical reactions … require a source of “energy,” … require water. Need a “catalyst.” Tend to proceed in a particular direction, but will eventually reach a state of “equilibrium.” (Brooker, 32-33) Typically reversible. Factors affecting reactions include: temperature, catalysts, and “concentration” of “reactants” and “products.” (Norton Lectures, 6/11/09) The “cell” is an intricate chemical factory, in which many chemical reactions are going on simultaneously, small molecules being changed one into another, and large molecules being built out of small ones. For every particular chemical reaction — every simple chemical step — there is a special catalyst that speeds up that step and that step only. (Crick, 34-35)


Aerobic: in biochemistry, reactions that need oxygen to happen or happen when oxygen is present. (NCIt) Process that occurs in the presence of oxygen. (Brooker, G1)

Anaerobic: a chemical process that does not require oxygen or occurs in the absence of oxygen. (NCIt) Process that occurs in the absence of oxygen. (Brooker, G2)

Bind (Binding): fasten, attach. (Oxford) The action of attracting something and forming a bond with it. (NCIt)

Binding Site: the parts of a “macromolecule” that directly participate in its specific combination with another molecule. (MeSH) A region (on a) “protein” that physically interacts with a specific “ligand,”  “substrate,” or a specific domain of some complex target biomolecule, such as a protein, lipid, carbohydrate, or nucleic acid. Typically, but not necessarily, the interaction results in protein “conformational” alteration and functional modification. (NCIt)

Catalyst: a substance which facilitates change. (Oxford) A substance that initiates or accelerates a chemical reaction without itself being affected. (NCIt) An agent that speeds up the rate of a chemical reaction without being consumed during the reaction. In living cells, the most common catalysts are “enzymes,” protein molecules that accelerate chemical reactions. (Brooker, 128) Speeds up a chemical reaction by lowering the “activation energy” required to initiate or complete the reaction. (Norman, 6/11/09) Adverb - ‘catalytic.’ 

Chemical Equations: describe what happens during reactions by identifying the reactants and products. (Hunt, 82) 

Condensation: a chemical reaction involving the joining together of two molecules with the removal of a molecule of water. Molecules which are formed in this way can usually be broken down by the addition of water molecules, a process known as “hydrolysis.” (Indge, 66) A chemical reaction involving the removal of a water molecule. An example is a “dimer.” (Brooker, 36) Also referred to as ‘dehydration synthesis.’

Decomposition Reaction: molecules converted to atoms. (Norton Lectures, 6/11/09)

Degradation: reduction to an inferior type, or to a simpler or more rudimentary structure. Conversion of matter to simpler substances; chemical breakdown. (Oxford) Converted into simpler substances - chemically broken down. (Kandel, 272) Degradation of protein aggregates and protein fragments is of vital importance, because they can form build-ups, or "plaques," that are highly toxic. "Alzheimer's disease," the "tremor" of "Parkinson's," and the relentless decline caused by the human form of mad cow disease, all result from the accumulation of toxic, insoluble protein aggregates. (Venter, 43)

Emulsification: a process during digestion that disrupts the large lipid droplets into many tiny droplets, thereby increasing their total surface area and exposure to catalyst action. (Brooker, G-12)

Emulsion: any combination of ‘immiscible’ (unable to be mixed) liquids (like oil and water) in which one is disbursed within the other in small droplets. (Oxford)

Equilibrium: the rate of forward reaction is balanced by the rate of the reverse reaction. All chemical reactions will eventually reach equilibrium. (Brooker, 33)

Exergonic Reaction: energy releasing reaction. (Norton Lectures, 6/11/09) A chemical reaction that releases free energy change and proceeds spontaneously (does not require energy.) (Brooker G-14)

Hydrolysis: a chemical reaction where water is used to break apart another molecule. (Brooker, 36) In a sense, water is wedging itself into a large molecule and breaking it down into two smaller molecules. During this process, water (H20) will break apart forming OH- and H+. The H+ will “bond” to one part of the large molecule and OH- will bond to the other part of the molecule, forming two smaller separate molecules. (Norman, 6/11/09) The breaking down of a large molecule into smaller molecules by the addition of water. The digestive enzymes found in the “gut” are all ‘hydrolases,’ that is they ‘hydrolyze’ their “substrates.” In this way, “starch” is digested to “maltose” and “glucose,” “fats” to “glycerol” and “fatty acids” and “proteins” to “amino acids.” Chemically, hydrolysis is the opposite reaction to condensation. (Indge, 141) From hydro - water, and lysis - to break apart. (Brooker, 36) Adjective - ‘hydrolytic.’

Oxidation: a process that involves the removal of electrons. Occurs during the breakdown of small organic molecules. (Brooker, G-26) A chemical reaction that takes place when a substance comes into contact with oxygen or another oxidizing substance. Examples of oxidation are rust and the brown color on a cut apple. (NCI1) A chemical reaction involving loss of electrons. Although oxidation is usually defined in these terms, it can also involve the addition of oxygen or the loss of hydrogen. Since electrons that are lost must go somewhere, oxidation of one substance is always accompanied by reduction of another. In a biological system, oxidation and reduction are controlled by enzymes. Oxidation of organic molecules is the basis of the process of “respiration.” (Indge, 195) Adjective - ‘oxidative.’

Antioxidants: substances that protect cells from the damage caused by free radicals.  Antioxidants include beta-carotene, lycopene, vitamins A, C, and E, and other natural and manufactured substances. (NCI1)

Free Radicals: a type of unstable molecule that is made during normal chemical changes that take place in a cell. Free radicals can build up in cells and cause damage to other molecules, such as DNA, lipids, and proteins. (NCIt) Free radicals may play a part in cancer, heart disease, stroke, and other diseases of aging. (NCI1)

Oxygen Free Radicals: a type of unstable molecule that contains oxygen and that easily reacts with other molecules in a cell. A build up of oxygen radicals in cells may cause damage to DNA, RNA, and proteins, and may cause cell death. An oxygen radical is a free radical. (NCI1) A molecule containing an atom with a single, unpaired electron in its outer “shell.” Can react with other molecules to ‘steal’ an electron from one of their atoms, thereby filling the “orbital” in the free radical. Can do considerable harm to living cells - for example, by causing a cell’s membrane to rupture or damaging the genetic material. Protection from free radicals is afforded by molecules that can donate electrons to the free radicals without becoming highly reactive themselves. Examples include certain “vitamins” and “flavonoids.” (Brooker, 32) Highly reactive forms of oxygen that arise during chemical reactions such as those of metabolism and transcription. May damage DNA. (Lewis, 228) Also referred to as ‘reactive oxygen species.’

Reactant: starting molecule in a chemical reaction. (Norton Lectures, 6/11/09)

Reduction: a process that involves the addition of electrons to an atom or molecule. (Brooker, G-31)

Reduction-Oxidation Reaction: a type of reaction in which the electron that is removed during the oxidation of an atom or molecule must be transferred to another atom or molecule, which becomes 'reduced.”' (Brooker, G-31) Also referred to as 'redox reaction.'

Substrates: reactant molecules and/or “ions” that bind to an enzyme at the “active site” and participate in a chemical reaction. (Brooker, G-36)

Synthesis: formation of a compound by combination of its elements or constituents. (Oxford) Verb - 'synthesize.'

Synthesis Reactions: atoms converted to molecules. (Norton Lectures, 6/11/09)

Anabolic Reaction: bond building reaction. (Norton Lectures, 6/11/09) A "metabolic pathway" that promotes the synthesis of larger molecules from smaller molecules. (Brooker, G-2)

Endergonic Reaction: energy storing reaction. (Norton Lectures, 6/11/09) A chemical reaction that has a positive free energy change and does not proceed spontaneously (it requires energy). (Brooker G-12)

Transition State: a state in a chemical reaction in which the original bonds have stretched to their limit. Once this state is reached, the reaction can proceed to the formation of products. (Brooker, G-37)