In examining every biological system one can always ask how it works; meaning how, from a knowledge of its parts, one can predict its behavior. Alternatively one can ask how the system got that way; in other words, how it evolved.
— Francis Crick, Of Molecules and Men

Biochemistry: chemical changes within living organisms. The branch of science which deals with the chemical and physiochemical processes which occur in living organisms. (Oxford) The study of the chemical substances and vital processes. (NCIt)

Biochemists have found that molecules can interact with one another within a "cell" and that these “chemical reactions” are organized in specific sequences known as biochemical "signaling pathways." The pathways convey information in the form of “molecules” from the surface of the cell to the interior. In addition, the pathways are ‘wireless.’ Molecules floating within the cell recognize and “bind” to specific molecular partners and regulate their activity. (Kandel, 223)

Acids: chemicals that gives off "hydrogen" "ions" in water and form salts by combining with certain metals. Acids have a sour taste and turn certain dyes red. Some acids made by the body, such as 'gastric acid,' can help "organs" work the way they should. An example of an acid is ‘hydrochloric acid.’ Acidity is measured on a scale called the “pH” scale. On this scale, a value of 7 is neutral, and a pH value of less than 7 to 0 shows increasing acidity. (NCI1) (Acids are) compounds that have the following characteristic properties: 1) in water they form “solutions” with a “pH” below '7',  2) they change the colors of ‘acid-base indicators', 3) they react with “metals” to produce hydrogen gas, 4) they react with 'carbonates' to form “carbon dioxide,” and 5) they react with basic “oxides” to form salts and water. (Hunt, 2) The more positive hydrogen ions a solution has, the more acidic the solution is. (Norman, 6/17/09)

Amino Acids: one of several molecules that join together to form proteins. There are 20 common amino acids found in proteins. (NCI1) Proteins consist of one or more chains of amino acids called "polypeptides." The sequence of the amino acid chain causes the polypeptide to fold into a shape that is biologically active. The amino acid sequences of proteins are encoded in the genes. (NHGRI) Today we know that amino acids are actually assembled into proteins in “ribosomes,” small cellular particles containing a form of ”nucleic acid” called “RNA.” (Watson, 69) Each of the amino acids in a protein has a central “carbon” atom attached to four other groups. (Hunt, 28) The general structure of an amino acid contains an “alpha-carbon” bonded to: 1) an amino group (NH2), a “carboxylic acid” group (COOH), a side group ("R-group"), and a hydrogen atom. There are twenty different amino acids which may be linked together to form proteins. All amino acids have the same basic chemical structure. It is only the R-group that differs. (Indge, 14) The 20 amino acids can be divided into categories, depending on whether their "side chains" are "hydrophobic" or "hydrophilic." (Batiza, 27) The side chains determine the characteristic properties of each amino acid. "Polar" or hydrophilic amino acids have side chains which react with water. 'Non-polar' or hydrophobic amino acids do not like water. (Micklos, 48) Amino acids are joined together by linking the carboxyl group of one amino acid to the amino group of another. A molecule of water is formed each time two amino acids are joined by a "dehydration reaction." (Brooker, 50) The adult brain is dependent on amino acids for producing "enzymes," transport molecules, structural materials, and "neurotransmitters." For example, the amino acids “tyrosine” and “phenylalanine” are needed to produce “epinephrine” and “dopamine.” (SAM Oct Nov 2007, 61)

Amine: any derivative of ammonia in which one or more hydrogen atoms are replaced by ‘alkyl’ or ‘aryl’ groups. (Oxford) A class of organic compounds that contain “nitrogen” as the pivotal atom for “functional groups.” There are several different types of amines and the class is extensive. (NCIt)

Amino: in chemistry, designating or containing the group NH2. (Oxford)

Cystine: an amino acid containing sulfur. Curly headed people have a lot of cistine in them. (Norman, 6/17/09) Not considered one of the 20 amino acids. It functions as an “antioxidant” and protects tissues against radiation and pollution, slowing the aging process. It also aids protein synthesis. Cystine is abundant in many proteins of skeletal tissues and skin, and found in insulin and digestive enzymes. (NCIt)

Glutamic Acid: an amino acid which occurs in proteins and is the source of the glutamate ion. (Oxford) One of twenty amino acids (molecules that join together to form proteins). Glutamic acid may help "nerve cells" send and receive information from other cells. It is being studied for its ability to decrease or prevent nerve damage caused by anticancer drugs. (NCIt)

Glycine: the simplest naturally-occurring amino acid. (Oxford) A non-essential amino acid. It is found primarily in gelatin and silk ‘fibroin’ and used therapeutically as a nutrient. It is also a fast “inhibitory neurotransmitter.” (MeSH)

Monoamine: any compound having a single amine group in its molecule especially one which is a neurotransmitter. (Oxford)

R-Group: general designation for an amino acid side chain. (Brooker, 50) “Chemical equation” designation for a group of atoms that contain carbon. (Brooker, 42) All amino acids have the same basic chemical structure. It is only the R-group that differs. (Indge, 14) The varying structures of the side chains are critical features of protein structure and function. The arrangement and chemical features of the side chains cause proteins to fold and adopt their three-dimensional shapes. Side chains found within the active sites of enzymes are important in “catalyzing” chemical reactions. (Brooker, 50) Also referred to as ‘amino acid side chains’ and ‘side chains.’

Fatty Acids: "carboxylic" acids with long hydrocarbon chains which are combined with "glycerol" to make “triglycerides” in “fats” and vegetable oils. (Hunt, 148) Organic, acids derived from "hydrocarbons" by the equivalent of “oxidation” of a “methyl group” to an “alcohol,”  ‘aldehyde,’ and then acid. Fatty acids are saturated and unsaturated. (MeSH)

Hyaluronic Acid: a type of “glycosaminoglycan" (GAG) which is found in the skin, eyes, and joint fluid. (Brooker, 195) A component of connective “tissue,” “skin,” “umbilical cord,” and the “capsule” of certain “microorganisms” contributing to adhesion, elasticity, and ‘viscosity’ of “extracellular” substances. (NCIt)

Lactic Acid: a product of “anaerobic respiration.” When a person exercises strenuously, the buildup of lactic acid causes a burning sensation or even cramps. Products of anaerobic respiration, such as lactic acid, are eventually secreted from cells. (Brooker, 145) The concentrated form is used internally to prevent gastrointestinal “fermentation.” Also referred to as ‘lactate.’

Base(s): an organic nitrogen-containing compound. (Bynum, 292) A molecule or ion which can accept a hydrogen ion from an acid. A base has a lone pair of “electrons” which can form a bond with a “proton.” Common bases are the oxide and hydroxide ions, ammonia and amines as well as the carbonate ions. (Indge, 51) Bases feel soapy or slippery on the skin and they can turn certain dyes blue. An example of a base is sodium hydroxide. ‘Basicity’ is measured on a scale called the pH scale. On this scale, a pH value of 7 is neutral, and a pH value of more than 7 to 14 shows increasing basicity. (NCIt) Often refers to one of the five "nitrogenous bases" which make up "nucleotides" and nucleic acids DNA and RNA. These compounds are bases in the chemical sense because they have lone pairs of nitrogen atoms which can accept hydrogen ions. (Hunt, 51) Adjective - ‘basic.' Also referred to as ‘alkali.’

Adenine: one of four chemical bases in DNA (and RNA), with the other three being "cytosine" (C), "guanine" (G), and "thymine" (T). Within the DNA molecule, adenine bases located on one strand form chemical bonds with thymine bases on the opposite strand. The sequence of four DNA bases encodes the cell's genetic instructions. A form of adenine called “adenosine triphosphate” (ATP) serves as an energy storage molecule and is used to power many chemical reactions within the cell. (NHGRI) Adenine is a type of “purine.” (NCIt)

Cytosine: one of the nucleotide bases found in nucleic acid molecules. (Indge) Within the DNA molecule, cytosine bases located on one strand form chemical bonds with guanine bases on the opposite strand. (NHGRI) It is a type of “pyrimidine.” (NCIt)

Guanine: one of four chemical bases in DNA (and RNA). Within the DNA molecule, guanine bases located on one strand form chemical bonds with cytosine bases on the opposite strand. (NHGRI) It is a type of purine. (NCIt)

Thymine: one of four chemical bases in DNA (and RNA). Thymine bases located on one strand form chemical bonds with adenine bases on the opposite strand. (NHGRI) It is a type of pyrimidine. (NCIt)

Uracil: one of the nucleotide bases found in nucleic acid molecules. (Indge) One of four chemical bases that are part of RNA. The other three bases are adenine, cytosine, and guanine. In DNA, the base thymine is used in place of uracil. (NHGRI) It is a type of pyrimidine. (NCIt)

Complex: of a substance or species: formed by combination of compounds. (Oxford) A molecular entity formed by loose association involving two or more component molecular entities. The “bonding” between the components is normally weaker than in a “covalent bond.” (NCIt)

Compound: in science, a substance that is made up of more than one ingredient. (NCIt)

Elastic: the ability of a material to recover its original shape or size once a deforming stress has been removed. (Chapple, 69)

Electrolytes: substances that dissociate into two or more ions, to some extent, in water. Solutions of electrolytes thus conduct an electric "current" and can be decomposed by it. (MeSH) Electrolytes regulate nerve and muscle function and water distribution between cells, plasma, and interstitial fluid. Imbalances can cause serious physiologic effects, including "seizures," cardiac "arrhythmias" and convulsions. (NCIt)

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) A suspension of liquid within another liquid or a ‘dispersion’ consisting of two or more liquid phases. (NCIt)

Ethanol: a colorless, volatile, flammable, liquid alcohol. (Oxford) Also referred to as ‘grain alcohol.’

Functional Groups: groups of atoms with special chemical features that are functionally important. Each type exhibits the same properties in all molecules in which it occurs. (Brooker, 43) The atoms and bonding which give a series of "organic" compounds its characteristic properties and are responsible for most of the reactions. (Hunt, 161)

Amino Group: biologically important functional group. Examples of where found include amino acids. (Brooker, 43) Designating or containing the group NH2. (Oxford)

Carbonyl Group: biologically important functional group. Includes "steroids," "eicosanoids," waxes, and proteins. Includes two main subcategories ‘ketones’ and ‘aldehydes.’ (Brooker, 43) The C==O double bond is “polar” with the electrons drawn towards the more (negatively charged) oxygen atom. (Hunt 73)

Carboxyl Group: the functional group which gives acids their characteristic properties. (Hunt, 73) The radical 'COOH' present in most organic compounds. (Oxford) Adjective - 'carboxylic.'

Hydroxyl Group: includes steroids, alcohol, carbohydrates, and some amino acids. (Brooker, 43) The group ‘OH’ in such compounds as bases and some acids and alcohols. (NCIt)

Phosphate Group: a functional group that when added to "ADP” creates ATP. (Batiza, 174) Involved in “gene expression.” (Lewis, 203) Bind to “histone” proteins, controlling “transcription.” (Lewis, 305) Composed of one "phosphorus" and four oxygen atoms. Examples of where found include in nucleic acids, in ATP, and attached to amino acids. (Brooker, 43) Phosphates are large molecules and can be thought of as anchors. (Norman, 6/16/09) Also referred to as ‘inorganic phosphate.’

Sulfate Group: examples of where found may include attachments to carbohydrates, proteins, and lipids. (Brooker, 43)

Glycerol: a colorless, sweet, viscous liquid. An alcohol formed as a by-product in the manufacture of soap. (Oxford) A three-carbon sugar alcohol. When combined with fatty acids it forms "fats" and 'oils" and membrane "lipids." (Lawrence) Also referred to as ‘glycerine.’

Gradient: an increase or decrease in the magnitude of a property, e.g. temperature, pressure, concentration, (electrical charge) etc., observed in passing from one point to another; the rate of such a change. (Oxford)  Can be an electrical gradient or a concentration gradient. (Norton Lectures, 6/3/09) Gradients involving ions have two components - electrical and chemical. (Brooker, 93)

Electrochemical Gradient: a dual gradient that has both an electrical gradient and a chemical gradient. An electrical gradient could exist in which the amount of net positive charge outside a cell is greater than inside. At the same time, a chemical gradient could exist in which the concentration (e.g. of Na+) outside is greater than inside. (Brooker, 93) Also referred to as 'ion electrochemical gradient.'

Transmembrane Gradient: the concentration of a solute is higher on one side of a membrane than the other. Transmembrane gradients of ions and other solutes are a universal feature of all living cells. (Brooker, 93)

Guanosine Diphosphate (GDP): involved in protein synthesis. (Brooker, 176)

Guanosine Triphosphate (GTP): a guanine nucleotide containing three phosphate groups. (NCIt) Involved in protein synthesis. (Brooker, 176)

Homotypic: adjective meaning relatively equal. (Blumenfeld, 881)

Hydrated: containing water. (Brooker, 45)

Insoluble: unable to be dissolved in a liquid. (Oxford)

Ions: electrically charged atoms (or molecules), such as "sodium," "potassium," and "chloride" contained in the extracellular fluid. The “cytoplasm” inside the cell also contains high "concentrations" of ions. An imbalance in the concentration of ions inside and outside the cell could give rise to current across the “membrane.” (Kandel, 80-81) These ions help move nutrients into cells, help move waste out of cells, and help nerves, muscles, the heart, and the brain work the way they should. (NCIt) Editor’s note - ions that can travel through “ionotropic receptors”  (such as those located on a “postsynaptic neuron”) include sodium, calcium, chlorine, and potassium (Na+, Cl-, Ca2+, and K+).

Anion: a molecule with a negative electrical charge. (Norton Lectures, 6/3/09)

Cation: a molecule with a positive electrical charge. (Norton Lectures, 6/3/09)

Nutrients: any substances taken in by the body that provide nourishment. (MeSH) Chemical compounds that make up foods. These compounds are used by the body to function and grow. (NCIt) A substance that must be consumed as part of the diet to provide a source of energy, material for growth, or a means of regulating growth or energy production. Nutrients include carbohydrates, fats, proteins, minerals, and vitamins. (OxfordMed)

Oxidants: chemicals found in foods (e.g. fava beans) that strip electrons from other compounds causing health issues. (Lewis, 227)

pH: a measurement of the concentration of hydrogen ions in a solution. The scale runs from 0 (the most H+ ions and most acidic) to 14 (the least H+ ions and most alkali). A pH of 7 is neutral. Describes the environment of a solution. Positive charges (i.e. H+ or Na+) attract negative charges (i.e. Cl-  OH-  O-). In an acidic environment, it is easy to see how some of the positive hydrogen ions floating around could attract to a negative charge on an enzyme and ‘pull’ it out of shape. The scale is logarithmic so each change in unit corresponds to a ten-fold change in the concentration of molecules. For example, a pH of 6 is ten times more acidic than a pH of 7. (Norman Labs, 34) In living cells, the pH ranges from 6.5 to 7.8 and is carefully regulated to avoid major shifts in pH. The blood of the human body has a normal range of pH 7.35 - 7.45. Certain diseases can reduce or increase blood pH by a few tenths of a unit. When this happens, the enzymes in the body needed for normal “metabolism” are rendered less functional, leading to illness and even death. An acidic solution has a pH that is below 7, while an 'alkaline' solution has a pH above 7. (Brooker, 38)

pH Buffer: a compound that acts to minimize pH fluctuations in the fluids of living organisms. Buffer systems can raise or lower pH as needed. (Brooker, G-5) 

Pheromones: chemical signals that provide information about social and sexual status to other members of the same species. (Hockenbury, 100) A substance which is produced and released into the environment by one organism and affects the behavior of another organism of the same species. Pheromones have a wide range of different functions. (Indge, 204) Although pheromones clearly carry signals, the degree to which they influence human behavior (or biology) is unknown. (Eagleman, 96) Also referred to as ‘human chemosignals.’

Phosphate: the phosphate anion. Phosphates are essential to the metabolism of living organisms because inorganic phosphate is required for the synthesis of the energy storage molecule ADP. Plants and microorganisms take up "phosphorus" mainly in the form of phosphates, and various phosphates are used as fertilizers. (Lawrence) Adding or removing phosphate chemical groups may affect the way proteins act in the body. (NCIt)

Products: the final molecules in a chemical reaction. (Norton Lectures, 6/11/09)

Radical: an element, atom, or group of atoms which can form the basis of a compound, and remain unaltered during ordinary chemical reactions. (Oxford)

Salt(s): generic name for a compound formed with a positive ion and a negative ion. Examples include baking soda, sodium chloride (table salt), calcium sulfate, ammonium sulfate, potassium chloride, and magnesium chloride. (Norton Labs, 25) Substances produced from the reaction between acids and bases. (MeSH)

Soluble: able to be dissolved. (Oxford) Able to be dissolved in a liquid. Capable of being dissolved in some "solvent." (NCIt)

Solute: a dissolved substance. (Brooker, 92)

Solution: a dissolved state or condition. (Oxford) A homogeneous mixture of two or more substances; frequently (but not necessarily) a liquid solution. (NCIt)

Hypertonic: when the solute concentration outside the cell is lower relative to the inside of the cell. (Brooker, G-18) Solutions that have a greater osmotic pressure than a reference solution such as blood, plasma, or interstitial fluid. (MeSH) In this case, water will try to move out of the cell due to osmotic pressure. (Norton Lectures, 6/3/09)

Hypotonic: when the solute concentration inside the cell is higher relative to the outside of the cell. (Brooker, G-18) Solutions that have a lesser “osmotic pressure” than a reference solution such as blood, plasma, or interstitial fluid. (MeSH) In this case, water will try to move into the cell due to osmotic pressure. (Norton Lectures, 6/3/09)

Isotonic: (condition) when the solute concentrations on both sides of the membrane are equal. (Brooker, 93) Of equal tension. Of equal "osmotic pressure." (Lawrence)

Osmolarity: the capacity of a solution to induce “osmosis.” The osmolarity of the interior of a cell is due mainly to the high concentration of small charged organic molecules and their (opposing) “ions.” (Lawrence) The concentration of body fluids measured in terms of the amount of dissolved substances per unit mass of water. (OxfordMed)

Solubility: the mass or amount of a substance that will dissolve in 100 grams of water. No chemical is completely "soluble" and none is completely insoluble. (Hunt, 321)

Solvent: a substance having the power of dissolving other substances. The major component in a solution in which the solute is dissolved. (Oxford)

Vitamins: nutrients that the body needs in small amounts to function and stay healthy. Sources of vitamins are plant and animal food products and dietary supplements. Some vitamins are made in the human body from food products. (NCIt) Groups of chemically unrelated organic substances which are needed in very small amounts in the diet. They can be divided into two groups. 'Fat-soluble vitamins' can be stored in the liver. 'Water-soluble vitamins,' however, cannot be stored and are removed from the body in the urine. It is essential, therefore to maintain a constant supply of water-soluble vitamins. (Indge, 285) Enables the body to use the carbohydrates, lipids, and proteins we eat. (Lewis, 21)