Bio-Chemistry Vocabulary:

• Isotope: One of the several atomic forms of an element, each with the same number of protons but different number of neutrons, thus differing in atomic mass.

• Valence electrons: unpaired electrons in the valence shell of an atom

• Covalent bonds: a chemical bond where electrons are shared between atoms.

• Ionic Bond: Chemical bond where electrons are transferred between atoms

• Hydrogen Bonds: A type of weak chemical force that is formed by the slightly positive H of a molecule is attached to a slightly negative polar covalent bond of another molecule/same region of a molecule (N,O,F).

• Polar Molecule: A molecule with unequal distribution of overall charge.

• Nonpolar Molecule: A molecule with equal distribution of overall charge

• Electronegativity: The attraction of a given atom for the electrons of a covalent bond.

• Cohesion: Property of H2O; H2O is attracted to itself and Hydrogen bonds to form water molecule.

• Adhesion: Property of H2O; H2O is attracted to other substances and bonds via hydrogen bonding.

• Surface tension: A measure of how mard/difficult is it to stretch or break the surface of a liquid. H2O has a high surface tension, due to Hydrogen bonding.

• Specific heat: the amount of heat needed to change the temperature 1°C for 1 gram of a substance. H2O has a high specific heat because a lot of heat is needed to break H-bonds than to move particles.   

• Heat of Vaporization: the amount of heat needed for a liquid to turn into a gaseous state. H2O has a high heat of vaporization, due to H-bonding.

• Evaporative Cooling: the “cool” remaining from evaporation. “Hot” molecules in gaseous state: “cool” are the rest. This provides stability, like sweat prevents overheating.

• Aqueous solution: H2O is the agent that dissolves a substance.

• Hydrophilic: a substance that readily absorbs or dissolves H2O.

• Hydrophobic: a substance that repels from H2O; they cannot form H-bonds (nonionic, nonpolar substances).

• pH: A measure of Hydrogen ion concentration, equal to the -log[H+} and ranging in value from 0-14.

• Buffer: Solution that helps maintain stable pH by donating and accepting H+ ions.

• Organic Chemistry: the study of all compounds that have Carbon atoms. Carbon is the basic element found in ALL living things.

• Isomers: One of several compounds with the same molecular formula but different structures and therefore different properties. There are three types of isomers.

• Structural isomers: One of several compounds that have the same structural formula but differ in the covalent arrangements of their atom (a.k.a. different structures).

• Cis-trans Isomer: One of several compounds that have the same molecular formula and covalent bonds between atoms, but differ in the spatial arrangement of their atoms owing to the inflexibility of double bonds; formerly called geometric isomer. Cis=X on the same side, Trans=X on different side.

• Enantiomer Isomer: One of two compounds that are mirror images of each other and that differ in the shape due to the presence of an asymmetric carbon.

• Hydroxyl: A chemical group consisting of an oxygen atom joined to a Hydrogen atom. Molecules processing this group are soluble in H2O and are called alcohols. -OH

• Carboxyl: A chemical group present in aldehydes and ketones and consist of a carbon atom double bonded to an oxygen atom C=O

• Carbonyl: A chemical group present in organic acids and consist of a single carbon atom double-bonded to an oxygen atom and also bonded to a hydroxyl group.

• Amino: A chemical group consisting of a nitrogen atom beded to two hydrogen atoms; can act as a base in a solution, accepting a hydrogen ion and acquiring a charge of 1+.

• Phosphate: A chemical group consisting of a phosphorus atom bonded to four oxygen atoms; important energy transfer.

• Methyl: A chemical group consisting of a carbon bonded to three Hydrogen atoms. The methyl group may be attached to a carbon or to a different atom.

• Macromolecule: a giant molecule formed by the joining of smaller molecules, usually by a dehydraion reactions. Polysaccharides, proteins, and nucleic acids are macromolecules.

• Monomers: The subunit that serves as the building blocks of polymers.

• Polymers: a long molecule consisting of many similar or identical monomers linked together by covalent bonds

• Dehydration Synthesis: A chemical reaction in which two molecules become covalently bonded to each other with the removal of an H2O molecule.

• Hydrolysis: A chemical reaction that breaks bonds between two molecules by addition of an H2O molecule; functions is disassembly of polymers to monomers.

• Carbohydrate: A sugar (monosaccharide) or one of its dimer (disaccharide) or polymers (polysaccharides)

• Monosaccharide: the monomer form of carbohydrates, for polysaccharide and disaccharides. a.k.a simple sugars and have molecular formulas of some multiple of CH2O.

• Polysaccharides: A polymer of many monosaccharide, formed by dehydration reactions

• Glycosidic linkage: A covalent bond formed between two monosaccharides by a dehydration synthesis.

• Cellulose: A structural polysaccharide of plant cell walls, consisting of glucose monomers joined by β glycosidic linkage.

• Lipid: Any group of large biological molecules, including fats, phospholipids, and steroid, that mix poorly, if at all, with H2O.

• Fatty Acids: A carboxylic acid with a long carbon chain, 3 Fatty acids with 1 glycerol form a fat molecule, commonly known as a triacylglycerol.

• Saturated fatty acids: A fatty acid with all single carbon bonds, generally sold at room temperature and aren’t healthy for you.

• Unsaturated fatty acids: A fatty acid that has at least one double bond, a “kink” in its carbon chain. they are usually solid at room temperature and healthier than saturated fatty acids.

• Phospholipids: A lipid that has 2 fatty acids and 1 glycerol and phosphate group. The chain acts as non polar, hydrophilic tails, and the rest act as hydrophilic, polar heads. They function as membranes.

• Steroids: A type of lipid characterized by a carbon skeleton that consists of 4 fused rings, with various chemical groups attached.

• Proteins: a biologically functional molecule consisting of one or more polypeptides folded and coiled into a specific 3-D structure.

• Polypeptide: The polymer of many amino acids (proteins) linked together by peptide bonds.

• Amino Acids: An organic molecule possessing both a carboxyl group and amino group. Amino Acids act as the monomers of polypeptides.

• Peptide bonds: The covalent bond between the carboxyl group on one amino acid and the amino group on another, formed by dehydration synthesis.

• Primary structure: The level of the protein structure that refers to the specific linear sequence of amino acids.

• Secondary structure: regions of repetitive coiling or folding of the polypeptide backbone of a protein, due to hydrogen bonding between the backbone (not side chains).

• Tertiary Structure: The overall, 3-D shape of a protein that results from amino acid side chains (which includes:hydrophobic interactions, ionic bonds, H-bonds, and disulfide bridges).

• Quaternary structure: THe particular shape of a complex, aggregated protein, defined by the characteristic 3-D arrangement of its subunits, each a polypeptide.

• Denatured: A process in which a protein loses its native shape due to the disruption of weak chemical bonds and interactions, thereby biologically inactive.

• Chaperonin: A protein complex that assists in the proper folding of other proteins.

• Nucleic Acids: A polymer (polynucleotide) consisting of many nucleotide monomers; serves as a blueprint for proteins, and through the actions of proteins, for all cellular activity. the two types are DNA and RNA.

• Nucleotide: the building block of a nucleic acid, consisting of a 5-carbon sugar, a phosphate group, and a covalently bonded nitrogenous base.

• Enzyme: A macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction.

• Activation Energy: The initial investment of energy for starting a reaction-the energy required to control the reaction molecules so the bonds can break free. Often supplied in thermal form (bent) so molecules collide more forcefully and often.

• Substrate: The reactant to which an enzyme acts on.

• Active site: The restricted region of an enzyme molecule in which the substrate actually binds to and catalysis occurs.

• Exergonic: A spontaneous chemical reaction, in which there is a net release of free energy.

• Endergonic: A nonspontaneous reaction that absorbs free energy from its surroundings to obtain a higher energy state.

• Catalytic Cycle: A multi step reaction mechanism that involves a catalyst.

• Coenzymes: An organic cofactor. They perform crucial chemical functions in catalysis (ex. vitamins)

• Cofactor: Nonprotein helpers for catalytic activity, which can be bound tightly to an enzyme (or not). They are inorganic (ex. Zn, Fe, Cu).

• Competitive inhibition: A process in which a substance reduces the activity of an enzyme by entering the active site in place of the substrate, whose structure it mimics.

• Noncompetitive inhibition: A process in which a substance reduces the activity of an enzyme by binding to a location remote from the active site, changing  the enzyme’s shape so that the active site no longer effectively catalyzes the conversion of substrate to product.

• Allosteric enzymes: Enzymes where its function is affected by the binding of a regulatory molecule at a separate site. It can result in inhibition or stimulation of enzyme’s activity (Multi-subunits).

• Feedback inhibition: A method metabolic control in which the end product of a metabolic pathway acts as inhibitor of an enzyme within the pathway.

• Cooperativity: A kind of allosteric regulation where a shape change in one subunit of a protein is caused by substrate binding. It is then transmitted to all the other subunits, facilitating binding of additional substrate molecules to those subunits.