Glossary of Biology and Chemistry Terms PDF

Module 1 Prokaryote: A unicellular organism with a single chromosome, no nuclear envelope and no membrane-bound organelles. Eukaryote: A unicellular or multicellular organism with celss having a membrane-bound nucleus, multiple chromosomes and internal organelles. Protein: A macromolecule compose...

Module 1 Prokaryote: A unicellular organism with a single chromosome, no nuclear envelope and no membrane-bound organelles. Eukaryote: A unicellular or multicellular organism with celss having a membrane-bound nucleus, multiple chromosomes and internal organelles. Protein: A macromolecule composed of one or more polypeptide chains, each with a characteristic sequence of amino acids joined by peptide bonds. Nucleic Acids: Biologically occurring polynucleotides in which the nucleotide residues are linked in a specific manner by phosphodiester bonds; DNA and RNA. Polysaccharide: A linear or branched polymer of monosaccharide units linked by glycosidic bonds. In vitro: “in glass”, that is, in the test tube. In vivo: ‘in life”, that is, in the living cell or organism. Conformation: The spatial arrange of substituent groups that are free to assume different positions in space, without breaking any bonds, because of the freedom of bond rotation. Configuration: The spatial arrangement of an organic molecules that is conferred by the presence of either (1) double bonds, about which there is no freedom of rotation, or (2) chiral centers, around which substituent groups are arranged in a specific sequence. Configurational isomers cannot be interconverted without breaking one or more covalent bonds. Geometric Isomers: Isomers related by rotation about a double bond: also called cis and trans isomers. Chiral Center: An atom with substituents arranged so that the molecule is not superimposable on its mirror image. Chiral Compound: A compound that contains an asymmetric center (chiral atom or chiral center) and that can occur in two non-superimposable mirror-image forms (enantiomers). Stereoisomers: Compounds that have the same composition and the same order of atomic connections but different molecular arrangements. Thermodynamics: A branch of science concerned with heat and its ​ relation to energy and work. First Law of Thermodynamics: The law stating that in all processes, the total energy of the universe remains constant. Second Law of Thermodynamics: The law stating that in any chemical or physical process, the entropy of the universe tends to increase. Enthalpy (H): The heat content of a system. Entropy (S): The extent of randomness or disorder in a system. Enthalpy Change (ΔH): For a reaction, is approximately equal to the difference between the energy used to break bonds and the energy gained by the formation of new bonds. Endergonic: A non-spontaneous process (DG > 0), needs input of free energy to proceed. Exergonic Reactions: A chemical reactions that proceeds with the release of free energy (that is, for which ΔG is negative). Exothermic Reaction: A chemical reaction that release heat (that is, for which ΔH is negative). Endothermic Reaction: A chemical reaction that takes up heat (that is, for which ΔH is positive). Genotype: The genetic constitution of an organism, as distinct from its physical characteristics, or phenotype. Phenotype: The observable characteristics of an organism. Module 2 pH: The negative logarithm of the hydrogen ion concentration of an aqueous solution. pKa: The negative logarithm of an equilibrium constant. Buffer: A solution of a weak acid and its conjugate base that resists changes in pH with the addition of acid or base. Buffering region: One pH unit on either side of the pKa. Henderson Hasselbalch: An equation relating the pH, the pKa and the ration of the concentrations of the proton accepts (A-) and proton donor (HA) species in a solution. Amphipathic: A molecule containing both polar and non-polar portions. Amphoteric: A molecule capable of donating and accepting protons, thus able to serve as an acid or a base. Ionic Interaction: An interaction between electrically charged groups; attractive between groups of opposite charge, repulsive between groups of the same charge. Hydrogen Bond: A weak electrostatic attraction between one electronegative atom (such as oxygen or nitrogen) and a hydrogen atom covalently linked to a second electronegative atom. Intramolecular: A process or characteristic limited within ​ the structure of a single molecule. Intermolecular: A process or characteristic limited within the structures of different molecules. For example, forces of attraction or repulsion between neighboring, different entities (atoms, molecules or ions). Module 3 Amino Acid: The smallest building block of proteins. There are 20 standard amino acids. Disulfide Bond: A covalent linkage formed between the sulfhydryl groups of two cysteine residues. Amphoteric: Capable of accepting and donating protons, able to serve as both an acid and a base. Buffering Region: The region extending one pH unit above and one pH unit below the pKa. Within this region there is no change in the pH of a solution with the addition of acid or base. Diprotic: A molecule with two functional groups that can accept/donate protons; corresponding to two buffering regions on a titration curve. Triprotic: A molecule with three functional groups that can accept/donate protons; corresponding to three buffering regions on a titration curve. Isoelectric Point: The pH at which the molecule has a net charge of zero. Module 4 Peptide Bond: A covalently linkage formed between the carboxyl group of one amino acid to the amino group of a second amino acid. The primary linkage of all peptide, polypeptide and protein structures. Residue: A single unit within a polymer; for example, an amino acid within a polypeptide chain. Native Conformation: The biologically active conformation of a biomolecule. Hydrogen Bond: A weak electrostatic interaction between an electronegative atom (such as oxygen or nitrogen) and a hydrogen covalently linked to a second electronegative atom. Ionic Interaction: Forces of attraction or repulsion between charged groups of opposite, or same, charge respectively. van der Waals Interaction: The attractive or repulsive forces between molecules (or between parts of the same molecule) due to induced or transient diploes. Hydrophobic Interaction: The association of non-polar groups with each other in aqueous system. A primary driving force of biomolecular structures. Denaturation: Partial or complete unfolding of the native conformation of a protein or nucleic acid. Primary Structure: The linear sequence of amino acids with a peptide, polypeptide or protein. Secondary Structure: Localized folding within a polypeptide chain to the generation of regions of defined structure. Examples include alpha helicies and beta sheets. Tertiary Structure: The pattern of folding of a single polypeptide in three dimensional space. Quaternary Structure: The folding and association of proteins consisting of multiple polypeptide chains. Phi Angle: The torsion angle within a polypeptide chain linking the alpha carbon to the amide nitrogen. There is theoretical freedom of rotation about the phi angle from -180 to +180 degrees. Psi Angle: The torsion angle within a polypeptide chain linking the alpha carbon to the carbonyl carbon. There is theoretical freedom of rotation about the phi angle from -180 to +180 degrees. Ramachandran Plot: A graph representing all the permutations of phi and psi on which specific values of phi and psi can be plotted for a polypeptide. Reveals common structural motifs such as elements of secondary structure. Alpha Helix: A helical conformation of a polypeptide chain, usually right-handed, with maximal intrachain hydrogen-bonding. Beta Sheet: An extended arrangement of a polypeptide chain. Beta sheets are made up of beta strands which may be either parallel or antiparallel. Helix Dipole: The uneven distribution of charge which forms over the length of an alpha helix due to the differential electronegativities of the amide and carobonyl groups of the peptide bond. The amino terminus of an alpha helix carries a partial positive charge while the carboxy terminus carries a partial negative charge. Pseudo-Seven Repeat: A repeating pattern found in the primary structure of keratin in which the first and four positions of the seven residue repeat tend to be occupied by hydrophobic residues. Amphipathic: Containing both polar and non-polar groups. Supercoil (Coiled-Coil): A protein structure motif marked by α-helical regions that self-associate to form stable, rod-like oligomeric proteins; commonly found in fibrous proteins, such as keratin and collagen. Scurvy: A disease associated with Vitamin C deficiency. Pathology results from the destabilization of collagen due to an inability of the body to introduce stabilizing post-translation modifications of collagen in the absence of Vitamin C. Conformation: The spatial arrangement of substituent groups that are free to assume different positions in three dimensional space, without breaking any bonds, because of the freedom of bond rotation. Configuration: The spatial arrangement of a molecule that is conferred by the presence of either double bonds or chiral centers around which substituent groups are arranged in a specific manner. Configurational isomers cannot be interconverted without breaking covalent bonds. Disulfide Bond: A covalent linkage formed between the sulfhydryl groups of two cysteine residues. Module 5 Ligand: A molecule that is bound reversibly by a protein. Binding Site: The crevice or pocket on a protein to which a ligand binds. Induced Fit: A change in the conformation of a protein in response to ligand binding. P50: The concentration of oxygen required to half saturate myoglobin or hemoglobin. Allosteric Protein: A protein (enzyme), generally with multiple subunits, with multiple ligand-binding sites, such that ligand binding at one site affects ligand binding at another. Allosteric Effector (Modulator): bind to allosteric proteins at a site distinct from the functional binding site. Homotropic Allosteric Effector: An allosteric modulator that is the same as the normal ligand of the protein (enzyme). Heterotropic Allosteric Effector: An allosteric modulator that is the different from the normal ligand of the protein (enzyme). Hemocyanin: An oxygen transport protein of select invertebrates that utilizes two copper atoms coordinated between histidines to enable reversible bidning of oxygen. Bohr Effect: Describes the pH dependence of hemoglobin’s affinity for oxygen; decreased affinity at decreased pH. Sickle Cell Anemia: A human disease characterized by defective hemoglobin molecules. Recognized by the sickling of red blood cells when exposed to low oxygen levels.