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CHM 554 Test 2 Terms
Ch 4-7: Structure, Proteins, & Enzymes
| Term | Definition |
|---|---|
| Conformation | A spatial arrangement of substituent groups that are free to assume different positions in space, without breaking any bonds, because of the freedom of bond rotation. |
| Native Conformation | The biologically active conformation of a macromolecule. |
| Solvation Layer | The solvation layer (or shell) describes the structured organization of a solvent (e.g. water) around a solute (e.g. a polypeptide or protein). |
| Secondary Structure | The local spatial arrangement of the main-chain atoms in a segment of a polymer (polypeptide or polynucleotide) chain. |
| Alpha Helix | A helical conformation of a polypeptide chain, usually right-handed, with maximal intrachain hydrogen bonding; one of the most common secondary structures in proteins. |
| Beta Conformation | An extended, zigzag arrangement of a polypeptide chain; a common secondary structure in proteins. |
| Beta Sheet | The side-by-side, hydrogen-bonded arrangement of polypeptide chains in the extended β conformation. |
| Beta Turn | A type of protein secondary structure consisting of four amino acid residues arranged in a tight turn so that the polypeptide turns back on itself. |
| Ramachandran Plot | A two-dimensional graph that shows the distribution of the phi (φ) and psi (ψ) torsion angles of a protein's backbone. |
| Circular Dichroism (CD) Spectroscopy | A method used to characterize the degree of folding in a protein, based on differences in the absorption of right-handed versus left-handed circularly polarized light. |
| Tertiary Structure | The three-dimensional conformation of a polymer in its native, folded state. |
| Quaternary Structure | The three-dimensional structure of a multisubunit protein, particularly the manner in which the subunits fit together. |
| Fibrous Proteins | Insoluble proteins that serve a protective or structural role; contain polypeptide chains that generally share a common secondary structure. |
| Globular Proteins | A protein that folds into a roughly spherical shape, making it water-soluble and allowing it to perform a wide range of functions within the cell, often including catalysis, transport, and regulation |
| Intrinsically Disordered Proteins | Proteins, or segments of proteins, that lack a definable three-dimensional structure in solution. In some cases folding can be dictated by binding partners. |
| Alpha Keratin | A polypeptide chain, typically high in alanine, leucine, arginine, and cysteine, that forms a right-handed α-helix |
| Collagen | A protein molecules made up of amino acids. It provides structural support to the extracellular space of connective tissues. |
| Fibrin | A protein factor that forms the cross-linked fibers in blood clots |
| Motif | Any distinct folding pattern for elements of secondary structure, observed in one or more proteins. A motif can be simple or complex, and can represent all or just a small part of a polypeptide chain. Also called a fold or supersecondary structure. |
| Domain | A distinct structural unit of a polypeptide; domains may have separate functions and may fold as independent, compact units. |
| Topology Diagrams | A structural representation in which the connections between elements of secondary structure are depicted in two dimensions. |
| Protein Family | A group of proteins that share a common evolutionary origin, reflected by their related functions and similarities in sequence or structure |
| Multimer | A protein molecule made up of two or more polypeptide chains, each referred to as a mono |
| Oligomer | A short polymer, usually of amino acids, sugars, or nucleotides; the definition of “short” is somewhat arbitrary, but usually fewer than 50 subunits. |
| Protomer | A DNA sequence at which RNA polymerase may bind, leading to initiation of transcription. |
| Proteostasis | The maintenance of a cellular steady-state collection of proteins that are required for cell functions under a given set of conditions. |
| Denaturation | Partial or complete unfolding of the specific native conformation of a polypeptide chain, protein, or nucleic acid such that the function of the molecule is lost. |
| Renaturation | The refolding of an unfolded (denatured) globular protein so as to restore its native structure and function. |
| Chaperone | Any of several classes of proteins or protein complexes that catalyze the accurate folding of proteins in all cells. |
| HSP70 | A molecular chaperone that helps maintain protein homeostasis in cells by regulating protein folding, degradation, and synthesis |
| Chaperonin | One of two major classes of chaperones in virtually all organisms; a complex of proteins that functions in protein folding: GroES/GroEL in bacteria; Hsp60 in eukaryotes. |
| Protein Disulfide Isomerase (PDI) | An enzyme that helps proteins fold by catalyzing the formation, rearrangement, and reduction of disulfide bonds |
| Peptide Prolyl Cis-Trans Isomerase (PPI) | Enzymes that catalyze the isomerization of peptide bonds, which helps proteins fold and re-fold |
| Amyloidoses | A variety of progressive diseases characterized by abnormal deposits of misfolded proteins in one or more organs or tissues. |
| Prion | A protein that can cause normal proteins in the brain to fold abnormally, leading to fatal neurodegenerative brain diseases |
| X-ray Crystallography | The analysis of x-ray diffraction patterns of a crystalline compound, used to determine the molecule’s three-dimensional structure. |
| Nuclear Magnetic Response (NMR) Spectroscopy | A technique that utilizes certain quantum mechanical properties of atomic nuclei to study the structure and dynamics of the molecules of which the nuclei are a part |
| Cryo-electron Microscopy (cryo-EM) | A technique for determining the structure of proteins; molecules are quick-frozen on a grid in random orientations and visualized by EM. Images of individual molecules are computationally aligned, yielding a three-dimensional map which can be modeled. |
| Ligand | A small molecule that binds specifically to a larger one; for example, a hormone is the ligand for its specific protein receptor. |
| Binding site | The crevice or pocket on a protein in which a ligand binds. |
| Induced Fit | An enzyme conformation change in response to substrate binding that renders the enzyme catalytically active; also denotes a conformation change in any macromolecule in response to ligand binding. |
| Hemoglobin | A heme protein in erythrocytes; functions in oxygen transport. |
| Heme | The iron-porphyrin prosthetic group of heme proteins. |
| Porphyrin | A complex nitrogenous compound containing four substituted pyrroles covalently joined in a ring; often complexed with a central metal atom. |
| Globin | a colorless protein obtained by removing heme from hemoglobin; the oxygen carrying compound in red blood cells |
| Globin Fold | A bundle of alpha-helices connected by rather short loops and arranged so that sequentially adjacent helices are not adjacent to each other in the 3D structure |
| Equilibrium Constant (Keq) | A constant, characteristic for each chemical reaction, that relates the specific concentrations of all reactants and products at equilibrium at a given temperature and pressure |
| Association Constant, Ka | The dissociation constant (Ka) of an acid, describing its dissociation into its conjugate base and a proton. |
| Dissociation Constant, Kd | An equilibrium constant for the dissociation of a complex of two or more biomolecules into its components; for example, dissociation of a substrate from an enzyme. |
| Allosteric Protein | The specific site on the surface of an allosteric protein molecule to which the modulator or effector molecule binds. |
| Modulator | A metabolite that, when bound to the allosteric site of an enzyme, alters its kinetic characteristics. |
| Homotropic | Describes an allosteric modulator that is identical to the normal ligand. |
| Heterotrophic | Describes an allosteric modulator that is distinct from the normal ligand |
| Hill Reaction | The evolution of oxygen and photoreduction of an artificial electron acceptor by a chloroplast preparation in the absence of carbon dioxide. |
| Hill Coefficient | A measure of cooperative interaction between protein subunits. |
| Bohr Effect | A decrease in the amount of oxygen associated with hemoglobin and other respiratory compounds in response to a lowered blood pH resulting from an increased concentration of carbon dioxide in the blood. |
| Immune response | The capacity of a vertebrate to generate antibodies to an antigen, a macromolecule foreign to the organism. |
| Antibody | A defense protein synthesized by the immune system of vertebrates and circulated in the blood. |
| Immunoglobulin (Ig) | An antibody protein generated against, and capable of binding specifically to, an antigen. |
| Lymphocytes | A subclass of leukocytes involved in the immune response. |
| B Lymphocytes (B Cell) | One of a class of blood cells (lymphocytes), responsible for the production of circulating antibodies. |
| T Lymphocytes (T Cell) | One of a class of blood cells (lymphocytes) of thymic origin, involved in cell-mediated immune reactions. |
| Antigen | A molecule capable of eliciting the synthesis of a specific antibody in vertebrates. |
| Epitome | Consisting all known antigen/antibody complex structures, a detailed description of the residues that are involved in the interactions, and their sequence/structure environments. |
| Hapten | A small molecule which, when combined with a larger carrier such as a protein, can elicit the production of antibodies which bind specifically to it (in the free or combined state). |
| Immunoglobulin Fold | a protein domain structure that is made up of two antiparallel beta-sheets in a Greek key topology. |
| Polyclonal Antibodies | A heterogeneous pool of antibodies produced in an animal by different B lymphocytes in response to an antigen. Different antibodies in the pool recognize different parts of the antigen. |
| Monoclonal Antibodies | Antibodies produced by a cloned hybridoma cell, which are therefore identical and directed against the same epitope of the antigen. |
| Immunoblotting (Western Blotting) | A technique using antibodies to detect the presence of a protein in a biological sample after the proteins have been separated by gel electrophoresis, transferred to a membrane, and immobilized; also called Western blotting. |
| Myosin | A contractile protein; the major component of the thick filaments of muscle and other actin-myosin systems. |
| Actin | A protein that makes up the thin filaments of muscle; also an important component of the cytoskeleton of many eukaryotic cells. |
| Myofibril | A unit of thick and thin filaments of muscle fibers. |
| Sacromere | A functional and structural unit of the muscle contractile system. |
| Enzyme | A biomolecule, either protein or RNA, that catalyzes a specific chemical reaction. It does not affect the equilibrium of the catalyzed reaction; it enhances the rate of the reaction by providing a reaction path with a lower activation energy. |
| Cofactor | The energy derived from noncovalent interactions between enzyme and substrate or receptor and ligand. |
| Coenzyme | An organic cofactor required for the action of certain enzymes; often is synthesized from a vitamin. |
| Prosthetic group | A metal ion or organic compound (other than an amino acid) covalently bound to a protein and essential to its activity. |
| Holoenzyme | A catalytically active enzyme, including all necessary subunits, prosthetic groups, and cofactors. |
| Apoenzyme | The protein portion of an enzyme, exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for catalytic activity. |
| Apoprotein | The protein portion of a protein, exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for activity. |
| Active Site | The region of an enzyme surface that binds the substrate molecule and catalytically transforms it; also known as the catalytic site. |
| Substrate | The specific compound acted upon by an enzyme. |
| Ground State | The normal, stable form of an atom or molecule, as distinct from the excited state. |
| Standard Free-Energy Change, Delta G | The free-energy change for a reaction occurring under a set of standard conditions: temperature, 298 K; pressure, 1 atm (101.3 kPa); and all solutes at 1 m concentration. |
| Biochemical Standard Free-Energy Change, Delta G" | The free-energy change for a reaction occurring under a set of standard conditions: temperature, 298 K; pressure, 1 atm (101.3 kPa); all solutes at 1 m concentration; at pH 7.0 in 55.5 m water. Also called standard transformed free-energy change. |
| Transition State | An activated form of a molecule in which the molecule has undergone a partial chemical reaction; the highest point on the reaction coordinate. |
| Activation Energy, Delta G+ | The amount of energy (in joules) required to convert all the molecules in 1 mol of a reacting substance from the ground state to the transition state. |
| Reaction Intermediate | Any chemical species in a reaction pathway that has a finite chemical lifetime |
| Rate-limiting Step | Generally, the step in an enzymatic reaction with the greatest activation energy or with the transition state of highest free energy. (2) The slowest step in a metabolic pathway. |
| Rate Constant | The proportionality constant that relates the velocity of a chemical reaction to the concentration(s) of the reactant(s). |
| Binding Energy, Delta Gb | The energy derived from noncovalent interactions between enzyme and substrate or receptor and ligand. |
| Specificity | The ability of an enzyme or receptor to discriminate among competing substrates or ligands. |
| Desolvation | In aqueous solution, the release of bound water surrounding a solute. |
| Specific Acid-Base Catalysis | Acid or base catalysis involving the constituents of water (hydroxide or hydronium ions). |
| General Acid-Base Catalysis | The inactive precursor protein of fibrin. |
| Covalent Catalysis | A mechanism that enzymes use to speed up reactions by forming a temporary covalent bond with a substrate |
| Pre-Steady State | In an enzyme-catalyzed reaction, the period preceding establishment of the steady state, often encompassing just the first enzymatic turnover |
| Steady State | A nonequilibrium state of a system through which matter is flowing and in which all components remain at a constant concentration. |
| V0 | Initial velocity, the initial rate of a reaction. |
| Vmax | The maximum velocity of an enzymatic reaction when the binding site is saturated with substrate |
| Michaelis-Menten Equation | The equation describing the hyperbolic dependence of the initial reaction velocity, V0, on substrate concentration, [S], in many enzyme-catalyzed reactions |
| Steady-State Assumption | The substrate concentration remains approximately constant during an initial transient, and the enzyme-substrate complex concentration builds up. |
| Michaelis Constant (Km) | The substrate concentration at which an enzyme-catalyzed reaction proceeds at one-half its maximum velocity. |
| Lineweaver-Burk Equation | An algebraic transform of the Michaelis-Menten equation, allowing determination of Vmax and Km by extrapolation of [S] to infinity. |
| Michaelis-Menten Kinetics | A kinetic pattern in which the initial rate of an enzyme-catalyzed reaction exhibits a hyperbolic dependence on substrate concentration. |
| Kcat | The turnover number and this describes how many substrate molecules are transformed into products per unit time by a single enzyme |
| Turnover Number | The number of times an enzyme molecule transforms a substrate molecule per unit time, under conditions giving maximal activity at saturating substrate concentrations. |
| Reversable Inhibition | Inhibition by a molecule that binds reversibly to the enzyme, such that the enzyme activity returns when the inhibitor is no longer present. |
| Competitive Inibition | A type of enzyme inhibition reversed by increasing the substrate concentration; a competitive inhibitor generally competes with the normal substrate or ligand for a protein’s binding site. |
| Irreversible Inhibitor | A substance that permanently blocks the action of an enzyme |
| Uncompetitive Inhibition | The reversible inhibition pattern resulting when an inhibitor molecule can bind to the enzyme-substrate complex but not to the free enzyme. |
| Suicide Inactivator | A relatively inert molecule that is transformed by an enzyme, at its active site, into a reactive substance that irreversibly inactivates the enzyme. |
| Transition State Analog | A stable molecule that resembles the transition state of a particular reaction and therefore binds the enzyme that catalyzes the reaction more tightly than does the substrate in the enzyme-substrate complex. |
| Serine Poteases | One of four major classes of proteases, having a reaction mechanism in which an active-site Ser residue acts as a covalent catalyst. |
| Retrovirus | An RNA virus containing a reverse transcriptase. |
| Regulatory Enzyme | An enzyme with a regulatory function, through its capacity to undergo a change in catalytic activity by allosteric mechanisms or by covalent modification. |
| Allosteric Enzyme | A regulatory enzyme with catalytic activity modulated by the noncovalent binding of a specific metabolite at a site other than the active site. |
| Allosteric Modulator | A substance that binds to a receptor at a site other than the orthosteric site, changing the receptor's response to stimuli |
| Regulatory Protein | Protein whose function is to regulate the activity of another protein or enzyme by binding to it. |
| Homotropic | Describes an allosteric modulator that is identical to the normal ligand. |
| Heterotopic | Describes an allosteric modulator that is distinct from the normal ligand. |
| Protein Kinases | Enzymes that transfer the terminal phosphoryl group of ATP or another nucleoside triphosphate to a Ser, Thr, Tyr, Asp, or His side chain in a target protein, thereby regulating the activity or other properties of that protein |
| Protein Phosphatases | Enzymes that hydrolyze a phosphate ester or anhydride bond on a protein, releasing inorganic phosphate, P. Also called phosphoprotein phosphatases. |
| Zygomen | An inactive precursor of an enzyme; for example, pepsinogen, the precursor of pepsin. |
| Platelets | Small, enucleated cells that initiate blood clotting; they arise from bone marrow cells called megakaryocytes. Also known as thrombocytes. |
| FIbrinogen | The inactive precursor protein of fibrin. |
| Thromboxane | Any of a class of eicosanoid lipids with a six-membered ether-containing ring; involved in platelet aggregation during blood clotting. |
| Intrinsic Pathway | A response to spontaneous, internal damage of the vascular endothelium |
| Extrinsic Pathway | Activated by external trauma, such as when tissue damage exposes blood to tissue factor, the first pathway to be activated |
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