Knopps notes definitions
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| configuration | the arrangement of atoms around a chiral center
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| conformation | the arrangement of atoms in space
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| isomers | two different compounds which have the same chemical composition but are physically distinct and seperable
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| anomers | a chiral center which is not initially present in a molecule and which is created by intramolecular bonding (newly created center)
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| chemical isomers | two different molecules which have the same chemical composition
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| enantiomer | two stereoisomers in which all chiral centers are switched
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| epimer | two stereoisomers which differ in only one chiral center
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| diastereomer | stereoisomers which contain more than one chiral center but are not mirror images of each other (all centers switched)
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| buffer | a weak acid or base which is present in an acid-base pair which resists changes in pH when another acid or base is added
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| pH | a negative of the logarithm of the hydronium ion concentration = -log[H+]
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| pKa | the negative of the logarithm of the acid dissociation constant
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| chiral atom | a single atom or group of atoms when the attached groups are interchanged the two molecules are not superimposable
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| residue | the monomeric component of a molecule minus the atoms which were removed to make the chemical linkage
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| side chain | "R-group" the atoms of an amino acid which were attached to the alpha carbon of an amino acid and which are not the carboxyl group, amino group or hydrogen
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| zwitter ion | a molecule which contains both positive and negative charges, but its electrically neutral
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| peptide bond | the covalent secondary amide linkage that joins the carbonyl group of one amino acid residue to the amino nitrogen of another in peptides and proteins
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| alpha helix | a type of secondary structure commonly found in proteins which is characterized by 3.6 residues per turn and a phi angle of 57 degrees and a psi angle of 47 degrees
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| beta sheet | a type of secondary structure commonly found in proteins which is characterized by 2 linear strands of the polypeptide backbone lying side by side and connected w/hydrogen bonds
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| chromatography | a technique of separation based on the movement of charged molecules in the prescence of an electric field
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| primary structure | the linear sequence of amino acids in a polypeptide or protein
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| proteins | polymer of alpha-amino acids linked by a peptide amide bond
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| quaternary structure | the association of multiple tertiary structures to form a complex
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| secondary structure | the regular or periodic folding of the primary structure
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| tertiary structure | the irregular or non-repeating folding of the primary and secondary structures
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| allosteric site | the location on an enzyme which is separate from the substrate binding site(s) and catalytic site(s) to which molecules bind and alter the activity of the enzyme
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| cooperativity | occurs when the change in one parameter influences the change in similar parameters
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| active site | the portion of an enzyme which is responsible for enzyme activity
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| catalytic site | the location on an enzyme where the substrates react with each other and/or portions of the enzyme
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| dalton | a unit of molecular weight where one mole of hydrogen atoms equals one dalton
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| enzymology | the study of enzymes and their properties by measuring enzyme activty (kinetics)
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| initial velocity | the rate of change in the concentration of a substrate or product per unit time at the beginning of a reaction where little product is formed and back reaction is negligible (t=0)
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| isozymes | one of two or more enzymes which catalyze the same biochemical reaction and can be separated by some physical method; eg: electrophoresis or chromotography
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| Ki | The equilibrium constant for the dissociation of an inhibitor from an enzyme inhibitor complex
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| Km | the concentration of a substrate which yields half of the maximum velocity for an enzyme catalyzed reaction, or is the concentration when the initial velocity is equal to half of the maximum velocity
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| specificity constant | kcat/Km - the ratio of kcat to Km
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| initial velocity | the rate of change in the concentration of a substrate or product per unit time at the beginning of a reaction where little product is formed and back reaction is negligible (t=0)
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| substrate binding site | the location on an enzyme where the substrate binds to the enzyme
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| Vmax | the rate of the enzyme catalyzed reaction with saturating concentrations of substrates and is the product of the catalytic rate constant or turnover number and the total enzyme concentration
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| Zymogens | an inactive precursor of an enzyme
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| intermediates | a quasi stable step between a substrate and a product
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| transition state analog | a stable molecule which resembles a proposed transition state (normally an effective inhibitor)
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| transition state | the fleeting and unstable stage of a substrate as it is converted to a product (distorted bond angles and lengths and cannot be detected or isolated)
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| apoenzyme | the protein component for an enzyme which requires a cofactor for activity
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| coenzyme | an organic cofactor
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| cofactor | a non-protein component which is required for enzyme activity
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| cosubstrate | coenzyme which is loosely bound to an enzyme and is consumed during the reaction
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| holoenzyme | an apoenzyme and its cofactor
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| metalloenzyme | an enzyme which contains one or more tightly bound metal ion(s) which are essential for activity
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| prosthetic group | a coenzyme which is tightly bound to an enzyme and which is not consumed by the reaction
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| simple enzyme | an enzyme which does not require a cofactor for activity
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| carbohydrate | a polyhydroxyl ketone or a polyhydroxyl aldehyde and its derivatives
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| biological membrane | lipid bilayer containing protein which completely surrounds and isoloates biomolecules
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| ionophore | a biomolecule which facilitates the movement of ions across a biological membrane
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| lipid | a biomolecule which is insoluble or slightly soluble in water and are usually extractable by organic (nonpolar) solvents
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| recepter | transmembrane protein component of a signal transduction pathway to which an external signal molecule will bind to cause a conformational change and subsequently activate a transducer molecule
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| transducer | a protein component of a single transduction pathway which is activated by a receptor and in turn alters the activity of an effector enzyme
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| effector enzyme | an enzyme component of a signal transduction pathway which is bound to a membrane, activated by a transducer and produces a second messenger
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| second messenger | a molecule which is part of a signal transduction pathway and which is produced as a consequence of the binding of an extracellular signal
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| nucleic acid | biopolymers consisting of nitrogenous bases which are linked to ribose or deoxyribose linked by phosphodiester bonds
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| mRNA | messenger RNA-a class of RNA molecules which carries a copy of the sequence of nucleic acid bases from the DNA to the ribosomes where these sequences are translated into a series of linked amino acids to form proteins
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| tRNA | transfer RNA-a series of RNA molecules composed of 75-95 nucleotides which are charged with an amino acid by the appropriate tRNA synthetase enzyme and which carry that activated amino acid to the ribosome
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| snRNA | small nuclear RNA - a series of RNA molecules ranging in size from about 100-200 nucleotides
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| rRNA | ribosomal RNA - this series of RNA molecules combine with proteins to form ribosomes
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| nucleoside | a purine or pyrimidine n-glycoside of ribose or deoxyribose (sugars)
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| nucleotide | the phosphate ester of a nucleoside consisting of a nitrogenous base linked to a pentose phosphate (phosphate)
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| Tm | the temperature at which a particular molecular transition is 50% complete
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| EMF | electron motive force-a measure of the difference between the reduction potentials of the reactions on the two sides of an electrochemical cell
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| enthalpy | the measure of the amount of heat in a system under constant pressure
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| entropy | the measure of the disorder of a system
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| gibbs free energy | the amount of energy available to do chemical work
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| energy charge | see formula pg 97 of workbook
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| macromolecules | large molecule (>10,000 daltons) composed of polymers of similar or identical parts
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