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Biochemistry
Knopps notes definitions
| Question | Answer |
|---|---|
| configuration | the arrangement of atoms around a chiral center |
| conformation | the arrangement of atoms in space |
| isomers | two different compounds which have the same chemical composition but are physically distinct and seperable |
| anomers | a chiral center which is not initially present in a molecule and which is created by intramolecular bonding (newly created center) |
| chemical isomers | two different molecules which have the same chemical composition |
| enantiomer | two stereoisomers in which all chiral centers are switched |
| epimer | two stereoisomers which differ in only one chiral center |
| diastereomer | stereoisomers which contain more than one chiral center but are not mirror images of each other (all centers switched) |
| 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 |
| pH | a negative of the logarithm of the hydronium ion concentration = -log[H+] |
| pKa | the negative of the logarithm of the acid dissociation constant |
| chiral atom | a single atom or group of atoms when the attached groups are interchanged the two molecules are not superimposable |
| residue | the monomeric component of a molecule minus the atoms which were removed to make the chemical linkage |
| 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 |
| zwitter ion | a molecule which contains both positive and negative charges, but its electrically neutral |
| 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 |
| 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 |
| 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 |
| chromatography | a technique of separation based on the movement of charged molecules in the prescence of an electric field |
| primary structure | the linear sequence of amino acids in a polypeptide or protein |
| proteins | polymer of alpha-amino acids linked by a peptide amide bond |
| quaternary structure | the association of multiple tertiary structures to form a complex |
| secondary structure | the regular or periodic folding of the primary structure |
| tertiary structure | the irregular or non-repeating folding of the primary and secondary structures |
| 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 |
| cooperativity | occurs when the change in one parameter influences the change in similar parameters |
| active site | the portion of an enzyme which is responsible for enzyme activity |
| catalytic site | the location on an enzyme where the substrates react with each other and/or portions of the enzyme |
| dalton | a unit of molecular weight where one mole of hydrogen atoms equals one dalton |
| enzymology | the study of enzymes and their properties by measuring enzyme activty (kinetics) |
| 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) |
| 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 |
| Ki | The equilibrium constant for the dissociation of an inhibitor from an enzyme inhibitor complex |
| 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 |
| specificity constant | kcat/Km - the ratio of kcat to Km |
| 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) |
| substrate binding site | the location on an enzyme where the substrate binds to the enzyme |
| 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 |
| Zymogens | an inactive precursor of an enzyme |
| intermediates | a quasi stable step between a substrate and a product |
| transition state analog | a stable molecule which resembles a proposed transition state (normally an effective inhibitor) |
| 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) |
| apoenzyme | the protein component for an enzyme which requires a cofactor for activity |
| coenzyme | an organic cofactor |
| cofactor | a non-protein component which is required for enzyme activity |
| cosubstrate | coenzyme which is loosely bound to an enzyme and is consumed during the reaction |
| holoenzyme | an apoenzyme and its cofactor |
| metalloenzyme | an enzyme which contains one or more tightly bound metal ion(s) which are essential for activity |
| prosthetic group | a coenzyme which is tightly bound to an enzyme and which is not consumed by the reaction |
| simple enzyme | an enzyme which does not require a cofactor for activity |
| carbohydrate | a polyhydroxyl ketone or a polyhydroxyl aldehyde and its derivatives |
| biological membrane | lipid bilayer containing protein which completely surrounds and isoloates biomolecules |
| ionophore | a biomolecule which facilitates the movement of ions across a biological membrane |
| lipid | a biomolecule which is insoluble or slightly soluble in water and are usually extractable by organic (nonpolar) solvents |
| 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 |
| 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 |
| 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 |
| 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 |
| nucleic acid | biopolymers consisting of nitrogenous bases which are linked to ribose or deoxyribose linked by phosphodiester bonds |
| 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 |
| 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 |
| snRNA | small nuclear RNA - a series of RNA molecules ranging in size from about 100-200 nucleotides |
| rRNA | ribosomal RNA - this series of RNA molecules combine with proteins to form ribosomes |
| nucleoside | a purine or pyrimidine n-glycoside of ribose or deoxyribose (sugars) |
| nucleotide | the phosphate ester of a nucleoside consisting of a nitrogenous base linked to a pentose phosphate (phosphate) |
| Tm | the temperature at which a particular molecular transition is 50% complete |
| EMF | electron motive force-a measure of the difference between the reduction potentials of the reactions on the two sides of an electrochemical cell |
| enthalpy | the measure of the amount of heat in a system under constant pressure |
| entropy | the measure of the disorder of a system |
| gibbs free energy | the amount of energy available to do chemical work |
| energy charge | see formula pg 97 of workbook |
| macromolecules | large molecule (>10,000 daltons) composed of polymers of similar or identical parts |
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