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Biochemistry

Knopps notes definitions

QuestionAnswer
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
Created by: vyc_torY_a