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81 Cards in this Set
- Front
- Back
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Hydrogen Bond
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A weak electrostatic attraction between one electronegative atom (such as oxygen or nitrogen) and a hydrogen atom covalently linked to a second electronegative atom.
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Bond Dissociation Energy
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The energy required to break a bond.
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Hydrophobic
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Nonpolar; describes molecules or groups that are insoluble in water.
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Amphipathic
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Containing both polar and nonpolar domains
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Micelle
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An aggregate of amphipathic molecules in water, with the nonpolar portions in the interior and the polar portions at the exterior surface, exposed to water
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Hydrophobic Interactions
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The association of nonpolar groups or compounds with each other in aqueous systems, driven by the tendency of the surrounding water molecules to seek their most stable (disordered) state.
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Buffer
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A system capable of resisting changes in pH, consisting of a conjugate acid-base pair in which in which the ratio of proton acceptor to proton donor is near unity.
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Henderson-Hasselbalch Equation
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An equation relation the pH, the pKa, and the ratio of the concentrations of proton-acceptor (A-) and proton-donor (HA) species in a solution:
pH = pKa + log [A-]/[HA] |
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Hydronium ions
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The hydrated hydrogen ion (H3O+)
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Equilibrium constant (Keq)
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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.
Keq = [H+][A-]/[HA] |
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Ion Product of Water (Kw)
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The product of the concentrations of H+ and OH- in pure water:
Kw = [H+][OH-] = 1x10^-14 (at 25 degrees C) |
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pH
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The negative logarithm of the hydrogen ion concentration of an aqueous solution.
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Conjugate Acid-Base Pair
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A proton donor and its corresponding deprotonated species; for example, acetic acid (donor) and acetate (acceptor)
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Dissociation Constant (Ka)
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An equilibrium constant (Ka) for the dissociation of a complex of two or more biomolecules into its components; for example, dissociation of a substrate from an enzyme.
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pKa
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The negative logarithm of an equilibrium constant
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Amino Acids
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α-Amino-substituted carboxylic acids, the building blocks of proteins
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Chiral Center
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An atom with substituents arranged so that the molecule is not superposable on its mirror image
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Optical Activity
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The capacity of a substance to rotate the plane of plane-polarized light
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Absolute Configuration
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The configuration of four different substituent groups around an asymmetric carbon atom, in relation to D- and L-glyceraldehyde
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Polarity
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Nonuniform distribution of electrons in a molecule; usually soluble in water if polar
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Glycine
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R = H
Gly, G Nonpolar, aliphatic |
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Alanine
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R = CH3
Ala, A Nonpolar, aliphatic |
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Proline
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R = -CH2-CH2-CH2- (NH2+)
Pro, P Nonpolar, aliphatic |
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Valine
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R = CH(CH3)2
Val, V Nonpolar, aliphatic |
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Leucine
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R = CH2-CH(CH3)2
Leu, L Nonpolar, aliphatic |
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Isoleucine
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R = CH(CH3)-CH2-CH3
Ile, I Nonpolar, aliphatic |
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Methionine
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R = -CH2-CH2-S-CH3
Met, M Nonpolar, aliphatic |
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Phenylalanine
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R = -CH2-Benzene
Phe, F Aromatic |
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Tyrosine
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R = -CH2-Benzene-OH
Tyr, Y Aromatic |
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Tryptophan
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R = -CH2-C(CH-NH-)Benzene
Trp, W Aromatic |
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Serine
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R = -CH2OH
Ser, S Polar, uncharged |
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Threonine
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R = CH,OH,CH3
Thr, T Polar, uncharged |
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Cysteine
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R = -CH2-SH
Cys, C Polar, uncharged |
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Asparagine
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R = -CH2-C(NH2)=O
Asn, N Polar, uncharged |
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Glutamine
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R = -CH2-CH2-C(NH2)=O
Gln, Q Polar, uncharged |
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Lysine
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R = -(CH2)4-NH3+
Lys, K Positively charged R group |
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Arginine
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R = -(CH2)3-NH-C=(NH2+)(NH2)
Arg, R Positively charged R group |
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Histidine
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R = -CH2-(C-NH-CH=N-CH=)
His, H Positively charged R group |
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Aspartate
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R = -CH2-COO-
Asp, D Negatively charged R group |
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Glutamate
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R = -CH2-CH2-COO-
Glu, E Negatively charged R group |
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Cystine
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Two Cysteine amino acids form a disulfide bond by oxidation; stabilizes many protein structures
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Zwitterion
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A dipolar ion with spatially separated positive and negative charges
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Amphoteric
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Capable of donating and accepting protons, thus able to serve as an acid or base
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Ampholyte
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A substance that can act as either a base or an acid
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Isoelectric Point, pI
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The pH at which a solute has no net electric charge and thus does not move in an electric field
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Peptide
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Two or more amino acids covalently joined by peptide bonds
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Protein
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A macromolecule composed of one or more polypeptide chains, each with a characteristic sequence of amino acids linked by peptide bonds
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Peptide Bond
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A substituted amide linkage between the α-Amino group of one amino acid and the α-Carboxyl group of another, with the elimination of the elements of water
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Oligopeptide
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A few amino acids joined by peptide bonds
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Polypeptide
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A long chain of amino acids linked by peptide bonds; the MW is generally less than 10,000.
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Amino-Terminal (N-terminal) Residue
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The only amino acid residue in a polypeptide chain with a free α-amino group; defines the amino terminus of the polypeptide
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Carboxyl-Terminal (C-terminal) Residue
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The only amino acid residue in a polypeptide chain with a free α-carboxyl group; defines the carboxyl terminus of the polypeptide
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Oligomeric Protein
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A multi-subunit protein having two or more identical polypeptide chains
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Conjugated Proteins
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A protein containing one or more prosthetic groups
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Prosthetic Group
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A metal ion or an organic compound (other than an amino acid) that is covalently bound to a protein and is essential to its activity
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Lipoproteins
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A lipid-protein aggregate that serves to carry water-insoluble lipids in the blood. The protein component alone is an apolipoprotein
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Glycoprotein
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A protein containing a carbohydrate group
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Metalloprotein
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A protein with a metal ion as its prosthetic group
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Primary Structure
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A description of the covalent backbone of a polymer (macromolecule), including the sequence of monomeric subunits and any interchain and intrachain covalent bonds
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Secondary Structure
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The local spatial arrangement of the main-chain atoms in a segment of a polypeptide chain
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Tertiary Structure
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The three-dimensional conformation of a polymer in its native folded state
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Quaternary structure
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The three-dimensional structure of a multisubunit protein, particularly the manner in which the subunits fit together
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Fractionation
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The process of separating the proteins or other components of a complex molecular mixture into fractions based on differences in properties such as solubility, net charge, molecular weight, or function
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Dialysis
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Removal of small molecules from a solution of a macromolecule by their diffusion through a semipermeable membrane into a suitably buffered solution
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Chromatography
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A process in which complex mixtures of molecules are separated by many repeated partitionings between a flowing (mobile) phase and a stationary phase.
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HPLC, High-Performance Liquid Chromatography
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Chromatographic procedure, often conducted at relatively high pressures, using automated equipment that permits refined and highly reproducible profiles
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Electrophoresis
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Movement of charged solutes in response to an electrical field; often used to separate mixtures of ions proteins, or nucleic acids
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Isoelectric Focusing
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An electrophoretic method for separating macromolecules on the basis of isoelectric pH
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Specific Activity
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The number of micromoles (μmol) of a substrate transformed by an enzyme preparation per minute per milligram of protein at 25degC; a measure of enzyme purity
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Ion-Exchange Resin
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A polymeric resin that contains fixed charged groups, used in chromatographic columns to separate ionic compounds
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Cation-Exchange Resin
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An insoluble polymer with fixed negative charges, used in the chromatographic separation of cationic substances
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Anion-Exchange Resin
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A polymeric resin with fixed cationic groups, used in the chromatographic separation of anions
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Size-Exclusion Chromatography
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A procedure for the separation of molecules by size, based on the capacity of porous polymers to exclude solutes above a certain size; also called gel filtration
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Activity
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The true thermodynamic activity or potential of a substance, as distinct from its molar concentration
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Homologous Proteins
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Proteins having similar sequences and functions in different species; for example, the hemoglobins
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Proteases
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Enzymes which catalyze the hydrolytic cleavage of peptide bonds
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Edman Degradation
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Labels and removes only the amino-terminal residue from a peptide, leaving all other peptide bonds intact
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Sequenator
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Machine in which the Edman Degradation is carried out in; mixes reagents in the proper proportions, separates the products, identifies them, and records the results
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α Helix
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A helical conformation of a polypeptide chain, usually right-handed, with maximal intrachain hydrogen bonding; one of the most common secondary structures in proteins
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Conformation
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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
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Native Conformation
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The biologically active conformation of a macromolecule
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