Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
81 Cards in this Set
- Front
- Back
|
Coulombs's Law |
increase dielectric constant decrease IMFs |
|
|
Van der Waals |
weak electrostatic forces that act over a short distance. create dipoles and reply on inherent repulsion of electron clouds |
|
|
Flicker Cluster |
short-lived areas of ordered water in a disordered solution |
|
|
Primary Hydration Sphere |
a tightly bound layer of water immediatly surrounding a charged or polar group |
|
|
dithiothreitol and dithioerythritol DTT and DTE |
reducing disulphide bonds, water soluble, don't smell, not reversible because it forms a stable ring, strong reducer --- replaced B-mercaptoethanol |
|
|
Speciation |
evolution of a new gene/protein that is genetically independent of the ancestor gene |
|
|
Homolog/Ortholog |
a gene/protein related to a second gene/protein by descent from a common ancestor |
|
|
Paralog |
gene/protein related by duplication of a common ancestor gene that evolved new functions (gives rise to divergent evolution) |
|
|
Convergent Evolution |
similar properties in proteins/gene of different genetic lineage |
|
|
Mutation |
single point changes in DNA, they occur with time |
|
|
Recombination |
exchange of genes between different chromosomes |
|
|
Gene Duplication |
duplication of a gene where the second set is free to evolve |
|
|
Retrotransposition |
incorporation of mRNA sequences back into DNA to create new expression patterns |
|
|
PAM |
Percent Acceptable Mutations, shows the difference between genes, want a lower number, global alignments |
|
|
BLOSUM |
The higher the number, the more similarities. Seeing what's the same, local alignments |
|
|
Statistic Coupling Analysis |
comparing mutations in a sequence and seeing if they're counter mutations (preserve function, usually catalytic sites) |
|
|
Metastable zone |
barely stable, just over soluble, where crystals grow |
|
|
Phase Problem |
what is the phase of the atom--where exactly is it located |
|
|
Isomorphous Replacement |
use heavy metals as a reference, its location can be determined with patterson and can be applied to rest of structure |
|
|
Molecular Replacement |
rotate and translate a homologous structure to get phase and apply it to your molecule |
|
|
Thermodynamics |
concerned with the initial and final state of the process |
|
|
Kinetics |
The rate at which the process occurs--the pathway it takes |
|
|
Collision Theory |
Need to collide with correct position and energy, formula states that increasing temp increases rate because it increases collisions,
|
|
|
Encounter Complex |
water acts as a barrier, as you get closer collision odds increase due to caging and shielding-->proximity effect |
|
|
Proximity Effect |
binding in active site increases local concentrations of reactant (part of enthalpy and binding energy) |
|
|
Orbital Steering |
orient reacting groups in the active site |
|
|
Desolvation |
removing H20 from the active site where it could prevent binding |
|
|
Microenvironment |
enhance reactivity of functional groups (using functional groups and phillic/phobic) |
|
|
Entrophy-Enthalpy Compensation |
using binding energy to offset unfavorable loss of entrophy due to restriction movements/loss of randomness of system |
|
|
Salting Out |
increase salt concentration to precipitate out proteins with hydrophobic interaction (ammonium sulfate) |
|
|
Dialysis |
lowers salt concentration |
|
|
HPLC |
high resolution, fast, automated, can separate out by all of these methods |
|
|
Ion Exchange Chromatography |
Cation exchange = capture + (- stationary) Anion exchange = capture - (+ stationary) pI matters |
|
|
Gel Filtration/ Size Exclusion |
small molecules retained in beads and large move right through, separate based on size, buffer and purity doesn't matter, V0 = void volume |
|
|
Affinity Chromatography |
use a ligand to bind to your molecule of interest and retain it |
|
|
Immunoaffinity Chromatography |
use an antibody to retain your desired molecule, very hard to remove antibody, try to retain tag |
|
|
Hydrophobic Interaction Chromatography |
stationary phase is hydrophillic and phobic groups attached, retain phobic |
|
|
Reverse-Phase Chromatography |
nonpolar substances retained, may need to denature proteins to get to phobic center |
|
|
Primary Sequence |
the amino acid sequence listed from a to c terminus |
|
|
Secondary Sequence |
recurring structural features stabilized by H bonds -- B sheets and A helixes |
|
|
Motif / supersecondary structure |
Highly conserved short aa sequence--do not necessarily have a function ex: alpha loop alpha |
|
|
Domain |
segment of protein structure that is autonomously stable and has a function, show evolution as they are conserved and identifiable by sequences |
|
|
Tertiary Structure |
stable independent protein from a single gene |
|
|
Quaternary Structure |
composed of 2 or more tertiary structures |
|
|
Heptad repeats |
every 7 aa there is a large hydrophobic aa like leu that acts like a zipper holding a chain together structure: H P P H C P C |
|
|
Rossman Fold |
repeating BAB motifs 7 times, Alpha used to connect 2 Parallel B sheets, Torroid shape (donut-like) |
|
|
Greek Key Motif |
BBB supersecondary structure (motif) up down up down up 52341 connection/order |
|
|
Hot Spot Residues |
areas that hold together oligomers in quaternary structure, they usually have complementary charge or phobicity to hold together in a specific way |
|
|
Pyruvate kinase domain |
takes phos from PEP to ADP in glycolysis, 4 distinct isozymes for metabolic pathways in different tissues |
|
|
Ramachandran Plot |
illustrates all possibile phi and psi angles around the sp2 planar peptide bond |
|
|
Alpha Helix |
stabilizes by internal H bonds, C=O attacks NH2 on n-4 aa, right handed, 3.6 residues per turn, proline causes bend, capping residues (Asn and Lys), dipole |
|
|
Beta Sheet |
parallel or anti-parallel, twisted into saddle shape, R groups are planar, right twist |
|
|
Intermolecular Forces |
weak short range attractive forces between atoms or molecules, additive, Van der Waals, H bonds, hydrophobic interactions, charge charge (coulombic) |
|
|
Dielectric Constant |
polarizability of the medium, the ability of the medium to diminish the force between 2 point charges at a constant distance vacuum-->air-->pressure air-->water |
|
|
London Jones Thought Experiment |
take 2 inert noble gases and push them together until they repel due to electron shell overlap. At first they attract due to induced dipoles. Repel just a little before van der waals radius |
|
|
Urea |
chaotropic agent that denatures protein by competing with water for H bonds. It binds up water decreasing phillic bonding (caging effect) 3so that protein can denature. nothing preventing phobic from exposure |
|
|
Amino acid |
average weight is 109, 20 aa residues, alanine is most common, hydrophobic, charged, and neutral, phillic polar and np groups. Rings abs in UV, all L if chiral, R group connected to a-Carbon, an amino and carboxyl group, form peptide bond with dehydration synthesis (carboxyl attacks amino) |
|
|
Extinction coefficient |
Abs =l conc E, how much an aa gives off /loses light at a specific wavelength, use to measure absorbance |
|
|
Insulin |
is a dimer connected by disulphide bonds that can't refold. regulate conc by splitting |
|
|
1st order rate |
Rate=k[A] only depends on one species, the k is 1st order rate constant (s-1) |
|
|
Cross Reaction |
antibody binding can give false positives at high concentrations, they'll bind to less specific active sites, keep low [ab] to prevent
|
|
|
Limit of Detection (Exposure time) |
Limit the exposure time to prevent burn out of a gel, bands expand and you can lose clarity |
|
|
Local Minimum Free Energy Structure |
lowest activation energy to get to structure (determined by primary sequence), global is theoretical as it takes too much energy to get to |
|
|
Reverse Turns |
connect segments of anti parallel beta sheets, type 1 (no steric hinderance, stabilized by H bonds, 2 structure) type 2 (need glycine due to steric hinderance, not energetically favorable, uncommon |
|
|
Gel Electrophoresis |
separation based off of size, shape, charge, and phobicity, matrix needed to decrease mobility and convection, compare relative mw to standards, gel made of polyacrylamide, cross-linking propagated by free radical (ammonium persulfate) and stabilized by TEMED |
|
|
Centrifugation |
gravitation force moves protein, tells absolute molecular weight and look at oligomers |
|
|
Oxidoreductases |
catalyze oxidation or reduction reactions. transfer of electrons |
|
|
Transferases |
transfer of a functional group, donor and acceptor |
|
|
Hydrolases |
breaking of chemical bonds with the addition of water |
|
|
Lyases |
generate a double bond, elimination reactions, synthase enzymes, two substrates required |
|
|
Isomerases |
catalyze structural changes in a molecule |
|
|
Ligases |
two substrates joined together using ATP, usually paired with another favorable reaction |
|
|
Disc Gel Electrophoresis |
concentration of proteins in stacker gel, initially Cl- is faster and glycine trails, Cl- moving pulls things along creating stacks. at running gel, proteins separate out by mw due to pH change in buffer ==> little sample and high resolution |
|
|
Tracking Dyes |
run with front, used to measure Rf, have little interaction with stationary phase, ex: bromophenol blue |
|
|
SDS aka sodium docecyl sulfate |
linearizes, gives uniform negative charge, binds 1.4 g to 1 g protein
|
|
|
SDS Page |
separation of protein on gel by basis of mw, -PO4+ can create doublet, if protein doesn't linearize or side chains don't bind SDS stokes radius will become smaller |
|
|
SILAC |
how much protein, incorporate heavy isotope AA to one cell line, fragment and run MS compare to control |
|
|
Mass Spec |
mass:charge, vaporize sample and ionize and read with detector, MALDI (excite via laser and detect via Time of Flight) vs. ESI (spray and vaporize read with quadrapole) more accurate |
|
|
Collision Induced Dissociation |
fragment ions from collision for tandem mass (polypeptide chains) |
|
|
Multiple Sequence Alignments |
local (long sequence suspected of containing similarity) and global (similar size and suspected similar sequence), scoring matrix = PAM, clustal, or BLOSUM, remove simple repeats, penalize gaps but not extensions, Expectation value (how easy is it to find similarities by random chance) |
|
|
Collagen |
3 left handed subunits (2) in a right handed helix, Gly-X-Y, with proline commonly modified to hyperoxygen Proline (prolyl hydroxylase), lysyl hydroxylase adds OH to epsilon C (=hydroxylysine), oxidative deamination (lysyl oxidase) crosslinked to hold microfibrils together |
