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75 Cards in this Set
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coenzymes |
organic compounds essential to many enzyme-catalyzed reactions |
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proteasomes |
degrade proteins no longer needed by the cell |
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oligomers |
shorter polymers |
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proteome |
sum of all proteins in a given cell |
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amphipathic |
contain regions that are polar (hydrophilic) and regions that are nonpolar (hydrophobic) |
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osmolarity |
osm = i*c = # of solutes*molarity |
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isotonic |
equal concentation on each side of a membrane |
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hypertonic |
higher concentration on the outside water moves out |
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hypotonic |
higher concentration on the inside - water moves in |
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zwitterion |
dipolar ion which can act as either an acid or a base |
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prosthetic group |
non-amino acid part of a conjugated protein, organic or inorganic |
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chymotrypsin |
digestive enzyme, cleaves carboxyl side of tyrosine, tryptophan, and phenylalanine |
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trypsin |
protease, cleaves carboxyl side of lysine or arginine except when followed by proline |
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carboxypeptidase |
cleaves peptide bond at carboxy-terminal end of peptide |
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van't hoff factor
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i, extent of a solute's dissociation into particles
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osmotic pressure |
RT(ic1 + ic2 + ...) |
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henderson-hasselbalch |
pH = pKa + log([A-]/[HA]) |
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Beer-Lambert Law |
log(I0/I) = EcI = A (absorbance) |
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specific activity |
units/mg |
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dialysis |
separation of particles in a liquid based on their ability to pass through a membrane |
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de-salting |
separating soluble macromolecules from smaller molecules |
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differential centrifugation |
separates membrane-associated material (pellet) from supernatant |
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isopycnic (sucrose-density) centrifugation |
separates particles into layers based on their density |
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cation exchange chromatography |
binds cations, resin is negative, mono S |
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anion exchange chromatography |
binds anions, resin is positive, DEAE A50 |
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molecular sieve/size-exclusion chromatography |
resin w/small holes to slow down small particles |
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affinity chromatography |
add ligand, add proteins, protein of interest binds to ligand, wash away unwanted proteins, protein of interest eluted by ligand solution |
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native PAGE (polyacrylamide gel electrophoresis) |
mobility depends on charge and size, protein kept intact, run at extreme (usually high) pH
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SDS PAGE |
protein must be denatured and coated w/negative charge, size proportional to charge |
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DTT and βME |
reduce disulfide bonds, separate peptides |
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isoelectric focusing |
gel pH gradient, proteins stop at their pI |
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2D electrophoresis |
isoelectric focusing and then SDS PAGE, 2D map of proteins |
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mass spectrometry |
measures mass to charge ratio |
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FDNB and dansyl chloride |
identifies amino terminus |
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Edman degradation (PITC) |
amino termini labeled, cleaved, and identified; repeat to sequence entire peptide |
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ϕ (phi) |
N - alpha C
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ψ (psi) |
alpha C - C |
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Ramachandran plots |
helps visualize phi and psi angles and see possible conformations |
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α-keratin |
2 α-helices, many disulfide bridges (hair, nails) |
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collagen |
left handed α-chains, 3 res/turn, triple coil (tendons, cartilage) |
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silk fibroin |
anitiparallel β-sheets, rich in ala, gly (chrysalis, spiderwebs) |
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domain |
section of protein w/its own structure or function (active sites) |
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amyloid |
misfolded protein structures that can form insoluble fibrils and lead to disease |
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amyloidosis |
buildup of amyloid |
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prions |
infections protein misfolding |
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θ |
= [PL]/{[PL]+P} = [L]/{[L]+kd}, fraction of P sites w/ligand, protein with ligand bound/total protein |
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kd |
1/ka, dissociation constant, where θ = 0.5 |
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myoglobin |
storage, high affinity |
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hemoglobin |
transport, myoglobin-like subunits, T (binding) and R (not binding) states |
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salt bridge |
bonds between oppositely charged residues |
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Bohr effect |
more oxygen dropped off as pH decreases |
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BPG altitude effect |
as altitude drops, oxygen levels drop and BPG rises = more drop off |
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immunoglobulins |
bind antigens |
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Fab |
antigen binding domain, transposable elements (variable) |
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Fc |
crystallizable tail (constant) |
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t-tubules |
deep invaginations of the muscle membrane so all parts can be signaled
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transverse tubules |
clefts lined with Ca channels in muscle fibers which allow quick Ca release throughout sarcomere |
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holoenzyme |
intact enzyme with prosthetic group |
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apoenzyme |
intact enzyme without prosthetic group |
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cofactor |
small non-protein required by enzyme |
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Michaelis-Menten |
1/V0 = Km/Vmax[S] + 1/Vmax |
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Michaelis constant, km |
how well the enzyme binds the substrate
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Vmax |
how quickly the enzyme turns substrate into product |
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protease digestion |
breaking up proteins with specific proteases one at a time and put pieces back together to sequence |
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tropomyosin |
blocks actin fibers |
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troponin C |
binds to Ca, moves tropomyosin away from actin filaments releasing inhibition |
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troponin T |
links to tropomyosin |
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troponin I |
inhibits myosin-actin connection |
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turnover number |
kcat |
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competitive inhibitor |
dilutes S, binds at active site, Vmax same, Km increases |
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uncompetitive inhibitor |
binds at other site when substrate is bound and prevents from turning into product, Vmax and Km decrease |
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mixed inhibitor |
binds to other side whether or not substrate is bound, Vmax decreases, Km increases (usually) |
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noncompetitive inhibitor |
mixed inhibitor when Km stays the same |
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racemase |
enzyme that changes stereochemistry, pull protein off alpha carbon and adds back to other side |
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transpeptidase |
enzyme required for production of bacterial cell walls |
