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137 Cards in this Set
- Front
- Back
Poiseulle’s Law
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Q = (pi * r^4 * ∆Pressure) / (8 * viscosity * length)
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conversion from liter
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1 L = 1 quart
1 L = (1000 gm)/(18 gm/mole) = 55.5 moles/L |
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dielectric effect
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a shielding effect where a slightly (-) charge is neutralized by a (+) charge due to polarity
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If you decrease order (increase entropy), what happens to energy change?
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-decreasing order is equivalent to going from high energy to low energy (spontaneous reaction)
-reactions want less order |
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Gibbs free energy (∆G)
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∆G = ∆H (heat) – T∆S (randomness)
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osmotic pressure
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osP = ([conc] * R * T) / (MW)
T is in kelvins (K = 273 + C) |
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Keq
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Keq = [products] / [reactants]
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pK & Keq of lactic acid
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Keq = 1.38 * 10^-4
pK = 3.86 |
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pK & Keq of ammonia
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Keq = 5.62 *10^-10
pK = 9.25 |
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Henderson-Hasselbalch Equation
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pH = pK + log [A-]/[HA] (conj. base/conj. acid)
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pK’s of phosphoric acid (H3PO4)
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pK1 = 2.1
pK2 = 7.2 pK3 = 10.0 |
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pH of the body
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pH = 7.4
*when the cell metabolizes products, the body’s pH decreases and becomes acidic *INC in CO2 levels decreases pH and causes the body to become acidic |
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pK of carbonic acid
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pK = 6.1
CO2 + H20 H2CO3 H+ + HCO3- |
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essential amino acids
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F, V, T, W, I, M, H, R, L, K
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polar amino acids
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G, S, T, C, Y, D, N, E, Q, H, R, K
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nonpolar amino acids
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A, V, L, I, M, F, W, P
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ordering of molecules for determining chirality
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1) COOH
2) NH3 3) R 4) H have 1 and 3 at up and down, away and have 2 and 4 at left and right, towards |
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pK’s of amino acids other than acidic and basic ones
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pK = 2.5 (for COOH)
pK = 9.5 (for NH2) |
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pK for acidic amino acids (ASP + GLU)
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pK = 2.5 (for COOH)
pK = 4.5 (for acidic proton) pK = 9.5 (for NH2) |
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pK for basic amino acid Lys
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pK = 2.5 (for COOH)
pK = 9.5 (for NH2) pK = 10.5 (for basic proton) |
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pK for basic amino acid Arg
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pK = 2.5 (for COOH)
pK = 9.5 (for NH2) pK = 12.5 (for basic proton) |
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pK for basic amino acid His
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pK = 2.5 (for COOH)
pK = 6.0 (for basic proton) pK = 9.5 (for NH2) |
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molecule used for cation exchange chromatography
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CMC-carboxy methyl cellulose, (-) charge
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molecule used for anion exchange chromatography
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DEAE-diethyl amino ethane, (+) charge
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how to detect whether or not an amino acid is a primary or secondary amine
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use ninhydrin
primary amines -> purple secondary amines -> yellow |
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beer-lambert law
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used in detection spectroscopy
abs = a (std absorbance) * c (concentration) * l (length of cuvette) abs. detects the density of a compound (think iced tea and amount of sugar) blood sugar levels determined using this |
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conditions for obtaining aa residues
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6 N HCL, 100 C, 24 hr
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properties of peptide bonds
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1. short
2. planar 3. trigonal 4. share electrons 5. don’t rotate -> trans in peptides 6. covalent partial double bond character (has 1.32 angstrom length) C-N 1.49 C=N 1.27 |
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Prosthetic Groups (of protein's primary structure)
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Heavy Metals: Fe, Zn, Cd, Hg, Pb
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when trying to estimate MW
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1. find gms of Fe, divide by MW (55.5) to give moles of Fe in protein
2. 1 gm protein/# of moles of Fe in protein = min. MW |
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average aa MW
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120 gm/mol
to find est. number of aa in a protein take min MW and divide by 120 gm/mol |
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Edman’s Reagent
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PITC (phenyl iso thio cyanate) interacts with primary amines (thus the amino end of a protein, may also be lysine or tyrosine) and cleaves off one aa at that end, can do 40-50 residues in sequence
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Sanger’s Reagent
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DNFB (dinitro fluoro benzene), hydrolyzes entire peptide chain so get individual aa’s but not order, gives the aa on the NH2 end
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Dansylation
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dansyl chloride, has fluoresces, destroys other peptide bonds
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aminopeptidase
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chews peptide from amino end down, gives new sample every 15 secs
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hydrazine
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tags each aa except for the COOH terminal aa, so tells what aa is on the COOH end, breaks every peptide bond
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trypsin and cleavage of aa’s
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cleaves basic aa’s (lys, arg)
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chymotrypsin and cleavage of aa’s
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cleaves aromatic aa’s (Phe, Tyr, Trp), sometimes His
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cyanogen bromide (CNBr) and cleavage of aa’s
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cleaves methionine
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To separate aa’s based on solubility/hydrophobicity:
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TLC, reverse phase
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To separate aa’s based on charge:
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ion exchange
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To separate aa’s based on size:
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gel exclusion, ultracentrifugation, dialysis, PAGE
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to separate aa’s based on function
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affinity purification
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reagent used to denature a protein
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SDS (sodium dodecyl sulfate), a detergent that stretches protein lengthwise), adds (-) charge to every 2 aa's
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sedimentation rate
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S = MWt (1 – (volume*density)) / (friction = 6 * pi * viscosity * strokes radius)
s is dependent on mass and shape |
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what determines where R groups are relative to each other on an aa peptide
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1. hydrophobic interactions (water, entropic effect) REPULSION (the primary driving force, all others are stabilizing forces)
2. ionic interactions (repulsion/ attraction) STABILIZATION 3. van der Waals forces (steric hinderance) REPULSION (bec. of space) 4. H-bonding (sharing of H+ between two electronegative atoms) STABILIZATION |
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alpha helix features
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right handed, driving force is hydrophobicity, stabilizing fore is H-bonds parallel to axis, found in wool, hair, horns, hooves, fingernails, 5.4 Angstroms/turn, 3.6 aa/turn
*long rigid rods with not much flexibility |
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alpha helical breakers
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1. run of negative charges on aa’s close to each other on folded alpha helix, causes repulsion
2. proline, causes a loss in twisting ability, may lead to beta turns |
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beta structure features
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1. rich in alanines
2. extended 3. antiparallel or parallel 4. perpendicular H-bonds 5. forms sheets 6. found in silk 1.5 aa's per turn |
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beta turn
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can turn anywhere, not just Beta sheets, can be alpha helical breakers, a proline, then a small R group (glycine), then a hydrophilic
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structure of collagen
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glycine, X (proline), Y, glycine, X (proline), Y…
perpendicular H-bonds |
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¼ stagger in bone due to collagen
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has a 700 angstrom nucleation site (for hydroxyapatite (650 A), caused by hydrophobic interactions), and 2800 angstrom for collagen
spontaneously forms (esp. with vitamin A and physiological salts) |
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mercaptoethanol
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CH3CH2SH used to reduce disulfide bonds to SH
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quaternary structure
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all interactions between multiple subunits are non-covalent (hydrophobic patches, ionic links or H-bonds)
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anabolic vs. catabolic
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anabolic (synthesis) or catabolic (degradation), cannot be used to determine the spontaneity of a reaction
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gibbs free energy and spontaneity
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∆G = (-) is spontaneous
∆G = 0 is at equilibrium ∆G = (+) is non-spontaneous |
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Standard State Conditions for ∆G
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1 mole/L each reactant and product
fixed temperature pH = 7.0 [H2O] = 55.5 moles/L ∆G°’ is inversely related to – Keq |
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∆G°’ equation (free energy at standard state)
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∆G°’ = -RT lnKeq = cal/mol
where R = 1.987 cal/(mole K) T = 298 K (room temperature ln = 2.303 * log or ∆G°’ = -1364 log Keq |
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actual free energy
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∆G = ∆G°’ + RT ln ([P]/[R])
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∆G°’ for glucose
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∆G°’ = -4000 cal/gm
* 180 gm/mole -720,000 cal/mole Keq = 10^528 |
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strategies that limit the ∆G°’ for glucose
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1. operating close to equilibrium (DEC ∆G°’ for glucose)
2. stepwise processes (gradual breakdown of glucoses 6 carbons) 3. coupling reactions 4. high energy barriers |
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energy in esters
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(-3 Kcal/mole), forms acid and alcohol (or amine if breaking down amide)
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energy in thiol-esters
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-6 to -8 Kcal/mole
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energy in anhydrides
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-7 to -10 Kcal/mole, ex: ATP
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what accounts for the difference in energy between different compounds
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entropic forces
1. 1 reactant 2 products (INC in entropy) 2. resonance stabilization of products (compared to reactants) a. INC resonance, INC entropy, ~50% of energy electronic forces 3. charge repulsion in ATP vs. ADP 4. charge separation in ATP vs. ADP |
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energy in guanidinum phosphates
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-10 Kcal/mole
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Creatine
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made from Arginine, composed of Gly, Met, Arg
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energy in enoyl phosphate
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-14 Kcal/mole, lots of energy present because of presence of tautomer form (a eneol form and a keto form (of which is favored energetically))
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oxidation states of C
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methane methanol formaldehyde formic acid carbon dioxide
tightly ordered ---------------------------------------------------------> loosest reduced -----------------------------------------------------------------> oxidized |
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energy in carbohydrates vs. fats
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carbs have 4 Kcal/mole, have more partially oxidized carbons
fats have 9 Kcal/mole, have far more reduced C’s, more constrained, more energy |
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energy in NADH or FADH
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-15 Kcal/mole
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velocity of a reaction
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dependent on the activation energy, v = k [R]
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Keq in terms of kinetics and thermodynamics
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Keq = [P]/[R] = kf/kr
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velocity of a reaction (Michaelis-Menton equation)
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v = vmax * ([S]) / (Km + [S])
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max. velocity of a reaction
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vmax = k3 * [Et]
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Km =
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Km = (k2 + k3) / (k1)
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inverse of affinity
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k2/k1
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turnover term
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k3/k1
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to determine enzyme specificity or enzyme preference
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Vmax/Km
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Lineweaver-Burk eq
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1/v = (Km/Vmax) * (1/[S]) + (1/Vmax)
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x-intercept of Lineweaver-Burk plot
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-1/Km
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y-intercept of Lineweaver-Burk plot
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1/Vmax
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slope of Lineweaver-Burk plot
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Km/Vmax
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irreversible inhibitors
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heavy metals and –SH groups (penicillin, Pb, Hg), when add to reaction, DEC Vmax but no effect on Km, works by binding to cysteine
ex: aspirin, it acetylates proteins and forms esters |
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competitive inhibitor
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binds to initial enzyme, reversible, same Vmax, different Km
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non-competitive inhibitor
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inhibitor can bind to enzyme or ES complex, same Km, DEC Vmax, looks like irreversible, tell difference through dialysis and see if inhibitor comes off, inhibitor binds to different spot on enzyme from substrate
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uncompetitive inhibitor
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inhibitor binds to ES complex, DEC Km and Vmax
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6 classes of enzymes
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OTHLIL (oxido-reductases, transferases, hydrolases, lyases, isomerases, ligases)
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Modification of amino acids (post-translational): hydroxylation
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proline-found in urine during bone remodeling, important in collagen, hydroxylate C 3 or 4
lysine-hydroxylate C 4 or 5 |
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Modification of amino acids (post-translational): esterifcation
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1. acetylation-adding acetic acid
2. phosphorylation aa's involved: serine, threonine, tyrosine |
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what form of amino acid is found in humans?
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L-form, it evolved the right turn alpha helix
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racemization and example of such:
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racemization-switching from the D to L form
EX: aspartic acid, racemizes @ 0.14%/year |
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Solvents used in TLC
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polar: water
nonpolar: isopropanol, butanol, phenol |
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carboxypeptidase
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similar to aminopeptidase but starts at the carboxy end and gives sample every 15 secs.
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Piezo Electric Effect
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found in inorganic systems, where crystals orient themselves perpendicular to a force
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random coils
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random in the sense that they are unpredictable, aa's in random coils are not rich in hydrophobics but have hydrophilics to react with the aqueous solution
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Affinson's Experiment
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looked at ribonuclease (which has 8 cysteines or 4 disulfide bonds) and determined the likely hood that those bonds would rejoin
expected: 1% chance they rejoined correctly and had activity observed: 80% retained activity, hydrophobic forces drive the bonds together |
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creatinine
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the spontaneous folding of creatine's COOH and NH2 end, is excreted through urine, detected during muscular damage
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oxidation and reduction forms of atoms
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"ic" oxidized
"ous" reduced |
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turnover constant/turnover number
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k3
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slowest step in the michalis-mentin equation
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v = k3 [E*S] complex
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First, Zero, and Mixed order reactions
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first-low [S] concentrations
zero-high [S] concentrations mixed-everywhere else |
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pseudo-first order reaction
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is second order, but if hold [E] constant (replenish E during the reaction), makes it appear to be 1st order
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ADH
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has a higher affinity for ethanol (which has a product of acetaldehyde, which is safe) as opposed to methanol (which has a product of formaldehyde, which is toxic)
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oxido-reductases
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EX: ADH, LDH, oxygenase
it oxidizes or reduces a compound |
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oxygenase
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EX: phenylalanine hydroxylase, turns phenylalanine into tyrosine
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PKU
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lack PH to make tyrosine, therefore there is an excess of phenylalanine in the body
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transferases
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all types of kinases, transfer a group from one compound to another
ex: creatine kinase, pyrophosphorylase |
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hydroxylases
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uses H2O to break or form a bond
ex: peptidases, carbohydrase, nuclease, lipase, phosphotases |
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lyases
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use H20 to break or form a double bond
ex: citric acid, fatty acid metabolism |
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isomerases
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switch a group within a compound
mutases-internal transferase epimerases-switch configuartion about a single atom |
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ligases
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join atoms together, uses ATP
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phosphatases
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remove a PO4
ex: phosphoproteinphosphatase |
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pyrophosphorylases
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break anhydride, form anhydride, used when you want to activate a sugar, release a pyrophosphate
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pyrophosphatases
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used to break down PPi into 2 PO4, makes sure pyrophosphorylase goes from left to right
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phosphorylases
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adds PO4 to bond and breaks a bond
ex: glycogen phosphorylase |
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How do enzymes work? How do they enhance the rate of a reaction?
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1. entropic effects
2. strain 3. acid-base catalysis 4. covalent catalysis |
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entropic effects for enhancing reaction rate
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ex: carbonic anhydrase
INC the likelihood that molecules will collide, affects the collicsion, proximity, orientation and orbital steering of reactants, has a 10-100X INC in rxn velocity |
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strain
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ex: glucokinase, lysozyme
induced fit, causes a change in the enzyme or substrate that INC the likelihood of reaction, 10^4-10^5 INC` |
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acid-base catalysis
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ex: lysozymes, carboxypeptidase, carbonic anhydrase
used to stabilize the charge of reactants, use Zn as cofactor that stabilizes the protein to break bond, INC 10^4-10^5 |
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covalent catalysis (reversible)
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ex: serine protease, chymotrypsin
have hydrophobic pocket, have covalent ES complex, INC rate by 10^4-10^5 |
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covalent irreversible
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zymogens, prohormones, collagen
make substances in active form and cleave or assemble when needed or in proper place |
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lactalbumin
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protein-protein interactions, acts ass allosteric effector of GT to change configuration of GT
pituitary->prolactin->mammary tissue->lactalbumin + GT->UDP-Glu + Gal->lactose |
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protein kinase A
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2 subunits: 2 catalitic and 2 regulatory, cAMP bind to regulatory to free active site on catalitic
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creatine kinase
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dimer
skeletal muscle-M-M, 95% of CK in serum heart muscle-M-B, 2-3%, 10-12 in MI brain tissue-B-B, <1% |
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LDH
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pyruvate <=> lactate
heart-H-H-H-H blood-H-H-H-L liver/skeletal muscle-L-L-L-L heart LDH has higher vmax/km for pyruvate, activated by pyruvate while L4 version is inhibited by high pyruvate PYR + LDH -> PYR-LDH -> LACT + LDH |
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Hexokinase
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HK, found in all tissues except liver, has a higher affinity for G-6-P than GK
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Glucokinase
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GK, found in liver, has a lower affinity for G6P
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HK in brain
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20* more than in other tissues
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resting glucose levels
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5*10^-3 M/L
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GAVLIMP
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0, 1, 3, 4, 4, 4, 4
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FYW
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ring, ring OH, 5 then ring
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STC
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CH2-OH, CH3-CH-OH, CH2-SH
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KRH
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4CH2 NH3+, 3CH2-N-C-N2, CH2-5-ring
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DENQ
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CH2COOH, CH2CH2COOH, CH2CONH2, CH2CH2CONH2
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What is the normal bicarbonate to CO2 ratio ([HCO3-] / 0.03 x pCO2) at physiological pH?
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24/(0.03*pCO2)
pCO2 = 40 |
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The insulin receptor:
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Undergoes autophosphorylation and Acquires kinase activity
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