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### 137 Cards in this Set

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 Poiseulle’s Law Q = (pi * r^4 * ∆Pressure) / (8 * viscosity * length) conversion from liter 1 L = 1 quart 1 L = (1000 gm)/(18 gm/mole) = 55.5 moles/L dielectric effect a shielding effect where a slightly (-) charge is neutralized by a (+) charge due to polarity If you decrease order (increase entropy), what happens to energy change? -decreasing order is equivalent to going from high energy to low energy (spontaneous reaction) -reactions want less order Gibbs free energy (∆G) ∆G = ∆H (heat) – T∆S (randomness) osmotic pressure osP = ([conc] * R * T) / (MW) T is in kelvins (K = 273 + C) Keq Keq = [products] / [reactants] pK & Keq of lactic acid Keq = 1.38 * 10^-4 pK = 3.86 pK & Keq of ammonia Keq = 5.62 *10^-10 pK = 9.25 Henderson-Hasselbalch Equation pH = pK + log [A-]/[HA] (conj. base/conj. acid) pK’s of phosphoric acid (H3PO4) pK1 = 2.1 pK2 = 7.2 pK3 = 10.0 pH of the body 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 pK of carbonic acid pK = 6.1 CO2 + H20  H2CO3  H+ + HCO3- essential amino acids F, V, T, W, I, M, H, R, L, K polar amino acids G, S, T, C, Y, D, N, E, Q, H, R, K nonpolar amino acids A, V, L, I, M, F, W, P ordering of molecules for determining chirality 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 pK’s of amino acids other than acidic and basic ones pK = 2.5 (for COOH) pK = 9.5 (for NH2) pK for acidic amino acids (ASP + GLU) pK = 2.5 (for COOH) pK = 4.5 (for acidic proton) pK = 9.5 (for NH2) pK for basic amino acid Lys pK = 2.5 (for COOH) pK = 9.5 (for NH2) pK = 10.5 (for basic proton) pK for basic amino acid Arg pK = 2.5 (for COOH) pK = 9.5 (for NH2) pK = 12.5 (for basic proton) pK for basic amino acid His pK = 2.5 (for COOH) pK = 6.0 (for basic proton) pK = 9.5 (for NH2) molecule used for cation exchange chromatography CMC-carboxy methyl cellulose, (-) charge molecule used for anion exchange chromatography DEAE-diethyl amino ethane, (+) charge how to detect whether or not an amino acid is a primary or secondary amine use ninhydrin primary amines -> purple secondary amines -> yellow beer-lambert law 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 conditions for obtaining aa residues 6 N HCL, 100 C, 24 hr properties of peptide bonds 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 Prosthetic Groups (of protein's primary structure) Heavy Metals: Fe, Zn, Cd, Hg, Pb when trying to estimate MW 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 average aa MW 120 gm/mol to find est. number of aa in a protein take min MW and divide by 120 gm/mol Edman’s Reagent 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 Sanger’s Reagent DNFB (dinitro fluoro benzene), hydrolyzes entire peptide chain so get individual aa’s but not order, gives the aa on the NH2 end Dansylation dansyl chloride, has fluoresces, destroys other peptide bonds aminopeptidase chews peptide from amino end down, gives new sample every 15 secs hydrazine tags each aa except for the COOH terminal aa, so tells what aa is on the COOH end, breaks every peptide bond trypsin and cleavage of aa’s cleaves basic aa’s (lys, arg) chymotrypsin and cleavage of aa’s cleaves aromatic aa’s (Phe, Tyr, Trp), sometimes His cyanogen bromide (CNBr) and cleavage of aa’s cleaves methionine To separate aa’s based on solubility/hydrophobicity: TLC, reverse phase To separate aa’s based on charge: ion exchange To separate aa’s based on size: gel exclusion, ultracentrifugation, dialysis, PAGE to separate aa’s based on function affinity purification reagent used to denature a protein SDS (sodium dodecyl sulfate), a detergent that stretches protein lengthwise), adds (-) charge to every 2 aa's sedimentation rate S = MWt (1 – (volume*density)) / (friction = 6 * pi * viscosity * strokes radius) s is dependent on mass and shape what determines where R groups are relative to each other on an aa peptide 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 alpha helix features 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 alpha helical breakers 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 beta structure features 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 beta turn can turn anywhere, not just Beta sheets, can be alpha helical breakers, a proline, then a small R group (glycine), then a hydrophilic structure of collagen glycine, X (proline), Y, glycine, X (proline), Y… perpendicular H-bonds ¼ stagger in bone due to collagen 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) mercaptoethanol CH3CH2SH used to reduce disulfide bonds to SH quaternary structure all interactions between multiple subunits are non-covalent (hydrophobic patches, ionic links or H-bonds) anabolic vs. catabolic anabolic (synthesis) or catabolic (degradation), cannot be used to determine the spontaneity of a reaction gibbs free energy and spontaneity ∆G = (-) is spontaneous ∆G = 0 is at equilibrium ∆G = (+) is non-spontaneous Standard State Conditions for ∆G 1 mole/L each reactant and product fixed temperature pH = 7.0 [H2O] = 55.5 moles/L ∆G°’ is inversely related to – Keq ∆G°’ equation (free energy at standard state) ∆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 actual free energy ∆G = ∆G°’ + RT ln ([P]/[R]) ∆G°’ for glucose ∆G°’ = -4000 cal/gm * 180 gm/mole -720,000 cal/mole Keq = 10^528 strategies that limit the ∆G°’ for glucose 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 energy in esters (-3 Kcal/mole), forms acid and alcohol (or amine if breaking down amide) energy in thiol-esters -6 to -8 Kcal/mole energy in anhydrides -7 to -10 Kcal/mole, ex: ATP what accounts for the difference in energy between different compounds 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 energy in guanidinum phosphates -10 Kcal/mole Creatine made from Arginine, composed of Gly, Met, Arg energy in enoyl phosphate -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)) oxidation states of C methane  methanol  formaldehyde  formic acid  carbon dioxide tightly ordered ---------------------------------------------------------> loosest reduced -----------------------------------------------------------------> oxidized energy in carbohydrates vs. fats 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 energy in NADH or FADH -15 Kcal/mole velocity of a reaction dependent on the activation energy, v = k [R] Keq in terms of kinetics and thermodynamics Keq = [P]/[R] = kf/kr velocity of a reaction (Michaelis-Menton equation) v = vmax * ([S]) / (Km + [S]) max. velocity of a reaction vmax = k3 * [Et] Km = Km = (k2 + k3) / (k1) inverse of affinity k2/k1 turnover term k3/k1 to determine enzyme specificity or enzyme preference Vmax/Km Lineweaver-Burk eq 1/v = (Km/Vmax) * (1/[S]) + (1/Vmax) x-intercept of Lineweaver-Burk plot -1/Km y-intercept of Lineweaver-Burk plot 1/Vmax slope of Lineweaver-Burk plot Km/Vmax irreversible inhibitors 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 competitive inhibitor binds to initial enzyme, reversible, same Vmax, different Km non-competitive inhibitor 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 uncompetitive inhibitor inhibitor binds to ES complex, DEC Km and Vmax 6 classes of enzymes OTHLIL (oxido-reductases, transferases, hydrolases, lyases, isomerases, ligases) Modification of amino acids (post-translational): hydroxylation proline-found in urine during bone remodeling, important in collagen, hydroxylate C 3 or 4 lysine-hydroxylate C 4 or 5 Modification of amino acids (post-translational): esterifcation 1. acetylation-adding acetic acid 2. phosphorylation aa's involved: serine, threonine, tyrosine what form of amino acid is found in humans? L-form, it evolved the right turn alpha helix racemization and example of such: racemization-switching from the D to L form EX: aspartic acid, racemizes @ 0.14%/year Solvents used in TLC polar: water nonpolar: isopropanol, butanol, phenol carboxypeptidase similar to aminopeptidase but starts at the carboxy end and gives sample every 15 secs. Piezo Electric Effect found in inorganic systems, where crystals orient themselves perpendicular to a force random coils 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 Affinson's Experiment 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 creatinine the spontaneous folding of creatine's COOH and NH2 end, is excreted through urine, detected during muscular damage oxidation and reduction forms of atoms "ic" oxidized "ous" reduced turnover constant/turnover number k3 slowest step in the michalis-mentin equation v = k3 [E*S] complex First, Zero, and Mixed order reactions first-low [S] concentrations zero-high [S] concentrations mixed-everywhere else pseudo-first order reaction is second order, but if hold [E] constant (replenish E during the reaction), makes it appear to be 1st order ADH 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) oxido-reductases EX: ADH, LDH, oxygenase it oxidizes or reduces a compound oxygenase EX: phenylalanine hydroxylase, turns phenylalanine into tyrosine PKU lack PH to make tyrosine, therefore there is an excess of phenylalanine in the body transferases all types of kinases, transfer a group from one compound to another ex: creatine kinase, pyrophosphorylase hydroxylases uses H2O to break or form a bond ex: peptidases, carbohydrase, nuclease, lipase, phosphotases lyases use H20 to break or form a double bond ex: citric acid, fatty acid metabolism isomerases switch a group within a compound mutases-internal transferase epimerases-switch configuartion about a single atom ligases join atoms together, uses ATP phosphatases remove a PO4 ex: phosphoproteinphosphatase pyrophosphorylases break anhydride, form anhydride, used when you want to activate a sugar, release a pyrophosphate pyrophosphatases used to break down PPi into 2 PO4, makes sure pyrophosphorylase goes from left to right phosphorylases adds PO4 to bond and breaks a bond ex: glycogen phosphorylase How do enzymes work? How do they enhance the rate of a reaction? 1. entropic effects 2. strain 3. acid-base catalysis 4. covalent catalysis entropic effects for enhancing reaction rate 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 strain ex: glucokinase, lysozyme induced fit, causes a change in the enzyme or substrate that INC the likelihood of reaction, 10^4-10^5 INC` acid-base catalysis 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 covalent catalysis (reversible) ex: serine protease, chymotrypsin have hydrophobic pocket, have covalent ES complex, INC rate by 10^4-10^5 covalent irreversible zymogens, prohormones, collagen make substances in active form and cleave or assemble when needed or in proper place lactalbumin protein-protein interactions, acts ass allosteric effector of GT to change configuration of GT pituitary->prolactin->mammary tissue->lactalbumin + GT->UDP-Glu + Gal->lactose protein kinase A 2 subunits: 2 catalitic and 2 regulatory, cAMP bind to regulatory to free active site on catalitic creatine kinase 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% LDH 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 Hexokinase HK, found in all tissues except liver, has a higher affinity for G-6-P than GK Glucokinase GK, found in liver, has a lower affinity for G6P HK in brain 20* more than in other tissues resting glucose levels 5*10^-3 M/L GAVLIMP 0, 1, 3, 4, 4, 4, 4 FYW ring, ring OH, 5 then ring STC CH2-OH, CH3-CH-OH, CH2-SH KRH 4CH2 NH3+, 3CH2-N-C-N2, CH2-5-ring DENQ CH2COOH, CH2CH2COOH, CH2CONH2, CH2CH2CONH2 What is the normal bicarbonate to CO2 ratio ([HCO3-] / 0.03 x pCO2) at physiological pH? 24/(0.03*pCO2) pCO2 = 40 The insulin receptor: Undergoes autophosphorylation and Acquires kinase activity