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Fichas

Biochem midterm

j_sunga Inglés 58 fichas

Fichas del conjunto (58)

  1. 1Very non polar amino acidsAla, Val, Leu, Ile, Phe, Met
  2. 2Moderately Non Polar Amino AcidsGly, Cys, Pro, Trp, Tyr
  3. 3Polar but uncharged amino acidsSer, Thr, Asn, Gln
  4. 4Positively Charged Amino AcidsHis, Lys, Arg
  5. 5Negatively Charged Amino AcidsAsp, Glu
  6. 6Hydrogen bondelectrostatic attractions between H-bond donor and an acceptor
  7. 7hydrogen acceptorelectronegative atom with available lone pair of electrons
  8. 8Henderson-Hasselbalck equationpH = pKa + log[deprotonated]/[protonated]
  9. 9factors affection pKa of amino acidpart of chain, chemical context (surroundings), ionizable groups
  10. 10residue:monomer of a polymer (example amino acid in a protein)
  11. 11peptide bond-C(=O)-N(-H)-
  12. 12polypeptidechain with many amino acids, usually a complete protein
  13. 13oligopeptidechain with a few amino acids, usually a fragment
  14. 14electronegativitytendency of an atom to attract or hold electrons
  15. 15Relative mobilitycharacteristic of each amino acid from thin layer chromatography (Xb/Xf = height travelled/solvent front)
  16. 16cation vs. anion exchangercation exchanger binds cations (contains anions), anion exchanger binds anions (contains cations)
  17. 17elution volumevolume of buffer needed to move compound through column
  18. 18basis of chemical reactivityunbalanced distribution of valence electrons
  19. 19metal affinity chromatographyNi2+ binds tightly to His clusters
  20. 20Gel filtration/molecular exclusion chromatographyelution of proteins based on size (larger elute first)
  21. 21Electrophoresisseparation based on movement of charged molecules in an electric field (based on size, shape and charge)
  22. 22Isoelectric Focusingseparation based on charge
  23. 23isoelectric pointpH at which net charge on a protein = 0
  24. 24selective hydrolysiscuts polypeptide at specific location to yield limited # of oligopeptides at definite size
  25. 25where do trypsin, chymotrypsin and cyanogen bromide cut peptides?Arg/Lys, Phe, Trp, Tyr, Met (trypsin and chymotrypsin have problem with Proline)
  26. 26steps in tandem mass spectrometry (4)1. hydrolyzed by proteases, 2. MS-1: separate peptides of different masses, 3. collision cell (random fragmentation), 4. MS-2, measures fragment masses
  27. 27nucleophileatom with lone pair available to share
  28. 28hydrolysisattack by H2O as nucleophile on electron deficient C of peptide bond
  29. 29benefit of Edman methodallows N-terminus to be removed without hydrolysing peptide bonds (can be repeated up to 50 times)
  30. 30coupling requires ______, cyclization requires ______base, acid
  31. 31amino acids that favour beta strandWYF VIT C
  32. 32amino acids that favour alpha helixAla, Arg, Gln, Glu, His, Leu, Lys, Met (Phe)
  33. 33secondary structure breaker amino acidsDPNGS
  34. 34conformation vs. configurationconformation can be changed by bond rotation, configuration only changed by breaking covalent bonds
  35. 35restoring disulfide structureremove urea THEN expose to oxygen (if exposed to oxygen first, will refold incorrectly)
  36. 36ion pairs (salt bridges)strong electrostatic interaction between charged side chains that are nearby in folded protein
  37. 37tertiary structure of alternating alpha helical and beta-strand segmentsforms parallel beta sheet, folds into beta barrel or sandwich structure
  38. 38Arrenhius equationRate = pZe^(-Ea/RT)
    Z- collision frequency, e - constant, Ea - activation energy, p - probability factor
  39. 39e^(-Ea/RT)=fraction of molecules at temperature T (in Kelvins) which possess energy Ea
  40. 40How do enzymes speed up reactions?remove randomness of collision, remove randomness of reaction process (proximity and orientation), decreases Ea (stabilize transition state)
  41. 41nucleophilic catalysisenzymes provide better nucleophile
  42. 42electrophilic catalysisenzymes use electron seeking group, initiate reaction by drawing electrons from substrate
  43. 43general acid/base catalysisdonate/remove H+ from reaction
  44. 44components of chymotrypsin catalytic triadAsp 102, His 57, Ser 195
  45. 45enzyme assaymeasuring enzyme catalyzed reaction rate
  46. 46enzyme kineticsmathematical analysis of how rate varies as function of [substrate]
  47. 47Absorbance equationA=log(Io/I)
  48. 48Beer-Lambert LawA=ɛcl,
    ɛ - extinction coefficient, c - concentration (mol/L), l - pathlength (cm)
  49. 49rate of reactionconcentration of substrate used or concentration of product formed per unit time
  50. 50enzyme activitymoles of substrate converted per unit time (rate x volume)
  51. 51specific activityactivity per unit mass of enzyme
  52. 52molar activityactivity per mole of enzyme (specific activity x molar mass of enzyme), also known as turnover number
  53. 53initial rate (vo) =K2[ES]
  54. 54steady state equation(k2+k-1)[ES]=k1[E][S]
  55. 55Michaelis- Mentin EquationVo=Vmax[S]/Km+[S] where Km[ES]=[E][S]
  56. 56Vmaxindicates catalytic rate when 100% of enzyme is occupied by substrate (saturated)
  57. 57Vmax=k2[E]total, upper limit for rate
  58. 58Kmindicates how well substrate fits catalytic site, concentration of S that gives initial rate of 50% Vmax (low Km means high recognition - better)

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(Winter 2014) Fichas sobre Biochem midterm, creado por j_sunga el 08/01/2014.
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j_sunga
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winter 2014
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