BCHE 5180 / 6180 FINAL EXAM

BCHE 5180 / 6180 FINAL EXAM Give the general Henderson-Hasselbalch equation and sketch the plot it describes (pH against amount of NaOH added to a weak acid). On your curve label the pKa for the weak acid, and indicate the region in which the buffering capacity of the system is greatest. [ A ] pH  pKa  log [HA] The inflection point, which occurs when the weak acid has been exactly one half titrated with NaOH, occurs at a pH equal to the pKa of the weak acid. The region of greatest buffering capacity (where the titration curve is flattest) occurs at pH values of pKa ±1. Name and briefly define four types of noncovalent interactions that occur between biological molecules. (1) Hydrogen bonds: weak electrostatic attractions between one electronegative atom (such as oxygen or nitrogen) and a hydrogen atom covalently linked to a second electronegative atom; (2) electrostatic interactions: relatively weak charge-charge interactions (attractions of opposite charges, repulsions of like charges) between two ionized groups; (3) hydrophobic interactions: the forces that tend to bring two hydrophobic groups together, reducing the total area of the two groups that is exposed to surrounding molecules of the polar solvent (water); (4) van der Waals interactions: weak interactions between the electric dipoles that two close-spaced atoms induce in each other. Draw the structure of alanine, leucine, isoleucine, tyrosine, lysine and histidine (At pH 7.0). Give also the three-letter and the one-letter codes. Indicate the pKa of the side groups. (Draw 1 amino acid completely, draw only the R group for the other amino acids) H +H3N C COO- CH3 Alanine (Ala, A) CH2 OH Tyrosine (Tyr, Y) pKa = 10.07 CH2 CH CH3 CH3 Leucine (Leu, L) CH2 CH2 CH2 CH2 NH3+ Lysine (Lys, K) pKa = 10.53 CH CH3 CH2 CH3 Isoleucine (Ile, I) H C N CH2 C N CH H Histidine (His, H) pKa = 6.00 Explain the differences between common and uncommon amino acids The 22 common or coded amino acids are used to make proteins. The proteins are synthesized on the ribosome where the sequence of amino acids are dictated by the sequence of codons on an mRNA molecule. The codons are recognized by the anti- codon on a tRNA molecules that have the amino acid attached. Each coded amino acid has its own set of tRNA molecules. Uncommon amino acids include the modified common amino acids as a result of post- translational modifications, and the group of amino acids that are 1) part of small polypeptides, 2) are metabolic or 3) are synthetic intermediates. 5 Given below is the structure of the polypeptide Glu-Gly-Leu-Ser-Leu-Ser-Lys. Glu Gly Leu Ser Leu Ser Lys pKa ~2.0 pKa ~9.6 H O H O H O H O H O H O H O- H3N+ C C N C C N C C N C C N C C N C C N C C H H CH2 CH2 C O O- H H3C H CH2 CH CH3 CH2 OH H H3C H CH2 CH CH3 CH2 OH H O CH2 CH2 CH2 CH2 pKa = 4.25 NH + pKa = 10.53 5a 6 points 5b 2 points What is the charge of the peptide at pH 3.0, pH 8.0, and pH 12? pH +H3N/H2N COOH/COO- +H3N/H2N COOH/COO- charge 3 + 0 + - +1 8 + - + - 0 12 0 - 0 - -2 What is the pI of the peptide? pI is in between pH 4.25 and 9.6: 4.25 9.6  6.93 2 6 A student has purified a protein. The table below describes the followed procedure: Step Volume Total Total Spec. activity protein Act. (ml) (U) (mg) Cell Extract 500 3,000 15,000 0.2 DEAE-Sepharose column (weak ion-exchange) 100 2,400 4,000 0.6 Mono-Q column (strong ion-exchange) 45 1,440 500 2.88 Phenyl-Sepharose column (hydrophic interaction) 50 1,000 125 8.0 The student also prepared an SDS-PAGE gel: Lane 1: Cell extract Lane 2: Sample after DEAE-Sepharose column Lane 3: After Mono-Q column Lane 4: After Phenyl-Sepharose column Lane M: Marker proteins