1 Biochemistry I, Fall 2007 Name:____________________________________ Biochemistry I - Exam I - Face Page This exam has 7 pages, including the face page. There are a total of 100 points. The following equations and constants may be useful but not necessarily required: T = 300K and pH = 7.0 unless otherwise stated. R = 8.3 J/mol-K ΔG° = ΔH° - TΔS° S = R ln W ln 9 = 2.2 ln (an) = n ln a ΔG° = -RT ln Keq For the reaction: ! N " U: Keq = [U]/[N] FU = Keq/(1+Keq) FN = 1/(1+Keq) Acid/Base: pH = pKa+log [A-]/[HA] ! [HA] = [AT]11+ R ! [A"] = [AT]R1+ R Ligand Binding: ! Y =[ML][M] + [ML]=[L]KD+ [L] Scatchard Plot: Y/[L] vs Y ! Y[L]="1KDY +1KD Amino Acid Names: Alanine: Ala Leucine: Leu Arginine: Arg Lysine: Lys Asparagine: Asn Methionine: Met Aspartic Acid: Asp Phenylalanine: Phe Histidine: His Cysteine: Cys Proline: Pro Isoleucine: Ile Glutamic Acid: Glu Serine: Ser Tyrosine: Tyr Glutamine: Gln Threonine: Thr Valine: Val Glycine: Gly Tryptophan: Trp2 Part A: (14 pts) Multiple Choice: Please circle the best answer (2 pts each). 1. The titration curve of a weak mono-protic acid is shown to the right. At pH 5.5: a) the acid is half deprotonated. b) the acid is completely deprotonated. c) the acid is mostly deprotonated. d) the acid is mostly protonated. 2. The surface of a globular protein: a) is mostly non-polar. b) has no non-polar residues. c) is charged, polar and non-polar. d) lacks hydrogen bonds. 3. The equilibrium constant KEQ for a protein folding reaction (UN) at 300 K is 0.1. At this temperature, the protein is: a) mostly folded. b) mostly unfolded. c) at its Tm. d) below its Tm 4. The three-dimensional structure adopted by a polypeptide depends on: a) the primary amino acid sequence of the polypeptide. b) the temperature. c) the pH of the solvent. d) all of the above. 5. The affinity with which a macromolecule binds ligand typically depends on: a) the rate constant, kon. b) the rate constant, koff. c) the number of ligand binding sites. d) both covalent and non-covalent interactions in the ligand binding site. 6. A saturation binding curve with which a macromolecule (M) binds its ligand (L) is shown to the right. At [L] = 1 mM: a) most of M is bound to L. b) all of M is bound to L. c) most of M is not bound to L. d) it is difficult to say how much of M is bound to L because [L] is too low. 7. A Scatchard plot: a) is only useful when binding data from low ligand concentrations is available. b) is only useful when binding data from high ligand concentrations is available. c) is useful for extrapolating to high ligand concentrations. d) is only useful for analyzing ligand binding to macromolecules with a single ligand binding site.3 Part B: 1. (20 pts) The side chains of 3 amino acids are shown below. (i) (ii) (iii) ______________ _______________ ________________ a) Write the name of the amino acid below each side chain structure (3 pts). b) Show how a water molecule might form a hydrogen bond with each of the above side chains. If there are multiple ways for water to interact with a single side chain, show just one of them. If the side chain is incapable of forming a hydrogen bond, also indicate this (3 pts). c) Indicate the side chain most likely to be found in the core of a globular protein (2 pts). [If you don’t know the name of the amino acid, indicate your answer with (i), (ii) or (iii)]. d) Indicate the side chain that is capable of participating in a covalent bond with another side chain (2 pts). e) Indicate which of the three amino acids listed above has the titration curve shown to the right (3 pts). f) Indicate the approximate net charge on the free amino acid containing the side chain shown in (i) at pH 7.0 (3 pts). g) Indicate which of the three amino acids listed above would make a good buffer at pH 6 (2 pts). h) Indicate the amino acid recognized by the enzyme chymotrypsin (2 pts). C! NNC!H S H C!4 2. (14 pts) Draw, in the space below, the extended chain structure of a di-peptide with any two distinct amino acid residues. Your drawing should reflect the ionization state of the di-peptide at pH 7. In your drawing, the peptide bond should be in trans (5 pts). a) Write the name of your di-peptide (1 pt). b) On your drawing, indicate the peptide bond (2 pts). c) Label an α-carbon in your dipeptide (2 pts). d) Indicate a bond about which there is no rotation (2 pts). e) Indicate a bond about which there is freedom of rotation (2pts). 3. (10 pts) The following questions concern the two major 2° structures found in proteins: α-helices and β-sheets. a) List one property that the two structures have in common (2 pts). b) How many main chain hydrogen bonds are formed by a non-polar amino acid residue when it is present in an α-helical conformation (1 pt)? c) How many main chain hydrogen bonds are formed by a non-polar amino acid residue when it is present in a β-sheet conformation (1 pt)? d) List two ways in which an α-helix differs from a β-sheet (6 pts).5 4. (12 pts) Please fill in the following table concerning the forces that impact protein stability. Force/effect Primary impact on ΔH° or ΔS°? Typically favors protein folding or unfolding? H-bonds Van der Waals Configurational entropy Solvent entropy 5. (a) Sketch the structure of an intact antibody molecule. Your sketch should indicate the number of subunits, number and location of antigen binding sites, and number of Ig folds per subunit (4 pts). (b) The affinity with which an antibody of interest binds its antigen is 1 nM (ie, the KD of the interaction is 1 nM). What is the standard free energy change (ΔG°) that occurs when the antibody binds its antigen at 300K (4 pts)?6 6. (4 pts) Sketch a pH titration curve of the tri-peptide Asp-Gly-His and indicate all inflection points and equivalence points. Label the x-axis in equivalents and indicate the net charge on the tripeptide at each equivalence point. 7. (6 pts) You are asked to construct 1 liter of a 10 mM buffered solution at pH 6.0. a) Indicate how you would construct your buffer using the tri-peptide described above (Asp-Gly-His). You have at hand the fully