University of Warwick Chemistry Past Paper - Bioorganic Chemistry - March 2015 - PDF

CH3CHx UNIVERSITY OF WARWICK THIRD YEAR EXAMINATIONS: March 2015 CHEMISTRY (BSc. Year 3, MChem Year 3) PAPER CH3CHG: Bioorganic Chemistry. Time allowed for candidates offering ONE SECTION: Time allowed for candidates offering TWO SECTIONS: 1½ hours 3 hours Read the rubric carefully. Percentages in s...

CH3CHx UNIVERSITY OF WARWICK THIRD YEAR EXAMINATIONS: March 2015 CHEMISTRY (BSc. Year 3, MChem Year 3) PAPER CH3CHG: Bioorganic Chemistry. Time allowed for candidates offering ONE SECTION: Time allowed for candidates offering TWO SECTIONS: 1½ hours 3 hours Read the rubric carefully. Percentages in square brackets are intended as a guide to the time candidates should spend in answering the corresponding part of the question. Read carefully the instructions given in each section that you attempt. Answers to each section should be written in a separate booklet. SECTION A: BIOORGANIC CHEMISTRY (CH3F5) Answer TWO questions from questions 4, 5 and 6 You should NOT attempt MORE than TWO questions in this section since ONLY the first TWO will be marked. UNSEEN EXAMPLE SIMILAR TO PROBLEM IN CLASS 4. The enthalpy of binding, HITC and association constant Ka for the immunosuppressant cyclosporin A (Figure 1) interacting with the protein cyclophilin A was measured in aqueous buffer at pH 7.5 using isothermal titration calorimetry (ITC; Table 1). Figure 1. Structure of cyclosporin A. 1 CH3CHx Table 1. ITC data for cyclosporin A interacting with cyclophilin A in buffer at pH 7.5. Ka / M-1 T/K 288.8 295.5 298.2 301.2 303.2 307.7 9.43 x 107 1.01 x 108 8.70 x 107 6.71 x 107 5.21 x 107 2.82 x 107 G˚ / kJ mol1) -44.1 -45.3 -45.3 -45.1 -44.8 -43.9 HITC / kJ mol1 – 40.1 – 58.9 – 61.0 – 68.1 – 72.7 – 74.4 SITC Stoichiometry Cp / J K-1 mol(n) /J K -1 mol-1 1 +13.8 -46.1 -52.6 -76.3 -92.1 -100.1 1.05 1.10 1.05 – 1.88 1.10 1.02 1.10 SIMILAR TO EXAMPLES IN CLASSES (a) Calculate the standard free energy of binding Go and hence entropy change SITC, due to interaction of cyclosporin A with cyclophilin A at each temperature, paying attention to units. 4 marks [20%] See completed Table above, from: G° = –RTlnKa S= −(G° - H)/T (units!) (b) Verify there is a linear relationship between HITC and T and hence determine the change in heat capacity at constant pressure, Cp. [10%] Plot graph of T vs ΔH and measure gradient, Cp. (green triangles, below) Cp = -1.88 J K -1 mol-1 from gradient of HITC or anywhere near 0.002 kJ K -1 mol-1 acceptable 2 marks 40.00 20.00 0.00 285 290 295 300 305 310 -20.00 DeltaG -40.00 -60.00 DeltaH -40.10 -58.90 -61.00 -80.00 -100.00 -120.00 2 y = -1.8765x + 498.69 R² = 0.9452 -68.10 -72.70 -74.70 DeltaS CH3CHx (d) X-ray structural analysis of the ligand protein complex reveals a network of bound water molecules between the ligand and protein in the binding site. With reference to this and the thermodynamic values you have calculated, comment on the nature of intermolecular forces involved on binding of ligand with protein. [20%] Recalling that G° = H - TS means that the increasingly negative value of SITC suggests there is an increase in order as temperature increases. Normally, a positive value for Cp is taken to indicate the hydrophobic effect is operating through release of water bound at a non-polar interface. The negative value for Cp indicates reorganisation of protein upon ligand binding but this is fact not substantially due to loss of water, but formation of polar contacts. G˚= H°-TSITC Hence, the negative enthalpy and overall negative G˚suggests that formation of hydrogen bonds to the water molecules observed to be bound in the active site plays an important part in the binding of cyclosporin A to cyclophilin A. This might be rationalised looking at the structure of the ligand, where one ‘face’ has exposed amide carbonyl moieties which can HB to water which remains in the active site. However most of the peptide amide groups are N-methylated suggesting a role in contact to nonpolar residues in the receptor protein cyclophilin, or another binding partner. Gibbs free energy stays constant over temperature range studied which can be interpreted as “entropy – enthalpy compensation” although this phenomenon has come under scrutiny (further reading given in Forum posts for example, JD Chodera, DL Mobley Annu Rev Biophys 2013 http://www.annualreviews.org/doi/abs/10.1146/annurev-biophys-083012-130318 ). 4 marks 3