Biochemistry 461 Section I May 21 1997 Final Exam Prof Jason D Kahn Your Printed Name Your SS Your Signature You have 120 minutes for this exam The exam has 6 questions worth 200 points Do all 6 questions Exams written in pencil or erasable ink will not be re graded under any circumstances Explanations should be concise and answer the specific question asked You will need a calculator for this exam No other study aids or materials are permitted There will be a viewing at a time and place to be announced on the class web page Final grades will be available only through MARS Possibly Useful Information Michaelis Menten equation v0 Vmax S Km S where Vmax k2 E t Type of inhibition Apparent Km Apparent Vmax Apparent Vmax Km Competitive aK m Vmax 1 a Vmax Km Uncompetitive 1 a Km 1 a Vmax Vmax Km Mixed a a Km 1 a Vmax 1 a Vmax Km Noncompetitive a a Km 1 a Vmax 1 a Vmax Km a 1 I KI a 1 I KI Henderson Hasselbach equation pH pKa log A HA DG DH TDS DG RTlnQ where Q has the form of an equilibrium constant Nernst equation DG nFDE F 96500 Coulomb mole electrons For transport of A from out to in DG RTln A in A out ZAFDY RT 2500 J mole today 2 1 40 pts Protein Structure and Folding a 8 pts What is the hydrogen bond pattern of an a helix specify functional groups on the n and n something residues Describe two differences between a helices and b sheets which rationalize why it easier to make small peptides 20 aa which fold into a helices than it is to make peptides which fold into small b sheets and why a helices are more common folding nuclei than b sheets b 7 pts Draw the Ala Pro dipeptide with a cis peptide bond Why is proline the only amino acid for which the cis form is energetically accessible Why is spontaneous cis trans interconversion of the peptide bond slow 3 DG folding kcal mole c 25 pts Proteins can always be denatured by heating though for some proteins this may require temperatures 100 C Some proteins also denature at low temperatures cold denaturation We want to understand the thermodynamics of these processes One simple model uses the temperature dependence of the hydrophobic effect As the temperature increases the hydrophobic effect becomes weaker as clathrates become less enthalpically stable and less ordered We will assume that London forces salt Protein Folding Thermodynamics 15 bridges and hydrogen bonds are temperature independent 10 contributing a favorable DH 0 and DS 0 while configurational 5 ordering of the peptide chain has a DGfolding temperature independent DH 0 0 and unfavorable DS 0 The Tc Tm graph sketches the temperature dependence of DGfolding for the reaction below U N 5 0 20 40 60 Temperature C 80 100 1 2 At the transition temperatures Tc cold and Tm melting where U N what is DG for folding 2 3 At low temperature DGfolding increases goes from negative to positive as temperature decreases through Tc Deduce the signs of DHfolding and DSfolding at low temperature Is folding enthalpy driven or entropy driven 3 6 Explain the physical origin of the signs of DH and DS from part 2 4 4 3 Around Tm DGfolding increases as temperature increases Deduce the signs of DHfolding and DSfolding at high temperature Is folding enthalpy driven or entropy driven 5 6 Explain the apparently contradictory results of parts 2 and 4 using the temperature dependent thermodynamics of the hydrophobic effect 6 5 Explain why proteins cold denature in terms of the hydrophobic effect 5 2 35 points Nucleic Acids Hoogsteen face a 10 pts Draw a possible base pair between guanosine and adenosine with at least two hygrogen bonds The structure of guanosine is given at the right What makes the four Watson Crick base pairs special O N N H G N N NH2 dR b 8 pts Seeman and Rich proposed that arginine should specifically recognize guanine and that asparagine should recognize adenine in protein DNA complexes Draw a reasonable recognition interaction between arginine and the Hoogsteen face of guanine the major groove edge 6 c 8 pts Why is the the major groove more informative than the minor groove Why is it difficult for a protein to specifically recognize the major groove of A form helical double stranded RNA e 9 pts Give a chemical rationale with a structure for the evolutionary advantage of the DNA sugar phosphate backbone as opposed to the RNA backbone for the genetic material 7 3 30 points Bioenergetics Transport a 20 pts The Na K ATPase pumps 3 Na sodium ions out of the cell and 2 K potassium in for each ATP hydrolyzed according to the equilibrium below 3 Na in 2 K out ATP H2O 3 Na out 2 K in ADP Pi Typical conditions are Na in 10 mM Na out 150 mM K in 120 mM K out 5 mM and DY 82 mV inside negative drives cations in 1 5 What is DG for transporting one Na ion from inside to outside 2 5 What is DG for transporting a K ion from out to in 3 5 What is the total DG for the transport performed by the ATPase This value is somewhat larger than the DG 30 5 kJ mole available from ATP hydrolysis How is this possible Hint I haven t told you the concentrations of ATP ADP and Pi 8 4 5 What effect would opening a potassium channel have under these conditions How about a sodium channel b 10 pts The DG for ATP hydrolysis is 30 5 kJ mole and for glucose 6 phosphate hydrolyis is 13 8 kJ mole Calculate DG and the equilibrium constant for the reaction below What is one likely physiological function for this phosphorylation Glucose ATP Glucose 6 phosphate ADP 9 4 35 pts Enzymology a 8 pts The first step in the lysozyme mechanism is shown below Draw the oxonium ion which results What is the role of Asp 52 in the reaction O Glu 35 H CH2 OH O NAG 3 OR H HO O NHAc Asp 52 b 6 pts Based on your answer to a which one of the following compounds could be a transition state analogue and therefore a good inhibitor of the enzyme Explain your reasoning A B C NAG 3 CH2 OH O AcN H CH2 OH O OR NAG 3 HO CH2 OH P OCH3 HO NHAc NAG 3 HO H O C NHAc O c 5 pts The enzyme ATCase is allosterically activated by ATP and deactivated by CTP In the presence of saturating amounts of the substrates aspartate and carbamoyl phosphate how will the binding constants for each of the two allosteric effectors change O 10 The beginning of the mechanism for Schiff s base catalyzed decarboxylation of a b keto carboxylic acid is drawn below as an aid in part d R RNH2 H O N O O O O d 11 pts The …