Chemistry 27 pring 2005 Exam 3 Chemistry 27 Professor Gavin MacBeath arvard University pring 2005 our Exam 3 Friday April 29 th, 2005 11:07 AM 12:00 PM Discussion ection (Day, Time): TF: Directions: 1. Do not write in red ink. othing in red ink will be graded. 2. Write your name on every page of the exam. 3. Provide your answers in the designated space. 4. The last page of the exam has a table of amino acids, cofactors, and DA bases for you to use. You may use the back of this amino acid page for scratch work but nothing written on this page will be graded. 5. You have 11 total pages. We have provided plenty of space for each answer. 6. All intermediates must be drawn as a distinct step. You need not draw out proton transfers as a distinct step unless explicitly told to do so. 7. Molecular model kits and calculators are permitted. 8. A significant fraction of your exams are photocopied before they are returned. Question core 1 /15 2 /25 3 /20 4 /20 5 /20 Total /100 Page 1 of 11
1. [15pts] Many anticancer and antiviral drugs are nucleoside analogs that get incorporated into DA or A. ne such drug is 5-iodo-2 -deoxyuridine (IDU), which is used in the treatment of herpes simplex virus. The iodine causes a shift in equilibrium to favor more of the enol tautomer of IDU. A) Draw the Watson-Crick base pairing of both the keto and enol tautomers with their complementary bases, indicating all hydrogen bonding. You may abbreviate the deoxyribose sugar with. (10pts) 5-iodo-2'-deoxyuridine (IDU) I I I adenine IDU keto tautomer guanine IDU enol tautomer 5pts for each base pair B) Using the base pairing information from your answer in part A, briefly describe how IDU induces mutations in DA. (5pts) During replication, if IDU is in the enol form, a G is place opposite of it in the growing strand. In the second round of replication, a C is placed opposite the G, fixing the mutation in the genome. 2pts for G opposite IDU 3pts for C opposite G/fixing mutation Page 2 of 11
3 2. [25pts] ebeccamycin, a potent anti-tumor agent, is biosynthesized starting from the amino acid, L-tryptophan. C L-Tryptophan AD 2 AD + - 2 2 FAD FAD 2 FAD 3 C L-Chlorotryptophan C (3) ebeccamycin A) how the mechanism for the FAD-dependent conversion of L-tryptophan to L- chlorotryptophan, accounting for the formation of all products. You may use the abbreviated structure of FAD and AD in your mechanism. int: The FAD derivative shown on the right is an intermediate in the conversion. (15pts) A A + 2 2-2 + + :B 3 C 3 C 3 C Page 3 of 11
B) how the mechanism for the formation of (3) from L-chlorotryptophan. (5pts) + C C C) The FAD 2 formed in part B is then used to catalyze the reduction of 2 to 2 2 for use later in the reaction sequence. how the mechanism for the formation of 2 2 and the regeneration of the FAD. (5pts) + 2 2 + + Page 4 of 11
3. [20pts] Most organisms use ATP as the source of energy. Bacterium Examobaccilus examicus however does not use ATP. Instead, it is found that E. examicus actually uses adenosine trisulfate (AT), the sulfur-analog of ATP, as its energy source. 2 AT A) cientists discovered that AT is much more susceptible to nucleophilic attack than ATP. Explain briefly why this is so. (4pts) The trisulfate portion of AT is substantially less negatively charged than the triphosphate of ATP. ence, nucleophilic attack on the sulfur atoms of AT is less kinetically disfavored than nucleophilic attack on the phosphorus atoms on ATP. B) It was found that nucleophilic substitutions at the sulfur atoms of AT do not proceed with 100% inversion of stereochemistry. Using the template below, provide a mechanism that leads to retention of stereochemistry at the atom. You must show all ground state intermediates in your mechanism. (8pts) u: 17 18-16 LG 17 18 - u LG 16 - pseudorotation 17 18 - - 16 u LG 17 18-16 u retention Must clearly show the pseudorotation for full credit Page 5 of 11
C) AT was found to be much more susceptible to nucleophilic attack on the β-sulfate than ATP on the β-phosphate. In fact, many reactions using AT involve nucleophilic displacement at the β-sulfate with either inorganic sulfate or adenosine monosulfate (AM) as the leaving group. ne of these reactions involving AT is shown below. AT + AM :C C 2- + 4 1 Propose a plausible mechanism for the reaction, accounting for all the products. You do not need to draw high energy, pentavalent intermediates but clearly indicate the flow of electrons for all steps. (8pts) 2-3 Adenosine 1 4 2- AM - :C -can attack from either face C 2 AM AM C 2 deprotonation could be by water AMP as first leaving group and 4 2- as second is acceptable for full credit Page 6 of 11
4) [20pts] Please provide a mechanism that shows how each of the enediynes below reacts under the indicated conditions to form an aryl diradical. A) (6pts) trong base :B B) (7pts) Me Mild base Me Page 7 of 11
C) (7pts) trong Base :B + + Taut.and Bergman Page 8 of 11
5) [20pts] The cyclic peptide shown below is synthesized on a non-ribosomal peptide synthase that contains a domain with nonstandard activity. 3 A) What amino acid is chosen by the first adenylation domain? (2pts) Cysteine B) Which domain is responsible for the formation of the bond indicated by the arrow? Give a reasonable mechanism for all reactions catalyzed by that domain. In your answer, represent all relevant domains as circles and show the side chain of relevant residues on the domains, if any. You can abbreviate phosphopantetheine as PA-. You do not need to draw the high energy, tetrahedral intermediates but clearly indicate the flow of electrons for all steps. (10pts) The TE domain is responsible for the indicated bond. PCP4 PA + 2 TE :B TE + 2 + PCP4 PA :B 3 + TE Page 9 of 11
C) Fill in the table below for the gene of the non-ribosomal peptide synthase responsible for the synthesis of this molecule. Please indicate the amino acid chosen by each adenylation domain. (8pts) A C PCP TE Module 1 X (Cys) X X Module 2 X (er) X X Module 3 X (Gly) X X Module 4 X (Val) X X X ne point off for each incorrect box Page 10 of 11
Useful Information 2 Me 3 Alanine Ala/A 3 Cysteine Cys/C 3 Aspartate Asp/D 3 3 Glutamate Glu/E 3 3 Phenylalanine Phe/F Glycine Gly/G adenine Me 2 3 3 3 3 3 3 2 istidine is/ Isoleucine Ile/I Lysine Lys/K Leucine Leu/L Methionine Met/M Asparagine Asn/ guanine 2 2 2 2 3C 3 C C 3 2 Proline Pro/P 3 Tryptophan Trp/W 3 3 Glutamine Gln/Q 3 Tyrosine Tyr/Y Arginine Arg/ 3 P 3 erine er/ P Threonine Thr/T P ATP 3 Valine Val/V 2 cytosine thymine 2 2 P P ADP + 2-3 P 2-3 P uracil 2 C 3 C 3 2 PLP PAP 3 C P P 3 C FAD Page 11 of 11