Lecture Assignment 1 McMurry & Begley (M&B) Chapter 1 #1-8 Week 2 2 M&B Chapter 1 # 12,16

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1 CEM 109 W Assignments, Lectures 111 (Exam 1 & 2) Lecture Assignment Due* 1 McMurry & Begley (M&B) Chapter 1 #18 Week 2 2 M&B Chapter 1 # 12,16 4/10 3 M&B Chapter 1 # 1.911, 1315 Week 3 4 Draw the ionic species for full p range (114) for acidic & basic amino acids. *No posted key for L4 W. Check your solutions with your TA in office hours or discussion 4/17 5 See W Set on p. W2 Week 4 6 McMurry 8 th Ed. Chapter 26 #38a, 44 (provide your answers at p 3, 7.4, and 10) 4/24 Design an enzyme active site for each reaction in the synthesis of glutamine from glutamate (Lecture 5). Try to keep the number of intermediates to a minimum, although it may not be possible to do each reaction in one step. Use appropriate amino acid residues as acids and bases as needed, as well was Mg 2+ to stabilize the negatively charged phosphates. Lecture Assignment Due* 7 McMurry 8 th ed. Chapter 26 #16, 17; Carbohydrate Activity #14 (p W3) Week 5 5/1 8 Carbohydrate Activity #58 (p. W4) Week 6 9 M&B (p. W5) 5/8 10 See p. W67 Week 7 11 See p. W78 5/15 12 TBD (lecture 12 not covered on exam 2) Week 8 *W is not checked for credit. W should be completed as soon as possible after lecture, but to keep you on track, plan on having your W done by Monday the following week. Monday dates are given in the table for clarity. Unannounced quizzes are given in section and are directly from the W due that week. Students may use their own W notebook during quizzes. W1

2 Lecture 5 omework You are not expected to memorize the schemes in the notes and W for the exams! You are expected to be able to work through the mechanisms given the starting materials, intermediates, products, and/or reaction names. This is more about understanding reactions than memorizing the complex reaction schemes. Biological Mechanisms: Assume that the reactions are taking place at physiological p (7.4). Take that into account when determining charges and proton movement. Use acids ( + ) and bases (:B) freely when needed. 1. n page L52, we covered the biosynthesis of asparagine from aspartate. The biosynthesis of glutamine from glutamate is strikingly similar! Show the mechanisms for each of the three steps in the synthesis of glutamine from glutamate: (1) hydrolysis of glutamine, (2) phosphate transfer with ATP, and (3) amide formation. The ammonia needed to make glutamine does actually come from the hydrolysis of glutamine. It is not uncommon for the degradation products of metabolic intermediates to be used to make the same molecule again! Glutamine + 2 Glutamate + N 3 N + 3 ATP ADP N + Pi 3 N C 2 3 P C 2 NC 2 Glutamate C 2 * Intermediate corrected 4/19 * 2. The final phase in the biosynthesis of proline is the reductive amination of glutamate 5 semialdehyde. Without looking at your notes, draw the arrowpushing mechanism for both steps. Check your mechanism with what was covered in lecture 5. C 2 Glutamine N 3 + C 2 Glutamate 5semialdehyde 2 N C 2 1Pyrroline 5carboxylate NAD NAD + N C 2 Proline 3. Go through your lecture 5 notes and make a list of the different types of mechanisms using terms in the mechanism review from lectures Explain the difference between glutamate and glutamic acid. Do the same for aspartate and aspartic acid. When is each name more appropriate? W2

3 Lecture 7 W CABYDATE ACTIVITY A. Define the following terms on a separate sheet while you complete Part B. Include formulas or structures, where appropriate. Carbohydrate Triose emiacetal Monosaccharide Tetrose Anomeric Carbon Disaccharide Pentose Anomers Trisaccharide exose Epimers Polysaccharide Penultimate Carbon Furanose Aldose DMonosaccharide Pyranose Ketose LMonosaccharide Glycosidic Bond B. Structural Conventions 1. Draw one example of each of the following types of monosaccharides (there may be several correct answers) and indicate the number of possible stereoisomers (while keeping the same D/L configuration). a. DAldotriose b. LKetotetrose c. LAldopentose d. DKetohexose e. LAldohexose 2. Draw Fischer projections of the following: a. The C2 epimer of DGlucose b. The C3 epimer of DGlucose c. The C4 epimer of DGlucose #36. Use the following templates when drawing sugars in aworth projections and chair conformations. 3. Draw aworth projections for the following (consult Fig 25.3 of McMurry; memorize the structure of DGlucose for the second exam). What is the relationship between a & b; between a & c? a. αdallopyranose b. βdaltropyranose c. αdglucopyranose d. βdmannopyranose e. αdgulopyranose f. βdidopyranose g. αdgalactopyranose h. βdtalopyranose 4. Draw the chair conformations for the monosaccharides in problem 4. W3

4 Lecture 8 W Carbohydrate Activity, Part 2 Disaccharides 1. There are at least eight common ways for two glucose units to be linked together to form eight different disaccharides. Show the mechanism for the linking of Dglucose units to make a disaccharide with loss of water. Use any glycosidic linkage or try a few! 2. Draw the aworth projection for βdidopyranosyl(1à6)αdallopyranoside, disaccharide formed between DIdose and DAllose linked by a β1,6glycosidic bond (consult Fig 25.3 of McMurry). 3. Draw the aworth projection for milk sugar (lactose). βdgalactopyranosyl(1à4)βdglucopyranoside disaccharide formed from D galactose and Dglucose linked by a β1,4glycosidic bond (consult Fig 25.3 of McMurry). 4. Draw the aworth projection for table sugar (sucrose). αdglucopyranosyl(1à2)βdfructofuranoside disaccharide formed between D glucose and Dfructose by a α1,2glycosidic bond (consult Fig 25.3 of McMurry and the structure below). 1 2 βdfructofuranose 5. Show the mechanism for the hydrolysis (addition of water) to a disaccharide into two D monosaccharides. W4

5 Lecture 9 W use amino acid residues as acids and bases. W5

6 Lecture 10 W ead all instructions carefully before attempting! efer to Lecture 10 notes to learn reactivity patterns in these new cofactors. 1. Show the mechanism for Step 4 of the citric acid cycle, conversion of α ketoglutarate into succinyl CoA. The reaction involves (1) an initial nucleophilic addition reaction to α ketoglutarate by TPP ylid, (2) decarboxylation, (3) reaction with lipoamide, (4) elimination of TPP ylid, and finally (5) a transesterification of the dihydrolipoamide thioester with coenzyme A. Use the structures below to complete this transformation, plus amino acid residues as acids and bases where appropriate. 2 C C 2 αketoglutarate CoAS C 2 Succinyl CoA N S S S TPP ylid Lipoamide SCoA Coenzyme A 2. Show the mechanism for Step 7 of the reductive pentose phosphate (PP) pathway. This is a transketolasecatalyzed reaction that involves (1) an initial nucleophilic addition reaction to fructose6phosphate by TPP ylid, (2) CC cleavage to release erythrose4phosphate, (3) nucleophilic addition of the TPP adduct to glyceraldehyde3phosphate, and (4) elimination of TPP ylid with release of xylulose5phosphate. Use the structures below and descriptions above to complete this transformation, plus amino acid residues as acids and bases where appropriate. N C 2 C + C 2 P 2 3 Fructose6 phosphate C C 2 P 2 3 Glyceraldehyde 3phosphate S TPP ylid C 2 C C 2 P 2 3 Xylulose5 phosphate + C C 2 P 2 3 Erythrose 4phosphate W6

7 Lecture 10 W (cont d) 3. Show the mechanism for Step 10 of the reductive pentose phosphate (PP) pathway. This is a transketolasecatalyzed reaction that involves (1) an initial nucleophilic addition reaction to seduheptulose7phosphate by TPP ylid, (2) CC cleavage to release ribose5phosphate, (3) nucleophilic addition of the TPP adduct to glyceraldehyde3phosphate, and (4) elimination of TPP ylid with release of xylulose5phosphate. Use the structures below and descriptions above to complete this transformation, plus amino acid residues as acids and bases where appropriate. Number. Your. Carbons. C 2 C + C 2 P 2 3 Sedoheptulose 7phosphate C C 2 P 2 3 Glyceraldehyde 3phosphate N S TPP ylid C 2 C C 2 P 2 3 Xylulose5 phosphate + C C 2 P 2 3 ibose5 phosphate Lecture 11 W 1. efer to the mevalonate pathway in your notes or the textbook when determining the final positions of the carbon14 labeled carbon atoms from Acetyl CoA into IPP, DMAPP, GPP, and Limonene. You are you not expected to memorize the pathways, but given the outline of the process, you should be able to follow a labeled atom. Indicate the positions with a star (*) C 3 C SCoA Acetyl CoA 14 C labeled carbonyl C Mevalonate Pathway Where are the 14 C's?? PP Isopentenyl Diphosphate + C 2 Limonene Where are the 14 C's?? PP Geranyl diphosphate (GPP) Where are the 14 C's?? PP Dimethylallyl diphosphate (DMAPP) Where are the 14 C's?? W7

8 Lecture 11 W (cont d) 2. The biosynthesis of terpenes often involves complex skeletal rearrangements, including hydride and methyl shifts. Add the arrows to complete the mechanism for the synthesis of trichodiene from FPP. Note that the last step requires base involvement, similar to the second step of an E1 mechanism. PP PP Farnesyl diphosphate (FPP) :B Trichodiene 3. Propose a mechanistic pathway for the synthesis of borneol from GPP and water. The first step should be to carefully number the carbons in the starting material to align with the product. You will find a somewhat similar addition of water to alkenes in your lecture 1 notes! PP PP Geranyl diphosphate (GPP) 2 Borneol W8