C485 Exam II Fall ‘15
Name______
Legible please!
Do not use acronyms. Use structures whenever they are asked for, or appropriate. Your explanations should be brief. Overly lengthy answers with irrelevant or erroneous material will receive deductions. Unless otherwise specified, all mechanisms should start at the beginning with a catalytically competent resting enzyme and end with a catalytically competent resting enzyme. GOOD LUCK
1. (15 Pts) There are two pathways for the degradation of serine. Outline (structures required) these pathways, showing all reaction products. A cofactor that is ubiquitous in amino acid metabolism is involved in a step in each of these two pathways. Draw the mechanism for one of these two cofactor-assisted transformations (your choice).
See transformations no. 3 and 5 in your PLP mechanism sheet (on the class web site).
2. (12 pts) Pick a branched chain amino acid. Outline its degradation (structures). Draw the mechanism for the first step of this pathway. (Just the first half of this mechanism is required.)
See branched chain amino acid metabolism on the class website.
See transamination reaction on PLP mechanism sheet.
3. (12pts) Outline the steps required to degrade this short chain fatty acid (structures). What would the energy yield (in ATP) be from this? Make sure you show how you arrive at this.
4. (8 pts) Which nucleotides are bound to G-proteins in their unactivated state and activated state, respectively? How does the 7TM activate a G protein? How is the activated state of a G protein returned to the unactivated form?
Ch 14 question 7 self test
5. (15 pts) Starting with alanine generated in muscle cells, diagram how the nitrogen in this compound winds up being excreted from the body. You should diagram the full journey, showing all chemical intermediates that accept and carry the nitrogen forward to the final excreted product. No curly arrow required, just structures and diagrams.
Figs 23.16 and .17 using structures
6. (8pts) Which of the following answers complete the sentence correctly? (Circle those answers)
Receptor tyrosine kinases
a) are seven-transmembrane helix receptors
b) are integral membrane enzymes
c) activate their targets via the G-protein cascade
d) are often activated by ligand-induced dimerization
e) can phosphorylate themselves on their own cytoplasmic domains when activated
f) that have been actiated by hormone binding are recognized by target poroteins hainvg SH2 (src protein homology region 2) sequences
g) are so named because they contain extraordinarily high amounts of tyrosine.
Ch 14 question 27 self test
7. (12 pts) Please briefly answer the following short questions (3pts each)
a) What are the two major sources of reducing power required for fatty acid synthesis?
Pentose phosphate pathway and citrate/pyruvate shuttle (exchange)
b) How is pyrophosphatase involved in the activation of fatty acids for beta oxidation?
Acyladenylate formed from cleavage of ATP yields pyrophosphate, which is degraded to 2Pi. This renders the reaction irreversible, because of the cleavage of 2 anhydride bonds.
c) Explain the involvement of carnitine in the beta oxidation of fatty acids.(structures not necessary)
Fatty acid CoA thioester must be transported to the mitochnodria, but it cannot pass through membranes. The fatty acid is temporarily transesterified with carnitine, which is transported and then transesterified back to CoA thioester.
d) What two properties make triacylglycerols more efficient than glycogen for the storage of energy?They are more reduced and do not hydrate. This means they yield more energy per unit weight.
8. (6pts) Outline the degradation pathway for ornithine.
9. (16 pts) Odd carbon number fatty acids leave a breakdown product that is different than that formed from even number fatty acids. What is it? Show how this can be converted into something that can enter a primary metabolic pathway. Draw the mechanism of this/these steps.
Propionyl CoA biotin dependent carboxylation to methyl malonyl CoA, B-12 dependent rearrangement to succinyl CoA. See mechanisms on web site and book.
10. (10 pts) Describe the structure of glycogen. Use chemical structures as necessary. What enzyme activities are required for glycogen breakdown? Describe what these enzymes do.
Figure 21.2 glycogen structure. Glycogen phosphorylase uses Pi to cleave a residue off the nonreducing end to yield alpha- glucose 1-P. Debranching enzyme cleaves residues off 1-6 branching chains by transferring blocks of 3 glucose molecules to nonreducing end. This leaves one glucose linked alpha 1-6. This is hydrolyzed by a glucosidase activity.
11. (12 pts) super duper extra extra credit. Draw the mechanism for oxidative decarboxylation of an alpha keto acid. Make sure to show all required cofactors and explicitly draw the mechanism of how all of them promote catalysis.
See TPP mechanism on class web site. Also see FAD oxidation of lipoamide on class web site.