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1 Sp12 BIBC102 final, page 1 Hello Young Metabolites! This is the Metabolic Biochemistry final. I am hoping you will agree that you have learned a lot of new things about some of the core processes of life as we know it. How boss! This test will be handed in, and will be available for pickup sometime next week. Although I will be away, there will be a way to get them. The key is posted on the website TONIGHT. Feel free to register complaints, comments, questions, or corrections to me by (don t use the text number for this). We just may fold those suggestions into the grading I have enjoyed teaching you and this class. To celebrate our completion, and commemorate our metabolisms, we will have a bunch of pizza outside the test room, which we can eat. Nummm! Happy Summer! Summation Page 2 (out of 12) Page 3 (out of 22) Page 4 (out of 20) Page 5 (out of 13) Page 6 (out of 21) Page 7 (out of 24) Page 8 (out of 17) Page 9 (out of 20) Page 10 (out of 17) Total (out of 166) adjustment to 150 (score time x 150/166 )

2 Sp12 BIBC102 final, page 2 Enzymes and Energetics (12pts) 1) 3pts You and a friend in the same lab class are each determining the activity of an enzyme at varying substrate concentrations. Each of your data sets yields straight lines on a Lineweaver-Burke plot. Knowing this feature of the enzyme, write the equation with S, Vo, Km, Vmax that describes the rate Vo as a function of S. You need use only variables. Vo = 2) 2pts It turns out that in your experiment, you used a concentration of enzyme that was three times higher than your lab mate. Draw a representation of your and your lab mates Lineweaver-Burke plots on the axis provided. Label the axes, and indicate which line is yours and which is your lab mates. 3) 3pts Since you and your lab mate used different enzyme concentrations, some of the numbers you measured are the same, and some are different. For kcat, Vmax, and Km, say which are the same between your experiments, and which are different K m : V max : k cat : 4) 2pts In an advanced class (for secondary metabolites), they study an allosteric enzyme. You measure the activity as a function of S with an allosteric activator present, and your lab mate measures the enzyme without an allosteric activator present. Draw and label the two rate graphs showing the enzyme activity with and without the allosteric activator. 5) 1pt An enzyme changes A) The forward rate of reaction only B) The reverse rate of a reaction only C) The forward and the reverse rate of a reaction D) The ΔG o of the reaction and hence the extent of product formation 6) 1pt T/F: Enzymes that catalyze large energy drop reactions are often allosteric

3 Sp12 BIBC102 final, page 3 Glucose, that sweetly rocks (22 pts) 7) 5pts The following five molecules are metabolites of the pentose phosphate pathway. Put them in order for that pathway, using numbers P-Gluconolactone Ribulose-5P Glu-6P Gluconic acid Ribose-5P 8) 1pt What cellular reducing agent is produced in the pentose phosphate pathway 9) 3pts Below is a representation of the non-reducing end of glycogen. The left glucose is the last one on a long glycogen chain. Write the reaction catalyzed by glycogen phosphorylase that liberates a glucose monomer from this awesome storage depot. I have drawn the smaller glycogen chain to save you work. Add the things you need to make the reaction complete. Draw the missing product, and name it. Glyc phos 10) a) 4pts In liver, what is the usual fate of the glucose monomer that is produced by this reaction? In muscle, what is the usual fate of the monomer that is produced? (one sentence) b) 2pts What enzyme underlies that particular difference between muscle and liver? 11) 1pt T/F: Glycolysis has a negative delta G o 12) 1pt T/F: Gluconeogenesis has a negative delta G o 13) 1pt T/F: Muscles are the largest source of glycogen-stored glucose 14) 1pt T/F: Muscles are the main source of glycogen for maintaining blood glucose levels 15) 1pt T/F: Muscles can convert lactate into glucose 16) 1pt T/F: Liver can convert lactate into glucose 17) 1pt T/F: Muscles can not use fatty acids as fuel

4 Sp12 BIBC102 final, page 4 Krebs Krebs Bo Bebs (20pts) 18) 5pts Write the number of carbons each molecule has. Oxalate Glutarate Malonate Succinate Citrate 19) 3pts Isocitrate dehydrogenase (IDH) is a currently popular enzyme due to its apparent role in some cancers. Its main purpose is as an enzyme of Old Roundy, the Krebs Cycle. Complete the Krebs cycle IDH reaction, including the product structure and name. isocitrate dehydrogenase isocitrate 20) Parts List! 9pts There are only so many ways to ask about the Krebs Cycle. Here is the parts list approach. Use the parts list to fill in the lines in the picture. The numbers refer to enzymes. The lines are where you will add the missing metabolites from the parts list. 21) 3pts Answer the following questions using either the enzyme numbers or the abbreviations for the metabolites from the parts list. a) Which reactions produce CO 2? b) What molecule is transported to the cytosol for fatty acid synthesis? c) What enzyme produces an α-keto acid? f) Which enzyme has a 5 carbon substrate? g) Which enzyme has a 4 carbon substrate? h) Which enzyme has a 3 carbon substrate?

5 Sp12 BIBC102 final, page 5 To (glyoxylate) cycle or not to cycle (13pts) 22) 6pts The glyoxylate cycle is a variant of the Krebs cycle that is used for anabolism. Let's compare the two cycles in this question, sort of like what we did on the midterm a) During each turn of the Krebs cycle, how many AcCoA are consumed?: and how many CO 2 are produced?: b) During each turn of the glyoxylate cycle, how many AcCoA are consumed?: and how many CO 2 are produced?: c) Why can't the Krebs cycle be used to make glucose (or other things) from AcCoA? (one sentence) d) Why CAN the glyoxylate cycle be used to make glucose (or other things from AcCoA? e) 3pts The structure of glyoxylate is shown below. It is a teeny aldehyde. Complete the glyoxalate cycle reaction catalyzed by malate synthase. Include the name of the product metabolite. Label the two carbons in the product that come from AcCoA (this question is full of hints) malate synthase 23) 4pts Bears hibernate over the winter, and they maintain a blood glucose level that keeps them alive, and healthy. They have a lot of fat stores, and no glyoxylate cycle, yet they synthesize glucose by gluconeogenesis over the long winter. Where does the carbon come from to make the glucose they need? Just one or two sentences is all we need

6 Sp12 BIBC102 final, page 6 Fruc-an-A! 24) 11pts This is a picture of the molecule fructose 2,6 bisphosphate (Fr2,6bP). It is a very special molecule in the coordination of glucose metabolism. It affects two key enzymes, and through these actions, two metabolic pathways that involve glucose. Let's make sure you know about this molecule! Brief (one or two word) answers needed a) How does Fr2,6bP affect glycolysis?: b) What glycolytic enzyme does Fr2,6bP regulate?: c) What does Fr2,6bP do to that glycolytic enzyme?: d) How does Fr2,6bP affect gluconeogenesis?: e) What gluconeogenic enzyme does Fr2,6bP regulate?: f) What does Fr2,6bP do to that gluconeogenic enzyme?: g) Does Fr2,6bP regulate glycogen breakdown or synthesis?: h) How does glucagon affect liver levels of Fr2,6bP?: i) How does insulin affect liver levels of Fr2,6bP?: j) What glycolytic pathway metabolite is Fr2,6bP most similar to?: k) Which is more boss, Fr2,6bP or GAPDH?: Cognate-tive dissonance 25) 10pts Below are pictures of two very familiar a-ketoacids. Write the name of each under the picture in the space provided. To the right of each, draw the cognate amino acid for each, write the name of that amino acid, and its one letter code in the spaces provided.

7 Sp12 BIBC102 final, page 7 Swatting Mis-ketos 26) 14pts Often diseases that alter a process are some of the best indicators of the normal function of that process. Patients with defects in the enzymes that synthesize ketone bodies show episodic hypoglycemia, that can be sometimes severe. For example, this is seen in patients with defects in HMG-CoA lyase, that produces the ketone body acetoacetate. Lets think about this class of molecules a) 2pts Draw the ketone body acetoacetate in the box provided to the right b) 2pts Where in the body are ketone bodies formed? c) 2pts Where in the cell are ketone bodies formed? d) 2pts What familiar metabolite is used to make ketone bodies? e) 2pts What is the proposed function of ketone bodies (one sentence): e) 4pts So why might an inability to make ketone bodies might lead to hypoglycemia in the patients with this syndrome, especially during fasting or prolonged activity? Another Fate of Citrate 27) 10pts Pictured is the citrate lyase (CL) reaction. This is a key reaction important in both normal cell metabolism and cancer. You should know some things about this reaction. You may even be treating patients based on it someday. a) 2pts What is the normal role of CL in metabolism? (one sentence) b) 2pts Where in the cell does CL function? : c) 2pts What two classes of molecules are made from the AcCoA produced by CL d) 2pts Where in the cell is the CL substrate citrate made?: e) 2pts Why is citrate lyase important in cancer cell growth (one sentence):

8 Sp12 BIBC102 final, page 8 FAS-inating anabolism 28) 17pts When fatty acids are synthesized, AcCoA is employed as a source of carbon. These questions are about fatty acid synthesis a) 3pts The first product generated from AcCoA for use in fatty acid synthesis is called: (hint: having read The Name Game would be useful ) b) 2pts What cofactor is needed to make this first product of AcCoA c) 2pts What is the name of the enzyme complex that uses this starter molecule to build fatty acids? d) 4pts Fatty acids are made by the repeated cycles of addition of a two carbon unit to a growing acyl chain, followed by modication of the resulting product. Put the list of descriptions of those reactions in the correct order for one of these cycles, using number 1-4 removal of H 2 O to make a double bond reduction of the double bond reduction to an β-oh acid formation of a β-keto acid and a new C-C sigma bond e) 2pts How many cycles of addition and modification does it take to build the 16 carbon fatty acid palmitate from AcCoA building blocks? f) 2pts If you are counting from the carboxyl group (as Carl Heoger taught you; the carboxyl carbon is number 1) what are the numerical postions of the two carbons added in the second round of reactions? ' positions and g) 2pts In fatty acid synthesis, what is the reducing agent used to do the reactions that occur during the cyclical reactions we are talking about?

9 Sp12 BIBC102 final, page 9 29) 16pts When Glucose is HERE or GONE! We have talked about glucose, glucagon, glycogen, glycolysis, gluconeogenesis and insulin. Confusing! The following questions put some of that together. Write the answer insulin, glucagon, both, or neither for the following questions: a) Affects both liver and muscle b) Affects only muscle c) Will lower blood glucose d) Will raise blood glucose e) Will be elevated after a meal f) Will be elevated after prolonged endurance exercise g) Increases glycogen synthesis in both liver and muscle h) Increases glycogen breakdown in both muscle and liver i) Increases glycogen breakdown in liver j) Is absent or low in type I diabetes k) Increases glycolysis in liver and muscle l) coordinates liver to produce free glucose for bloodstream m) stimulates phosphorylation of glycogen synthase n) stimulates activity of glycogen synthase o) stimulates phoshphorylation of glycogen phosphorylase p) stimulates activity of glycogen phosphorylase 30) Krebs' other child 4pts This is arginine (single letter R), one of the 20 amino acids. It is also a metabolite of the Urea Cycle. Show the reaction that it undergoes, that yields the product for which the cycle is named. Include structures of products. I'll even provide the water + H 2 O arginase

10 Sp12 BIBC102 final, page 10 31) Let Truth and Freedom Ring- 17pts these are all TF questions culled from old exams. A gallery of greatest hits. Answer T or F for each a) Rubisco can react with O 2 in an undesired side-reaction b) Plants can not make net glucose from acetyl-coa c) The Krebs cycle has oxygen-dependent reactions d) UDP is a carrier for lipids and carbohydrates e) Transamination reactions are part of the malate-aspartate shuttle f) Type IIb muscle fibers are more dependent on anaerobic metabolism than Type IIa fibers g) The Levine study described in the last class indicates that obesity causes lower levels of NEAT in humans. h) The inner mitochondrial membrane is impermeable to aspartate (amino acid D) i) Pyruvate carboxylase is needed in the Cori cycle j) A Michaelis-Menton enzyme with a Km of 10mM is operating at 75% maximal rate in 30 mm substrate k) Reduction of DHAP to glycerol-3-p can provide a route for NAD + regeneration for use in glycolysis l) Anaerobic energy metabolism accounts for 90% of the energy needed for sprinters and other high intensity exercises m) In amino acid catabolism, the nitrogen is directly removed from each amino acid by an enzyme to produce free ammonium ion n) Regulatory phosphorylation always causes enzymes to have higher activity o) Type II diabetes is caused by tissue insensitivity to insulin p) Hydrolysis of triglycerides produces fatty acids and glycerol q) In the balanced Calvin cycle (sorry Bensen), 5 molecules of G3P are used to make 3 molecules of Ribulose 1,5bP You have crossed the finish line! (looking better than me doing the same in the picture ) Have a great summer and thanks for being a fun and energetic class. It is a great privilege to be part of your education. Thanks! Read Fast Food Nation, and watch Forks over Knives. Trust me