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MCMP 208 Exam III Key - 1 Examination III Key MCMP 208 – Biochemistry for Pharmaceutical Sciences I April 9, 2012 Correct answers in multiple choice questions are indicated in RED and underlined. Correct answers to essay questions are indicated in RED in comic book font. In some cases and explanation is provided in BLUE/BLUE MATCHING. For problems 1 to 3, a set of numbered answers is provided immediately below. For each problem, select from the list of answers the single choice that best matches the item described in the problem. Mark that answer on your answer sheet. An answer may be used more than once or not at all. [3 points each] Stearic acid Prostaglandin Phosphatidylcholine Phosphatidylinositol Triacylglycerol Ceramide Sphingomyelin Cholesterol Cholesterol ester Cholic acid 1. Triacylglycerol 2. Phosphatidylinositol MCMP 208 Exam III Key - 2 3. Cholesterol ester MULTIPLE CHOICE. For problems 4 to 20, select from the list immediately following each question the single most correct choice to complete the statement, solve the problem, or answer the question. Mark that answer on your answer sheet. [3 points each] 4. Which of the following statements is INCORRECT about gangliosides? Gangliosides are sphingolipids Gangliosides contain one or more sialic acids. Gangliosides contain an amide bond between sphingosine and a fatty acid. Gangliosides are phospholipids. Gangliosides do not have phosphate group. Sphingomyelin is the only phospholipid in sphingolipids. Gangliosides have one or more sugar residues. Tay-Sachs disease occurs when a ganglioside accumulates in lysosome. 5. _____________ scavenges excess cholesterol and cholesterol ester and transports them to the liver. Chylomicron Chylomicron remnant Very-low-density lipoprotein Intermediate-density lipoprotein Low-density lipoprotein High-density lipoprotein Because of this role, the high level of HDL in the plasma inversely correlates with the incidence of coronary heart diseases. 6. Which of the following descriptions is INCORRECT about membrane proteins? The transverse movement (flipping) of integral membrane proteins occurs readily. The transverse movement of integral membrane proteins requires the passage of hydrophilic residues through hydrophobic region of lipid bilayer, which is energetically costly. The proper orientation of integral membrane proteins is critical for their functions. Peripheral membrane proteins can be removed from the membrane with mild treatments. Channels and transporters are all integral membrane proteins. Transmembrane domains of integral membrane proteins are mostly composed of hydrophobic residues. Some peripheral membrane proteins are anchored to the membrane through a covalent modification with a lipid. MCMP 208 Exam III Key - 3 7. Which of the following uses energy to transport molecules or ions against their concentration gradient? Voltage-gated Na+ channel Acetylcholine receptor Glucose transporter ATP-ADP transporter Na+/K+-ATPase Na+/K+-ATPase uses ATP as an energy source to transport Na+ and K+ against their concentration gradient and maintain the concentration gradients of Na+ and K+. 8. Membrane potential can affect the direction of the transport of _____________. Water Not charged O2 Not charged K+ Charged Glucose Not charged Cholesterol Not charged 9. The molecule that fatty acids are bonded to when fatty acids are transported into the mitochondria of cells is coenzyme A coenzyme Q acyl carrier protein glutathione carnitine cysteine glutamate serum albumin pyrophosphate phosphate 10. In addition to the mitochondria, fatty acids are also subject to beta-oxidation in the proteosome endosome peroxisome nucleosome chylomicron lipid droplet lipoprotein MCMP 208 Exam III Key - 4 11. Typically, fatty acids found in humans are stearate, oleate and even longer structures. Part of their synthesis is accomplished by fatty acid synthase. The remainder of their synthesis involves lengthening in the mitochondria adding cis double bonds in the mitochondria both lengthening and adding cis double bonds in the mitochondria isomerizing trans double bonds to cis double bonds in the mitochondria lengthening in the endoplasmic reticulum adding cis double bonds in the endoplasmic reticulum both lengthening and adding cis double bonds in the endoplasmic reticulum isomerizing trans double bonds to cis double bonds in the endoplasmic reticulum condensing two shorter fatty acids (each one longer than acetate) together to make a longer and sometimes unsaturated fatty acid The additional synthesis does not occur in the mitochondria, because that is where only fatty acid degradation occurs. The question hints at the fact that both lengthening and addition of cis bonds are needed since oleic acid is C18:1, while FAS only makes C16:0 12. Phosphatidyl serine is made from serine and phosphatidic acid diacylglycerol CDP-diacylglycerol phosphatidylethanolamine by head group exchange triacylglycerol 13. The regulation of fatty acid synthesis primarily occurs by regulation of acyl carrier protein fatty acid synthase acyl coA carboxylase phospho-enolpyruvate carboxy kinase HMG-CoA reductase phosphofuctose kinase glucose transport pyruvate dehydrogenase lipoprotein lipase triacylglycerol lipase (also known as hormone-sensitive lipase) 14. Which one of the following is a bile salt? mevalonate eicosanoate adipate cholate cholesteryl ester 7-dehydrocholesterol lanosterol MCMP 208 Exam III Key - 5 15. The process of converting N2 to two molecules of ammonia is called nitrogenolysis hydrazonolysis nitrification denitrification mineralization nitrogen fixation hydrolysis hydrogenolysis 16. The only enzyme-catalyzed reaction that can remove the alpha amino group of glutamate as ammonia involves another amino acid an alpha-keto acid other than alpha-ketoglutarate transaminase asparagine ATP N-acetylglutamate glutamine glutamate dehydrogenase aspartate 17. An individual with a negative nitrogen balance always indicates that the individual’s tissues are growing wasting away neither growing nor wasting away not able to biosynthesize urea have too many essential amino acids and not enough non-essential amino acids This may be the cause, but is not always the cause have inadequate levels of glucogenic amino acids available from his/her diet This may be the cause, but is not always the cause 18. Though it can function in several different ways, the primary biochemical function of Sadenosylmethionine is to produce homocysteine to produce cysteine to produce propionyl CoA to produce mevalonate to produce methylene-THF Something like the opposite of this is true (methylene-THF makes met) to reduce tetrahydrobiopterin to methylate macromolecules and complex lipids to donate one-carbon units during biosynthetic reactions of amino acids and nucleotides This is the role of THF with one-carbon units. SAM does not do this as its primary function, though it sometimes does this, e.g., during epinephrine synthesis. to accept one-carbon units during reactions catabolizing amino acids and nucleotides MCMP 208 Exam III Key - 6 19. Ubiquitin is the receptor for ubiquinone a lipid that regulates the process of macroautophagy a protease a small protein that enzymes covalently link to other proteins To tag then for degradation at the proteosome a coenzyme for proteases a component of the proteosome a small protein that regulates endocytosis and membrane remodeling 20. Urea is made in a single enzyme-catalyzed reaction from carbamoyl phosphate arginine This is the last step in the cyclic part of urea synthesis, also yielding ornithine which continues the urea cycle by accepting a carbamate from carbamolyl phosphate asparagine glutamine citrulline ornithine arginino-succinate alanine glutamate ammonia and carbon dioxide ESSAY PROBLEMS. Write your answers to problems 21 to 28 in the space immediately below each problem. 21. [3 points] The abbreviated name for α-linolenic acid is 18:3Δ9,12,15. Draw the structure of α-linolenic acid. It is a fatty acid with 18 carbon atoms and three double bonds at 9th, 12th, and 15th carbon from the carboxylic side. All the double bonds are cis. 22. [3 points] In lipoproteins, phospholipids are present in the shell, but triacylglycerol is present in the core. Explain briefly why they are distributed differently. Phospholipids are amphipathic, and the polar head groups need to be exposed to the aqueous phase. However, triacylglycerol is hydrophobic and should be sequestered from the aqueous phase. MCMP 208 Exam III Key - 7 + 23. [3 points] Bacterial lactose permease is a symporter of lactose and H . When the lactose concentrations in the cytosol and in the extracellular space are identical but the pH’s in the two locations are different as indicated below, which direction would lactose be transported? Explain briefly why you think that way. Lactose permease Extracellular space pH = 5 Cytosol pH = 7 Cell membrane Lactose moves from the extracellular space to the cytosol. The greater proton concentration in the extracellular space (pH 5.0) than in the cytosol (pH 7.0) drives the transport of lactose. Conceptually, this transporter is similar to Na+/glucose cotransporter, which utilizes the Na+ concentration gradient to drive the transport of glucose against its concentration gradient. 24. [4 points] There are three types of cells that add lipids to the general blood circulation. a. [1 point] What are these three cell types? Adipocytes, hepatocytes, enterocytes Acceptable alternative names: fat cells, liver cells, intestinal cells (respectively) b. [3 points] The form of lipid added to the blood circulation vary among these three cell types. For each of these three cell types, describe (i) the one name that best describes the dominant class of lipid that is added to the blood circulation and (ii) the way in which the dominant lipid class is released from the cell and enters the general blood circulation. Adipocytes: (i) fatty acid (ii) released directly into blood (across the plasma membrane) Hepatocytes: (i) VLDL (ii) exocytosis directly into blood MCMP 208 Exam III Key - 8 Enterocytes: (i) chylomicron (ii) exocytosis (to extracellular space) and flow through lymphatics to blood 25. [7 points] In the biosynthesis of fatty acids starting from acetyl-CoA, there is only one enzyme-catalyzed step that uses ATP. Answer the following questions about this enzyme. a. [1 point] What is the name of this enzyme? Acetyl CoA carboxylase (the abbreviation ACC is acceptable) b. [2 points] What is the ATP used for during the mechanism of this reaction? ATP is used to phosphorylated bicarbonate to make phosphocarbonate (which is used to regenerate the carboxybiotin form of the prosthetic group) c. [2 points] What is the name and structure of the product produced by this enzyme (the product that is used in fatty acid synthesis)? [You may indicate the location of Coenzyme A in your structure by using “CoA”] Malonyl-CoA (The S is not required and the anionic form is acceptable) O HO H O C C C SCoA H d. [2 points] Why is this step needed for the synthesis of fatty acids? The carboxylate on the beta carbon activates the alpha carbon by making it more acidic, which stabilizes its carbanion character after deprotonation. Without this carbanion stabilization, acetyl-CoA is much less reactive in the condensation step of fatty acid synthesis. 26. [7 points] As with other types of lipids, sterols can be considered to be oligomers of an oligomer. Given this context, answer the following questions. a. [1 point] What is oligomerized to produce the first (smaller size) level of oligomer? Acetyl-CoA (“acetate” is also acceptable) b. [1 point] How many copies of your answer to (a) are oligomerized to produce the first level oligomer? 3 It takes three acetyl-CoA to make HMG-CoA, the precursor of isoprene c. [1 point] How many carbons are in the basic unit that is oligomerized in the second level of oligomerization? 5 MCMP 208 Exam III Key - 9 d. [1 point] How many copies of the basic unit described in (c) are in the final oligomer used to make sterols? 6 Squalene is made by dimerization of faresylPP; farnesy is made from 3 isoprene units e. [1 point] What is the generic chemical name of the carbon part of the basic unit described in (c)? Isoprene (“isopentene” is also acceptable) f. [1 point] What is the name of the final oligomer used to make sterols? squalene g. [1 point] Other than oligomerization during sterol synthesis, what is the other function of the intermediates in the second stage of oligomerization (the stage referred to in (c) through (e))? Protein prenylation (post-translational addition of an oligo-isoprene to proteins) 27. [6 points] Consider the enzymes that catalyze the synthesis of tyrosine as well as that catalyze the first step in the formation of catecholamines and the formation of serotonin. The substrates for each of these three enzymes share three structures and/or structural characteristics. Describe these three shared structures and/or structural characteristics? (i) one substrate is O2 (molecular oxygen and dioxygen are also acceptable) (ii) one substrate is an aromatic amino acid (iii) the third substrate is tetrahydrobiopterin 28. [7 points] Serine, generally available within cells in an unlimted amount, can be metabolized to a key metabolic intermediate that can be used to spare some methionine from being degraded. a. [3 points] What is the name of this key metabolic intermediate? Methylene-tetrahydrofolate (methylene-THF is also acceptable) Also, methyl-tetrahydrofolate and methyl-THF are also acceptable (but see below) b. [2 points] Describe (with words or reactions) how can serine be used to generate this intermediate? [Hint: Each serine can be used to generate two of these molecules.] Serine is catabolized to glycine and methylene-THF, then glycine is catabolized to another methylene-THF plus ammonia and carbon dioxide. If answer to (a) is Methyl-THF: Methylene-THF must then be reduced to methyl-THF c. [2 points] How is this key intermediate used to spare some methionine from degradation? 1. If answer to (a) is Methylene-THF: Methylene-THF must first be reduced to methyl-THF (this part is not required if the answer to part a is methylene-THF) 2. Methyl-THF is used to make methionine from homocysteine (by adding a methyl)
