biochem exam solution 06

biochem exam solution 06 - INTRODUCTORY BIOCHEMISTRY FINAL...

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Unformatted text preview: INTRODUCTORY BIOCHEMISTRY FINAL EXAM FALL 2006 SEMESTER PAGE - 13 ANSWERS TO FALL 2006 FINAL EXAM SECTION A MULTIPLE CHOICE QUESTIONS Detailed Solutions to Multiple Choice Questions 1. (B) O rnithine is produced by the action of the enzyme arginase on amino acid L-arginine, creating urea. Therefore, ornithine is a central part of the urea cycle, which allows for the disposal of excess nitrogen. 2. (D) Substrate and c ompetitive inhibitors s hare similar structure and shape, thus compete each other to bind to enzyme’s active site . Competitive inhibitors bind irreversibly to free enzyme, not the ES complex, to form an enzyme-inhibitor (EI) complex. This type of inhibition can be overcome b y increasing the concentration of substrate. At high [S], all the active sites are saturated with substrate, and reaction velocity reaches the V max value observed without an inhibitor. 3. (E) R iboflavin is Vitamin B2 (e.g. FAD, FMN) and has a n atural orange-yellow color due to the presence of isoalloxazine ring. The nutritional supplements usually contain B vitamins, which is a powerful detoxifying agent. Riboflavin releases the toxins and helps them excrete out of the body in the urine. At first, the urine would become more brightly yellow colored , but eventually it will clear up after the last toxins are released. 4. (C) H ydrolysis of ATP into ADP and P i requires the cleavage of “high-energy” phosphoanhydride bond to yield )G°’ = s35 kJ/mol. On the other hand, h ydrolysis of AMP into adenosine and P i requires the cleavage of “low-energy” phosphate ester bond. As a result, the latter h ydrolysis of AMP w ill release less )G°’ (-s9 kJ/mol). 5. (E) N ADPH functions as a reducing agent (electron donor) in various reductive biosynthetic p athways (i.e. a nabolism ; energy-requiring process, )G°’ = r) such as fatty acid biosynthesis. On the other hand, N AD + serves as an oxidizing agent (electron acceptor) used in the o xidative degradation p rocess (i.e. catabolism ). NADP H h as the same reducing equivalent as NAD H . 6. (C) A conitase c atalyzes the isomerization of citrate to isocitrate in the citric acid cycle, via a reversible h ydration o f an alkene, cis-aconitate intermediate. 7. (E) T he shown compound is o xalic acid (HOOC-COOH), a dicarboxylic acid. The acetic acid is simply CH 3-COOH (two carbon mono-acid). The fumaric acid (HOOCCH=CH-COOH) and succinic acid (HOOC-CH 2-CH 2-COOH) are the molecules found in citric acid cycle. P yruvic acid (HOOC-(C=O)-CH 3) is the final product of a naerobic glycolysis. The decarboxylation of o xalic acid yields formic acid (H-COOH). 8. (E) A ll of the statements are correct. INTRODUCTORY BIOCHEMISTRY FINAL EXAM FALL 2006 SEMESTER PAGE - 14 9. (A) C arnitine is used to transport fatty acids across the mitochondrial membranes (outer and inner) in the form of fatty acyl esters. One form of carnitine acyltransferase acts at the outer mitochondrial membrane, converting the fatty acyl-CoA thioester into a fatty acyl carnitine ester. A transport protein then moves this ester across the inner mitochondrial membrane (which is highly impermeable to most solutes). Once inside the matrix, the fatty acyl carnitine ester is reconverted to a fatty acyl-CoA thioester in a reaction catalyzed by another form of carnitine acyltransferase, prior to $-oxidation. 10. (A) C lass 5: Isomerase catalyzes several types of intramolecular rearrangements s uch as functional group isomers of aldehyde and ketone. Both p hosphohexose isomerase and triose phosphate isomerase convert phosphorylated a ldoses (glucose-6-phosphate and glyceraldehyde-3-phosphate) into phosphorylated k etoses (fructose-6-phosphate and dihydroxyacetone phosphate, respectively). Both enzymes involve the interconversion of an isomeric aldose/ketose pair. Thus, the catalytic mechanisms of both enzymes are similar. However, m utase c atalyzes the intramolecular transfer of specific group at different positions. 11. (C) R eaction C catalyzes o xidative decarboxylation o f 6-phosphogluconate (6C aldose) to yield the ribulose-5-phosphate (5C ketose). The hydroxyl group at C-3 (C-2 of the product) is o xidized to a ketone. This promotes loss of the carboxyl group at C-1 as C O 2. The reaction is catalyzed by p hosphogluconate dehydrogenase (Class 1: Oxidoreductase). N ADP + serves as an oxidizing agent (electron acceptor). 12. (D) R eaction D shows the interconversion of two stereoisomers (epimers). E pimers are isomers which d iffer in the optical configuration at one carbon atom . This epimerization is catalyzed by ribulose-5-phosphate epimerase (Class 5: Isomerase), which interconverts the stereoisomers ribulose-5-phosphate and xylulose-5-phosphate. Thus, epimerase involves the inversion of asymmetric carbon atoms. 13. (E) T here is NO reaction required ATP input because the molecule has no further phosphorylation (i.e. the molecule remains one phosphate group). 14. (C) R eaction A catalyzes o xidation o f the a ldehyde (hemiacetal) at C -1 o f glucose-6phosphate, to a carboxylic acid in ester linkage (lactone). The reaction is catalyzed by glucose-6-phosphate dehydrogenase (Class 1: Oxidoreductase). N ADP + s erves as an oxidizing agent (i.e. electron acceptor) and is r educed to N ADPH . Reduction of oxidized N ADP + (as with NAD +) involves transfer of 2 eG + 1 H + (1 H G h ydride anion) to the nicotinamide moiety. 15. (E) R eaction B u ndergoes h ydrolysis o f the ester linkage (lactone) and results in ring opening. The product is 6-phosphogluconate (an acid sugar). This reaction is catalyzed by 6 -phosphogluconolactonase (Class 3: Hydrolase). INTRODUCTORY BIOCHEMISTRY FINAL EXAM FALL 2006 SEMESTER PAGE - 15 16. (D) P hosphatidylcholine is a phospholipid with p olar p hosphate headgroup and nonpolar h ydrocarbon tail, which aggregates to form micelles at lower concentration and form lipid bilayer structure at high concentration, in aqueous environment. Arachidonic acid (C20:4) is a poly-unsaturated fatty acid, giving four “kinks” enough to form almost a complete “loop”, and is a precursor of “eicosanoids’ such as prostaglandins and leukotrienes involved in inflammatory and immune processes. Triacylglycerol, also known as “fat”, possesses three long fatty acyl chains for energy conservation, and is so hydrophobic that stored in adipose tissue in animals. Sodium salts of the fatty acids are called “soap” which are soluble in water because of the hydrophilic negatively charged carboxylate headgroup, forming m icelles. Saturated (palmitate, C16:0) and unsaturated (linolenate, C18:3) fatty acids are nonpolar hydrocarbon components found in the acyl chains of phospholipids and triacylglycerol. 17. (A) U nder anaerobic condition (i.e. n o involvement of mitochondrial processes such as citric acid cycle and electron transport chain), glycolysis takes place solely in cytoplasm . Formation of lactic acid implies the r educed cofactor NADH is oxidized by lactate dehydrogenase and the o xidized cofactor NAD + is utilized by glyceraldehyde-3phosphate dehydrogenase (i.e. n o net gain of NADH). A t the first stage of glycolysis, one ATP is consumed in hexokinase step and one ATP is utilized by phosphofructokinase. A t the second stage of glycolysis, 2 ATP are produced by phosphoglycerate kinase, and another 2 ATP are formed by pyruvate kinase. Thus, glycolysis under anaerobic conditions yields n et two ATP p er mole of glucose. 18. (A) A ll of the statements are correct. 19. (D) P aul Boyer carried kinetic experiments to measure the exchange of phosphate groups among ADP and ATP and P i. It was found that the equilibrium constant for the reaction ADP + P i ÷ A TP + H 2O is close to 1 (i.e. )G = 0, under these conditions), when the reaction occurs in the active site of the ATP synthase, without release of product ATP from the active site as ATP is bound very tightly to the active site. 20. (E) S uccinate dehydrogenase catalyzes the oxidation of succinate into fumarate with a reduction of cofactor NAD + into NADH in citric acid cycle. S uccinate dehydrogenase is also known as C omplex II in electron transport chain and is situated in the inner mitochondrial membrane. C arnitine acyltransferase involves the transport of fatty acids in the form of esters with an alcohol (i.e. carnitine) across the mitochondrial membranes (outer and inner). E noyl-CoA hydratase catalyzes the hydration step in $-oxidation which takes place in the matrix of mitochondria (same location as citric acid cycle). P yruvate dehydrogenase, which is found in the matrix of mitochondria , catalyzes the oxidative decarboxylation of pyruvate (3C) into acetyl-CoA (2C) with a release of CO 2. P yruvate kinase is the last glycolytic enzyme located in the cytosol, which catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate to ADP to form pyruvate and ATP. INTRODUCTORY BIOCHEMISTRY FINAL EXAM SECTION B 21. (a) (b) (c) (d) (e) (f) (g) (h) 22. FALL 2006 SEMESTER PAGE - 16 SHORT-ANSWER QUESTIONS 10 . The transmembrane core of F o is an assembly of multiple copies of the subunit called “c ”. Multiple c m onomers aggregate into a ring as a “rotor” part of rotary engine. In the mammalian F oF 1 -ATPase enzyme, the ring of c subunits (c10 ) rotates with respect to the stator (a , b 2, and *), powered by the proton gradient. 4 . The reduction (gaining eG) half-reaction of one molecule of O 2 is: O 2 + 4 H + + 4 e G ÷ 2 H 2O 2 . During alcoholic fermentation under a naerobic g lycolysis, one glucose (6C ) is o xidized to two pyruvate (3C ). Pyruvate decarboxylase catalyzes the removal of CO 2 from pyruvate and produces acetaldehyde (2C), which is further r educed to ethanol (2C ) by alcohol dehydrogenase. Thus, glucose (6C) produces two moles of ethanol (2C) and 2 moles of CO 2 (1C) during a naerobic g lycolysis. 20 . Arachidic acid is a saturated fatty acid containing 2 0 carbon atoms. 1 . Heme is a p rosthetic group found in many hemeproteins such as hemoglobin, myoglobin, cytochrome oxidase, catalase e tc.. The heme ring joins four pyrrole rings (five-membered rings with one N atom) together into a tetrapyrrole ring, which forms a large conjugated aromatic system. The four N atoms are positioned to form a pocket that can bind o ne iron (Fe) m etal ion. 9 . Nine turns of $-oxidation is required to o xidize C 20:0 fatty acid into 1 0 molecules of acetyl-CoA (2C) with production of 9 NADH and 9 FADH 2. 10 . Ten enzymes are involved in the glycolytic pathway from glucose to pyruvate: there are four Class 2: Transferases - kinases (hexokinase, phosphofructokinase, phosphoglycerate kinase and pyruvate kinase); three Class 5: Isomerases (phosphohexose isomerase, triose phosphate isomerase and phosphoglycerate mutase); two Class 4: Lyases (aldolase and enolase); and one Class 1: Oxidoreductase (glyceraldehyde-3-phosphate dehydrogenase). 3 . There are three intermolecular h ydrogen bondings found between the pyrimidine base C a nd purine base G (C /G ). (a) The reaction scheme proposed by Michaelis and Menten kinetics is: (b) The Michaelis-Menten equation is expressed as: INTRODUCTORY BIOCHEMISTRY FINAL EXAM 23. (a) (b) FALL 2006 SEMESTER PAGE - 17 Two glucose molecules in pyranose form must join together h ead-to-head to tie up the two C -1 anomeric carbons to form a n on-reducing d isaccharide (i.e. the glycosidic linkage must be joined between the two anomeric !OH groups). Three d ifferent isomeric forms of trehalose with 3 possible glycosydic linkages: Î Glc("1 ÷"1)Glc ("-D-glucopyranosyl- (1 ÷1)-"-D-glucopyranoside) Ï Glc($1 ÷$1)Glc ($-D-glucopyranosyl- (1 ÷1)-$-D-glucopyranoside) Ð Glc("1 ÷$1)Glc ("-D-glucopyranosyl- (1 ÷1)-$-D-glucopyranoside), which is the same molecule as: Glc($1 ÷"1)Glc ($-D-glucopyranosyl- (1 ÷1)-"-D-glucopyranoside) because both monosaccharide components are glucose. Three possible isomeric forms of Trehalose G lc("1 ÷"1)Glc 2 4. 25. G lc($1 ÷$1)Glc G lc("1 ÷$1)Glc = Glc($1 ÷"1)Glc )G = ! n F )E ; where n = number of electrons transferred, F = Faraday constant N ADPH (reduced form) (Nicotinamide Adenine Dinucleotide Phosphate) consists of the following components: Î first nucleotide (reduced n icotinamide ring + ribose + P) Ï second nucleotide (AMP) (adenine + ribose + phosphate) Ð extra p hosphate attached to C-2’ in ribose of AMP Ñ adenine is a bicyclic purine base Ò C-1’ is $-glycosylic-linked to N-9 in adenine base INTRODUCTORY BIOCHEMISTRY FINAL EXAM FALL 2006 SEMESTER PAGE - 18 25. 2 6. (a) (b) (c) fumarase (from citric acid cycle) enolase (from glycolysis) enoyl-CoA hydratase (from $-oxidation) 27. Chemical Mechanism catalyzed by glycolytic enzyme phosphohexose isomerase Î Phosphohexose isomerase c atalyzes the reversible isomerization of glucose-6phosphate (an aldose) to fructose-6-phosphate (a ketose). C This reaction provides a good example of “general base catalysis”. Ï A basic group on the enzyme (Enz-COO G, the carboxylate anion form (!COO G) of a glutamate residue in the active site) abstracts (accepts) a proton (H +) from the C-2 hydroxyl (!OH) group of glucose-6-phosphate, as the C-1 aldehyde O picks up a H + from water. Thus, “Enz-COO G” undergoes “general base catalysis. C The product of these protonation / deprotonation steps is an “ene-diol” (alkene + two hydroxyl groups) intermediate, bound to the enzyme. Ð In the second step, a H + is lost from the C-2 hydroxyl (!O !H) group to solution, as the C-1 carbon picks up a H + from the p rotonated g lutamate residue on the enzyme (Enz-COO H ). or or * Y ou o nly n eed to draw the above diagram to obtain the full marks. INTRODUCTORY BIOCHEMISTRY FINAL EXAM 27. FALL 2006 SEMESTER PAGE - 19 Chemical Mechanism catalyzed by $-oxidation enzyme thiolase Î Thiolase catalzyes the cleavage of $-ketoacyl-CoA (i.e. thiolysis) to split off the carboxyl-terminal two-carbon fragment of the original fatty acid as acetyl-CoA (2 C). The other product is the coenzyme A thioester of the fatty acid, now s hortened b y two carbon atoms (fatty acyl-CoA (n !2)). Balanced Equation: $-ketoacyl-CoA + CoASH ÷ fatty acyl-CoA (n !2) + CoA-SAc C This is an example of the reaction of a nucleophile with an electrophilic carbonyl carbon atom . The C !C bond cleavage is made possible by the reactive $-dicarbonyl substrate (i.e. $-ketoacyl-CoA ). Ï Coenzyme A (CoA !SH) binds to thiolase (a basic group on the enzyme removes the proton (H +) from the thiol group of CoA-SH, converting it to its ionized thiolate anion form (CoA !S:G), a strong n ucelophile. C The lone pair electrons from the n ucleophile (CoA !S:G) attacks the electrophilic carbonyl $-carbon a tom, resulting in a C !S bonded tetrahedral intermediate. Ð This intermediate a lso has a second carbonyl group at C-1position . That oxygen atom “pulls” at the electrons, which flow towards it, breaking the bond between the "- and $-carbons. Ñ Acetyl-CoA is released as an a nion , following protonation by the enzyme, which gives acetyl-CoA as a product. The other product is simply a fatty acyl-CoA , now shortened by two carbon atoms. * Y ou o nly n eed to draw the above diagram to obtain the full marks. INTRODUCTORY BIOCHEMISTRY FINAL EXAM FALL 2006 SEMESTER PAGE - 20 29. (a) Oxaloacetate (4 C "-keto acid) is r educed b y lactate to L -malate; whereas lactate is o xidized to p yruvate (3 C "-keto acid). (b) 28. The reduction of oxaloacetate by lactate can be achieved in two enzymatic steps (dehydrogenase) with cofactors (NAD +/NADH ) as follows: (i) Enzyme: L-malate dehydrogenase Cofactor: NADH + oxaloacetate + NADH + H ÷ L -malate + NAD + (ii) Enzyme: lactate dehydrogenase Cofactor: NAD + lactate + NAD + ÷ p yruvate + NADH + H + Secondary Structure of the DNA Double-Helix (Watson & Crick, 1953) (a) DNA is composed of 2 r ight-handed polydeoxyribonucleotide chains (similar, but not identical) showing antiparallel directions (5’ ÷ 3 ’) of each strand (b) Polar sugar-phosphate backbone projects outward into the polar water environments. Bases are perpendicular to axis, and project inward to facilitate the inter-chain H-bond formation, (purine :::: pyrimidine) A = T and G / C and are stacked above each other via hydrophobic and van der Waals interaction Overall DNA structure displays major and minor grooves (reflecting the glycosidic linkages) which can accommodate protein. There are 10.4 base-pairs per helical turn (i.e. pitch of 3.4 nm). major groove minor groove (c) (d) (e) ...
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