Unit 10 Objectives

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Unit 10 U NIT 10 P ART A: B IOENERGETICS P ART B: C HEMISTRY OF C ARBOHYDRATES P ART C: G LYCOLYSIS P ART A: B IOENERGETICS Assignment: Nelson & Cox, pp. 461 – 485, 488 - 496. All living cells must obtain energy from their surroundings and expend it as efficiently as possible. Plants gather most of their energy from sunlight; animals use the energy stored in plants or other foods that they consume. The processing of this energy is central to the understanding of biochemistry. Bioenergetics, the quantitative analysis of how organisms gain and utilize energy, is a special part of the general science of energy transformation which is called thermodynamics. 1. Use Fig. 2 (p. 462) to distinguish between catabolic and anabolic pathways. 2.  G =  H - T  S a. Name and define each of the terms in the above equation (p. 467). What units are used for each of these terms? (Note this equation is almost never used by biochemists because we work at one temperature and don't measure heat formation.) b. Distinguish between  G,  G°, and  G'° (p. 468). 1

Unit 10 3.  G'° = -RT ln K'eq (equation 13-3, p. 468) a. What is the sign of  G'° when the reaction proceeds in the written direction (Table 13-3, p. 469)? b.  G '° is determined by measuring the equilibrium constant. Using the sample calculations on pp. 469 and 471 as a guide, do problems 2, 3, and 6 (p. 504). c. Using Table 13-4 (p. 469), compare the free energy content of acid anhydride and ester bonds. 4. Of the equations shown in the textbook, the Gibbs equation is the most useful for biochemists because it involves concentrations that can be measured (equation 13-4; p. 470). To analyze the energetics of a pathway in vivo we first measure K eq in vitro , calculate  G'°, and then measure  G in vivo by measuring the concentrations of products and reactants and applying equation 13-4 (p. 470). For aA + bB ⇌ cC + dD ∆G = ∆G ' ˚ + RT ln [ C ] c [ D ] d [ A ] a [ B ] b a. Which term in the Gibbs equation can be used to predict whether a reaction will proceed? Note : It is  G, not  G '° , which determines whether a reaction will go spontaneously or not. Thus, why do the authors of most texts talk about coupled reactions, thermodynamic feasibility, etc . in terms of  G '° ? The reason is mostly a matter of convenience because these values can easily be looked up in tables. Sometimes  G and  G'° can, however, be very different! For example, one reaction in the citric acid cycle has a  G'° of +7.1 Kcal/mol and a negative  G. Although the  G'° would not suggest it, the reaction occurs spontaneously in the citric acid cycle due to the concentration term in the Gibbs equation. b. What does  G tell you about the rate of the reaction (p. 470)? c. What effect do enzymes have on  G (p. 470)? 2

Unit 10 5. Hydrolysis of phosphoanhydride linkages in ATP has a large negative  G '° (pp. 479 – 481) a. Draw the structure of ATP (Fig. 13-11, p. 479). You may use A to abbreviate the structure of the base. b. Give at least two reasons why  G '° is such a large negative number (ca. -30.5 kJ/mol) for the reaction (Fig. 13-11, p. 479): ATP + H 2 O  ADP + P i Note that since, by convention, H 2 O is omitted when calculating equilibrium constants, K eq for ATP hydrolysis has units of molar. Also, note you must use values of M (and not mM) when performing calculations. c. Although the free-energy change for ATP hydrolysis is -30.5 kJ/mol, ATP is kinetically stable in water in the absence of enzymes. Suggest why (p. 470). 6. Use Table 13-6 (p. 481) to show that thioester bonds (eg. Acetyl-CoA) and acid anhydride bonds (eg. 1,3-bisphosphoglycerate, ATP, etc.) are high energy bonds. Use Fig. 13-17 (p. 483) to explain why thioester, but not oxygen ester, bonds are high energy. 7. It is possible for a reaction with a positive  G'° to be driven by a coupled reaction which has a negative  G'°. Explain why this can occur. Using the example on page 484 as a guide, do problems 9, 12, and 13 (p. 505). 8. Oxidation-Reduction (redox) Reactions (pp. 488 – 492) a. Distinguish between a reducing agent (reductant) and an oxidizing agent (oxidant; p. 489). b. Define standard reduction potential, E° and E'° (p. 490). c. Which half reaction contains the strongest oxidant - one with a more positive E'°, or one for which it is more negative (p. 492)? d. Which half reaction contains the strongest reductant - one with a more positive E'°, or one for which it is more negative (p. 492)? e. Pick two half reactions from Table 13-7 (p. 491) and identify which half reaction contains the strongest oxidant and which contains the strongest reductant then specifically identify the strongest oxidant and 3

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Unit 10 reductant in each of these half reactions. Calculate  E’° by subtracting E’° values (E’° value oxidant – E’° value reductant). f. Using Worked Example 13-3 (p. 492) as a guide, do problems 28, 30, 32, and 33 (pp. 507 - 508; Note: For question 28, use a redox potential of -0.185 instead of -0.19 for pyruvate/lactate.). 9. Coenzymes (pp. 492 – 496): a. What words do the letters of NAD + stand for (Fig. 13-24a, p. 493)? Using words, not structures, show how the component parts of the molecule are arranged and linked together. How does NADP + differ from NAD + ? Distinguish between the physiological role of NADH and NADPH (pp. 493 - 494). b. Use Figure 13-24b to explain how redox reactions involving NAD + /NADH can be monitored in vitro . c. What words do the letters of FMN stand for (Fig. 13-27, p. 495)? Using words, not structures, show how the component parts are arranged and linked together. d. Draw the active part of the molecule for NAD + , NADP + , and FAD (Fig. 13-24 [p. 493] and Fig. 13-27 [p. 495]). Show the conversion from oxidized to reduced form. Include protons and electrons in your structures and note how many of each are incorporated. e. Coenzyme A is also a coenzyme used in the transfer of acyl groups in metabolic reactions. For FAD: For NAD+ and NADP+: 4

Unit 10 P ART B: C HEMISTRY OF C ARBOHYDRATES The oxidation of carbohydrates is the central energy-yielding pathway in most nonphotosynthetic cells. Also, carbohydrate polymers serve as structural and protective elements in the cell walls of bacteria and plants. The following objectives will give you a brief introduction to the major classes of carbohydrates and their roles in the cell. Assignment Nelson & Cox pp. 229 - 242. 1. Monosaccharides a. Define monosaccharide in terms of functional groups and empirical formula (p. 229). b. Distinguish between aldose and ketose sugars (p. 230). 2. Monosaccharides occur in cyclic forms (pp. 233 - 235). a. Using a structural formula of the type ROH, represent the reaction of an alcohol with an aldehyde to form a hemiacetal and with a ketone to form a hemiketal. (Fig. 7-5, p. 234; Use arrows to underscore the nucleophilic attack mechanism.) b. Show that a pyranose ring results from intramolecular hemiacetal formation in glucose (Fig. 7-6, p. 234). Show that a furanose ring results from intramolecular hemiketal formation in fructose. Note that the ring forms of monosaccharides are always in equilibrium with the open chain form, i.e . with the free aldehyde or ketone. 3. Disaccharides and polysaccharides contain glycosidic bonds (p. 237 - 242). a. Formation of glycosidic linkages . Recall the formation of a hemiacetal in the above objective (Fig. 7-5, p. 234). Now show the reaction of this hemiacetal with another alcohol R"OH to form the acetal (Fig. 7-10, p. 237). Similarly, show the reaction of a hemiketal with an alcohol. The product (formerly called a ketal) is also called an acetal. 5

Unit 10 b. For glycogen (Fig. 7-13, p. 242): 1) Identify the repeating monosaccharide. 2) Indicate the nature of the most prevalent glycosidic linkage (   1  X). 3) Indicate the nature of the glycosidic linkage at the branch points. 4) What is meant by the "reducing end" (p. 237)? Point out the reducing and non-reducing ends on glycogen (Fig. 7-13, p. 242). A N O VERVIEW OF C ARBOHYDRATE M ETABOLISM The generation of metabolic energy from carbohydrates begins with glycolysis. Glycolysis is an ancient metabolic pathway that was probably used by the earliest known bacteria some 3.5 billion years ago. Since this was about one billion years before the earliest known photosynthetic organisms began contributing O 2 to the earth's atmosphere, glycolysis had to function under completely anaerobic conditions. Far more energy is generated in the reactions by which pyruvate is completely oxidized to CO 2 in the citric acid cycle. This cycle is the central oxidative pathway in respiration, the process by which all metabolic fuels, carbohydrates, lipid, and protein, are catabolized in aerobic organisms and tissues. The energy released, in this pathway, is in the form of exergonic dehydrogenation reactions that generate reduced electron carriers. These carriers are next re-oxidized in the mitochondrial respiratory (electron transport) chain. The free energy released from some of these reactions drives the synthesis of ATP from ADP and orthophosphate, through oxidative phosphorylation. 6

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Unit 10 P ART C: G LYCOLYSIS Assignment: Nelson & Cox, pp. 510 – 521, 525 – 530 (skip Boxes 14-1 and 14-2 and stop at “Fermentations Produce Some Common Foods…”), 541 - 542. 1. Overview a. What are the two phases of glycolysis (p. 511 - 513)? What is invested in the preparatory phase? Name two molecules in which energy is conserved in the payoff phase. b. The pathway is more complex than would be needed chemically because the cell membrane must be impermeant to all the intermediates. How is this accomplished (Fig. 14-3, p. 513)? 2. Compounds in the glycolytic cycle We suggest that you make a summary diagram of glycolysis based on Figs. 14-2 and 14-3 (pp. 512 - 513) on which you will write additional notes as you learn more about the pathway. Note that the enzymes of glycolysis are located in the cytoplasm of eukaryotic cells. Also note that the objectives below examine some of the reactions in more detail. This one is mainly to give you an overview to begin with and a diagram on which you can put further notes. By the time you take the Unit 10 quiz we hope you will be able to write out the pathway (using structures) by understanding the steps. 3. ATP is both utilized and generated in glycolysis a. Mark on your diagram the two reactions in which ATP is used in Phase 1. What types of enzymes catalyze these reactions? b. Mark on your diagram the two reactions in which ATP is generated in Phase 2. Name the two compounds which donate phosphate to ADP. 7

Unit 10 c. To what kind of energy rich group is the aldehyde of glyceraldehyde 3-phosphate converted in the oxidation step of glycolysis? Circle this group on the structure given below. 1) Name the type of linkage by which the other phosphate group is linked to this molecule. 2) Estimate the  G °' of hydrolysis of these two phosphate groups by finding similar groups in Table 13-6 (p. 481). d. In Table 13–6 (p. 481) find the  G '° of hydrolysis of the second energy rich molecule which forms ATP in glycolysis. How does it compare with the ∆G’° of other compounds in the table? 4. Enzymes in Glycolysis a. Indicate the general type of reaction catalyzed by: 1) kinases 2) isomerases 3) dehydrogenases 4) mutases 5) aldolase 6) enolase You are not responsible for the names of specific enzymes in the glycolytic pathway, but you should know which reactions are catalyzed by the types listed above. C - O - P - O O H - C - OH O CH - O - P - O O 2 O O - - - - 8

Unit 10 b. The last three enzymes listed above generally catalyze reversible reactions whereas kinase-catalyzed reactions are usually irreversible (for all practical purposes). However, one of the four kinase-catalyzed reactions in glycolysis is reversible under cellular conditions. Look at Table 14-2 (p. 535) to decide which one is reversible. 5. A thioester is formed in the oxidation of glyceraldehyde 3-phosphate Use Fig. 14-7 (p. 519) to show how glyceraldehyde 3-phosphate dehydrogenase uses a strategy involving a covalent enzyme-bound intermediate as a mechanism of energy coupling (i.e. the energy released during oxidation is used to make a high energy mixed anhydride bond). Note that the product of the oxidation is a thioester which is subsequently cleaved by HOPO 3 2 - (P i ). 6. In order for glycolysis to continue, NAD + must be regenerated (pp. 525 – 530; skip Boxes 14-1 and 14-2). a. Use Fig. 14-11 (p. 525) to discuss the three catabolic fates of the pyruvate formed in glycolysis. What do these three reaction pathways have in common (p. 525)? b. How is NAD + regenerated under aerobic conditions (p. 525)? (Just name the process. You will learn how it works in Unit 12.) c. Write the reactions by which NADH is oxidized to NAD + in: 1) anaerobic muscle (p. 526) 2) anaerobic yeast (p. 530) Note: Yeast form ethanol because it is less toxic than lactic acid. When NAD + is regenerated with concomitant formation of ethanol, the whole process (glucose to ethanol or lactic acid) is traditionally called fermentation instead of glycolysis. 9

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Unit 10 7. Mechanisms by which the rate of glycolysis is controlled. (pp. 541 - 542) In every metabolic pathway in the cell there is at least one reaction that is far from equilibrium because of the relative low activity of the enzyme that catalyzes the reaction. The rate of this reaction is not limited by substrate availability, but only by the activity of the enzyme. The reaction is therefore said to be enzyme-limited , and because its rate limits the rate of the whole reaction sequence, the step is called the rate-limiting step in the pathway. These rate-limiting steps are highly exergonic reactions and are essentially irreversible. Enzymes that catalyze these exergonic, rate-limiting steps are commonly the target of metabolic regulation. These enzymes are often allosterically controlled by a variety of regulators that signal the need for the products of the pathway. a. Phosphofructokinase-1 is the key regulatory enzyme in glycolysis. How is it regulated (i.e. allosteric, covalent modification, etc.; Fig. 14-22, p. 541)? b. Name five substances that regulate the activity of this enzyme and explain why their action is logical (Fig. 14-22, p. 541). Note the regulatory logic of fructose 2,6-bisphosphate will be discussed extensively in future units. 10