Biochem Exam 4
How does the presence of alpha-bonds versus beta-bonds influence the digestibility of glucose polymers by humans? Hint: There are two effects.
Humans can digest glucose polymers containing alpha-bonds but not beta. For this reason, glycogen and starch are digestible, whereas cellulose is not. In addition, cellulose is fibrous rather than branched, which makes the polymer insoluble in water and inaccessible to digestion by humans.
Explain how the pentose phosphate pathway can respond to a cell's need for ATP, NADPH, and ribose-5-phosphate.
If a cell needs NADPH, all the reactions of the pentose phosphate pathway take place. If a cell needs ribose-5-phosphate, the oxidative portion of the pathway can be bypassed; only the nonoxidative reshuffling reactions take place. The pentose phosphate pathway does not have a significant effect on the cell's supply of ATP.
How does an increase in the ADP/ATP ratio affect the activity of isocitrate dehydrogenase?
If the amount of ADP in a cell increases relative to the amount of ATP, the cell needs energy (ATP). This situation not only favors the reactions of the citric acid cycle, which release energy, activating isocitrate dehydrogenase, but also stimulates the formation of NADH and FADH2 for ATP production by electron transport and oxidative phosphorylation.
How does an increase in the NADH/NAD+ ratio affect the activity of pyruvate dehydrogenase?
If the amount of NADH in a cell increases relative to the amount of NAD+, the cell has completed a number of energy-releasing reactions. There is less need for the citric acid cycle to be active; as a result, the activity of pyruvate dehydrogenase is decreased.
What is the chemical difference between a sugar phosphate and a sugar involved in a glycosidic bond?
In a sugar phosphate, an ester bond is formed between one of the sugar hydroxyls and phosphoric acid. A glycosidic bond is an acetal, which can be hydrolyzed to regenerate the two original sugar hydroxyls.
What role does the proton gradient play in chemiosmotic coupling?
In chemiosmotic coupling, the proton gradient is related to ATP production. The proton gradient leads to conformational changes in a number of proteins, releasing tightly bound ATP from the synthase as a result of the conformational change.
How does the role of glucose-6-phosphate in gluconeogenesis differ from that in glycolysis?
In gluconeogenesis, glucose-6-phosphate is dephosphorylated to glucose (the last step of the pathway); in glycolysis, it isomerizes to fructose-6-phosphate (an early step in the pathway).
How does phosphorolysis differ from hydrolysis?
In phosphorolysis, a bond is cleaved by adding the elements of phosphoric acid across that bond, whereas in hydrolysis, the cleavage takes place by adding the elements of water across the bond.
What is the metabolic basis for the observation that many adults cannot ingest large quantities of milk without developing gastric difficulties?
In some cases, the enzyme that degrades lactose (milk sugar) to its components—glucose and galactose—is missing. In other cases, the enzyme isomerizes galactose to glucose for further metabolic breakdown.
How does substrate-level phosphorylation differ from phosphorylation linked to the electron transport chain?
In substrate-level phosphorylation, the energy of hydrolysis of some compound provides sufficient energy to allow the endergonic phosphorylation of ADP to ATP to take place. In the next chapter, we will see how the electron transport chain generates energy to allow the conversion of ADP to ATP.
How does control of the glucose-6-phosphatase reaction differ from that of the fructose-1,6-bisphosphatase reaction?
In the glucose-6-phosphatase reaction, the concentration of substrate is the main determinant of reaction velocity. In the fructose-1,6-bisphosphatase reaction, allosteric effects are the main determinant of reaction velocity.
What are the metabolic effects of not being able to produce the M subunit of phosphofructokinase?
Individuals who lack the gene that directs the synthesis of the M form of the enzyme can carry on glycolysis in their livers but experience muscle weakness because they lack the enzyme in muscle.
What role does insulin play in glycogen synthesis?
Insulin triggers the series of events that leads to glycogen synthesis.
You are a teaching assistant in a general chemistry lab. The next experiment is to be an oxidation-reduction titration involving iodine. You get a starch indicator from the stockroom. Why do you need it?
Iodine is the reagent that will be added to the reaction mixture in the titration. When the end point is reached, the next drop of iodine will produce a characteristic blue color in the presence of the indicator.
Which enzymes of the citric acid cycle are missing from the glyoxylate cycle?
Isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase, and succinyl-CoA synthetase.
Why would enzymes be found as isozymes?
Isozymes allow for subtle control of the enzyme to respond to different cellular needs. For example, in the liver, lactate dehydrogenase is most often used to convert lactate to pyruvate, but the reaction is often reversed in the muscle. Having a different isozyme in the muscle and liver allows for those reactions to be optimized.
Define isozymes and give an example from the material discussed in this chapter.
Isozymes are oligomeric enzymes that have slightly different amino acid compositions in different organs. Lactate dehydrogenase is an example, as is phosphofructokinase.
A researcher claims to have discovered a variant form of glycogen. The variation is that it has very few branches (every 50 glucose residues or so) and that the branches are only three residues long. Is it likely that this discovery will be confirmed by later work?
It is unlikely that this finding will be confirmed by other researchers. The highly branched structure of glycogen is optimized for release of glucose on demand.
What does it mean when an enzyme has the name synthase?
It means that the reaction catalyzed by the enzyme produces the product that is part of the name and does not require a direct input of energy from a high-energy phosphate. Thus, citrate synthase catalyzes the synthesis of citrate without using ATP to do it.
Using the information in Chapters 17, 18, and 19, calculate the amount of ATP that can be produced from one molecule of lactose metabolized aerobically through glycolysis and the citric acid cycle.
Lactose is a disaccharide of glucose and galactose. There is no energy cost in the hydrolysis of the bond between the two monosaccharides, so essentially there are two hexoses to consider. Because the processing of any of the hexoses yields the same amount of energy, the aerobic processing of lactose would lead to 60 to 64 ATPs, depending on the tissue and on the shuttle system used.
Briefly describe the dual role of lipoic acid in the pyruvate dehydrogenase complex.
Lipoic acid plays a role both in redox and in acetyl-transfer reactions.
Why is acetyl-CoA considered the central molecule of metabolism?
Many compounds can form acetyl-CoA, such as fats, carbohydrates, and many amino acids. Acetyl-CoA can also form fats and ketone bodies, as well as feed directly into the citric acid cycle.
How does mitochondrial structure contribute to aerobic metabolism, particularly to the integration of the citric acid cycle and electron transport?
Mitochondrial structure confines the reduced electron carriers produced by the citric acid cycle to the matrix. There they are close to the respiratory complexes of the electron transport chain that will pass the electrons from the carriers produced by the citric acid cycle to oxygen, the ultimate recipient of electrons and hydrogens.
Suggest a reason or reasons why the Cori cycle takes place in the liver and in muscle.
Muscle tissue uses large quantities of glucose, producing lactate in the process. The liver is an important site of gluconeogenesis to recycle the lactate to glucose.
What electron acceptors play a role in the citric acid cycle?
NAD+ and FAD are the primary electron acceptors of the citric acid cycle.
What three molecules produced during the citric acid cycle are an indirect or direct source of high-energy compounds?
NADH and FADH2 are indirect sources of energy produced in the TCA cycle. GTP is a direct source of energy.
Which of the enzymes discussed in this chapter are NADH-linked dehydrogenases?
NADH-linked dehydrogenases: Glyceraldehyde-3-phosphate dehydrogenase, lactate dehydrogenase, and alcohol dehydrogenase.
Avidin, a protein found in egg whites, binds to biotin so strongly that it inhibits enzymes that require biotin. What is the effect of avidin on glycogen formation? On gluconeogenesis? On the pentose phosphate pathway?
Of the three processes—glycogen formation, gluconeogenesis, and the pentose phosphate pathway—only one, gluconeogenesis, involves an enzyme that requires biotin. The enzyme in question is pyruvate carboxylase, which catalyzes the conversion of pyruvate to oxaloacetate, an early step in gluconeogenesis.
Describe the multiple ways that PDH is controlled.
PDH is controlled allosterically. It is inhibited by ATP, acetyl-CoA, and NADH. In addition, it is subject to control by phosphorylation. When PDH kinase phosphorylates PDH, it becomes inactive. Removing the phosphate with the PDH phosphatase reactivates it.
Aldolases
Performing an aldol cleavage of a sugar to yield two smaller sugars or sugar derivatives.
What are the possible metabolic fates of pyruvate?
Pyruvate can be converted to lactate, ethanol, or acetyl-CoA.
Which reaction or reactions discussed in this chapter require ATP? Which reaction or reactions produce ATP? List the enzymes that catalyze the reactions that require and that produce ATP.
Reactions that require ATP: formation of UDP-glucose from glucose-1-phosphate and UTP (indirect requirement, because ATP is needed to regenerate UTP), regeneration of UTP, and carboxylation of pyruvate to oxaloacetate. Reactions that produce ATP: none. Enzymes that catalyze ATP-requiring reactions: UDP-glucose phosphorylase (indirect requirement), nucleoside phosphate kinase, and pyruvate carboxylase. Enzymes that catalyze ATP-producing reactions: none.
What reactions in this chapter require acetyl-CoA or biotin?
Reactions that require acetyl-CoA: none. Reactions that require biotin: carboxylation of pyruvate to oxaloacetate.
Earlier biochemists called substrate cycles "futile cycles." Why might they have chosen such a name? Why is it something of a misnomer?
Substrate cycles are futile in the sense that there is no net change except for the hydrolysis of ATP. However, substrate cycles allow for increased control over opposing reactions when they are catalyzed by different enzymes.
Suggest a reason why sugar nucleotides, such as UDPG, play a role in glycogen synthesis, rather than sugar phosphates, such as glucose-6-phosphate.
Sugar nucleotides are diphosphates. The net result is hydrolysis to two phosphate ions, releasing more energy and driving the addition of glucose residues to glycogen in the direction of polymerization.
What is the Cori cycle?
The Cori cycle is a pathway in which there is cycling of glucose due to glycolysis in muscle and gluconeogenesis in liver. The blood transports lactate from muscle to liver and glucose from liver to muscle.
Is mitochondrial ATP synthase an integral membrane protein?
The F0 portion of mitochondrial ATP synthase lies within the inner mitochondrial membrane, but the F1 portion projects into the matrix.
Describe the role of the F1 portion of ATP synthase in oxidative phosphorylation.
The F1 portion of the mitochondrial ATP synthase, which projects into the matrix, is the site of ATP synthesis.
Why is the citric acid cycle considered part of aerobic metabolism, even though molecular oxygen does not appear in any reaction?
The NADH and FADH2 produced by the citric acid cycle are the electron donors in the electron transport chain linked to oxygen. Because of this connection, the citric acid cycle is considered part of aerobic metabolism.
What is the advantage of having a Q cycle in electron transport in spite of its complexity?
The Q cycle allows for a smooth transition from two-electron carriers (NADH and FADH2) to one-electron carriers (cytochromes).
What does the material of this chapter have to do with beer? What does it have to do with tired and aching muscles?
The bubbles in beer are CO2, produced by alcoholic fermentation. Tired and aching muscles are caused in part by a buildup of lactic acid, a product of anaerobic glycolysis.
What are some of the main differences between the cell walls of plants and those of bacteria?
The cell walls of plants consist mainly of cellulose, whereas those of bacteria consist mainly of polysaccharides with peptide crosslinks.
Briefly summarize the main arguments of the chemiosmotic coupling hypothesis.
The chemiosmotic coupling mechanism is based on the difference in hydrogen ion concentration between the intermembrane space and the matrix of actively respiring mitochondria. The hydrogen ion gradient is created by the proton pumping that accompanies the transfer of electrons. The flow of hydrogen ions back into the matrix through a channel in the ATP synthase is directly coupled to the phosphorylation of ADP.
What are the different names used to describe the pathway discussed in this chapter?
The citric acid cycle is also called the Krebs cycle, the tricarboxylic acid cycle, and the TCA cycle.
Describe the various purposes of the citric acid cycle.
The citric acid cycle is the central metabolic pathway and indirect producer of energy. It receives fuels from the other pathways at many points and generates reduced electron carriers that go into the electron transport chain. It is also involved in anabolism, as many of its intermediates can be drawn off to synthesize other compounds.
In what part of the cell does the citric acid cycle take place? Does this differ from the part of the cell where glycolysis occurs?
The citric acid cycle takes place in the mitochondrial matrix. Glycolysis takes place in the cytosol.
What are two advantages of the components of the electron transport chain being embedded in the inner mitochondrial membrane?
The components are in the proper orientation for the electrons to be transferred rapidly from one component to the next; if the components were in solution, speed would be limited to the rate of diffusion. A second advantage, which is actually a necessity, is that the components are properly positioned to facilitate the transport of protons from the matrix to the intermembrane space.
How can the synthesis and breakdown of fructose-2,6-bisphosphate be controlled independently?
The concentration of fructose-2,6-bisphosphate in a cell depends on the balance between its synthesis (catalyzed by phosphofructokinase-2) and its breakdown (catalyzed by fructose-1,6-bisphosphatase). The separate enzymes that control the formation and breakdown of fructose-2,6-bisphosphate are themselves controlled by a phosphorylation/dephosphorylation mechanism.
Which reactions are the control points in glycolysis?
The control points in glycolysis are the reactions catalyzed by hexokinase, phosphofructokinase, and pyruvate kinase.
Is the conversion of fumarate to malate a redox (electron transfer) reaction? Give the reason for your answer.
The conversion of fumarate to malate is a hydration reaction, not a redox reaction.
What are the unique reactions of the glyoxylate cycle?
The conversion of isocitrate to succinate and glyoxylate catalyzed by isocitrate lyase and the conversion of glyoxylate and acetyl-CoA to malate catalyzed by malate synthase.
No animal can digest cellulose. Reconcile this statement with the fact that many animals are herbivores that depend heavily on cellulose as a food source.
The digestive tract of these animals contains bacteria that have the enzyme to hydrolyze cellulose.
Would eating candy bars, high in sucrose rather than complex carbohydrates, help build up glycogen stores?
The disaccharide sucrose can be hydrolyzed to glucose and fructose, which can both be readily converted to glucose-1-phosphate, the immediate precursor of glycogen. This is not the usual form of "glycogen-loading."
Why is it reasonable to compare the electron transport process to a battery?
The electron transport chain translocates charged particles by chemical means. Interconversion of chemical and electrical energy is exactly what a battery does.
Acetyl-CoA and succinyl-CoA are both high-energy thioesters, but their chemical energy is put to different uses. Elaborate.
The energy released by hydrolysis of acetyl-CoA is needed for the condensation reaction that links the acetyl moiety to oxaloacetate, yielding citrate. The energy released by hydrolysis of succinyl-CoA drives the phosphorylation of GDP, yielding GTP.
Why is it useful to have a primer in glycogen synthesis?
The enzyme that catalyzes addition of glucose residues to a growing glycogen chain cannot form a bond between isolated glucose residues; thus we have the need for a primer.
What are the major differences between the oxidations in the citric acid cycle that use NAD+ as an electron acceptor and the one that uses FAD?
The enzymes that reduce NAD+ are all soluble, matrix enzymes, while succinate dehydrogenase is membrane-bound. The NAD+-linked dehydrogenases all catalyze oxidations that involve carbons and oxygens, such as an alcohol group being oxidized to an aldehyde or aldehyde to carboxylic acid. The FAD-linked dehydrogenase oxidizes a carbon-carbon single bond to a double bond.
Why is it reasonable to expect that glucose-6-phosphate will be oxidized to a lactone rather than to an open-chain compound?
The ester bond is more easily broken than any of the other bonds that form the sugar ring. Hydrolysis of that bond is the next step in the pathway.
Why is the formation of fructose-1,6-bisphosphate a step in which control is likely to be exercised in the glycolytic pathway?
The formation of fructose-1,6-bisphosphate is the committed step in the glycolytic pathway. It is also one of the energy-requiring steps of the pathway. Control is exercised here.
Define substrate-level phosphorylation and give an example from the reactions discussed in this chapter.
The free energy of hydrolysis of a substrate is the energetic driving force in substrate-level phosphorylation. An example is the conversion of glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate.
Is the glycogen synthase reaction exergonic or endergonic? What is the reason for your answer?
The glycogen synthase reaction is exergonic overall because it is coupled to phosphate ester hydrolysis.
How does the result in the question above differ from the gross yield of ATP?
The gross yield is four ATP molecules per glucose molecule, but the reactions of glycolysis require two ATP per glucose.
In what way is the observed mode of action of hexokinase consistent with the induced-fit theory of enzyme action?
The hexokinase molecule changes shape drastically on binding to substrate, consistent with the induced-fit theory of an enzyme adapting itself to its substrate.
How does the hydrolysis of fructose-1,6-bisphosphate bring about the reversal of one of the physiologically irreversible steps of glycolysis?
The hydrolysis of fructose-1,6-bisphosphate is a strongly exergonic reaction. The reverse reaction in glycolysis, phosphorylation of fructose-6-phosphate, is irreversible because of the energy supplied by ATP hydrolysis.
What is unique about TPP that makes it useful in decarboxylation reactions?
The important part of TPP is the five-membered ring, in which a carbon is found between nitrogen and sulfur. This carbon forms a carbanion that is extremely reactive, making it able to perform a nucleophilic attack on carbonyl groups, leading to decarboxylation of several compounds in different pathways.
What should be the net ATP yield for glycolysis when fructose, mannose, and galactose are used as the starting compounds? Justify your answer.
The net yield of ATP from glycolysis is the same, two ATP, when either of the three substrates is used. The energetics of the conversion of hexoses to pyruvate are the same, regardless of hexose type.
Many NADH-linked dehydrogenases have similar active sites. Which part of glyceraldehyde-3-phosphate dehydrogenase would be the most conserved between other enzymes?
The part of the active site that binds to NADH would be the part that is most conserved, since many dehydrogenases use that coenzyme.
If lactic acid is the buildup product of strenuous muscle activity, why is sodium lactate often given to hospital patients intravenously?
The problem with lactic acid is that it is an acid. The H+ produced from lactic acid formation causes the burning muscle sensation. Sodium lactate is the conjugate weak base of lactic acid. It is reconverted to glucose by gluconeogenesis in the liver. Giving sodium lactate intravenously is a good way to supply an indirect source of blood glucose.
Why do the electron-transfer reactions of the cytochromes differ in standard reduction potential, even though all the reactions involve the same oxidation-reduction reaction of iron?
The protein environment of the iron differs in each of the cytochromes, causing differences in the reduction potential.
What is the metabolic purpose of lactic acid production?
The purpose of the step that produces lactic acid is to re duce pyruvate so that NADH can be oxidized to NAD+, which is needed for the step catalyzed by glyceraldehyde-3-phosphate dehydrogenase.
With respect to stereochemistry, what is unique about the reaction catalyzed by aconitase?
The reaction involves an achiral molecule (citrate) being converted to a chiral one (isocitrate).
Is the reaction of 2-phosphoglycerate to phosphoenolpyruvate a redox reaction? Give the reason for your answer.
The reaction of 2-phosphoglycerate to phosphoenolpyruvate is a dehydration (loss of water) rather than a redox reaction.
Which steps of aerobic metabolism of pyruvate through the citric acid cycle are control points?
The reactions are catalyzed by pyruvate dehydrogenase, citrate synthase, isocitrate dehydrogenase, and alpha-ketoglutarate dehydrogenase.
Which reactions in glycolysis are coupled reactions?
The reactions catalyzed by hexokinase, phosphofructokinase, glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerokinase, and pyruvate kinase.
What are the similarities and differences between the reactions catalyzed by pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase?
The reactions proceed by the same mechanism and use the same cofactors. The difference is the initial substrate, which is pyruvate or alpha-ketoglutarate. During the course of the reaction, pyruvate dehydrogenase shuttles an acetyl unit through the reaction while alpha-ketoglutarate dehydrogenase shuttles a succinyl unit.
The concentration of lactate in blood rises sharply during a sprint and declines slowly for about an hour afterward. What causes the rapid rise in lactate concentration? What causes the decline in lactate concentration after the run?
The sprint is essentially anaerobic and produces lactate from glucose by glycolysis. Lactate is then recycled to glucose by gluconeogenesis.
Which steps in glycolysis are physiologically irreversible?
The steps catalyzed by hexokinase, phosphofructokinase, and pyruvate kinase.
The malate-aspartate shuttle yields about 2.5 moles of ATP for each mole of cytosolic NADH. Why does nature use the glycerol-phosphate shuttle, which yields only about 1.5 moles of ATP?
The transport "product" (in the matrix) of the malate-aspartate shuttle is NADH, whereas that of the glycerol-phosphate shuttle is FADH2. The latter shuttle can thus go against a transmembrane NADH concentration gradient, whereas the former cannot.
What is the metabolic advantage of having both hexokinase and glucokinase to phosphorylate glucose?
The two enzymes can have different tissue locations and kinetic parameters. The glucokinase has a higher Km for glucose than hexokinase. Thus, under conditions of low glucose, the liver does not convert glucose to glucose-6-phosphate, using the substrate that is needed elsewhere. When the glucose concentration is much higher, however, glucokinase helps phosphorylate glucose so that it can be stored as glycogen.
How many chiral centers are there in the open-chain form of glucose? In the cyclic form?
There are four chiral centers in the open-chain form of glucose (carbons two through five). Cyclization introduces another chiral center at the carbon involved in hemiacetal formation, giving a total of five chiral centers in the cyclic form.
Does the net gain of ATP in glycolysis differ when glycogen, rather than glucose, is the starting material? If so, what is the change?
There is a net gain of three, rather than two, ATP when glycogen, not glucose, is the starting material of glycolysis.
How does pyruvate from glycolysis get to the pyruvate dehydrogenase complex?
There is a transporter on the inner mitochondrial matrix that allows pyruvate from the cytosol to pass into the mitochondria.
What type of reaction is catalyzed by isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase?
These enzymes catalyze oxidative decarboxylations.
What do cytochromes have in common with hemoglobin or myoglobin?
They all contain the heme group, with minor differences in the heme side chains in most cytochromes.
Briefly discuss the role of thiamine pyrophosphate in enzymatic reactions, using material from this chapter to illustrate your points.
Thiamine pyrophosphate is a coenzyme in the transfer of two-carbon units. It is required for catalysis by pyruvate decarboxylase in alcoholic fermentation.
Beriberi is a disease caused by a deficiency of vitamin B1 (thiamine) in the diet. Thiamine is the precursor of thiamine pyrophosphate. In view of what you have learned in this chapter, why is it not surprising that alcoholics tend to develop this disease?
Thiamine pyrophosphate is a coenzyme required in the reaction catalyzed by pyruvate carboxylase. Because this reaction is a part of the metabolism of ethanol, less will be available to serve as a coenzyme in the reactions of other enzymes that require it.
Would you expect delta G for the hydrolysis of a thioester to be (a) large and negative, (b) large and positive, (c) small and negative, or (d) small and positive? Give the reason for your answer.
Thioesters are "high-energy" compounds that play a role in group-transfer reactions; consequently, their delta G of hydrolysis is large and negative to provide energy for the reaction.
Do all the respiratory complexes generate enough energy to phosphorylate ADP to ATP?
Three of the four respiratory complexes generate enough energy to phosphorylate ADP to ATP. Complex II is the sole exception.
Which steps of glycolysis are irreversible? What bearing does this observation have on the reactions in which gluconeogenesis differs from glycolysis?
Three reactions of glycolysis are irreversible under physiological conditions. They are the production of pyruvate and ATP from phosphoenolpyruvate, the production of fructose-1,6-bisphosphate from fructose-6-phosphate, and the production of glucose-6-phosphate from glucose. These reactions are bypassed in gluconeogenesis; the reactions of gluconeogenesis differ from those of glycolysis at these points and are catalyzed by different enzymes.
How does the cyclization of sugars introduce a new chiral center?
Two different orientations with respect to the sugar ring are possible for the hydroxyl group at the anomeric carbon. The two possibilities give rise to the new chiral center.
Can an uncoupler of oxidative phosphorylation inhibit electron transport from one component of the electron transport chain to another? Why or why not?
Uncouplers and respiratory inhibitors act in different ways. Uncouplers lead to increased permeability of the inner mitochondrial membrane, making oxidative phosphorylation less effective. Respiratory inhibitors block the transfer of electrons from one component of the electron transport chain to the next component.
Briefly describe the role of uncouplers in oxidative phosphorylation.
Uncouplers overcome the proton gradient on which oxidative phosphorylation depends.
Kinases
Using a high-energy phosphate to phosphorylate a substrate.
Give an example of substrate-level phosphorylation in a pathway other than the citric acid cycle.
We have previously encountered substrate-level phosphorylation in glycolysis. An example is the transfer of a phosphate from 1,3-bisphosphoglycerate to ADP to afford 3-phosphoglycerate and ATP.
Most metabolic pathways are relatively long and appear to be very complex. For example, there are 10 individual chemical reactions in glycolysis, converting glucose to pyruvate. Suggest a reason for the complexity.
With few exceptions, a biochemical reaction typically results in only one chemical modification of the substrate. Accordingly, several to many steps are needed to reach the ultimate goal.
Many soft drinks contain citric acid as a significant part of their flavor. Is this a good nutrient?
Yes, not only is citric acid completely degraded to carbon dioxide and water, but it is also readily absorbed into the mitochondrion.
Enzymes that catalyze reactions requiring NAD+:
glyceraldehyde-3-phosphate dehydrogenase.
Enzymes that catalyze reactions requiring ATP:
hexokinase, glucokinase, and phosphofructokinase.
Enzymes that catalyze reactions requiring NADH:
lactate dehydrogenase and alcohol dehydrogenase.
Reactions that require NAD+:
oxidation of glyceraldehyde-3-phosphate to give 1,3-diphosphoglycerate.
Enzymes that catalyze reactions producing ATP:
phosphoglycerate kinase and pyruvate kinase.
Reactions that require ATP:
phosphorylation of glucose to give glucose-6-phosphate and phosphorylation of fructose-6-phosphate to give fructose-1,6-bisphosphate.
Reactions that require NADH:
reduction of pyruvate to lactate and reduction of acetaldehyde to ethanol.
Reactions that produce ATP:
transfer of phosphate group from 1,3-bisphosphoglycerate to ADP and transfer of phosphate group from phosphoenolpyruvate to ADP.
Briefly describe "going for the burn" in a workout in terms of the material in this chapter.
"Going for the burn" in a workout refers to the sensation that accompanies lactic acid buildup. This in turn arises from anaerobic metabolism of glucose in muscle.
What is the effect on gluconeogenesis and glycogen synthesis of (a) increasing the level of ATP, (b) decreasing the concentration of fructose-1,6-bisphosphate, and (c) increasing the concentration of fructose-6-phosphate?
(a) Increasing the level of ATP favors both gluconeogenesis and glycogen synthesis. (b)Decreasing the level of fructose-1,6-bisphosphate would tend to stimulate glycolysis, rather than gluconeogenesis or glycogen synthesis. (c)Levels of fructose-6-phosphate do not have a marked regulatory effect on these pathways of carbohydrate metabolism.
What is the net gain of ATP molecules derived from the reactions of glycolysis?
2 ATP per molecule of glucose
What is the approximate P/O ratio that can be expected if intact mitochondria are incubated in the presence of oxygen, along with added succinate?
A P/O ratio of 1.5 can be expected because oxidation of succinate passes electrons to coenzyme Q via a flavoprotein intermediate, bypassing the first respiratory complex.
Why is the reaction catalyzed by citrate synthase considered a condensation reaction?
A condensation reaction is one in which a new carbon-carbon bond is formed. The reaction of acetyl-CoA and oxaloacetate to produce citrate involves formation of such a carbon-carbon bond.
Define furanose
A furanose is a cyclic sugar that contains a five-membered ring similar to that in furan.
Define glycoprotein
A glycoprotein is formed by the covalent bonding of sugars to a protein.
define glycosidic bond
A glycosidic bond is the acetal linkage that joins two sugars.
Do any of the respiratory complexes play a role in the citric acid cycle? If so, what is that role?
A part of complex II catalyzes the conversion of succinate to fumarate in the citric acid cycle.
Define polysaccharide
A polysaccharide is a polymer of simple sugars, which are compounds that contain a single carbonyl group and several hydroxyl groups.
Define pyranose
A pyranose is a cyclic sugar that contains a six-membered ring similar to that in pyran.
Define the term reducing sugar
A reducing sugar is one that has a free aldehyde group. The aldehyde is easily oxidized, thus reducing the oxidizing agent.
What does it mean when an enzyme is called a synthetase?
A synthetase is an enzyme that synthesizes a molecule and uses a high-energy phosphate in the process.
How does the action of allosteric effectors differ in the reactions catalyzed by phosphofructokinase and fructose-1,6-bisphosphatase?
AMP and fructose-2,6-bisphosphate are allosteric activators of phosphofructokinase. They are allosteric inhibitors of fructose-1,6-bisphosphatase.
What are the two most common inhibitors of steps of the citric acid cycle and the reaction catalyzed by pyruvate dehydrogenase?
ATP and NADH are the two most common inhibitors.
How does ATP act as an allosteric effector in the mode of action of phosphofructokinase?
ATP inhibits phosphofructokinase, consistent with the fact that ATP is produced by later reactions of glycolysis.
Discuss the logic of the nature of the allosteric inhibitors and activators of glycolysis. Why would these molecules be used?
ATP is an inhibitor of several steps of glycolysis as well as other catabolic pathways. The purpose of catabolic pathways is to produce energy, and high levels of ATP mean the cell already has sufficient energy. Glucose-6-phosphate inhibits hexokinase and is an example of product inhibition. If the glucose-6-phosphate level is high, it may indicate that sufficient glucose is available from glycogen breakdown or that the subsequent enzymatic steps of glycolysis are going slowly. Either way, there is no reason to produce more glucose-6-phosphate. Phosphofructokinase is inhibited by a special effector molecule, fructose-2,6-bisphosphate, whose levels are controlled by hormones. It is also inhibited by citrate, which indicates that there is sufficient energy from the citric acid cycle, probably from fat and amino acid degradation. Pyruvate kinase is also inhibited by acetyl-CoA, the presence of which indicates that fatty acids are being used to generate energy for the citric acid cycle. The main function of glycolysis is to feed carbon units to the citric acid cycle. When these carbon skeletons can come from other sources, glycolysis is inhibited to spare glucose for other purposes.
Explain the origin of the name of the enzyme aldolase.
Aldolase catalyzes the reverse aldol condensation of fructose-1,6-bisphosphate to glyceraldehyde-3-phosphate and dihydroxyacetone phosphate.
Name which, if any, of the following groups are not aldose-ketose pairs: -ribose and D-ribulose, D-glucose and D-fructose, D-glyceraldehyde and dihydroxyacetone.
All groups are aldose-ketose pairs.
What is meant by the statement that a pathway is amphibolic?
Amphibolic means that the pathway is involved in both catabolism and anabolism.
Define aldose
An aldose is a sugar that contains an aldehyde group; a ketose is a sugar that contains a ketone group.
Why does ATP production require an intact mitochondrial membrane?
An intact mitochondrial membrane is necessary for compartmentalization, which in turn is necessary for proton pumping.
What is the difference between an isomerase and a mutase?
An isomerase is a general term for an enzyme that changes the form of a substrate without changing its empirical formula. A mutase is an enzyme of the isomerase class that moves a functional group, such as a phosphate, to a new location in a substrate molecule.
Define oligosaccharide
An oligosaccharide is a compound formed by the linking of several simple sugars (monosaccharides) by glycosidic bonds.
Which pathways are involved in the anaerobic metabolism of glucose? Which pathways are involved in the aerobic metabolism of glucose?
Anaerobic glycolysis is the principal pathway for the anaerobic metabolism of glucose. The pentose phosphate pathway can also be considered. Aerobic glycolysis and the citric acid cycle are responsible for the aerobic metabolism of glucose.
How many ATPs can be produced from one molecule of glucose anaerobically? Aerobically?
Anaerobically, two ATPs can be produced from one glucose molecule. Aerobically, this figure is 30 to 32, depending on in which tissue it is occurring.
Most hunters know that meat from animals that have been run to death tastes sour. Suggest a reason for this observation.
Animals that have been run to death have accumulated large amounts of lactic acid in their muscle tissue, accounting for the sour taste of the meat
Glycogen is highly branched. What advantage, if any, does this provide an animal?
Because of the branching, the glycogen molecule gives rise to a number of available glucose molecules at a time when it is being hydrolyzed to provide energy. A linear molecule could produce only one available glucose at a time.
What is the role of biotin in gluconeogenesis?
Biotin is the molecule to which carbon dioxide is attached to the process of being transferred to pyruvate. The reaction produces oxaloacetate, which then undergoes further reactions of gluconeogenesis.
What is the main structural difference between cellulose and starch?
Both cellulose and starch are polymers of glucose. In cellulose, the monomers are joined by a beta-glycosidic linkage, whereas in starch they are joined by an alpha-glycosidic linkage.
Show the carbon atom that changes oxidation state during the reaction catalyzed by glyceraldehyde-3-phosphate dehydrogenase. What is the functional group that changes during the reaction?
Carbon-1 of glyceraldehyde is the aldehyde group. It changes oxidation state to a carboxylic acid, which is phosphorylated simultaneously.
Isomerases
Changing the form of a molecule without changing its empirical formula (i.e., replacing one isomer with another).
Dehydrogenases
Changing the oxidation state of a substrate by removing hydrogens while simultaneously changing the oxidation state of a coenzyme (NADH, FADH2, etc.).
How does chitin differ from cellulose in structure and function?
Chitin is a polymer of N-acetyl-Beta-D-glucosamine, whereas cellulose is a polymer of D-glucose. Both polymers play a structural role, but chitin occurs in the exoskeletons of invertebrates and cellulose primarily in plants.
Why is the polysaccharide chitin a suitable material for the exoskeleton of invertebrates such as lobsters? What other sort of material can play a similar role?
Chitin is a suitable material for the exoskeleton of invertebrates because of its mechanical strength. Individual polymer strands are cross-linked by hydrogen bonding, accounting for the strength. Cellulose is another polysaccharide cross-linked in the same way, and it can play a similar role.
Which of the following does not play a role in respiratory complexes: cytochromes, flavoproteins, iron-sulfur proteins, or coenzyme Q?
Coenzyme Q is not bound to any of the respiratory complexes. It moves freely in the inner mitochondrial membrane.
What is the metabolic advantage in the conversion of glucose to lactate, in which there is no net oxidation or reduction?
Conversion of glucose to lactate rather than pyruvate recycles NADH.
In which steps of the aerobic processing of pyruvate is CO2 produced?
Conversion of pyruvate to acetyl-CoA, conversion of isocitrate to alpha-ketoglutarate, and conversion of alpha-ketoglutarate to succinyl-CoA.
In which steps of the aerobic processing of pyruvate are reduced electron carriers produced?
Conversion of pyruvate to acetyl-CoA, conversion of isocitrate to alpha-ketoglutarate, conversion of alpha-ketoglutarate to succinyl-CoA, conversion of succinate to fumarate, and conversion of malate to oxaloacetate.
Two sugars are epimers of each other. Is it possible to convert one to the other without breaking covalent bonds?
Converting a sugar to an epimer requires inversion of configuration at a chiral center. This can be done only by breaking and reforming covalent bonds.
Two biochemistry students are about to use mitochondria isolated from rat liver for an experiment on oxidative phosphorylation. The directions for the experiment specify addition of purified cytochrome c from any source to the reaction mixture. Why is the added cytochrome c needed? Why does the source not have to be the same as that of the mitochondria?
Cytochrome c is not tightly bound to the mitochondrial membrane and can easily be lost in the course of cell fractionation. This protein is so similar in most aerobic organisms that cytochrome c from one source can easily be substituted for that from another source.
How do the cytochromes differ from hemoglobin and myoglobin in terms of chemical activity?
Cytochromes are proteins of electron transport; the heme ion alternates between the Fe(II) and Fe(III) states. The function of hemoglobin and myoglobin is oxygen transport and storage, respectively. The iron remains in the Fe(II) state.
Name which, if any, of the following are epimers of D-glucose: D-mannose, D-galactose, D-ribose.
D-Mannose and D-galactose are both epimers of D-glucose, with inversion of configuration around carbon atoms 2 and 4, respectively; D-ribose has only five carbons, but the rest of the sugars named in this question have six.
Explain how the minor structural difference between alpha- and beta-glucose is related to the differences in structure and function in the polymers formed from these two monomers.
Differences in structure: cellulose consists of linear fibers, but starch has a coil form. Differences in function: cellulose has a structural role, but starch is used for energy storage.
What is the source of the energy needed to incorporate glucose residues into glycogen? How is it used?
Each glucose residue added to a growing phosphate chain comes from uridine diphosphate glucose. The cleavage of the phosphate ester bond to the nucleoside diphosphate moiety supplies the needed energy.
Briefly outline the role of UDPG in glycogen biosynthesis.
Each glucose residue is added to the growing glycogen molecule by transfer from UDPG.
You are planning to go on a strenuous hike and are advised to eat plenty of high-carbohydrate foods, such as bread and pasta, for several days beforehand. Suggest a reason for the advice.
Eating high-carbohydrate foods for several days before strenuous activity is intended to build up glycogen stores in the body. Glycogen will be available to supply required energy.
Are electron transport and oxidative phosphorylation the same process? Why or why not?
Electron transport and oxidative phosphorylation are different processes. Electron transport requires the respiratory complexes of the inner mitochondrial membrane, whereas oxidative phosphorylation requires ATP synthase, also located on the inner mitochondrial membrane. Electron transport can take place in the absence of oxidative phosphorylation.
Briefly summarize the steps in the electron transport chain from NADH to oxygen.
Electrons are passed from NADH to a flavin-containing protein to coenzyme Q. From coenzyme Q, the electrons pass to cytochrome b, then to cytochrome c, via the Q cycle, followed by cytochromes a and a3. From the cytochrome aa3 complex, the electrons are finally passed to oxygen.
What is the difference between an enantiomer and a diastereomer?
Enantiomers are nonsuperimposable, mirror-image stereoisomers. Diastereomers are nonsuperimposable, nonmirrorimage stereoisomers.
Why would you expect to see that reactions of substrate cycles involve different enzymes for different directions?
Enzymes, like all catalysts, speed up the forward and reverse reaction to the same extent. Having different catalysts is the only way to ensure independent control over the rates of the forward and reverse process.
Is it possible to have proton pumping in the absence of electron transport?
Experiments with model systems have shown that electron transport and proton pumping can take place separately.
What is the advantage to the organization of the PDH complex?
Five enzymes are all in close proximity for efficient shuttling of the acetyl unit between molecules and efficient control of the complex by phosphorylation.
How many enzymes are involved in mammalian pyruvate dehydrogenase? What are their functions?
Five enzymes are involved in the pyruvate dehydrogenase complex of mammals. Pyruvate dehydrogenase transfers a two-carbon unit to TPP and releases CO2. Dihydrolipoyl transacetylase transfers the two-carbon acetyl unit to lipoic acid and then to coenzyme A. Dihydrolipoyl dehydrogenase reoxidizes lipoic acid and reduces NAD+ to NADH. Pyruvate dehydrogenase kinase phosphorylates PDH. PDH phosphatase removes the phosphate.
What is fluoroacetate? Why is it used?
Fluoroacetate is a poison that is produced naturally in some plants and is also used as a poison against undesirable pests. It is poisonous because it is used by citrate synthase to make fluorocitrate, which is an inhibitor of the citric acid cycle.
How many possible epimers of D-glucose exist?
Four epimers of D-glucose exist, with inversion of configuration at a single carbon. The possible carbons at which this is possible are those numbered two through five.
At what point in glycolysis are all the reactions considered doubled?
From the point at which aldolase splits fructose-1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde-3-phosphate; all reactions of the pathway are doubled (only the path from one glyceraldehyde-3-phosphate is usually shown).
Why is the formation of fructose-1,6-bisphosphate the committed step in glycolysis?
Fructose-1,6-bisphosphate can only undergo the reactions of glycolysis. The components of the pathway up to this point can have other metabolic fates.
How does fructose-2,6-bisphosphate play a role as an allosteric effector?
Fructose-2,6-bisphosphate is an allosteric activator of phosphofructokinase (a glycolytic enzyme) and an allosteric inhibitor of fructose-1,6-bisphosphatase (an enzyme in the pathway of gluconeogenesis).
Explain how fructose-2,6-bisphosphate can play a role in more than one metabolic pathway.
Fructose-2,6-bisphosphate is an allosteric activator of phosphofructokinase (a glycolytic enzyme) and an allosteric inhibitor of fructose-1,6-bisphosphatase (an enzyme in the pathway of gluconeogenesis). It thus plays a role in two pathways that are not exactly the reverse of each other.
Why are furanoses and pyranoses the most common cyclic forms of sugars?
Furanoses and pyranoses have five-membered and six-membered rings, respectively. It is well known from organic chemistry that rings of this size are the most stable and the most readily formed.
Why can we say that production of a GTP is equivalent to production of an ATP?
GTP is equivalent to ATP because an enzyme, nucleoside diphosphate kinase, is able to interconvert GTP and ATP.
What roles do glucagon and epinephrine play in glycogen breakdown?
Glucagon and epinephrine start the chain of events leading to glycogen breakdown.
What are four possible metabolic fates of glucose-6-phosphate?
Glucose-6-phosphate can be converted to glucose (gluconeogenesis), glycogen, pentose phosphates (pentose phosphate pathway), or pyruvate (glycolysis).
High levels of glucose-6-phosphate inhibit glycolysis. If the concentration of glucose-6-phosphate decreases, activity is restored. Why?
Glucose-6-phosphate inhibits hexokinase, the enzyme responsible for its own formation. Because G-6-P is used up by additional reactions of glycolysis, the inhibition is relieved.
Why is it advantageous that breakdown of glycogen gives rise to glucose-6-phosphate rather than to glucose?
Glucose-6-phosphate is already phosphorylated. This saves one ATP equivalent in the early stages of glycolysis.
How does glycogen differ from starch in structure and function?
Glycogen and starch differ mainly in the degree of chain branching. Both polymers serve as vehicles for energy storage, glycogen in animals and starch in plants.
What is the main structural difference between glycogen and starch?
Glycogen exists as a highly branched polymer. Starch can have both a linear and a branched form, which is not as highly branched as that of glycogen.
What are glycoproteins? What are some of their biochemical roles?
Glycoproteins are ones in which carbohydrates are covalently bonded to proteins. They play a role in eukaryotic cell membranes, frequently as recognition sites for external molecules. Antibodies (immunoglobulins) are glycoproteins.
Suggest a reason why a different reducing agent (NADPH) is used in anabolic reactions rather than NADH, which plays a role in catabolic ones.
Having different reducing agents for anabolic and catabolic pathways keeps the pathways separate metabolically. Thus, they are subject to independent control and do not waste energy.
What is the advantage of having mobile electron carriers in addition to large membrane-bound complexes of carriers?
Having mobile electron carriers in addition to membrane-bound respiratory complexes allows electron transport to use the most readily available complex rather than to use the same one all the time.
Blood samples for research or medical tests sometimes have heparin added. Why is this done?
Heparin is an anticoagulant. Its presence prevents blood clotting.
How do glucokinase and hexokinase differ in function?
Hexokinase can add a phosphate group to any of several six-carbon sugars, whereas glucokinase is specific for glucose. Glucokinase has a lower affinity for glucose than does hexokinase. Consequently, glucokinase tends to deal with an excess of glucose, particularly in the liver. Hexokinase is the usual enzyme for phosphorylating six-carbon sugars.
Which molecules act as inhibitors of glycolysis? Which molecules act as activators?
Hexokinase is inhibited by glucose-6-phosphate. Phosphofructokinase is inhibited by ATP and citrate. Pyruvate kinase is inhibited by ATP, acetyl-CoA, and alanine. Phosphofructokinase is stimulated by AMP and fructose-2,6-bisphosphate. Pyruvate kinase is stimulated by AMP and fructose-1,6-bisphosphate.