Cell Bio Chapter 9 Problem Set

9-3 Glycolysis in 25 Words or Fewer. Complete each of the following statements about the glycolytic pathway in 25 words or fewer. A)Although the brain is an obligately aerobic organ, it still depends on glycolysis because . . .

Glycolysis is the first state in aerobic energy metabolism for any cell that depends on glucose as its energy source, as brain cells do.

The History of Glycolysis. B) Alcoholic fermentation does not take place in the absence of inorganic phosphate.

(b) Alcoholic fermentation does not occur in the absence of inorganic phosphate. Explanation: Explanation: The absence of inorganic phosphate inhibits alcoholic fermentation, indicating that phosphate is essential for some steps in the glycolytic pathway. Phosphate might be necessary for phosphorylation reactions, such as the conversion of glucose to glucose-6-phosphate. Justification: This observation highlights the importance of phosphate-dependent reactions in glycolysis, emphasizing the role of phosphorylation steps in the pathway.

The History of Glycolysis. C) In the presence of iodoacetate, a known inhibitor of glycolysis, fermenting yeast extracts accumulate a doubly phosphorylated hexose.

(c) In the presence of iodoacetate, an inhibitor of glycolysis, fermenting yeast extracts accumulate a doubly phosphorylated hexose. Explanation: Explanation: Iodoacetate inhibits a specific enzyme in glycolysis, likely one of the early enzymes involved in converting glucose to hexose phosphates. The accumulation of a doubly phosphorylated hexose indicates that glycolysis is blocked at an earlier step, preventing the conversion of hexose phosphates to triose phosphates. Justification: This observation helps establish the sequence of enzymatic reactions in glycolysis and identifies where the inhibition by iodoacetate occurs.

DATA ANALYSIS Regulation of Phosphofructokinase-1. C) What assumptions do you have to make about the concentration of ATP in Figure 9-15a and about the concentration of F2,6BP in Figure 9-15b? Explain.

(c) What assumptions do you have to make about the concentrations of ATP in Figure 9-15a and about the concentration of F2,6BP in Figure 9-15b? Explain.In Figure 9-15a, we assume that the concentration of ATP is constant and that it is not limiting the activity of PFK-1. This is because we are only interested in the effect of F2,6BP on enzyme activity. In Figure 9-15b, we assume that the concentration of F2,6BP is constant and that it is not affecting the activity of PFK-1. Explanation: This is because we are only interested in the effect of ATP concentration on enzyme activity. In Figure 9-15a, we assume that the concentration of ATP is not limiting the activity of PFK-1. In Figure 9-15b, we assume that the concentration of F2,6BP is not affecting the activity of PFK-1.

The History of Glycolysis. D) In the presence of fluoride ion, another known glycolytic inhibitor, fermenting yeast extracts accumulate two phosphorylated three-carbon acids.

(d) In the presence of fluoride ion, another known glycolytic inhibitor, fermenting yeast extracts accumulate two phosphorylated three-carbon acids. Explanation: Explanation: Fluoride ions interfere with specific enzymes in glycolysis, likely enzymes involved in the conversion of three-carbon compounds to two-carbon compounds like pyruvate. The accumulation of two phosphorylated three-carbon acids indicates that glycolysis is disrupted closer to the end of the pathway. Justification: This observation helps identify the site of inhibition by fluoride ions and provides insight into the latter stages of glycolysis.

9-6 Ethanol Intoxication and Methanol Toxicity. C)The medical treatment for methanol poisoning usually involves administration of large doses of ethanol. Why is this treatment effective?

-Methanol and ethanol are both substrates of the enzyme alcohol dehydrogenase.The body is flooded with a large amount of ethanol to provide an effective competitor of methanol, thereby minimizing the production of formaldehyde.

QUANTITATIVE Glycolysis and Gluconeogenesis C) Explain why gluconeogenesis requires the input of six molecules of nucleoside triphosphates (four ATPs and two GTPs) per molecule of glucose synthesized, whereas glycolysis yields only two molecules of ATP per molecule of glucose.

.The four additional PHOSPHOANHYDRIDE bonds provide the extra energy needed to ensure that the pathway is driven strongly enough in the gluconeogenic direction so that it is essentially IRREVERSIBLE in that direction.

9-7 Propionate Fermentation. B)Suggest an overall scheme for propionate production that generates only one additional product, and indicate what that product might be.

=> C6H12O6 --> 2CH3CH2COO- + O2 + 2H+ => CH3CH2COO- is propionate => O2 is an additional product => Option 2nd is correct

QUANTITATIVE Glycolysis and Gluconeogenesis. As Figure 9-12 indicates, gluconeogenesis is accomplished by what is essentially the reverse of the glycolytic pathway but with bypass reactions in place of the first, third, and tenth reactions in glycolysis. A) Explain why it is not possible to accomplish gluconeogenesis by a simple reversal of all the reactions in glycolysis.

A reaction sequence that is thermodynamically feasible (exergonic) in one direction will not function in the other direction by simple reversal of each of the reactions because it will be endergonic in that direction under the same conditions. The thermodynamic driving force − that is, the ΔG for the reaction sequence in the forward direction − is usually sufficiently great for most metabolic pathways.

9-9 Wrong Again. For each of the following false statements, change the statement to make it true, and explain why it was false. D) Because energy production is so important in the cell, glycolytic enzymes function solely to degrade glucose.

ATP is the ideal energy currency because the delta G for hydrolysis of ATP is an intermediate among cellular phosphorylated compounds. to produce ATP, ADP can be phosphorylated by compounds with a more -delta G of hydrolysis such as PEP. It can also be used to phosporylate compounds with a less -delta G of hydrolysis such as (G6P)

9-6 Ethanol Intoxication and Methanol Toxicity. B)Most of the unpleasant effects of hangovers result from an accumulation of acetaldehyde and its metabolites. Where does the acetaldehyde come from?

Acetaldehyde is the immediate product of ethanol oxidation. Ethanol+NAD+→acetaldehyde+NADH+H+

9-11 Arsenate Poisoning. Arsenate is a potent poison to almost all living systems. Among other effects, arsenate is known to uncouple the phosphorylation event from the oxidation of glyceraldehyde-3-phosphate. This uncoupling occurs because the enzyme involved, glyceraldehyde-3-phosphate dehydrogenase, can utilize arsenate instead of inorganic phosphate, forming glycerate-1-arseno-3-phosphate. This product is a highly unstable compound that immediately undergoes nonenzymatic hydrolysis into glycerate-3-phosphate and free arsenate. A)In what sense might arsenate be called an uncoupler of substrate-level phosphorylation?

Arsenate can be used by the enzyme glyceraldehyde-3-phosphate dehydrogenase in place of inorganic phosphate to make glycerate-1-arseno-3-phosphate. This makes arsenate an uncoupler of substrate-level phosphorylation. This product is very unstable and breaks down right away into glycerate-3-phosphate and free arsenate without the help of enzymes. Explanation: This mechanism separates the phosphorylation event from the oxidation of glyceraldehyde-3-phosphate because the enzyme can no longer speed up the reaction to make the desired product. Arsenate is harmful to a living thing because it can mess up the metabolic pathways that the living thing needs to make energy. In particular, it can mess up glycolysis, the part of metabolism that breaks down glucose to make energy.

9-11 Arsenate Poisoning. B) Why is arsenate such a toxic substance for an organism that depends critically on glycolysis to meet its energy needs?

As was said before, arsenate can stop this process by separating the phosphorylation event. This stops glycolysis from finishing since the glucose can't be broken down to make energy. Because of this, the creature can't make the energy it needs to stay alive. Other reactions that are likely to be uncoupled by arsenate in the same way as the glyceraldehyde-3-phosphate dehydrogenase reaction include the reaction of pyruvate kinase, which catalyzes the conversion of phosphoenolpyruvate to pyruvate, and the reaction of hexokinase, which catalyzes the conversion of glucose to glucose-6-phosphate. Phosphorylation is a part of each of these reactions, and arsenate is likely to mess them up. Explanation: Arsenate is also likely to change other reactions that involve oxidative phosphorylation, such as the electron transport chain. This is because the electron transport cycle needs electrons to be moved to oxygen, which arsenate stops from happening. Because of this, the creature can't make the energy it needs to stay alive.

9-10 You've Got Some Explaining to Do. Explain each of the following observations. B)In 1905, Arthur Harden and William Young found that addition of inorganic phosphate to a yeast extract stimulated and prolonged the fermentation of glucose.

B) Red blood cells do not require oxygen in the solution because red blood cells do not perform aerobic respiration. Red blood cells are unique in that they lack mitochondria, which are the cellular organelles responsible for aerobic respiration. Instead, red blood cells rely on anaerobic glycolysis for their energy needs. Explanation: Anaerobic glycolysis is a metabolic pathway that breaks down glucose without the need for oxygen, producing a small amount of ATP. Since red blood cells do not have mitochondria and are specifically designed to transport oxygen throughout the body, they don't consume the oxygen in their surroundings. In fact, they serve to transport oxygen to other tissues in the body, where oxygen is utilized for aerobic respiration.

9-3 Glycolysis in 25 Words or Fewer. B)Although one of its reactions is an oxidation, glycolysis can proceed in the absence of oxygen because . . .

The oxidation that occurs at one step is balanced by the reduction that occurs when pyruvate is concerted to lactate or ethanol and carbon dioxide.

9-3 Glycolysis in 25 Words or Fewer. D)If you bake bread or brew beer, you depend on glycolysis for . .

The pyruvate that is then reductively decarboxylated to generate the ethanol present in the beer and the carbon dioxide that causes the bread to rise.

9-3 Glycolysis in 25 Words or Fewer. E)Two organs in your body that can use lactate are

The liver and heart muscle.

QUANTITATIVE Glycolysis and Gluconeogenesis D) Assuming concentrations of ATP, ADP, and are such that for the hydrolysis of ATP is about , what is the approximate value for the overall reaction for gluconeogenesis that you wrote in part b?

The ΔG' for the glucolytic pathway under typical cellular conditions is about -20 kcal/mol and therefore +20 kcal/mol in the opposite direction. Because four additional phosphoanhydride bonds are hydrolyzed to drive the pathway n the opposite direction and each of those bonds has a ΔG' of about -10 kcal/mol, the net driving force in the gluconeogenic direction is ΔG'= 20+ 4(-10) = -20 kcal/mol

Fritz Lipmann in 1941 B) Energy is always released whenever a covalent bond is formed and is always required to break a covalent bond.

True

9-3 Glycolysis in 25 Words or Fewer. C)What happens to the pyruvate generated by the glycolytic pathway depends on

Whether an external electron acceptor is available, which in most cases means whether oxygen is available (i.e., whether the cell is functioning under aerobic conditions).

Fritz Lipmann in 1941 D) Phosphoester bonds are low-energy bonds because they require less energy to break than the high-energy bonds of phosphoanhydrides

false

Fritz Lipmann in 1941 E) Phosphoester bonds are low-energy bonds because they require less energy to break than the high-energy bonds of phosphoanhydrides.

false

9-9 Wrong Again. For each of the following false statements, change the statement to make it true, and explain why it was false. A)A lthough the reactions of gluconeogenesis are simply the reverse of the reactions of glycolysis, gluconeogenesis requires more energy than glycolysis releases.

gluconeogenesis does require more ATP but they are not simply the reverse of eachother, the 3 essentially irreversible rxns of glycolysis (Gly -1,-3,-10) are replaced by 3 bypass rxns that are unique to gluconeogenesis

Fritz Lipmann in 1941 C) To a physical chemist, high-energy bond means a very stable bond that requires a lot of energy to break, whereas to a biochemist, the term is likely to mean a bond that releases a lot of energy upon hydrolysis.

true

Fritz Lipmann in 1941 F)The term high-energy molecule should be thought of as a characteristic of the reaction the molecule is involved in—not as an intrinsic property of a particular bond within that molecule.

true

9-10 You've Got Some Explaining to Do. Explain each of the following observations. A)In his classic studies of glucose fermentation by yeast cells, Louis Pasteur observed that the rate of glucose consumption by yeast cells was much higher under anaerobic conditions than under aerobic conditions.

(A) Louis Pasteur observed that the rate of glucose consumption by yeast cells was much higher under anaerobic conditions than under aerobic conditions. This observation can be explained by the differences in energy production pathways between anaerobic and aerobic metabolism. Explanation: Under anaerobic conditions, yeast cells primarily undergo a process called fermentation. In this process, glucose is partially metabolized without the need for oxygen. The main goal of fermentation is to generate ATP (adenosine triphosphate), which is the cell's primary energy currency. However, fermentation is less efficient in terms of ATP production compared to aerobic respiration. Under aerobic conditions, yeast cells use oxygen to perform aerobic respiration, a highly efficient process that results in the complete oxidation of glucose to produce a large amount of ATP. When oxygen is available, yeast cells preferentially use aerobic respiration to maximize energy production. This is why the rate of glucose consumption is higher under anaerobic conditions, as the cells are trying to generate energy even without oxygen, although less efficiently.

9-10 You've Got Some Explaining to Do. Explain each of the following observations. C)An alligator is normally very sluggish but, if provoked, is capable of rapidly moving its legs, jaws, and tail. However, such bursts of activity must be followed by long periods of recovery.

(C) The runner's situation in the marathon can be explained by the different energy systems at play during various phases of the race. At the start of the marathon, the runner maintains a steady pace, primarily relying on aerobic metabolism to produce ATP from oxygen and stored energy sources. However, during the short sprint, the runner switches to anaerobic metabolism, which is less sustainable for longer durations. Explanation: The sprint likely depletes the runner's glycogen stores and results in the accumulation of lactic acid, causing fatigue. When the runner returns to a steady jog, they are still in an anaerobic state due to the accumulated lactic acid. This hinders their ability to continue, and they must exit the race because they cannot clear the lactic acid and switch back to efficient aerobic metabolism quickly enough.

9-10 You've Got Some Explaining to Do. Explain each of the following observations. D)Fermentation of glucose to lactate is an energy-yielding process, although it involves no net oxidation (i.e., even though the oxidation of glyceraldehyde-3-phosphate to glycerate is accompanied by the reduction of pyruvate to lactate and no net accumulation of NADH occurs).

(D) Fermentation of glucose to lactate is an energy-yielding process despite no net oxidation because it involves a partial reduction-oxidation reaction. In this process, glucose is partially oxidized to form two molecules of lactate from two molecules of pyruvate. Explanation: The key to understanding why this is energy-yielding lies in the role of coenzymes like NADH (nicotinamide adenine dinucleotide) and NAD+ (the oxidized form of NADH). During glycolysis (the initial step of glucose metabolism), NADH is produced, and this NADH is consumed in the subsequent step of reducing pyruvate to lactate. This transfer of electrons from NADH to pyruvate releases energy and regenerates NAD+ for further use in glycolysis. As a result, some energy is produced in the form of ATP despite no net oxidation of glucose.

The History of Glycolysis. Following are several historical observations that led to the elucidation of the glycolytic pathway. In each case, suggest a metabolic basis for the observed effect, and explain the significance of the observation for the elucidation of the pathway a)Alcoholic fermentation in yeast extracts requires a heat-labile fraction originally called zymase and a heat-stable fraction (cozymase) that is necessary for the activity of zymase.

(a) Alcoholic fermentation in yeast extracts requires a heat-labile fraction called zymase and a heat-stable fraction (cozymase). Explanation: Alcoholic fermentation in yeast extracts is a complex process involving various biochemical reactions. Zymase, a heat-labile fraction, is likely to contain enzymes responsible for converting glucose into ethanol. Cozymase, the heat-stable fraction, probably plays a role in supplying coenzymes or cofactors needed for zymase's enzymatic activity. Justification: The need for both zymase and cozymase suggests that multiple enzymes are required for the fermentation process. This observation led to the realization that glycolysis (fermentation) is not a single reaction but a series of stepwise enzymatic reactions. Understanding the involvement of various enzymes and cofactors in glycolysis paved the way for unraveling the entire metabolic pathway.

9-9 Wrong Again. For each of the following false statements, change the statement to make it true, and explain why it was false. C) ATP is ideal for the energy currency of the cell because it has the most negative standard free energy change () of hydrolysis of any phosphorylated compound in the cell.

ATP is the ideal energy currency because the delta G for hydrolysis of ATP is an intermediate among cellular phosphorylated compounds. to produce ATP, ADP can be phosphorylated by compounds with a more -delta G of hydrolysis such as PEP. It can also be used to phosporylate compounds with a less -delta G of hydrolysis such as (G6P)

9-3 Glycolysis in 25 Words or Fewer. F) The synthesis of glucose from lactate in a liver cell requires more molecules of nucleoside triphosphates (ATP and GTP) than are formed during the catabolism of glucose to lactate in a muscle cell because . . .

Energy is always lost (as heat and entropy) whenever a reaction occurs, so glucose formation from lactate requires more energy than glucose catabolism releases.

QUANTITATIVE Glycolysis and Gluconeogenesis E) With all of the enzymes for glycolysis and gluconeogenesis present in a liver cell, how does the cell "know" whether it should be synthesizing or catabolizing glucose at any given time?

Changes in the concentrations of AMP, ADP, ATP, ACETYLCoA, and F2,6BP either activate or inhibit the regulatory enzymes, thereby effectively turning the pathway on in one direction and off in the other.

9-6 Ethanol Intoxication and Methanol Toxicity. The enzyme alcohol dehydrogenase was mentioned in this chapter because of its role in the final step of alcoholic fermentation. However, the enzyme also occurs commonly in aerobic organisms, including humans. The ability of the human body to catabolize the ethanol in alcoholic beverages depends on the presence of alcohol dehydrogenase in the liver. One effect of ethanol intoxication is a dramatic decrease in the concentration in liver cells, which decreases the aerobic utilization of glucose. Methanol, on the other hand, is not just an intoxicant; it is a deadly poison due to the toxic effect of the formaldehyde to which it is converted in the liver. A) Why does ethanol consumption lead to a reduction in concentration and to a decrease in aerobic respiration?

Ethanol catabolism in the body begins with its oxidation (dehydrogenation), with NAD+as the electron acceptor. The more ethanol is consumed, the greater the demand is for NAD+ and the more serious is the reduction in NAD+ concentration. The supply of NAD+ may be inadequate for aerobic respiration of glucose.

When first introduced by Fritz Lipmann in 1941, the term high-energy bond was considered a useful concept for describing the energetics of biochemical molecules and reactions. However, the term can lead to confusion when relating ideas about cellular energy metabolism to those of physical chemistry. To check out your own understanding, indicate whether each of the following statements is true or false A) Energy is stored in special high-energy bonds in molecules such as ATP and is released when these bonds are broken.

False

DATA ANALYSIS Regulation of Phosphofructokinase-1. Shown in Figure 9-15 are plots of initial reaction velocity (expressed as % of ) versus fructose-6-phosphate concentration for liver phosphofructokinase (PFK-1) in the presence and absence of fructose-2,6-bisphosphate (F2,6BP) (Figure 9-15a) and in the presence of a low or high concentration of ATP (Figure 9-15b). A)Explain the effect of F2,6BP on enzyme activity as shown in Figure 9-15a.

Fructose-2,6-bisphosphate (F2,6BP) is an allosteric activator of phosphofructokinase-1 (PFK-1). This means that it binds to a site on the enzyme that is different from the active site and increases the enzyme's activity. As shown in Figure 9-15a, the presence of F2,6BP increases the initial reaction velocity of PFK-1 at all concentrations of fructose-6-phosphate (F6P). Explanation: This is because F2,6BP stabilizes the enzyme in its active conformation, making it more likely to bind to F6P and catalyze its conversion to fructose-1,6-bisphosphate (F1,6BP). F2,6BP is a potent allosteric activator of PFK-1. F2,6BP is produced from F6P by the enzyme PFK-2. The concentration of F2,6BP is regulated by hormones such as glucagon and insulin

9-11 Arsenate Poisoning. C)Can you think of other reactions that are likely to be uncoupled by arsenate in the same way as the glyceraldehyde-3-phosphate dehydrogenase reaction?

In short, arsenate is an uncoupler of substrate-level phosphorylation because the enzyme glyceraldehyde-3-phosphate dehydrogenase can use it instead of inorganic phosphate to make glycerate-1-arseno-3-phosphate. This process breaks the link between the phosphorylation event and the oxidation of glyceraldehyde-3-phosphate. This stops glycolysis from finishing and stops the organism from making the energy it needs to stay alive. Arsenate may also impact other pathways that involve oxidative phosphorylation, such as the electron transport chain. Because of this, the organism can't make the energy it needs to stay alive. This makes arsenate poisonous for an organism that gets its energy via glycolysis.

9-7 Propionate Fermentation. Although lactate and ethanol are the best-known products of fermentation, other pathways are also known, some with important commercial applications. Swiss cheese production, for example, depends on the bacterium Propionibacterium freudenreichii, which converts pyruvate to propionate . Fermentation of glucose to propionate always generates at least one other product as well. A)Why is it not possible to devise a scheme for the fermentation of glucose with propionate as the sole end-product?

Propionate differs from pyruvate in that its middle carbon atom is at the (hydrocarbon) level rather than at the (carbonyl) level. To (reduce) pyruvate to propionate would therefore require two molecules of NADH. Considering that the stoichiometry of glycolysis provides only one molecule of NADH per molecule of pyruvate, all of the pyruvate cannot be (reduced) to propionate

DATA ANALYSIS Regulation of Phosphofructokinase-1. B) Explain the effect of the ATP concentration on the data shown in Figure 9-15b.

b) Explain the effect of the ATP concentration on the data shown in Figure 9-15b.ATP is an allosteric inhibitor of PFK-1. This means that it binds to a site on the enzyme that is different from the active site and decreases the enzyme's activity. As shown in Figure 9-15b, the initial reaction velocity of PFK-1 is lower at high concentrations of ATP than at low concentrations of ATP. Explanation: This is because ATP stabilizes the enzyme in its inactive conformation, making it less likely to bind to F6P and catalyze its conversion to F1,6BP. ATP is an allosteric inhibitor of PFK-1. ATP is a product of glycolysis. The concentration of ATP is an indicator of the cell's energy status

9-9 Wrong Again. For each of the following false statements, change the statement to make it true, and explain why it was false. B)Because glycolysis involves the partial oxidation of glucose, it cannot proceed in the absence of oxygen.

glycolysis does and can proceed in the absence of 02. the partial oxidation of glucose is performed by NAD+ which gets reduced to NADH as it accepts electrons during the sole oxidation step in glycolysis

9-12 Life Without Phosphofructokinase. Many bacteria do not have phosphofructokinase-1 (Gly-3) and thus cannot convert glucose to fructose-1,6-bisphosphate. Instead, they use a pathway known as the Entner-Doudoroff pathway to partially oxidize glucose and convert it to two three-carbon molecules. See if you can draw the products of the first three steps of the pathway based on the following description. A) In the first step, the ring form of glucose-6-phosphate is oxidized at carbon 1 to form 6-phosphogluconolactone, as the coenzyme is reduced to .

he coenzyme involved in this oxidation reaction is likely NADP⁺, and it is reduced to NADPH during the process.

9-7 Propionate Fermentation. C)If you know that Swiss cheese production actually requires both propionate and carbon dioxide and that both are produced by Propionibacterium fermentation, what else can you now say about the fermentation process that this bacterium carries out?

the pyurvate must be further metabolized by decarboxylation