SaplingPlus for Lehninger Principles of Biochemistry (Six-Month Access)
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ISBN: 9781319108236
Author: David L. Nelson, Michael M. Cox
Publisher: W. H. Freeman
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Chapter 6, Problem 5P
(a)
Summary Introduction
To determine: The distance (Å) between
Introduction: Enzyme contains an active site, a region of enzyme where substrate binds. After binding of enzyme with substrate, enzyme-substrate complex is formed and initiates
(b)
Summary Introduction
To explain: How the two amino acids residues that can catalyze a reaction that occurs in space of few angstroms.
Introduction: Amino acids are the building blocks of proteins. It is an organic compound that contains an
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Classify each coenzyme or distinguishing characteristic based on whether it corresponds to catalytic or
stoichiometric coenzymes.
Catalytic coenzymes
Answer Bank
Stoichiometric coenzymes
lipoic acid
FAD
used once
coenzyme A
regenerated
thiamine pyrophosphate (TPP)
NAD+
The oxidation of malate by NAD+ to form oxaloacetate is a highly endergonic reaction under standard conditions.
AG +29 kJ mol¹ (+7 kcal mol-¹)
Malate + NAD+ oxaloacetate + NADH + H+
The reaction proceeds readily under physiological conditions.
=
Why does the reaction proceed readily as written under physiological conditions?
The NADH produced during glycolysis drives the reaction in the direction of malate oxidation.
The steady-state concentrations of the products are low compared with those of the substrates.
The reaction is pushed forward by the energetically favorable oxidation of fumarate to malate.
Endergonic reactions such as this occur spontaneously without the input of free energy.
Assuming an [NAD+ ]/[NADH] ratio of 8, a temperature of 25°C, and a pH of 7, what is the lowest [malate]/[oxaloacetate] ratio
at which oxaloacetate can be formed from malate?
[malate]
[oxaloacetate]
Calculate and compare the AG values for the oxidation of succinate by NAD+ and FAD. Use the data given in the table to find
the E of the NAD+: NADH and fumarate:succinate couples, and assume that E for the enzyme-bound FAD: FADH2 redox
couple is nearly +0.05 V.
Oxidant
Reductant
"
E' (V)
NAD+
NADH + H+
2
-0.32
Fumarate
Succinate
AG°' for the oxidation of succinate by NAD+:
AG°' for the oxidation of succinate by FAD:
2
-0.03
Why is FAD rather than NAD+ the electron acceptor in the reaction catalyzed by succinate dehydrogenase?
The electron-transport chain can regenerate FAD, but not NAD+.
FAD is an oxidant, whereas NAD+ is a reductant.
The oxidation of succinate requires two NAD+ molecules but only one FAD molecule.
The oxidation of succinate by NAD+ is not thermodynamically feasible.
kJ mol-1
kJ mol-1
Chapter 6 Solutions
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- Use the cellular respiration interactive to help you complete the passage. 2,4-dinitrophenol (DNP) was a popular ingredient in diet pills in the 1930s before it was discovered that moderate doses of the compound cause exceptionally high body temperature and even death. Complete the passage detailing how DNP's mechanism of action explains why it causes both high body temperature and weight loss. 2,4-dinitrophenol (DNP) causes of returning to the mitochondrial matrix through to pass directly across the inner mitochondrial membrane instead proteins. Because of DNP's effect on the mitochondrion, less energy is captured in the form of energy is instead wasted as heat. and more protons electrons ATP NADH sugars cytochrome ATP synthase heatarrow_forwardTo answer this question, you may reference the Metabolic Map. Select the reactions of glycolysis in which ATP is produced. 1,3-Bisphosphoglycerate 3-phosphoglycerate Glyceraldehyde 3-phosphate 1,3-bisphosphoglycerate Fructose 6-phosphate fructose 1,6-bisphosphate Phosphoenolpyruvate pyruvate Glucose glucose 6-phosphate Suppose 17 glucose molecules enter glycolysis. Calculate the total number of inorganic phosphate (P) molecules required as well as the total number of pyruvate molecules produced. P required: pyruvate produced: molecules moleculesarrow_forwardSuppose a marathon runner depletes carbohydrate stores after a four-hour run. The runner's nutritionist suggests replenishing carbohydrate stores by eating carbohydrates. However, the runner is also concerned about weight loss and wants to know if fats can be directly converted into carbohydrates. How should the nutritionist respond to the runner? Yes, the glyoxylate cycle can be used to convert acetyl CoA into succinate, which can then be converted into carbohydrates. No, the two decarboxylation reactions of the citric acid cycle preclude the net conversion of acetyl CoA into carbohydrates. No, the citric acid cycle converts acetyl CoA into oxaloacetate, but there is no pathway to form glucose from oxaloacetate. Yes, pyruvate carboxylase can convert acetyl CoA into pyruvate, which can be used to form glucose through gluconeogenesis.arrow_forward
- The crossover technique can reveal the precise site of action of a respiratory-chain inhibitor. Britton Chance devised elegant spectroscopic methods for determining the proportions of the oxidized and reduced form of each carrier. This determination is feasible because the forms have distinctive absorption spectra, as illustrated in the graph for cytochrome c. Upon the addition of a new inhibitor to respiring mitochondria, the carriers between NADH and ubiquinol (QH2) become more reduced, and those between cytochrome c and O₂ become more oxidized. Where does your inhibitor act? Complex I Complex II Complex III Complex IV Absorbance coefficient (M-1 cm x 10-5) 10 1.0 0.5 400 Reduced Oxidized 500 Wavelength (nm) 600arrow_forwardWhy are the electrons carried by FADH2 not as energy rich as those carried by NADH? FADH2 carries fewer high-energy electrons than NADH. OFADH2 is less negatively charged than NADH. OFADH2 has a lower phosphoryl-transfer potential than NADH. FADH₂ has a lower reduction potential than NADH. What is the consequence of this difference? Electrons flow from NADH to FADH2 before they are transferred to O₂. Electron flow FADH₂ to O, results in the production of more ATP than does electron flow from NADH. Electron flow from FADH₂ to O, pumps fewer protons than does electron flow from NADH. Electron flow from FADH, to O, consumes more free energy than does electron flow from NADH. A simple equation relates the standard free-energy change, AG", to the change in reduction potential, AE. AG=-FAE Then represents the number of transferred electrons, and F is the Faraday constant with a value of 96.48 kJ mol¹ V-¹. Use the standard reduction potentials provided to determine the standard free energy…arrow_forwardMatch each enzyme with its description. catalyzes the formation of isocitrate synthesizes succinyl CoA generates malate generates ATP converts pyruvate into acetyl CoA converts pyruvate into oxaloacetate condenses oxaloacetate and acetyl CoA catalyzes the formation of oxaloacetate synthesizes fumarate catalyzes the formation of a-ketoglutarate Answer Bank succinate dehydrogenase a-ketoglutarate dehydrogenase aconitase fumarase citrate synthase malate dehydrogenase pyruvate carboxylase pyruvate dehydrogenase complex isocitrate dehydrogenase succinyl CoA synthetasearrow_forward
- coo ☐ CH2 coo Malonate Determine how the concentration of each citric acid cycle intermediate will change immediately after the addition of malonate. The concentration of citrate will The concentration of isocitrate will The concentration of α-ketoglutarate will The concentration of succinyl CoA will The concentration of succinate will The concentration of fumarate will The concentration of malate will The concentration of oxaloacetate will Why is malonate not a substrate for succinate dehydrogenase? Malonate lacks a thioester bond that has high transfer potential. Malonate has two carboxylic acid groups. Malonate is not large enough to bind to the enzyme. Malonate only has one methylene group.arrow_forwardAnalysis of the a-ketoglutarate formed showed that none of the radioactive label had been lost. Decarboxylation of a-ketoglutarate then yielded succinate devoid of radioactivity. All the label was in the released CO₂. Use an asterisk (*) to indicate the location of "C in the intermediates and products of the pathway that converts [C]oxaloacetate into succinate. Coo Coo CH₂ CH₂ Tooc-c-OH ooc-CH CH₂ CH₂ HC OH 14Coo coo -Coo [14C]oxaloacetate Citrate Isocitrate 0000 Coo coo CH₂ CH₂ S-COA Succinate Succinyl CoA ☐ ☐ CH₂ a-Ketoglutarate Why do all the labeled carbons emerge as carbon dioxide? Citrate is a symmetric molecule, and each -CH, COO group reacts identically. Both of citrate's -CH, COO groups are decarboxylated on the pathway to succinate. Citrate is a chiral molecule, and each-CH,COO- group reacts differently. An enzyme in this pathway holds its substrate in a specific orientation. Anwer Bankarrow_forwardAlthough both hexokinase and phosphofructokinase catalyze irreversible steps in glycolysis and the hexokinase-catalyzed step is first, phosphofructokinase is nonetheless the pacemaker of glycolysis. What does this information tell you about the fate of the glucose 6-phosphate formed by hexokinase? Glucose 6-phosphate must be wasted when it is produced in excess. Glucose 6-phosphate must be unstable and release its phosphoryl group over time. Glucose 6-phosphate must allosterically inhibit phosphofructokinase, but not hexokinase. Glucose 6-phosphate must be utilized by other metabolic pathways.arrow_forward
- Complete the table by predicting the effect of each mutation on the pace of glycolysis in liver cells. Mutation Loss of the allosteric site for ATP in phosphofructokinase Loss of the binding site for citrate in phosphofructokinase Loss of the phosphatase domain of the bifunctional enzyme that controls the level of fructose 2,6-bisphosphate Loss of the binding site for fructose 1,6-bisphosphate in pyruvate kinase Pace of glycolysis increase decrease no changearrow_forwardMatch each enzyme of glycolysis with its description. forms fructose 1,6-bisphosphate generates the first intermediate compound with a high phosphoryl-transfer potential that is not ATP converts glucose 6-phosphate into fructose 6-phosphate enolase Answer Bank hexokinase pyruvate kinase phosphoglycerate mutase phosphorylates glucose generates the second molecule of ATP cleaves fructose 1,6-bisphosphate generates the second intermediate compound with a high phosphoryl-transfer potential catalyzes the interconversion of three-carbon isomers converts 3-phosphoglycerate into 2-phosphoglycerate generates the first molecule of ATP aldolase triose phosphate isomerase phosphoglucose isomerase phosphofructokinase glyceraldehyde 3-phosphate dehydrogenase phosphoglycerate kinasearrow_forwardFatty acid breakdown generates a large amount of acetyl CoA. What is the effect of fatty acid breakdown on glycolysis and pyruvate dehydrogenase complex activity? The amount of glucose broken down by glycolysis because the acetyl CoA generated by fatty acid breakdown the pyruvate dehydrogenase complex.arrow_forward
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