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medical sciences
biochemistry

Questions and Answers of Biochemistry

What structural features distinguish the T conformation of glycogen phosphorylase from the R conformation of the enzyme?
Glycogen phosphorylase is activated in vigorously active muscle without significant changes in intracellular [cAMP]. Explain.
Which target enzyme in glycogen metabolism requires both α- and β-adrenoreceptors to be activated for full enzyme activity?
What is the fate of H14CO3- added to a liver homogenate that is active in gluconeogenesis?
Write a balanced equation for the formation of PEP from pyruvate and compare it with the reverse reaction of glycolysis.
While acetyl-CoA, the end product of fatty acid oxidation, cannot be converted into glucose, another product of fat degradation, glycerol, can be converted to glucose. Where does glycerol enter the
UDP-galactose can donate is sugar residue to glucose to form the disaccharide lactose. For the structures of UDP-galactose and glucose below, indicate the reactive electrophilic and nucleophilic
What feature of the structure of glycogen phosphorylase is consistent with the observation that the enzyme cannot cleave a glycosidic bond within five residues of a branch point?
What would be the product of the nonenzymatic phosphorolysis of glycogen?
In the diagram of glycogen shown below, circle the substrates for glycogen debranching enzyme.
The rate of debranching is much slower than that of phosphorolysis. Explain how highly branched glycogen molecules release glucose-1-phosphate at a greater rate than relatively unbranched ones.
How is the thermodynamic barrier to glycogen synthesis overcome by cells?
In the diagram below, each circle represents a glycosyl unit. By the action of branching enzyme, show the most branched structure this molecule can assume. Indicate the reducing and nonreducing ends
Explain why the glycogen phosphorylase reaction ((G(( = 3.1 kJ ( mol-1) is exergonic in the cell.
Subjects who consumed a meal containing a high amylose:amylopectin ratio showed a lower increase in blood glucose levels than subjects who consumed a meal with a low amylose:amylopectin ratio.
Many diabetics do not respond to insulin because of a deficiency of insulin receptors on their cells. How does this affect (a) The levels of circulating glucose immediately after a meal and (b) The
Why does it make metabolic sense for the same hormone signal to stimulate glycogenolysis and inhibit glycolysis in the liver while stimulating both glycogenolysis and glycolysis in muscles?
Write the balanced equation for the sequential conversion of glucose to pyruvate and of pyruvate to glucose.
Write the balanced equation for the catabolism of six molecules of G6P by the pentose phosphate pathway followed by conversion of ribulose-5-phosphate back to G6P by gluconeogenesis.
In the Cori cycle, the lactate product of glycolysis in muscle is transformed back into glucose by the liver. (a) List the enzymes involved in the lactate ( glucose pathway. (b) What is the net
(a) What amino acid, other than alanine, can be converted by transamination to a gluconeogenic precursor? (b) Calculate the cost, in ATP equivalents, of converting two molecules of this amino acid to
The pathways of carbohydrate metabolism described in Chapters 15 and 16 include two reactions involving the transfer of onecarbon groups. (a) Name the enzymes and the pathways where these reactions
Predict the effect of a fructose-1,6-bisphosphatase deficiency on blood glucose levels (a) Before and (b) After a 24-hour fast.
Would you expect the allosteric regulator AMP to increase or decrease fructose-1,6-bisphosphatase activity?
Explain why it makes metabolic sense for acetyl-CoA, which is not a substrate for gluconeogenesis, to activate pyruvate carboxylase.
Fill in the blanks in the following diagram representing sucrose synthesis in plants.
Starch synthase in plants contains a single active site that accommodates ADP-glucose. However, cellulose synthase may contain two UDP-glucose-binding active sites. Given the structural differences
Individuals with McArdle's disease often experience a "second wind" resulting from cardiovascular adjustments that allow glucose mobilized from liver glycogen to fuel muscle contraction. Explain why
A sample of glycogen from a patient with liver disease is incubated with Pi, normal glycogen phosphorylase, and normal debranching enzyme. The ratio of G1P to glucose formed in the reaction mixture
One molecule of dietary glucose can be oxidized through glycolysis and the citric acid cycle to generate a maximum of 32 molecules of ATP. Calculate the fraction of this energy that is lost when the
The free energy of hydrolysis of an ((1(4) glycosidic bond is - 15.5 kJ ( mol-1, whereas that of an ((1(6) glycosidic bond is -7.1 kJ ( mol-1. Use these data to explain why glycogen debranching
Calculations based on the volume of a glucose residue and the branching pattern of cellular glycogen indicate that a glycogen molecule could have up to 28 branching tiers before becoming impossibly
The citric acid cycle can be divided into two phases with respect to the oxidation of acetyl- CoA. Describe each phase and write its balanced equation.
How would the rapid accumulation of succinyl-CoA affect the rate of glucose oxidation?
How does acetyl-CoA affect the activity of pyruvate carboxylase? Why is this advantageous for the cell?
Write a balanced equation for the synthesis of glucose from acetyl-CoA via the glyoxylate cycle.
Early experiments showed that malonate, which inhibits succinate dehydrogenase, blocks cellular respiration. This led to the idea that succinate participates in oxidative metabolism as an
For each reaction listed below, indicate the appropriate enzyme(s) in the pyruvate dehydrogenase complex and the relevant cofactor(s), if applicable.
What are the roles of FAD and NAD+ in the pyruvate dehydrogenase catalytic mechanism?
You are given two preparations of purified pyruvate dehydrogenase complex enzymes with all the required cofactors. You add pyruvate to each preparation and then measure the rate of production of
Which of the following labeled glucose molecules would yield 14CO2 following glycolysis and the pyruvate dehydrogenase reaction? (a) 1-[14C]-glucose (b) 3-[14C]-glucose (c) 4-[14C]-glucose (d)
What is the energetic function of the thioester bond of CoA in the citrate synthase reaction?
For the half-reactionFAD + 2 e- + 2 H+ ⇆ FADH2E °′≈ 0.00 V for FAD bound to succinate dehydrogenase.(a) Calculate ΔG°′ for the oxidation of succinate to fumarate by enzyme-bound FAD.(b)
The CO2 produced in one round of the citric acid cycle does not originate in the acetyl carbons that entered that round. If acetyl CoA is labeled with 14C at its carbonyl carbon, how many rounds of
Refer to Table 14-4 to explain why FAD rather than NAD+ is used in the succinate dehydrogenase reaction.
Certain microorganisms with an incomplete citric acid cycle decarboxylate (- ketoglutarate to produce succinate semialdehyde. A dehydrogenase then converts succinate semialdehyde to succinate.These
Given the following information, calculate the physiological (G of the isocitrate dehydrogenase reaction at 25°C and pH 7.0: [NAD+] / [NADH] = 8, [(-ketoglutarate] = 0.1 mM, and [isocitrate] = 0.02
Calculate the ratio of [fumarate] to [succinate] under cellular conditions at 37°C.
What is the ratio of [isocitrate] to [citrate] under cellular conditions at 37°C?
Why is it advantageous for citrate, the product of Reaction 1 of the citric acid cycle, to inhibit phosphofructokinase, which catalyzes the third reaction of glycolysis?
If acetyl-CoA is labeled with 14C at its methyl group, how many rounds of the cycle are required before 14CO2 is released?
When blood [glucose] is high and a cell's energy needs are met, insulin stimulates glycogen synthesis. Is it counterproductive for insulin to also promote the conversion of pyruvate to acetyl-CoA?
(a) Explain why obligate anaerobes contain some citric acid cycle enzymes. (b) Why don't these organisms have a complete citric acid cycle?
The catabolism of several amino acids generates succinyl-CoA. Describe the series of reactions that are required to convert mitochondrial succinyl-CoA to cytosolic oxaloacetate that can be used for
Many amino acids are broken down to intermediates of the citric acid cycle. (a) Why can't these amino acid "remnants" be directly oxidized to CO2 by the citric acid cycle? (b) Explain why amino acids
Anaplerotic reactions permit the citric acid cycle to supply intermediates to biosynthetic pathways while maintaining the proper levels of cycle intermediates. Write the equation for the net
Although animals cannot synthesize glucose from acetyl-CoA, if a rat is fed 14C-labeled acetate, some of the label appears in glycogen extracted from its muscles. Explain.
The malaria parasite Plasmodium falciparum does not carry out oxidative phosphorylation and therefore does not use the citric acid cycle to generate reduced cofactors. Instead, the parasite converts
Which one of the five steps of the pyruvate dehydrogenase complex reaction is most likely to be metabolically irreversible? Explain.
Explain why an individual with a deficiency of pyruvate dehydrogenase phosphatase (PDP) is unable to tolerate exercise.
Draw a cross-section of a mitochondrion and label the following structural features: Outer membrane (OM)..........................Inner membrane (IM) Matrix
What amino acid residues would you expect to find at the cytochrome c-binding sites of Complex III and Complex IV?
What key observations support the chemiosmotic hypothesis?
Can a pH gradient exist without ΔΨ? Can ΔΨ exist without a ΔpH?
(a) What is a P/O ratio? (b) What happens to oxygen consumption when electron donors and inorganic phosphate are present in a suspension of mitochondria in the absence of ADP? (c) What happens when
(a) Valinomycin, an antibiotic ionophore, allows the free passage of only K+ ions across a membrane. If K+ and valinomycin are added to respiring, fully coupled ATP-synthesizing mitochondria, what
The free energy-requiring step in the synthesis of ATP is not the formation of ATP from ADP and Pi (ΔG ≈ 0), but the release of tightly bound ATP. Explain why this is not inconsistent with the
Dicyclohexylcarbodiimide (DCCD) reacts with Asp and Glu residues in the c subunits of F0 and blocks ATP synthase activity. What happens to the rate of electron transport when DCCD is added to
What does an H+/P ratio measure? Why would it be impractical to determine an H+/P ratio?
The conversion of glucose to 2 lactate has ΔG°′ = -196 kJ⋅mol-1. The complete oxidation of glucose to 6 CO2 has ΔG°′ = -2823 kJ⋅mol-1. Compare the efficiencies of ATP synthesis by each of
Match the following enzyme or other molecule with its location:
On an average day, an adult dissipates about 7000 kJ of free energy. Assuming that this occurs under standard conditions, (a) How many moles of ATP must be hydrolyzed to provide this quantity of free
What is the irreversible step in electron transport and how is its rate controlled?
Cytochrome P450 (Section 12-4D) catalyzes a reaction in which two electrons supplied by NADPH reduce the heme Fe atom so that it can then reduce O2 preparatory to the hydroxylation of a substrate
Rats that are fed a "cafeteria" diet (in which food is always available) tend to die sooner than rats whose dietary intake is limited. Propose an explanation for this observation.
About half the volume of the mitochondrial matrix is water, and the rest is protein. If a single protein of molecular mass 40,000 were as concentrated, what would be its molar concentration? Assume
Oxidative phosphorylation requires the transfer of electrons donated by NADH. (a) Is NADH imported directly into the mitochondria? Explain. (b) Describe two import mechanisms that transfer cytosolic
Which reactions of the citric acid cycle donate electron pairs to the mitochondrial electrontransport chain?
The half-cell reduction potential is provided by the Nernst equation (Equation 14-8):(a) On the graph below, plot the reduction potentials for the FADH2/FAD half-cell (E°€² = - 0.219 V)
Inhibitors of electron transport have been used to determine the order of electron carriers. What would be the expected redox states of cytochromes a, bL, and c when (a) Stigmatellin, (b) Antimycin
Which mitochondrial electron carriers are potentially proton carriers? Which are more abundant-proton carriers or electron carriers? What does this suggest about the mechanism of transmembrane proton
Explain why a liver cell mitochondrion contains fewer cristae than a mitochondrion from a heart muscle cell.
Sketch the O2-consumption curves obtained for the mitochondria in Problem 9 when (a) CN- is added at t = 1 and succinate is added at t = 2 and (b) oligomycin (which binds to F0 and prevents ATP
Why is it possible for electrons to flow from a redox center with a more positive to one with a more negative within an electron-transfer complex?
A family of proteins known as cupredoxins contain a single redox-active Cu ion coordinated by a Cys, a Met, and two His residues. The reduction potentials of cupredoxins range from about 0.15 V to
Bombarding a suspension of mitochondria with high-frequency sound waves (sonication) produces submitochondrial particles derived from the inner mitochondrial membrane. These membranous vesicles seal
The difference in pH between the internal and external surfaces of the inner mitochondrial membrane is 1.4 pH units (external side acidic). If the membrane potential is 0.06 V (inside negative), what
For the mitochondrial membrane described in Problem 15, how many protons must be transported to provide enough free energy for the synthesis of 1 mol of ATP (assuming standard biochemical conditions)?
Consider the mitochondrial ADP-ATP translocator and the Pi-H+ symport protein. How do the activities of the two transporters affect the electrochemical gradient across the mitochondrial membrane?
How do the P/O ratios for NADH differ in ATP synthases that contain 10 and 15c subunits?
Certain genetic diseases caused by defective mitochondrial proteins are inherited only maternally, in contrast to most genetic diseases, in which either parent can pass on the defect. Explain.
How many protons are required to synthesize one ATP by F1F0 ATPase containing (a) 10 or (b) 15c subunits?
Dicyclohexylcarbodiimide (DCCD) is a reagent that reacts with Asp or Glu residues.Explain why the reaction of DCCD with the c subunits of F1F0 ATPase blocks its ATP-synthesizing activity.
The antibiotic oligomycin B blocks proton transport through F0. Explain why lactate concentrations build up in rats who have been treated with oligomycin B.
Explain why compounds such as DNP increase metabolic rates.
What is the advantage of hormones activating a lipase to stimulate nonshivering thermogenesis in brown fat rather than activating UCP1 directly?
Describe the changes in [NADH]/[NAD+] and [ATP]/[ADP] that occur during the switch from anaerobic to aerobic metabolism. How do these ratios influence the activity of glycolysis and the citric acid
During cell signaling events that increase cytosolic calcium concentrations, Ca2+ enters the mitochondria via Ca2+ channels in the inner membrane. (a) Explain why it is necessary for these channels
In coastal marine environments, high concentrations of nutrients from terrestrial runoff often lead to algal blooms. When the nutrients are depleted, the algae die and sink and are degraded by other
Chromium is most toxic and highly soluble in its oxidized Cr(VI) state but is less toxic and less soluble in its more reduced Cr(III) state. Efforts to detoxify Cr-contaminated groundwater have

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