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medical sciences
biochemistry

Biochemistry Concepts and Connections 1st edition Dean R. Appling, Spencer J. Anthony Cahill, Christopher K. Mathews - Solutions

At 37 C, the serine protease subtilisin has kcat = 50 s-1 and KM = 1.4 × 10-4 M. It is proposed that the N155 side chain contributes a hydrogen bond to the oxyanion hole of subtilisin. J. A. Wells and colleagues reported (1986, Phil. Trans. R. Soc. Lond. A 317:415-423) the following kinetic
On the figure below are shown three Line weaver-Burk plots for enzyme reactions that have been carried out in the presence, or absence, of an inhibitor. Indicate what type of inhibition is predicted based on each Line weaver-Burk plot. For each plot indicate which line corresponds to the reaction
The steady-state kinetics of an enzyme are studied in the absence and presence of an inhibitor (inhibitor A). The initial rate is given as a function of substrate concentration in the following table:a. What kind of inhibition (competitive, uncompetitive, or mixed) is involved?b. Determine Vmax and
The same enzyme as in Problem 14 is studied in the presence of a different inhibitor (inhibitor B). In this case, two different concentrations of inhibitor are used. Data are as follows:a. What kind of inhibitor is inhibitor B?b. Determine the apparent Vmax and KM at each inhibitor concentration.c.
Enalapril is an anti-hypertension "prodrug" (i.e., a drug precursor) that is inactive until the ethyl ester (arrow in figure) is hydrolyzed by esterases pre-sent in blood plasma. The active drug is the dicarboxylic acid ("enalaprilat") that results from this hydrolysis reaction.a. Enalapril is
Initial rate data for an enzyme that obeys Michaelis-Menten kinetics are shown in the following table. When the enzyme concentration is 3 nmol ml-1, a Line weaver-Burk plot of this data gives a line with a y-intercept of 0.00426 (Î¼mol-1ml s).a. Calculate kcat for the reaction. b.
Suggest the effects of each of the following mutations on the physiological role of chymotrypsinogen: a. R15S b. C1S c. T147S
The inhibitory effect of an uncompetitive inhibitor is greater at high [S] than at low [S]. Explain this observation.
The allosterically regulated enzyme ATCase binds aspartic acid as a substrate and acylates the a -amino group. Succinate acts as a competitive inhibitor of ATCase because it binds the active site but can't be acylated. The dependence of v0 on aspartic acid for ATCase is shown in panel (a) of the
An enzyme contains an active site aspartic acid with a pKa = 5.0, which acts as a general acid catalyst. On the template below, draw the curve of enzyme activity (reaction rate) versus pH for the enzyme (assume the protein is stably folded between pH 2-12 and that the active site Asp is the only
The folding and unfolding rate constants for a myoglobin mutant have been determined. The unfolding rate constant kF → U = 3.62 × 10-s S-1 and the folding rate constant kU→F = 255 S-1, where F is the folded protein and U is the unfolded (denatured) protein. For wild-type myoglobin, Δ
In some reactions, in which a protein molecule is binding to a specific site on DNA a rate greater than that predicted by the diffusion limit is observed. Suggest an explanation.
The initial rate for an enzyme-catalyzed reaction has been determined at a number of substrate concentrations. Data are as follows:a. Estimate Vmax and KM from a direct graph of v versus [S]. Do you find difficulties in getting clear answers? b. Now use a Lineweaver-Burk plot to analyze the same
a. If the total enzyme concentration in Problem 7 was 1 nmol/L, how many molecules of substrate can a molecule of enzyme process in each minute? b. Calculate kcat/KM for the enzyme reaction in Problem 7. Is this a fairly efficient enzyme?
Figure 8.19 shows a proposed mechanism for carboxypeptidase A.In Figure 8.19a. What is the role of Glu 270 in catalysis? b. What is the role of Arg 145 in catalysis?
Draw Haworth projections for the following:In Î±-furanose form. Name the sugar.(a)(b) The l isomer of (a) (c) Î± -D-GlcNAc (d) Î± -D-Fructofuranose
The reagent periodate (IO4-) oxidatively cleaves the carbon--carbon bonds between two adjacent carbons carrying hydroxyl groups. Explain how periodate oxidation might be used to distinguish between methyl glycosides of glucose in the pyranose and furanose forms.
Draw (using Haworth projections) the fragments of xylan and glucomannan structures shown on page 291.In page 298Chitin
Why do you suppose that the influenza virus protein that binds the virus to an infected cell is called hemagglutinin? Hemagglutination is the clumping together of red blood cells.
The diversity of functional groups on sugars that can form glycosidic bonds greatly increases the information content of glycans relative to oligopeptides. Consider three amino acids, A, B, and C. How many tripeptides can be formed from one molecule of each amino acid? Now consider three
Are mannose and galactose epimers? Allose and altrose? Gulose and talose? Ribose and arabinose? Consider only d-sugars. Explain your answers.
Explain in about one sentence why it is important to animals for the major carbohydrate storage polymer, glycogen, to be branched rather than unbranched.
Write the structure of UDP-N-acetyl glucosamine and UDP-galactosamine.
Consider the dextran sucrase reaction. Why do you suppose there is not an ATP requirement to energetically drive the creation of glycosidic bonds in the dextran product?
α-D-Galactopyranose rotates the plane of polarized light, but the product of its reduction with sodium borohydride (galactitol) does not. Explain the difference.
Provide an explanation for the fact that α-D-mannose is more stable than β-D-mannose, whereas the opposite is true for glucose.
Why is a type O individual considered a universal blood donor? Why is a type AB individual considered a universal acceptor?
The disaccharide Î±, Î²-trehalose differs from the Î±, Î± structure in Figure 9.14(a) by having an (a1†’Î²1) linkage. Draw its structure as a Haworth projection.In Figure 9.14
Dextrans are polysaccharides produced by certain species of bacteria. They are glucans, with primarily α(1 → 6) linkages and with frequent a (1 → 3) branching. Draw a Haworth projection of a portion of a dextran, including one (1 → 3) branch point.
Give structures for the following, based on the data in Table 10.1.In Table 10.1a. cis-9-Dodecenoic acid b. 18:1c ˆ†11 c. A saturated fatty acid that should melt below 30 °C
Calculate the equilibrium membrane potentials to be expected across a membrane at 37 °C, with a NaCl concentration of 0.10 M on the right and 0.01 M on the left, given the following conditions. In each case, state which side is (+) and which is (-). a. Membrane permeable only to Na+. b. Membrane
List two differences you would expect to see in the composition of lipids in the E. coli membrane when the cells are incubated at 25 °C compared to incubation at 37 °C.
Many transmembrane proteins are oligomeric, with several identical subunits. The oligomers are usually found to have some form of Cn symmetry, rather than Dn or any higher order. Suggest a reason for this observation.
The average human generates approximately his or her weight in ATP every day. A resting person uses about 25% of this in ion transport-mostly via the Na+ - K+ ATPase. About how many grams of Na+ and K+ will a sedentary 70-kg person pump across membranes in a day?
The concentration of glucose in your circulatory system is maintained near 5.0 mM by the actions of the pancreatic hormones glucagon and insulin. Glucose is imported into cells by protein transporters that are highly specific for binding glucose. Inside the liver cells the imported glucose is
ATP is synthesized from ADP, Pi, and a proton on the matrix side of the inner mitochondrial membrane. We will refer to the matrix side as the "inside" of the inner mitochondrial membrane (IMM).a. H+ transport from the outside of the IMM into the matrix drives this process. The pH inside the matrix
The Na+/glucose symport transports glucose from the lumen of the small intestine into cells lining the lumen. Transport of 1 glucose molecule is directly coupled to the transport of 1 Na+ ion into the cell.Assume the following conditions at 37 °C: [Na+]in = 12 mM, [Na+]out = 145 mM,
The classic demonstration that cell plasma membranes are composed of bilayers depends on the following kinds of data: • Te membrane lipids from 4.74 × 109 erythrocytes will form a mono-layer of area 0.89 m2 when spread on a water surface. • Te surface of one erythrocyte is approximately 100
The lipid portion of a typical bilayer is about 30 Å thick. a. Calculate the minimum number of residues in an α-helix required to span this distance. b. Calculate the minimum number of residues in a β-strand required to span this distance. c. Explain why α-helices are most commonly observed in
In the situations described below, what is the free energy change if 1 mole of Na+ is transported across a membrane from a region where the concentration is 1 μM to a region where it is 100 μM? (Assume T = 37 oC.)a. In the absence of a membrane potential.b. When the transport is opposed by a
Propose an experiment that would distinguish pore-mediated diffusion (e.g., by gramicidin) from carrier-mediated diffusion (e.g., by valinomycin).
In contrast to phospholipids, the transport of fatty acids across membranes is much more rapid (less than a second). Propose an explanation for this observation.
Peptide hormones (such as insulin) must bind to receptors on the outside surfaces of their target cells before their signal is transmitted to the inside of the cell. In contrast, the receptors for steroid hormones (such as estradiol, shown below) are found inside cells. What features of these two
Suppose calcium ion is maintained within an organelle at a concentration 1000 times greater than outside the organelle (T = 37 oC). What is the contribution of Ca+ to the membrane potential? Which side of the organelle membrane is positive, and which is negative?
Write a balanced equation for the complete oxidation of each of the following, and calculate the respiratory quotient for each substance.(a) Ethanol(b) Acetic acid(c) Stearic acid(d) Oleic acid(e) Linoleic acid
Mammalian cells growing in culture were labeled with [3H]-thymidine to estimate the rate of DNA synthesis. Te thymidine administered had a speciﬁc activity of 3000 cpm / pmol. At intervals, samples of culture were taken and acidiﬁed to precipitate nucleic acids. Te rate of incorporation of
Suppliers of radioisotopically labeled compounds usually provide each product as a mixture of labeled and unlabeled material. Unlabeled material is added deliberately as a carrier, partly because the speciﬁc activity of the carrier-free product is too high to be useful and partly because the
Predict the product(s) of the following reactions:
Given what you know about the involvement of nicotinamide nucleotides in oxidative and reductive metabolic reactions, predict whether the following intracellular concentration ratios should be 1, > 1, or < 1. Explain your answers. (a) [NAD+] / [NADH] (b) [NADP+] / [NADPH] (c) Since NAD+ and NADP+
On page 345 we showed that the oxidation of glucose and palmitic acid yields 15.64 kJ / g and 38.90 kJ / g, respectively. Calculate these values in terms of kJ / mol and kJ per carbon atom oxidized for both glucose and palmitic acid.
Free energy changes under intracellular conditions diﬀer markedly from those determined under standard conditions. ΔG°′ = - 30.5 kJ/mol for ATP hydrolysis to ADP and Pi. Calculate ΔG for ATP hydrolysis in a cell at 37 ° C that contains |ATP| = 3 mM, |ADP| = 1 mM, and |P i| = 1 mM.
(a) Consider the following hypothetical metabolic pathway:Under intracellular conditions, the activity of enzyme X is 100 pmol/106 cells/s. Calculate the eï¬€ect on metabolic ï¬‚ux rate (pmol/106 cells/s) of B †’ C of the following treatments. Calculate as % change (increase or
Te glucose / glucose-6-phosphate substrate cycle involves distinct reactions of glycolysis and gluconeogenesis that interconvert these two metabolites. Assume that under physiological conditions, [ATP] = [ADP] and [Pi] = 1 mM.Consider the following glycolytic reaction catalyzed by hexokinase:ATP +
Wheeler and Mathews (J.Biol.Chem.286:16992-16996,2011) reported the concentrations of adenine nucleotides in rat liver mitochondria as follows: ATP, 5.5 mM; ADP, 5.1 mM; AMP, 1.8 mM.(a) Calculate the adenylate energy charge within the mitochondrion.(b) Most measurements of adenylate energy charge
Two-dimensional gel electrophoresis of proteins in a cell extract provides a qualitative way to compare proteins with respect to intracellular abundance. Describe a quantitative approach to determine the number of molecules of an enzyme per cell.
Intracellular concentrations in resting muscle are as follows: fructose-6-phosphate, 1.0 mM; fructose-1,6-bisphosphate, 10 mM; AMP, 0.1 mM; ADP, 0.5 mM; ATP, 5 mM; and Pi , 10 mM. Is the phosphofructokinase reaction in muscle more or less exergonic than under standard conditions by how much?
Briefly discuss why each of the three common forms of galactosemia involves impaired utilization of galactose. Which metabolic process is blocked in each condition?
Some anaerobic bacteria use an alternative pathway for glucose catabolism, shown below, that converts glucose to acetate rather than to pyruvate. The first part of this pathway (glucose to fructose-1, 6-bisphosphate) is identical to the glycolytic pathway. In the second part of the alternative
Sketch a curve that would describe the expected behavior of phosphofructokinase activity as a function of the adenylate energy charge.
Methanol is highly toxic, not because of its own biological activity but because it is converted metabolically to formaldehyde, through action of alcohol dehydrogenase. Part of the medical treatment for methanol poisoning involves administration of large doses of ethanol. Explain why this treatment
Write a balanced equation for each of the following reactions or reaction sequences. (a) The reaction catalyzed by PFK-2 (b) The conversion of 2 moles of oxaloacetate to glucose (c) The conversion of glucose to UDP-Glc (d) The conversion of 2 moles of glycerol to glucose (e) The conversion of 2
Sketch curves for reaction velocity versus [fructose-6-phosphate] for the phosphorylated and non-phosphorylated forms of PFK-2 in liver.
Based on information presented on pages 402-403, sketch curves relating glycogen synthase reaction velocity to [UDP-glucose], for both the a and b forms of the enzyme, in the presence and absence of glucose-6-phosphate.
What is the metabolic significance of the following observations?(1) Only the liver form of pyruvate kinase is inhibited by alanine, (2) Only gluconeogenic tissues contain appreciable levels of glucose-6-phosphatase.
Write a one-sentence explanation for each of the following statements.(a) In liver, glucagon stimulates glycogen breakdown via cAMP. Although you might expect glucagon to stimulate catabolism of the glucose formed as well, glucagon inhibits glycolysis and stimulates gluconeogenesis in liver.(b)
Write a balanced chemical equation for the pentose phosphate pathway in the first two modes depicted in Figure 12.36, where(a) ribose-5-phosphate synthesis is maximized(b) NADPH production is maximized, by con- version of the sugar phosphate products to glucose-6-phosphate for repeated operations
Pyruvate carboxylase is thought to activate CO2 by ATP, through formation of carboxyphosphate as an intermediate. Propose a mechanism for the formation of this intermediate.
Refer to Figure 12.8, which indicates Î”G for each glycolytic reaction under intracellular conditions. Assume that glyceraldehyde-3-phosphate dehy-drogenase was inhibited with iodoacetate, which reacts with its active site cysteine sulfhydryl group. Which glycolytic intermediate would
Xylulose-5-phosphate is an intermediate in the pentose phosphate pathway (see Figure 12.36). As xylulose-5-phosphate levels rise in response to excess glucose shunting through the pentose phosphate pathway, does flux through glycolysis increase or decrease?
In different organisms sucrose can be cleaved either by hydrolysis or by phosphorolysis. Calculate the ATP yield per mole of sucrose metabolized by anaerobic glycolysis starting with.(a) Hydrolytic cleavage(b) Phosphorolytic cleavage.
Write balanced chemical equations for each of the following: (a) Anaerobic glycolysis of 1 mole of sucrose, cleaved initially by sucrose phosphorylase; (b) Aerobic glycolysis of 1 mole of maltose; (c) Fermentation of one glucose residue in starch to ethanol, with the initial cleavage involving α
Suppose that you made some wine whose alcohol content was 10% w/v (i.e., 10 g of ethanol per 100 mL of wine). The initial fermentation mixture would have had to contain what molar concentration of glucose or its equivalent to generate this much ethanol? Is it likely that an initial fermentation
Design a radiotracer experiment that would allow you to determine which proportion of glucose catabolism in a given tissue preparation occurs through the pentose phosphate pathway and which proportion occurs through glycolysis and the citric acid cycle. Assume that you can synthesize glucose
Certain microorganisms with a modified citric acid cycle decarboxylate a -ketoglutarate to produce succinate semi-aldehyde:(a) Succinate semialdehyde is then converted to succinate, which is further metabolized by standard citric acid cycle enzymes. What kind of reaction is required to convert
Draw a plausible mechanism for the oxidation of dihydrolipoamide to lipoamide by the E3 subunit (dihydrolipoamide dehydrogenase) of pyruvate dehydrogenase complex.
Predict which one of the five steps of the a-ketoglutarate dehydrogenase complex reaction is metabolically irreversible under physiological conditions and explain why.
Draw a plausible mechanism for the oxidative decarboxylation of isocitrate by isocitrate dehydrogenase.
Aconitase catalyzes the reaction: citrate ‡† isocitrateThe standard free energy change, ˆ†G°€², for this reaction is + 6.3 kJ / mol however, the observed free energy change (ˆ†G) for this reaction in mammalian mitochondria at 25°C is ˆ¼ 0
The same E1 -E2 -E3 multienzyme structure found in the pyruvate dehydrogenase and the α-ketoglutarate dehydrogenase complexes is also used in the branched-chain α-ketoacid dehydrogenase complex, which participates in the catabolism of branched chain amino acids. Draw the reaction product when the
When the O2 supply from blood fails to meet the demand of O2 -consuming cells, oxygen deprivation (hypoxia) occurs. This is common, for example, in exercising muscle. It has been recognized for over 100 years that O2 -deprived cells show increased conversion of glucose to lactate, known as the
Some bacteria use the citric acid cycle intermediate, Î±-ketoglutarate, plus acetyl-CoA, as the starting point for lysine biosynthesis. The first part of this biosynthetic pathway uses the same chemical strategy found in the citric acid cycle. Propose a four-step pathway for the
Suppose that aconitase did not bind its substrate asymmetrically. What fraction of the carbon atoms introduced in one cycle as acetyl-CoA would be released in the first turn of the cycle? What fraction of the carbon atoms that entered in the first cycle would be released in the second turn?
Assume you have a solution containing the pyruvate dehydrogenase complex and all the enzymes of the TCA cycle, but none of the metabolic intermediates. When you supplement this solution with 5 μ moles each of pyruvate, oxaloacetate, coenzyme A, NAD+, FAD, GDP, and Pi, you find that 5 μ moles of
Outline the mechanism of the conversion of a-ketoglutarate to succinyl-CoA catalyzed by a-ketoglutarate dehydrogenase complex. Include all products, coenzymes, and reactions in your discussion.
Briefly describe the biological rationale for each of the following allosteric phenomena:(a) Activation of pyruvate carboxylase by acetyl-CoA;(b) Activation of pyruvate dehydrogenase kinase by NADH;(c) Inhibition of isocitrate dehydrogenase by NADH; (d) Activation of isocitrate dehydrogenase by
As a representation of the respiratory chain, what is wrong with this picture? There are four deliberate errors.
GSSG + NADPH + H+ †’ 2GSH + NADP+(a) Calculate ˆ†G°€² for the glutathione reductase reaction in the direction shown, using E°€² values from Table 14.1.(b) Suppose that a cell contained an isoform of glutathione reductase that used NADH instead of NADPH as the reductive coenzyme.
To carefully prepared mitochondria were added succinate, oxidized cytochrome c, ADP, orthophosphate, and sodium cyanide. Referring to Figure 14.16, answer the following.(a) List the sequence of electron carriers in this system.(b) Write a balanced equation for the overall reaction occurring in this
In order to function as an oxidative phosphorylation uncoupler, 2, 4-dinitrophenol must act catalytically, not stoichiometrically. What does this mean? Identify and discuss an important implication of this conclusion.
(a) Calculate the standard free energy change as a pair of electrons is transferred from succinate to molecular oxygen in the mitochondrial respiratory chain. (b) Based on your answer in part a, calculate the maximum number of protons that could be pumped out of the matrix into the inter-membrane
Four electron carriers, a, b, c, and d, whose reduced and oxidized forms can be distinguished spectrophotometrically, are required for respiration in a bacterial electron-transport system. In the presence of substrates and oxygen, three different inhibitors block respiration, yielding the patterns
Biochemists working with isolated mitochondria recognize five energy "states" of mitochondria, depending on the presence or absence of essential substrates for respiration-O2 , ADP, oxidizable substrates, and so forth. The characteristics of each state are:State 1: mitochondria alone (in
FAD is a stronger oxidant than NAD+; FAD has a higher standard reduction potential than NAD+. Yet in the last reaction of the pyruvate dehydrogenase complex (Chapter 13), FADH2 bound to the E3 subunit is oxidized by NAD+. Explain this apparent paradox.
When pure reduced cytochrome c is added to carefully prepared mitochondria along with ADP, Pi , antimycin A, and oxygen, the cytochrome c becomes oxidized, and ATP is formed, with a P/O ratio approaching 1.0.(a) Indicate the probable flow of electrons in this system.(b) Why was antimycin A
Freshly prepared mitochondria were incubated with b -hyroxybutyrate, oxidized cytochrome c, ADP, Pi, and cyanide. b -Hyroxybutyrate is oxidized by an NAD+ -dependent dehydrogenase.The experimenter measured the rate of oxidation of Î²-hyroxybutyrate and the rate of formation of ATP.(a) Indicate
Of the various oxidation reactions in glycolysis and the citric acid cycle, the only one that does not involve NAD+ is the succinate dehydrogenase reaction. What would ∆G°′ be for an enzyme that oxidizes succinate with NAD+ instead of FAD? If the intramitochondrial concentration of succinate
Intramitochondrial ATP concentrations are about 5 mM, and phosphate concentration is about 10 mM. If ADP is five times more abundant than AMP, calculate the molar concentrations of ADP and AMP at an energy charge of 0.85. Calculate ˆ†G for ATP hydrolysis at 37°C under these
According to Figure 15.11(b), upon excitation the P700 reaction center is raised in potential from about + 0.4 to - 1.3 volts. To what value of Î”Go' does this correspond? How does it compare with the energy in an einstein of 700 nm photons?
J. C. Servaites, in Plant Physiol. (1985) 78:839-843, observed that Rubisco from tobacco leaves collected before dawn had a much lower specific activity than the enzyme collected at noon. This difference persisted despite extensive dialysis, gel filtration, or heat treatment. However, precipitation
If a photosynthetic organism is illuminated in a closed, sealed environment, it is observed that the CO2 and O2 levels in the surrounding atmosphere reach a constant ratio.(a) Suggest an explanation.(b) What factor would you think primarily determines the value of this ratio?

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