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medical sciences
biochemistry

Fundamentals of biochemistry Life at the Molecular Level 4th edition Donald Voet, Judith G. Voet, Charlotte W. Pratt - Solutions

Suppose the concentration differences across a membrane for glucose and sodium are both 104 (that is, the concentrations are 104 greater on one side of the membrane). Is the free energy change for the transmembrane movement of these solutes the same? Explain.
Determine whether each of the following transport systems is uniport, symport, or antiport. Which systems are active transport systems? (a) Glucose transporter in erythrocytes (b) Valinomycin (c) Plasma membrane (Na+-K+)-ATPase (d) Na+-glucose transporter of intestinal epithelium (e) E. coli
Fill in the diagram below showing glucose transport across a brush border cell from the intestinal lumen to the capillary bed. Also, draw arrows to show the flow of solutes and to indicate which transporter requires ATP hydrolysis. Note: not all blanks and circles may be relevant.
What is the electrochemical potential difference when the intracellular [Ca2+] = 1 μM and the extracellular [Ca2+] = 1 mM? Assume ΔΨ = -100 mV (inside negative) and T = 25°C.
Rank the molecules below from lowest to highest according to their ability to diffuse across a lipid bilayer. Explain your rationale.
The following data (using arbitrary units) were obtained for the transmembrane movements of compounds A and B from outside to inside a cell:Which compound enters the cell by mediated transport? Explain.
Which graph below shows the expected relationship between temperature and flux (J, rate of flow) of an ion transported across a biological membrane via a carrier ionophore? Explain.
K+ channels have openings that are much wider than Na+ ions, yet sodium ions cannot pass through efficiently. Explain.
Calculate the free energy change for glucose entry into cells when the extracellular concentration is 5 mM and the intracellular concentration is 3 mM.
In addition to neurons, muscle cells undergo depolarization, although smaller and slower than in the neuron, as a result of the activity of the acetylcholine receptor. (a) The acetylcholine receptor is also a gated ion channel. What triggers the gate to open? (b) The acetylcholine receptor/ion
The compound shown below is the antiparasitic drug miltefosine.(a) Is this compound a glycerophospholipid? (b) How does miltefosine likely cross the parasite cell membrane? (c) In what part of the cell would the drug tend to accumulate? Explain. (d) Miltefosine binds to a protein that also binds
In eukaryotes, ribosomes (approximate mass 4 × 106 D) are assembled inside the nucleus, which is enclosed by a double membrane. Protein synthesis occurs in the cytosol. (a) Could a protein similar to a porin or the glucose transporter be responsible for transporting ribosomes into the cytoplasm?
The rate of movement (flux) of a substance X into cells was measured at different concentrations of X to construct the following graph.(a) Does this information suggest that the movement of X into the cells is mediated by a protein transporter? Explain.(b) What additional experiment could you
Endothelial cells and pericytes in the retina of the eye have different mechanisms for glucose uptake. The figure shows the rate of glucose uptake for each type of cell in the presence of increasing amounts of sodium. What do these results reveal about the glucose transporter in each cell type?
Explain why Na+ and K+ ions usually move more slowly through pumps than through channels.
Why would overexpression of an MDR transporter in a cancer cell make the cancer more difficult to treat?
Cells in the wall of the mammalian stomach secrete HCl at a concentration of 0.15 M. The secreted protons, which are derived from the intracellular hydration of CO2 by carbonic anhydrase, are pumped out by an (H+ -K+)-ATPase antiport. A K+- Cl co-transporter is also required to complete the
(a) Calculate the chemical potential difference when intracellular [Na+] = 10 mM and extracellular [Na+] = 150 mM at 37°C. (b) What would the electrochemical potential be if the membrane potential were -60 mV (inside negative)?
Kidney cells contain a channel that allows intracellular ammonia to exit the cells. (a) Why did researchers originally believe that cells had no need for such a channel? (b) What is the free energy source for ammonia transport via the channel? (c) The same kidney cells also contain a proton pump
If the ATP supply in the cell shown in Fig. 10-21c suddenly vanished, would the intracellular glucose concentration increase, decrease, or remain the same?In Figure 10.21c
The bacterial Na+ -H+ antiporter is a secondary active transport protein that excretes excess Na+ from the cell. Is the extracellular pH higher or lower than the intracellular pH?
For the problem in Sample Calculation 10-1, calculate ∆G at 37°C when the membrane potential is (a) -50 mV (cytosol negative) and (b) + 150 mV. In which case is Ca2+ movement in the indicated direction thermodynamically favorable?
Calculate the free energy required to move 1 mol of K+ ions from the outside of the cell (where [K+] = 4 mM) to the inside (where [K+] = 140 mM) when the membrane potential is -70 mV and the temperature is 37°C.
How long would it take 100 molecules of valinomycin to transport enough K+ to change the concentration inside an erythrocyte of volume 100 μm3 by 10 mM?
If a protonated His residue acts as the proton donor in an acid-catalyzed enzymatic reaction, what happens to the enzyme's activity as the pH increases to a value that exceeds the pKR of that residue?
The pK values of two essential catalytic residues in RNase A are 5.4 and 6.4. (a) Which corresponds to His 12 and which to His 119? (b) Draw a titration curve for these two residues.
A good covalent catalyst is highly nucleophilic and can form a good leaving group. What structural properties support these seemingly opposite characteristics?
Classify each of the following groups as an electrophile or nucleophile: (a) Amine (b) Carbonyl (c) Cationic imine (d) Hydroxyl (e) Imidazole
For each of the following reactions, indicate the nucleophilic center and the electrophilic center. Draw curved arrows to indicate the movement of electrons and draw the reaction products.(a) Carbonyl phosphate + ammonia ‡† carbamic acid + Pi(b) NADH + acetaldehyde ‡† ethanol +
What is the role of Zn2+ in carbonic anhydrase?
What are the roles of Glu 35 and and Asp 52? What is the role of water in catalysis?
Explain why enzymes are stereospecific.
Hydrogen bonding of substrates to enzymes often involves the polypeptide backbone rather than amino acid side chains. What backbone-substrate hydrogen bond helps distort NAM in the D subsite of lysozyme? Can this hydrogen bond form when N-acetylxylosamine is in the active site?
Draw the resonance forms of the half-chair conformation of the oxonium ion transition state of the lysozyme reaction.
What is the role of the following amino acids in the active site of chymotrypsin? (a) Asp 102 (b) His 57 (c) Ser 195 (d) Gly 193 (e) Which three constitute the "catalytic triad?"
What two catalytic residues in chymotrypsin were identified by chemical modification? Could the same reagents used to identify these residues be used to label the catalytic residues of other serine proteases?
The different substrate specificities of chymotrypsin and trypsin have been attributed to the presence of different amino acid residues in the binding pocket. What problems can arise when site-directed mutagenesis is used to test predictions about the roles of such residues in substrate specificity?
The cleavage of the ester p-nitrophenylacetate (shown below) by chymotrypsin occurs in two stages. In the first stage, the product p-nitrophenolate is released in a burst, in amounts equivalent to the amount of active enzyme present. In the second stage, p-nitrophenolate is generated at a steady
Lys 15 of bovine pancreatic trypsin inhibitor binds to the active site of trypsin but is not cleaved. Explain why the proteolytic reaction cannot proceed.
Since trypsin activation is autocatalytic, what is the role of enteropeptidase in activating trypsin?
What is an apoenzyme and how does it differ from a holoenzyme? Which form is active?
What is the relationship between vitamins and coenzymes?
Proteins can be chemically modified by a variety of reagents that react with specific amino acid residues. How can such reagents be used to identify residues involved in an enzyme's activity? What are the shortcomings of this method?
Answer yes or no to the following questions and explain your answer. (a) Can the absolute value of ΔG for a reaction be larger than ΔG‡? (b) Can ΔG‡ for an enzyme-catalyzed reaction be greater than ΔG‡ for the nonenzymatic reaction? (c) In a two-step reaction, such as the one diagrammed
An increase in temperature increases the rate of a reaction. How does the temperature affect ΔG‡?
ΔΔG‡ for an enzymatic reaction at 25°C is 13 kJ·mole-1. (a) Calculate the rate enhancement. (b) What is ΔΔG‡ when the rate enhancement is 105?
Using the reaction shown in Box 11-1 (the attack of an amine on the carbonyl group of a ketone) as a starting point, draw curved arrows to represent the acid-catalyzed reaction (when the group ¬A¬H is present).
Explain why enzyme activity varies with temperature, as shown here.
The covalent catalytic mechanism of an enzyme depends on a single active site Cys whose pK is 8. A mutation in a nearby residue alters the microenvironment so that this pK increases to 10. Would the mutation cause the reaction rate to increase or decrease? Explain.
Urease, the first enzyme to be crystallized, is inhibited in the presence of Hg, Cd, or Co ions. What does this information suggest about the catalytic mechanism of urease?
What feature of RNA would allow it to function as a ribozyme? Why are there no naturally occurring DNA enzymes?
Wolfenden has stated that it is meaningless to distinguish between the "binding sites" and the "catalytic sites" of enzymes. Explain.
Suggest a transition state analog for proline racemase that differs from those discussed in the text. Justify your suggestion.
Explain why lysozyme cleaves the artificial substrate (NAG)4 ~4000 times more slowly than it cleaves (NAG)6.
What is the relationship between the rate of an enzyme-catalyzed reaction and the rate of the corresponding uncatalyzed reaction? Do enzymes enhance the rates of slow uncatalyzed reactions as much as they enhance the rates of fast uncatalyzed reactions?
Would you expect lysozyme to hydrolyze cellulose? Why or why not?
Design a chloromethylketone inhibitor of elastase.
Diagram the hydrogen-bonding interactions of the catalytic triad His-Lys-Ser during catalysis in a hypothetical hydrolytic enzyme.
The comparison of the active site geometries of chymotrypsin and subtilisin under the assumption that their similarities have catalytic significance has led to greater mechanistic understanding of both these enzymes. Discuss the validity of this strategy.
Why is the broad substrate specificity of chymotrypsin advantageous in vivo? Why would this be a disadvantage for some other proteases?
Tofu (bean curd), a high-protein soybean product, is prepared in such a way as to remove the trypsin inhibitor present in soybeans. Explain the reason(s) for this treatment.
Many of the cell's hydrolytic enzymes are located in the lysosome, where the pH is ~5. What would you expect to be the optimum pH for these enzymes, and why would this protect the rest of the cell from the destructive power of these enzymes upon the accidental rupture of a lysosome?
A genetic defect in coagulation factor IX causes hemophilia b, a disease characterized by a tendency to bleed profusely after very minor trauma. However, a genetic defect in coagulation factor XI has only mild clinical symptoms. Explain this discrepancy in terms of the mechanism for activation of
On the free energy diagram shown, label the intermediate(s) and transition state(s). Is the reaction thermodynamically favorable?
Draw a transition state diagram of (a) a nonenzymatic reaction and the corresponding enzyme-catalyzed reaction in which (b) S binds loosely to the enzyme and (c) S binds very tightly to the enzyme. Compare ∆G‡ for each case. Why is tight binding of S not advantageous?
Using the reaction shown in Box 11-1 (the attack of an amine on the carbonyl group of a ketone) as a starting point, draw curved arrows to represent the base-catalyzed reaction (when the group ¬B: is present).
For each of the following reactions, write a rate equation and determine the reaction order. (a) A → P (b) A + B → P + Q (c) 2A → P
Assume that k2 = kcat for a highly purified enzyme for which you seek to determine ΔG‡. Using the Arrhenius equation, k = Ae-ΔG‡/RT, where k is a reaction rate constant and A is a constant, you can determine the activation energy to a good approximation. (a) Derive a mathematical relationship
There are three general mechanisms for the reversible inhibition of enzymes that follow the Michaelis-Menten model. How does the mode of inhibitor-enzyme binding differ among the three mechanisms?
The catalytic behavior of an enzyme may depend on ionizable amino acids. Therefore, a change in pH may influence an enzyme's catalytic behavior. How can you tell whether pH affects substrate binding or catalytic activity?
The movement of glucose across the erythrocyte membrane is "catalyzed" by a transport protein (Section 10-2E and Box 10-2). (a) What is the kinetic behavior of this process? (b) Can glucose transport be subject to competitive, uncompetitive, or mixed inhibition? Explain.
In hen egg white lysozyme (Section 11-4), the substitution of Ala for Asn at position 37 or for Trp at position 62 may alter the enzyme's kinetics. What changes would you predict and why?
Draw velocity versus [Asp] curves for the reaction catalyzed by the ATCase catalytic trimer and by the intact enzyme. Explain why the curves differ.
What biochemical parameters are likely to vary among different allelic isozymes of cytochrome P450?
Draw a flow diagram that summarizes the steps involved in developing a drug from the generation of a lead compound through FDA approval. Which is the most time-consuming step?
List two different ways to measure the progress of a chemical reaction.
A first-order reaction has a t1/2 of 20 minutes. (a) What is the rate constant k? (b) What time is required to form 20% of the product? (c) What time is required to form 80% of the product? (d) How much starting material remains after 15 min? (e) Compare the rate constant for this reaction to that
The energy of binding a transition state complex (X‡) can be determined by writing an equilibrium expression for the formation of the complex. (a) For the reaction A ⇆ X‡, what is the equilibrium expression? (b) What is the expression for the free energy of binding to the transition state
For the following reaction:(a) What is meant by the term "enzyme-substrate complex"? (b) Write a rate equation for the production of ES. (c) What is the rate of product formation from ES? (d) If all the enzyme is bound to substrate, what is the effect of adding more substrate on the forward rate of
What is meant by (a) the steady state assumption, (b) KM, (c) kcat, (d) turnover number, (e) catalytic efficiency, and (f) diffusion-controlled limit?
The following data were obtained for the reaction A ⇆ B, catalyzed by the enzyme Aase. The reaction volume was 1 mL and the stock concentration of A was 5.0 mM. Seven separate reactions were examined, each containing a different amount of A. The reactions were initiated by adding 2.0 μL of a 10
Can you use kinetic data to prove that a particular model for an enzymatic reaction mechanism is correct? Explain.
Why is it possible for sequential bisubstrate reactions to be Ordered or Random, whereas a Ping Pong reaction always has an invariant order of substrate addition and product release?
Consider the nonenzymatic elementary reaction A → B. When the concentration of A is 20 mM, the reaction velocity is measured as 5 μM B produced per minute. (a) Calculate the rate constant for this reaction. (b) What is the molecularity of the reaction?
Calculate KM and Vmax from the following data:
Explain why each of the following data sets from a Lineweaver-Burk plot are not individually ideal for determining KM for an enzyme-catalyzed reaction that follows Michaelis- Menten kinetics.
Is it necessary for measurements of reaction velocity to be expressed in units of concentration per time (M ∙ s-1, for example) in order to calculate an enzyme's KM?
Is it necessary to know [E]T in order to determine (a) KM, (b) Vmax, or (c) kcat?
You are trying to determine the KM for an enzyme. Due to a lab mishap, you have only two usable data points:Use these data to calculate an approximate value for KM. Is this value likely to be an overestimate or an underestimate of the true value? Explain.
You are constructing a velocity versus [substrate] curve for an enzyme whose KM is believed to be about 2 μM. The enzyme concentration is 200 nM and the substrate concentrations range from 0.1 μM to 10 μM. What is wrong with this experimental setup and how could you fix it?
Enzyme A catalyzes the reaction S → P and has a KM of 50 μM and a Vmax of 100 nM ∙ s-1, Enzyme B catalyzes the reaction S → Q and has a KM of 5 mM and a Vmax of 120 nM ∙ s-1. When 100 μM of S is added to a mixture containing equivalent amounts of enzymes A and B, after 1 minute which
For the same enzyme sample described in Problem 25, what would your results show if a reversible inhibitor is present? In Problem 25 Based on some preliminary measurements, you suspect that a sample of enzyme contains an irreversible enzyme inhibitor. You decide to dilute the sample 100-fold and
Determine the type of inhibition of an enzymatic reaction from the following data collected in the presence and absence of the inhibitor.
Calculate the half-life, in years, for the reaction 2 X → Y when the starting concentration of X is 6 μM and the rate constant is 3.6 × 10-3 M-1 ∙ s-1.
From the reaction data below, determine whether the reaction is first order or second order and calculate the rate constant.
From the reaction data below, determine whether the reaction is first order or second order and calculate the rate constant.
For an enzymatic reaction, draw curves that show the appropriate relationships between the variables in each plot below.
Explain why it is usually easier to calculate an enzyme's reaction velocity from the rate of appearance of product rather than the rate of disappearance of a substrate.
At what concentration of S (expressed as a multiple of KM) will vo = 0.95Vmax?
The α- and β-adreonoreceptors stimulate different cellular effects in response to their ligands or agonists; however, the ultimate physiological response is the same. What is the net result of the activation of both kinds of receptors?

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