Biochemistry
6th Edition
ISBN: 9781305577206
Author: Reginald H. Garrett, Charles M. Grisham
Publisher: Cengage Learning
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Chapter 26, Problem 17P
Interpretation Introduction
Interpretation:
Explanation about the structure of DHFR reductase.
Concept introduction:
In the hydrophobic region, the parallel sheets are connected by crossover structures with helices and random coils that make an open pocket. The amino acid residue of dihydrofolate is that the surface of the macromolecule and is exposed to the solvent.
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#1 Specify the role each of the following amino acids play within the crystal structure and/or active site for Be as specific as possible, with pictures (and mechanistic arrows) as necessary. His11
Arg140
Glu89
Trp68
#2 Provide a step-wise mechanism for the reaction Bisphosphoglycerate mutase catalyzes, using the amino acids responsible for aiding in catalysis. You do not need to add surrounding amino acids that aid in substrate specificity. (drawn out)
What is the catalytic efficiency of Catalase ?
Table. The values of KM and kcat for some Enzymes and Substrates
Enzyme
Carbonic anhydrase
Substrate
CO2
HCO3
KM (M)
1.2 x 10-2
2.6 x 10-2
Kcat (s-1)
1.0 x 106
4.0 x 105
Catalase
H2O2
2.5 x 10-2
1.0 x 107
Urease
Urea
2.5 x 10-2
4.0 x 105
O A. 4 x 108 M-s-1
O B. 4 x 108 M-1.s-1
OC25x 10-9 M-s1
D. 2.5 x 102 M-1.s-1
OE 1.0 x 107 s1
Consider the role of Histidine in the Serine protease mechanism and sketch a plot showing
the predicted pH profile of chymotrypsin which has a pH optimum of approximately ~8. The pk,
for the His in the catalytic triad is 7.3 in free chymotrypsin which increases to greater than 8 with
a bound peptide. Be sure to label the plot axes and indicate the pka of His on the plot,
Chapter 26 Solutions
Biochemistry
Ch. 26 - Prob. 1PCh. 26 - Prob. 2PCh. 26 - Allosteric Regulation of Purine and Pyrimidine...Ch. 26 - Inhibition of Purine and Pyrimidine Metabolism by...Ch. 26 - Prob. 5PCh. 26 - Allosteric Regulation of Ribonucleotide Reductase...Ch. 26 - Prob. 7PCh. 26 - Prob. 8PCh. 26 - Prob. 9PCh. 26 - Prob. 10P
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- (b) the activity of the malate-aspartate shuttle (MAS) system of isolated rat brain mitochondria suspended in an isotonic me- dium buffered to pH 7.4. Diagram A illustrates NADH fluo- rescence emission upon addition of Glutamate in the ab- sence and presence of Aspartate. Diagram B illustrates sim- ilarly NADH fluorescence emission upon addition of Gluta- mate in the presence of Aspartate followed by additions of submicromolar concentrations of Ca2+. As is well estab- lished, the MAS in brain, skeletal muscle, and cardiac mus- Diagrams A and B on the right show changes in Glu A Glu В -No Asp + 0 +0.12 -0.48 + 16 0.81 +1.8 ++ Asp 10 min 2 min cle mitochondria is activated by cytosolic concentrations of Ca2* < 3 µM. To simulate the cytosolic part of the MAS, the following reagents were added to the medium: 4 units/ml glutamate-oxaloacetate transaminase, 6 units/ml malate dehydrogenase, 66 µM NADH, 5 mM aspartate, 5 mM malate, 0.5 mM ADP, 200 nM ruthenium red (to block the mitochondrial…arrow_forwardPage of 6 ZOOM + name: 3. In the last reaction of the citric acid cycle, malate is dehydrogenated to regenerate the oxaloacetate necessary for the entry of acetyl-CoA into the cycle: L-Malate + NAD+ → oxaloacetate + NADH + H* AG'° = 30.0 kJ/mol (a) Calculate the equilibrium constant for this reaction at 25 °C. (b) Because AG°' assumes a standard pH of 7, the equilibrium constant calculated in (a) corresponds to [oxaloacetate][NADH] Keq [L-malate][NAD*] The measured concentration of L-malate in rat liver mitochondria is about 0.20 mM when [NAD*]/[NADH] is 10. Calculate the concentration of oxaloacetate at pH 7 in these mitochondria. (c) To appreciate the magnitude of the mitochondrial oxaloacetate concentration, calculate the number of oxaloacetate molecules in a single rat liver mitochondrion. Assume the mitochondrion is a sphere of diameter 2.0 microns.arrow_forwardGlucosidase I catalyzes hydrolysis of specific glucosidase I is a synthetic trisaccharide, glucose-al-2- glucose-al-3-glucose-a-O(CH₂) #COOCH3. Kinetic measurements oligosaccharides containing glucose. obtained using this trisaccharide as substrate in the deoxynorjirimycin at concentrations of 50 μM (), 100 μM absence (x-x) and presence of the inhibitor 1- A) were used to prepare the (-), and 200 μM (4 Lineweaver-Burk plot below: b) Page 3 12) 7. a) V/V (nmol/hr)-1 1.S 1.0- 0.5 1/Trisaccharide (mM)-! Estimate the values for Vmax and KM for the trisaccharide substrate in the absence of the inhibitor. 0.0 -1.0 0.0 One substrate for 1.0 2.0 Determine whether inhibition by 1-deoxynorjirimycin is competitive, non-competitive or neither.arrow_forward
- The protein catalase catalyzes the reaction 2H,O,(aq) — 2H,O(l) + O,(g) and has a Michaelis-Menten constant of KM = 25 mM and a turnover number of 4.0 × 107 s¯¹. The total enzyme concentration is 0.010 µM and the initial substrate concentration is 4.83 µM. Catalase has a single active site. Calculate the value of Rmax (often written as Vmax) for this enzyme. Rmax Calculate the initial rate, R (often written as V), of this reaction. R = ×10 mM.s-1 mM-s-1arrow_forwardDistinguishing the Mechanisms of Class I and Class I Aldolases Fructose bisphosphate aldolase in animal muscle is a class 1 aldolase, which forms a Schiff base intermediate between substrate (for example. fructose-1, 6-bisphosphate or dihydroxyacetone phosphate) and a lysine at the active site (see Figure I8.12). The chemical evidence for this intermediate conies from studies with aldolase and the reducing agent sodium borohydride, NaBH4. Incubation of the enzyme with dihydroxyacetone phosphate and NaBH4 inactivates the enzyme. Interestingly, no inactivation is observed if NabH4 is added to the enzyme in the absence of substrate. Write a mechanism that explains these observations and provides evidence for the formation of a Schiff base intermediate in the aldolase reaction.arrow_forwardUsing the ActiveModel for enoyl-CoA dehydratase, give an example of a case in which conserved residues in slightly different positions can change the catalytic rate of reaction.arrow_forward
- Extending the Mechanism of Methylmalonyl-CoA Mutase to Similar Reactions Based on the mechanism for the methylmalonyl-CoA mutase (see problem 14), write reasonable mechanisms for the following reactions shown.arrow_forwardmolecule A Plot of velocity versus substrate B Lineweaver-Burk plot 1/v Km 1 Vmax (S) Vmx 1 V max 1/2Vmax 1/Vmax -1/Km Km [S] 1/[S] fppt.com molecule Exercise The following data describe an enzyme-catalyzed reaction. Plot these results using the Lineweaver-Burk method, and determine values for KM and Vinax- The symbol mM represents millimoles per liter; 1 mM = 1 × 10 3 mol L. (The concentration of the enzyme is the same in all experiments.) Velocity (mM sec-) Substrate Concentration (тм) 2.5 0.024 5.0 0.036 10.0 0.053 15.0 0.060 20.0 0.061 fppt.comarrow_forwardRuBP carboxylaseis by no means an idesl enzyme. Describe some of the problems with its active site and its substrate specificity. If we compare the amino acid sequences of this enzyme from many different species, they are almost identical. What is the significance of this uniformity?arrow_forward
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