Biochemistry: Concepts and Connections (2nd Edition)
2nd Edition
ISBN: 9780134641621
Author: Dean R. Appling, Spencer J. Anthony-Cahill, Christopher K. Mathews
Publisher: PEARSON
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Chapter 6, Problem 22P
A Leu → Ala mutation at a site buried the core of the enzyme lysozyme is found to be destabilizing. Explain observed effect of this mutation on lsozyme stability by predicting how enthalpy (ΔH''), conformational entropy (ΔS0peptide), and the hydrophobic effect (ΔS0solvent) are expected to change for the mutant compared to wild-type lysozyme. Explain how for unfolding affected by your predicted changes enthalpy or entropy.
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Lysozyme is an enzyme that hydrolyzes bacterial cell wall polysaccharides. When this reaction is carried out in the presence of H218O, it is observed that there is retention of configuration at the C1 carbon of the D site sugar as shown below:
Would this result suggest that the enzyme mechanism involves the direct nucleophilic attack of water at C1 or that the enzyme mechanism involves attack by a nucleophilic amino acid side chain of the enzyme that generates a transient covalent intermediate?
The enzyme lysozyme kills certain bacteria by attacking a
sugar called N-acetylglucosamine (NAG) in their cell walls.
At an enzyme concentration of 2 × 10-6 M, the maximum
rate for substrate (NAG) reaction, found at high substrate
concentration, is 1 × 10-6 mol L¯'s1. The rate is reduced
by a factor of 2 when the substrate concentration is
reduced to 6 x 10-6 M. Determine the Michaelis-Menten
constants Km and k, for lysozyme.
Lysozyme is an enzyme that hydrolyzes bacterial cell wall polysaccharides. When this reaction is carried out in the presence of H218O, it is observed that there is retention of configuration at the C1 carbon of the D site sugar as shown below
Two key amino acid side chains (an Asp and a Glu) essential for lysozyme’s catalytic activity are positioned above and below the C1-O bond that is cleaved as shown below. Suggest a plausible mechanism for the reaction that starts with a nucleophilic attack at C1.
Chapter 6 Solutions
Biochemistry: Concepts and Connections (2nd Edition)
Ch. 6 - Prob. 1PCh. 6 - Bovine pancreatic trypsin inhibitor (BPTI; Figure...Ch. 6 - A schematic structure of the subunit of...Ch. 6 - In the protein adenylate kinase, the C-terminal...Ch. 6 - Give two reasons to explain why a proline residue...Ch. 6 - Consider a small protein containing 101 amino acid...Ch. 6 - a. Based on a more conservative answer to Problem...Ch. 6 - The following sequence is part of a globular...Ch. 6 - a. A protein is found to be a tetramer of...Ch. 6 - Under physiological conditions, the protein...
Ch. 6 - Theoretical and experimental measurements show...Ch. 6 - The peptide hormone vasopressin is used in the...Ch. 6 - A protein gives under conditions of buffer...Ch. 6 - A protein gives a single band on SDS get...Ch. 6 - It has been postulated that the normal...Ch. 6 - Below are shown two views of the backbone...Ch. 6 - Do you expect a Pro Gly mutation in a...Ch. 6 - Rank the following in terms of predicted rates...Ch. 6 - Shown below are two cartoon views of the small...Ch. 6 - Prob. 20PCh. 6 - In most cases, mutations in the core of protein...Ch. 6 - A Leu Ala mutation at a site buried the core of...Ch. 6 - Disulfide bonds have been shown to stabilize...Ch. 6 - Cartoon renderings of the proteins Top 7 and adaH2...
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Need a deep-dive on the concept behind this application? Look no further. Learn more about this topic, biochemistry and related others by exploring similar questions and additional content below.Similar questions
- An active site of a hypothetical serine protease with a peptide substrate bound is shown below: This serine protease has 3 specificity pockets (S1, S2, S1') as shown in the figure above. S1 pocket has a glutamic acid in the bottom, the S2 pocket is small and hydrophobic, and the S1' pocket is deep and hydrophobic. Based on this information you can conclude that R1 is most likely side chain of a. Asp b. Lys c. Lle d. Gly e. Phearrow_forwardConsider 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,arrow_forwardIf a small amount of ATP labeled with radioactive phosphorus in the terminal position, [γ-32P]ATP, is added to a yeast extract, about half of the 32P activity is found in Pi within a few minutes, but the concentration of ATP remains unchanged. Explain. If the same experiment is carried out using ATP labeled with 32P in the central position, [β-32P]ATP, the 32P does not appear inPi within such a short time. Why?arrow_forward
- Bovine ribonuclease folds with ΔH° = -280 kJ mol-1 and ΔS° = -0.79 kJ mol-1 K -1. Assume ΔH° and ΔS° are independent of temperature. What fraction of bovine ribonuclease is unfolded at 42 °C?arrow_forwardLike ribonuclease A, lysozyme from T4 phage is a model enzyme for understanding the energetics and pathways of protein folding. Unlike ribonuclease A, T4 lysozyme does not contain any disulfide bonds. A number of studies have quantified the thermodynamic contributions individual amino acid residues and their interactions make to lysozyme folding. An ion pair between an Asp residue and a His residue in lysozyme contributes 13-21 kJ/mol of favorable folding energy at pH 6.0. However, this ion pair contributes much less to lysozyme folding at either pH 2.0 or pH 10.0. Why does the Asp-His ion pair contribute more energy at pH 6.0 than at low or high pH? At pH 10.0, Asp is protonated and His may be deprotonated. At pH 6.0, Asp is protonated and His may be deprotonated. At pH 2.0, Asp and His are both deprotonated. At pH 10.0, Asp and His are both protonated. ● At pH 6.0, Asp is deprotonated and His may be protonated.arrow_forwardThe enzymatic activity of lysozyme is optimal at pH 5.2 and decreases above and below this pH value. Lysozyme contains two amino acid residues in the active site essential for catalysis: Glu35 and Asp52. The pK value for the carboxyl side chains of these two residues are 5.9 and 4.5 respectively. What is the ionization state of each residue at the pH optimum of lysozyme? How can the ionization states of these 2 amino acid residues explain the pH-activity profile of lysozyme?arrow_forward
- Consider a protein with two surface-exposed histidine residues: HisA is a “typical” histidine residue with a pKa = 6.2 HisB is involved in a stabilizing interaction (His-NH+ ..... -O2C-Glu) with a neighboring glutamic acid residue. For HisB, the Gibbs free energy of deprotonation at pH = 7.0 and T = 293K is ΔG'o = +15 kj mol-1. If you had a solution, at pH = 7.0 and T = 293K, containing this protein: a) What fraction of HisA residues are protonated? b) What fraction of HisB residues are protonated? c) What is the pKa of HisB?arrow_forward8) A Leu > Ala mutation at a site buried in the core of the enzyme lysozyme ends up being destabilizing. Explain why in terms of AH", AS" (for both the protein and solvent), and AG".arrow_forwardThe distal Histidine (His 64) in myoglobin is subjected to three different mutations, this is one of them: H64N. (Histidine to Aparagine) For the mutation, draw a theoretical binding curve and CO relative to the O2 and CO binding curves for wild-type Mb (see example below). Provide a clear rationale for the binding curve.arrow_forward
- The figure shows an example of a thermal denaturation plot. The melting temperature (T) is the midpoint of the temperature range over which denaturation occurs. Percent unfolded 100 80 60 40 20 0 20 Tm E 40 60 Temperature (°C) 80 100 Suppose that a Met residue buried in the folded, hydrophobic core of T4 lysozyme is replaced by mutation with a Lys residue.arrow_forwardUsing the pKa data in as shown and the Henderson-Hasselbalch equation,calculate the approximate net charge on each of the four common ribonucleoside 5′-monophosphates (rNMPs) at pH 3.8. If a mixture of these rNMPs was placed in an electrophoresis apparatus, as shown, draw four bands to predict the direction and relative migration rate of each.arrow_forwardWhat is the smallest number of molecules of ATP and GTP consumed in the synthesis of a 200- residue protein, starting from amino acids? Assume that the hydrolysis of PP i is equivalent to the hydrolysis of ATP for this calculation.arrow_forward
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