The figure shows an example of a thermal denaturation plot.The melting temperature (T) is the midpoint of thetemperature range over which denaturation occurs.Percent unfolded10080604020020TmE4060Temperature (°C)80100Suppose that a Met residue buried in the folded, hydrophobic core of T4 lysozyme is replaced by mutation with a Lys residue. How would the Met to Lys mutation affect the thermal denaturation of lysozyme at pH 3.0?It will destabilize the protein and lower the Tm, shifting the curve to the left.It will stabilize the protein and raise the Tm, shifting the curve to higher temperatures.It will not change the T at pH 3.0 because the Lys side chain pK, is 10.53.It will not affect stability, but it will decrease the Tm and shift the curve to lower temperatures.

The proteins re folded into their proper three dimensional structure and this folding is driven by…

Answered: The figure shows an example of a…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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= A different Fab fragment binds to lysozyme with a dissociation constant of Ka 10-6 M. A 1 nM (10-9 M) solution of lysozyme is treated with increasing concentrations of this Fab fragment. At what concentration of added Fab will half of the lysozyme be bound to this Fab? [F] = ab M
Equilibrium constants are always dependent upon temperature. In determining equilibrium constants for biochemical reactions the equilibrium constant also depends upon ion concentration and proton concentration. Write down an equation in differential form that describe the dependence of an equilibrium constant K for a protein binding to DNA, where the equilibrium constant, K is a function of Temperature, [NaCI], and [H*], i.e. dK(T, [NaCl], [H*]).
An Fab fragment binds to lysozyme with a dissociation constant of Ka = 10-11 M. A 1 nM (10-9 M) solution of lysozyme is treated with increasing concentrations of the Fab fragment. At what concentration of added Fab will half of the lysozyme be bound to the Fab? [Fab] 9.9 Incorrect nM
Proteinase K should be used as the first step of DNA purification (before applying phenol CIA mixture) to remove most proteins. Proteinase K alone cannot remove all proteins from the lysate. Explain why the Proteinase K enzyme cannot remove ALL proteins from the cell lysate.
After calculating the extinction coefficient for lysozyme above, you convert it into ml mg cm1 units. (You need not do the calculation, just suppose you did). To calculate the protein concentration in your column fractions (W1-3, E1-2), would your calculated extinction coefficient be a better choice than 1.5 mL mg 1 cm1 value listed in the theory section of your pre-lab? Why or why not? (Choose the best response) Yes, because we expect all of the column fractions to be mainly lysozyme. No, because most, if not all, the column fractions are mixtures of 2 or more proteins. Trick question, we should use the values calculated by EXPASY for lysozyme. Yes, because my calculated value is more accurate than values from the literature. ONo, because lysozyme is still stuck to the column and shouldnot be in any of our column fractions.
Cell wall bullding block D-Ala-D-Alal-Lys-tail NH,Me Heptapeptide backbone R1 R. R2 ii) With the aid of the figure above showing the important features of the binding of Vancomycin (lower part) to a bacterial cell wall peptia discuss the antibiotic effect of Vancomycin. i) Vancomycin resistant strains often have a mutation in which one of the D-Ala moieties is exchanged to a D-lactate moiety. Discuss why this mutation makes the strain Vancomycin- resistant but still viable. iv) Glycoconjugate vaccines based on bacterial capsular polysaccharides have been used for 30 years without any need for changes in their structures, while the flu vaccine, based on attenuated or killed virus particles, requires many different structures and a check each time when there is an epidemic that the right vaccine is used. Discuss the reason behind this.
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?
What would the order of migration be (bottom to top in the gel) in a SDS-PAGE for the following proteins? Concanavalin A (ConA) (a homotetramer of 106 kDa), lysozyme (a monomer of 14.3 kDa) & horse liver alcohol dehydrogenase (ADH) (a homodimer of 80 kDa). a. ADH, ConA, lysozyme b. ConA, ADH, lysozyme c. Lysozyme, ADH, ConA Od. Lysozyme, ConA, ADH
Like 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.
High salt concentrations tend to cause protein aggregation. Suggest a way to identify proteins normalexpressed in particular bacterial species that can retaintheir solubility despite high salt conditions.
In each of the following cases, predict whether the pKa value of the first residue will be upshifted or downshifted relative to the typical pKa value (Table 2.1) based on the microenvironment. Briefly (in no more than 2-3 sentences) explain your reasoning. (a) A His residue adjacent to two Arg residues on the surface of a protein(b) A Cys residue adjacent to an Asp residue in the active site of an enzyme(c) A Lys residue buried in the hydrophobic core of a globular protein
To approximate the concentration of enzymes in a bacterial cell, assume that the cell contains equal concentrations of 1,000 different enzymes in solution in the cytosol and that each protein has a molecular weight of 100,000. Assume also that the bacterial cell is a cylinder (diameter 1.0 μm, height 2.0 μm), that the cytosol (specific gravity 1.20) is 20% soluble protein by weight, and that the soluble protein consists entirely of enzymes. Calculate the average molar concentration of each enzyme in this hypothetical cell.

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The figure shows an example of a thermal denaturation plot. The melting temperature (Tm) is the midpoint of the temperature range over which denaturation occurs. Percent unfolded 100 80 60 40 20 0 20 Tm 40 60 Temperature (°C) 80 100