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 2, Problem 22P
Consider a protein in which a negatively charged glutamic acid side chain (pks = 4.2) makes a salt bridge (ion—ion interaction) with a positively charged histidine side chain (pKa = 6.5).
a. Do you predict that this salt bridge will become stronger, become weaker, or be unaffected as pH increases from pH = 7.0 to pH = 7.5?
b. Justify your answer with calculations of partial charges on these amino acid side chains. (Hint Consider lessons from Coulomb's law, and the Henderson-Hasselbalch equation)
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Consider a protein in which a negatively charged glutamic acid side chain (pKa = 4.2) makes a salt bridge (ion–ion interaction) with a positively charged histidine side chain (pKa = 6.5). (a) Do you predict that this salt bridge will become stronger, become weaker, or be unaffected as pH increases from pH = 7.0 to pH = 7.5? (b) Justify your answer with calculations of partial charges on these amino acid side chains.
Currently, aspartic acid is forming an ionic interaction with arginine in a protein.
Part a) If arginine is replaced with glutamic acid, would the ionic interaction have its stability increased, decreased, or have no effect on the ionic interaction?
Part b) If arginine is replaced with Lysine, would the ionic interaction have its stability increased, decreased, or have no effect on the ionic interaction?
Part c) If arginine is replaced with isoleucine, would the ionic interaction have its stability increased, decreased, or have no effect on the ionic interaction?
At a pH equal to the isoelectric point of alanine, the net charge on alanine is zero. Two structures can be drawn that have a net charge of zero, but the predominant form of alanine at its pI is zwitterionic.(a) Why is alanine predominantly zwitterionic rather than completely uncharged at its pI?(b) What fraction of alanine is in the completely uncharged form at its pI? Justify your assumptions.
Chapter 2 Solutions
Biochemistry: Concepts and Connections (2nd Edition)
Ch. 2 - Suppose a chloride ion and a sodium ion are...Ch. 2 - Draw two different possible hydrogen-bonding...Ch. 2 - Prob. 3PCh. 2 - 4. What is the pH of each of the following...Ch. 2 - Prob. 5PCh. 2 - The weak acid HA is 2% ionized (dissociated) in a...Ch. 2 - 7. Calculate the pH values and draw the titration...Ch. 2 - What is the pH of the following buffer mixtures?...Ch. 2 - a. Suppose you wanted to make a buffer of exactly...Ch. 2 - Prob. 10P
Ch. 2 - You need to make a buffer whose pH is 7.0, and you...Ch. 2 - Describe the preparation of 2.00 L of 100 glycine...Ch. 2 - Carbon dioxide is dissolved in blood (pH 7.4) to...Ch. 2 - What is the molecular basis for the observation...Ch. 2 - The anno acid arginine ionizes according to the...Ch. 2 - It is possible to make a buffer that functions...Ch. 2 - A student is carrying out a biological preparation...Ch. 2 - Histidine is an amino acid with three titratable...Ch. 2 - Prob. 19PCh. 2 - A biochemical reaction takes place in a 1.00 ml...Ch. 2 - Is RNA-binding enzyme RNase A more likely to have...Ch. 2 - Consider a protein in which a negatively charged...Ch. 2 - Prob. 23PCh. 2 - Prob. 24P
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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
- Draw Ramachandran plot for: a) regular secondary structure with Φ = 60-65 and Ψ = 60-80 b) regular secondary structure with Φ = -170 and Ψ = 170 c) intrinsically disordered proteins d) explain why these Ramachsndran plots will be different, and what secondary structures are described in A and in Barrow_forwardFor the following pentapeptides: Ser-Glu-Gly-His-Ala and Gly-His-Ala-Glu-Ser A. Compute their isoelectric pH (pI). Show full solution. Use standard pKa values. B. Do these peptides with the same amino acid composition have different net charges at pH 7.0? Explain briefly. C. Would you expect the titration curves of the two peptides to differ? Why or Why not?arrow_forwardAssume that some protein molecule, in its folded native state, has one favored conformation. But when it is denatured, it becomes a “random coil,” with many possible conformations. (a) If we only consider the change in entropy for the protein, what must be the sign of ∆S for the change: native → denatured? (Note: As suggested in the next problem, this does not include solvent effects, which also make significant contributions to ∆S.) (b) How will the contribution of ∆S for native → denatured affect the favorability of the process? What apparent requirement does this impose on ∆H if proteins are to be stable structures?arrow_forward
- Consider two proteins, Protein A and Protein B: A is a monomeric protein, whereas B is a subunit of a homo-tetrameric protein. Both A and B are soluble. Additionally, both A and B have similar 3D structures. What differences would you expect to see between the amino acids exposed on the surfaces of A and B? Explain the reasons for the differences observed.arrow_forwardLet’s consider histidine as a free amino acid in aqueous solution. a) Draw the most likely structure of histidine under biochemical standard state conditions. b) Given that free histidine has the following three pKa values, assign each to its corresponding acidic hydrogen or conjugate base in your structure from part a). pKa1 = 1.7; pKa2 = 6.2; and pKa3 = 9.1 c) For each pKa, give the corresponding expression for the equilibrium constant. It helps to write out the chemical equation for each. d) Create a speciation diagram for histidine by plotting Xi vs pH from pH = 4 to pH = 8 where Xi is the mole fraction of the two histidine species involved in the K2 equilibrium in part c).arrow_forwardYou are given a protein solution with a concentration of 0.15 mg/ml. Suppose that we want to prepare a solution containing 100 μg of the protein at a concentration of 1 mg/ml. To achieve this, we will first dry down enough protein solution to obtain 100 μg of proteins. How much solution do we need for drying down? How much volume of H2O do we need to add to the dried protein to obtain the desired concentration?arrow_forward
- A protein hypothetically consists of two polypeptide chains with the given sequences in the picture. Based on the said sequences, a. Do you think it is possible that interchain disulfide bonds is present in the protein? Explain. b. Do you think it is possible that intrachain disulfide bonds is present in the protein? Explain.arrow_forwardAmong these amino acid combinations listed above, only the combination of Lys and Glu have side chains with groups that have the greatest ability to stabilize the tertiary structure of a protein. Explain by drawing (a) why Lys and Glu side chain interaction stabilizes the tertiary structure of a protein (b) why the pairs of Glu and Asp & Arg and Pro cannot provide the stability to the protein structure.arrow_forwardA sample of the amino acid tyrosine is barely soluble in water. Would a polypeptide containing only Tyr residues, poly(Tyr), be more or less soluble, assuming the total number of Tyr groups remains constant?arrow_forward
- Considering the chemical characteristics of the amino acids valine and glutamic acid (see Figure 5.14), propose a possible explanation for the dramatic effect on protein function that occurs when valine is substituted for glutamic acid.arrow_forwardAssume that some protein molecule, in its folded native state, has onefavored conformation. But when it is denatured, it becomes a “random coil,” with many possible conformations.(a) If we only consider the change in entropy for the protein, what mustbe the sign of ΔS for the change: native → denatured? (Note: As suggestedin the next problem, this does not include solvent effects, which also make significant contributions to ΔS.)(b) How will the contribution of ΔS for native → denatured affect thefavorability of the process? What apparent requirement does this imposeon ΔH if proteins are to be stable structures?arrow_forwardAs an example, consider albumin, a protein made of a single polypeptide weighing 66,000 daltons (66 kDa). On the other hand, gamma globulin has quaternary structure: is made of four polypeptides, two of which weigh 23,000 daltons (23 kDa) each, and two of which weigh 53,000 daltons (53 kDa) each. When treated with reducing agent and SDS, the subunits separate and they all linearize. If albumin and gamma globulin were run through gel electrophoresis, which polypeptides would move the fastest? Which would move the slowest?arrow_forward
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