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 11P
Theoretical and experimental measurements show that in many cases, the contributions of ionic and hydrogen-bonding interactions to ΔH for protein folding are close to zero. Provide an explanation for this result. (Hint: Consider the environment in which protein folding occurs.)
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Many plasma proteins found in an aqueous environment are globular in shape. Which amino acid side chains would you expect to find on the surface of a globular protein and in contact with the aqueous environment? Which would you expect to find inside, shielded from the aqueous environment? Explain.
Q.) Arg
For the binding of a ligand to a protein, what is the relationship between the Ka (association constant), the Kd (dissociation constant), and the affinity of the protein for the ligand?
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?
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
- In what type of intra and intermolecular interactions does a valine within a protein backbone typically participate?arrow_forwardMost protein dissolve in neutral salt solution, is that true? Provide reasoningarrow_forward"To judge the biological importance of an interaction between protein A and protein B, we need to know quantitative details about their concentrations, affinities, and kinetic behaviors" is true or false.arrow_forward
- List and discuss the types of interactions that stabilize the tertiary structure of proteins. For each stabilizing interaction, identify one example of denaturant and describe how the interactions are disrupted.arrow_forwardInsulin possesses two polypeptide chains denoted A and B that are linked by disulfide bonds. Upon denaturation by reduction of the SH groups of insulin, followed by reoxidation, only 7% of the hormone activity is recovered. This is the level of activity expected for random pairing of cysteine residues to form disulfide bonds. How can these data be reconciled with the hypothesis that the amino acid sequence directs protein folding?arrow_forwardConsidering 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_forward
- Which of the following amino acids is most likely to be found on the outside of a soluble protein, and which of them is more likely to be found on the inside? Explain each answer. (Hint: Consider the effect of the amino acidside chain in each case and that the protein is folded up into its globular form.)(a) Valine (b) Aspartate(c) Histidine (d) Alaninearrow_forwardThe simplest form of the Ramachandran diagram is calculated by ignoring hydrogen bonding, interactions with water, and the hydrophobic effect. Why is this simple form of the diagram still an effective predictor of protein backbone conformation?arrow_forwardAre peptide bonds free to rotate in folded protein? Can they be ionized at extreme pH values?arrow_forward
- Consider protein folding that results when the following components interact: Where the solution is at a pH of 7, green (thick-dotted line) represents aspartic acid (R group contains a carboxylic acid with pKa = 4), orange (thick-solid line) represents lysine (R group contains an amine with pKa = 10), and blue (thin-solid line) represents hydrophilic groups. Rank the three complexes in order from lowest to highest dissociation constants Kd (low Kd values correspond to good binding constants and low energy, while high Kd values correspond to low binding constants and high energy) as determined by intermolecular charge-charge interactions. For those complexes with charge-charge interactions being equal, look at the possibility for the formation of hydrogen bonds via carboxylic acid dimers (only possible when the carboxylic acid is protonated) which are low energy structures.arrow_forwardUnder what conditions can a single binding site have a chemical specificity for more than one type of ligand?arrow_forwardConsider 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_forward
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