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 21P
In most cases, mutations in the core of protein that replace a smaller nonpolar side chain in the wild-type (e.g., Ala, Val) with a larger nonpolar side chain (e.g., Leu, lle, Phe, Trp) in the mutant, result in significant destabilization and misfolding of the mutant. What feature of the protein core explains this observation? Why would such a mutation prevent a protein from folding properly?
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In most cases, mutations in the core of a protein that replace a smaller nonpolar side chain in the wild-type (e.g., Ala, Val) with a larger nonpolar side chain (e.g., Leu, Ile, Phe, Trp) in the mutant, result in significant destabilization and misfolding of the mutant. What feature of the protein core explains this observation? Why would such a mutation prevent a protein from folding properly?
Why would the mutation Ile -> Asp be likely to destabilize a protein? Why would the mutation Ile ->Val be likely to destabilize a protein? Why would the mutation Val -> Ile be likely to destabilize a protein?
A hypothetical protein has a molar mass of 23,300 Da. Assume that the average molar mass of an amino acid is 120.
• How many amino acids are present in this hypothetical protein?
• What is the minimum number of codons present in the mRNA that codes for this protein?
• What is the minimum number of nucleotides needed to code for this protein?
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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- Imagine a globular protein with a histidine that is involved in a salt bridge to an aspartic acid, in an internal (hydrophobic) region of the protein. What would happen to the pKa of that histidine R group if the protein was mutated, and the aspartic acid was replaced with an alanine? (i.e., would the pKa increase, decrease, or stay the same?). Assume that the location of the histidine stays the same. Explain your answer clearlyarrow_forward. Disulfide bonds have been shown to stabilize proteins (i.e., make them less likely to unfold). Consider the cases shown schematically below for two variants of the same protein. In case #1 the disulfide forms between Cys residues that have been introduced near the protein N- and C-termini, and in case #2 the disulfide forms between Cys residues that have been introduced in the middle of the protein sequence. Which protein is likely to be more stable? (Note: Assume the disulfide bond is intact in both the unfolded and folded states). Explain your reasoning.arrow_forwardThe folding of intrinsically disordered proteins is prevented by the presence of Ser, Lys, and Glu residues. What do these amino acids have in common? Why do they disrupt IDPs?arrow_forward
- Once the chains of peptides that make up lysyl-tRNA synthetase protein are synthesized in ribosomes, lysyl-tRNA synthetase needs to have the proper active site in order to perform its function, explain the process of protein folding necessary to have a proper 3-D structure, include effect of thermodynamics and different states in folding, including what happen when there are prolines that form peptide bonds with other amino acids, and any disulfide bridgesarrow_forwardIf a new isolated protein called STICKY and this STICKY protein contains a bHLH domain. Now, how we predict the function of STICKY and the rationale for the importance of these domains in the STICKY function?arrow_forwardOn average, how many phosphoanhydride bonds (P;-P; bonds) are directly hydrolyzed in thecourse of synthesizing a 200 amino acid protein? Assume that you begin with the mature mRNA,ribosomal subunits, tRNAs, free amino acids, and all necessary factors.arrow_forward
- Which amino acid replacement would result in the biggest structural change in a protein if a Cys residue was replaced with Ser or Phe amino acid, and why?arrow_forwardPeptides and small proteins fold spontaneously in aqueous solution at room temperature. Thus, for a small protein in water, we can say ΔG FOLD < 0. Denoting the unfolded protein as Unf and the folded protein as Fld, we can write the following equation:Unf(aq)--DELTA G FOLD----> Fld(aq)Considering the transition from the unfolded state (in which there are many possible conformations) to the folded state (only one conformation), there is clearly a decrease in the entropy of the protein. However, protein folding is (correctly) described as an entropically driven process.a) Resolve this apparent paradox by identifying the enthalpy (ΔH) and entropy (−TΔS)components involved in protein…arrow_forwardIf an Arg residue in a protein was replaced with either Lys or Glu amino acid, whichsubstitution would you expect to result in the greatest structural change and why?arrow_forward
- The effect of base-pair substitution mutations on protein function varies widely from no detectable effect to the complete loss of a protein function. Why the functional consequences of base-pair substitution vary so widely?arrow_forwardWhich of the following statements are true? Electrostatic interactions are the dominant forces in protein molecular recognition. When two proteins form a complex there is an unfavorable loss of rotational-translational entropy. Protein-protein interfaces are most often dry. The exclusion of water results in an unfavorable loss in rotational-translational entropy. The free energy change associated with the formation of an enzyme-substrate complex almost always results in an unfavorable reduction in conformational entropy of the proteins. Burial of an uncompensated positive charge inside proteins is usually unfavorable. So-called van der Waals’ interactions are essentially electrostatic in origin. Steric complementarity of the two partners forming a complex is essential to achieve optimal free energy of binding. Structural models of proteins obtained from low temperature crystallography are excellent descriptions of all biochemically relevant aspects of their function.arrow_forwardBased on the N-terminal amino acid sequence, what is the approximate half-life of the protein after methionine is cleaved off?arrow_forward
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