Estimate the net charge at pH 7.0 of a cyclic tetrapeptide that consists of two Pro and two Tyr residues. The net charge isin charge, andsince the Pro side chains arein charge. Tyr side chains arevandthere is no free N-terminus or C-terminus in the cyclic molecule.

Amino acids are organic compounds that serve as the building blocks of proteins. They consist of an…

Answered: Estimate the net charge at pH 7.0 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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Consider the phenolic hydroxyl group of a particular Tyr residue in a protein. Suppose the hydroxyl group in the unfolded protein in aqueous solution, where the group is exposed to H2O, has a pKa of 10.0. If that group is found in a hydrophobic environment in the interior of the protein when the protein is folded into its native tertiary structure, would you expect the pKa of the phenolic hydroxyl to be higher or lower in the folded protein interior than in H2O? Explain your reasoning.
A schematic diagram of the helical structure of cytochrome b562 is reproduced below. Thisprotein belongs to the family of -proteins that have a four-helix bundle. Number the helices 1 – 4according to their N  C direction. Indicate relative orientations of the macrodipoles of helices 1 – 4adjacent to the diagram of cytochrome b562. Remember that according to the definition of a dipolethat the arrow points towards the positive end.
Suppose you have a solution of a protein, which contains a specific Tyr residue that has an actual (measured) pKa of 8.8. The protein binds a ligand by several noncovalent interactions, one of which is a hydrogen bond in which the Tyr phenolic hydroxyl group must serve as a hydrogen bond donor. Calculate the percentage of the protein molecules in which that tyrosyl residue's phenolic hydroxyl group could serve as a hydrogen bond donor at pH 8.5
The peptide aspartyl-glutamyl-leucyl-threonyl-alanine, shown in the sketch drawing window, has several ionizable groups. Adjust the charges to show the molecule as it would exist at pH 5.00. Use the pk values in the table below. pK, Values for Ionizable Groups of Amino Acids. Amino Acid pA, of a-COOH pA, of e-NH, pA, of Side Chain Isoelectric Point (pI) Alanine 235 9.87 6.11 Arginine 2.01 9.04 12.48 10.76 Asparagine 2.02 8.80 5.41 Aspartic acid 210 9.82 3.86 298 Cysteine 2.05 10.25 8.00 5.02 Glutzmic acid 2.10 9.47 4.07 3.08 Glutamine 217 9.13 5.65 Glycine 235 9.78 6.06 Histidine 7.11 9.18 6.10 7.64 Isoleucine 232 9.76 6.04 Leucine 233 9.74 6.04 Lysine 218 8.95 10.53 9.74 Methionine 2 28 9.21 5.74 Phenylalanine 2 58 9.24 5.91 Proline 2.00 10.60 6.30 Serine 221 9.15 5.68 Threonine 2.09 9.10 5.60 Trуptophan 238 9.39 5.88 Tyrosine 2 20 9.11 10.07 5.63 Valine 2 29 9.72 6.00 • Use the wedge hash bond tools to indicate stereochemistry where it exists. • If a group is 2chiral, do not use…
An organic chemist is generally happy with 95% yields. If you synthesized a polypeptide and realized a 95% yield with each amino acid residue added, what would be your overall yield after adding 10 residues (to the first amino acid)? After adding 50 residues? After 100 residues? Would these low yields be biochemically “satisfactory”? How are low yields avoided, biochemically?
Based on the pK, table for amino acids (Table 1.1), draw the structures with net charge, and the equilibria representing the complete deprotonation of aspartate. Table 1.1 Name pK pk2 pKR Glycine Alanine 2.4 9.8 2.3 9.7 Valine 2.3 2.4 9.6 Leucine 9.6 Isoleucine 2.4 9.7 Methionine 2.3 9.2 Phenylalanine Proline Serine 1.8 9.1 2.0 10.6 2.1 9.2 Threonine 2.6 10.4 Cysteine Asparagine Glutamine 1.8 10.8 8.3 2.0 8.8 2.2 9.1 Tyrosine Tryptophan Aspartate Glutamate 2.2 9.1 10.9 2.4 9.4 2.0 2.2 10.0 3.9 9.7 4.3 Histidine 1.8 9.2 6.0 10.8 Lysine Arginine 2.2 9.2 1.8 9.0 12.5
The major difference between a protein molecule in its native state and in its denatured state lies in the number of conformations avail- able. To a first approximation, the native, folded state can be thought to have one conformation. The unfolded state can be estimated to have three possible orientations about each bond between residues. (a) For a protein of 100 residues, estimate the entropy change per mole upon denaturation. (b) What must be the enthalpy change accompanying denaturation to allow the protein to be half-denatured at 50 °C? (c) Will the fraction denatured increase or decrease with increasing temperature?
Consider an amino acid (A) with no ionizable side chains, and call the three species involved in the acid/base equilibria H2A+, HA, and A- (see scheme below). Assume that pKa(1) = 2.0 and that pKa(2) = 9.0. Suppose that the total concentration of the amino acid is 1.0 mM. Report to two significant digits. pH [H2A+] (mM) [HA] (mM) [A-] (mM) 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0 11.0 12.0
Draw graphs of optical densities of the amino acid ninhydrin complexes at different wavelengths
Histidine is an amino acid containing an ionizable group in its side chain. This ionizable group has a pka of 6.0, meaning that His is in its deprotonated form at physiological pH (7.0-7.4). However, His is included in the positively charged amino acid category. Calculate the ratio of deprotonated/protonated His at pH 7.0, and use your answer to justify why this amino acid is included in the positively charged amino acid category. Show all work for full credit.
9L.11.5

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Estimate the net charge at pH 7.0 of a cyclic tetrapeptide that consists of two Pro and two Tyr residues. The net charge is in charge, and since the Pro side chains are in charge, Tyr side chains are vand there is no free N-terminus or C-terminus in the cyclic molecule.