aAll amino acids have at least two ionizable groups: an a-amino group (average pK₁ of 8.0) andan α-carboxylic acid group (average pK₂ of 3.1). Histidine also has an ionizable side chain (Rgroup) with a pKa of about 6.0. One of the possible ionization states of histidine is shown inathe image.Select the pH values at which the charged form of the R group would predominate.6.0At what pH would the structure shown be the predominant ionization state? Consider the ionization state of all three of thefunctional groups.2.2+The protonated form of the R group of histidine is shown in the structure. The ratio of the charged (protonated) form to thedeprotonated form depends on the pK₁ of the R group and the pH of the solution.4.9H₂N-CH-C-OH|CH₂11.5+HN-NH

pKa is the pH at which a weak acid is 50% dissociated into a proton and conjugate base.At pH <…

Answered: All amino acids have at least two…

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 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). Part C: Justify your answer with calculations of partial charges on these amino acid side chains at pH=7.9.(Hint: Consider lessons from Coulomb's law, and the Henderson-Hasselbalch equation.)
Draw a schematic of the chemical structure of the Leu-Tyr-Met-Lys tetrapeptide, with the correct ionization at neutral pH (pH 7). Also, give an estimate the pl of this tetrapeptide (you are given that the pKa of any acidic R group is 4, the pKa of any basic R group is 11.5, and the pKa of the α-COOH is 2, and the a-NH3 is 9.5). Provide rationale!
What average positive charge of an amino acid side chain with pKa 10.9 at a pH value of 11.9? Answer up to two decimals. (Please type answer no write by hend)
The pka of the side chain of histidine is 6.00. What is the percent of protonated histidine at pH 6.4? 15.3% 28.5% 45.3% O 66.6%
Discuss the reaction conditions you would need to carry out the PEGylation reaction of this peptide and explain how the pH affects the selectivity of these reactions.
Amino acid structure For any ionizable group, indicate the pka value and draw the structure that would be expected at the pH inside the cell (~7.4).
The amino acid glycine is often used as an ingredient in buffers for biochemistry experiments. The amino group of glycine has a pKa of 9.6. Glycine exists in either a protonated form (-NH3+) or a free base (-NH₂). a) In what pH range can glycine be used as an effective buffer? b) In a 0.1M solution of glycine at pH 9.0, what fraction has its amino group in the protonated form? c) When 99% of the glycine is in the protonated from, what is the numerical relation between the pH of the solution and the pKa of the amino group?
Draw the titration curves for the following AA’s: Aspartic acid, Alanine, Lysine, Valine, Serine, and Trrosine.
At which pH would the peptide with the amino acid sequence 'KEYHR' be found in an IPG (Immobilized pH gradient) strip after successful isoelectric focusing. Show calculation. lonizable groups Alpha amine group of K Side chain group of K Side chain group of E Side chain group of Y Side chain group of H Side chain group of R Alpha carboxylic acid group of R pka 8.95 10.53 4.25 10.07 6 12.48 2.17
The amino acid arginine ionizes according to the following scheme: (a) Calculate the isoelectric point of arginine. You can neglect contributions from form I. Why? (b) Calculate the average charge on arginine when pH = 9.20. (c) Is the value of average charge you calculated in part b reasonable, given the pI you calculated in part a? Explain your answer
A cytosolic protein has an important alpha amino group. The pKa of this group is approximately 8 when exposed to water outside of a protein. 1. What would happen to the pKa if this group was instead buried in the hydrophobic interior of the protein? Explain. 2. Let’s say in the hydrophobic interior of the protein, the group forms an ionic bond with a carboxylate group of the side chain of a charged Asparagine residue. How would the pKa of this alpha amino group compare with the pKa of the alpha amino group in the hydrophobic interior of the protein without a nearby Asparagine residue to form this ionic bond? Explain.
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

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