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=7.1 to pH=7.5? b) Justify your answer with calculations of partial charges on these amino acid side chains at pH=7.1. (Hint: Consider lessons from Coulomb's law, and the Henderson-Hasselbalch equation.)
Added by Adrian G.
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1 using the Henderson-Hasselbalch equation. Show more…
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pKa of the side chain R-groups: D (3.9), E (4.2), H (6.0), C (8.3), Y (10.1), K (10.5), and R (12.5). pKa of amino acids α-amino group (9.6) and α-carboxyl group (2.1). pKa of N-terminal oligopeptide α-amino group (7.4) and C-terminal α-carboxyl group (3.6). 1. An oligopeptide X was obtained from blood plasma with the sequence W-P-T-I-H-E. (a) Draw the structure of this X oligopeptide in the form that would predominate at pH 7.0 (b) Calculate the overall net charge of X oligopeptide at that pH (7.0) to the nearest 0.01 (with a precision of two decimal places)?
Adi S.
(b) The amino acid lysine has the following values of pKa: pK1 =2.2, pK2 = 8.9, pKR = 10.5 (the pKa of the amino group in the side chain). At pH 7 it has the structure shown below (6). Draw the structure that you would expect for lysine at pH 9.7, indicating the charges as appropriate. (c) Phenol (C6H5OH) and 2,4,6-trichlorophenol (C6H2Cl3OH) are both weak acids with pKa values of 9.89 and 6.21, respectively, at 298.15 K. (i) Write down the dissociation reaction and corresponding expression for the equilibrium constant for 2,4,6-trichlorophenol. What is the conjugate base of this acid? (ii) Which of these two acids is the stronger? Considering the difference in electron density of the OH group in each molecule and the effect that this will have on the acidic hydrogen, suggest a reason for the difference in the strength of the two acids.
A naturally occurring amino acid such as alanine has a group that is a carboxylic acid and a group that is a protonated amine. The $\mathrm{p} K_{\mathrm{a}}$ values of the two groups are shown. a. If the $\mathrm{p} K_{\mathrm{a}}$ value of a carboxylic acid such as acetic acid is about 5 (see Table 2.1 ), then why is the $\mathrm{p} K_{\mathrm{a}}$ value of the carboxylic acid group of alanine so much lower? b. Draw the structure of alanine in a solution at $\mathrm{pH}=0$. c. Draw the structure of alanine in a solution at physiological pH (pH 7.4). d. Draw the structure of alanine in a solution at $\mathrm{pH}=12$. e. Is there a pH at which alanine is uncharged (that is, neither group has a charge)? f. At what pH does alanine have no net charge (that is, the amount of negative charge is the same as the amount of positive charge)?
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