My textbook shows that all the acidic amino acids are negatively charged and all the basic amino acids are positively charged. I would think it should be the reverse. Shouldn't a negatively charged amino acid attract protons, hence decomposing water, increasing the hydroxide concentration and therefore forming a basic solution?
Textbooks most often illustrate amino acids in their charged states at pH 7 (physiological pH). The charged state of the amine and carboxylic acid functionalities on amino acids depends on the pH of the solution, which in turn is related to the functional groups' pKa (-log Ka). Very simply put, when the pH of the solution is above the pKa, the group will be in its deprotonated state. Conversely, when the pH of the solution is below the pKa, the group will be in its protonated state. As a rule of thumb, carboxylic acids have pKa's of ~5 and amines have pKa's of ~10. Therefore, at pH 7, amines will be protonated (NH3+) and carboxylic acids will be deprotonated (COO-). To extend this principle further, if you raise the pH to 12, both the carboxylic acid and the amine will be deprotonated (i.e. NH2 and COO-) and if you lower the pH to 3, then both the carboxylic acid and amine will be protonated (i.e. NH3+ and COOH). Your comment about the carboxylate (COO-) deprotonating water can also be addressed using pKa values. If you want to deprotonate something with an x pKa value, you'll need to use a base that has a pKa which is higher than x. While a carboxylate can act as a base, water has a pKa of 15.6, so there's no way a carboxylate will deprotonate water. Hope that helps.
The charged state of the amine and carboxylic acid functionalities on amino acids depends on the pH of the solution. Finally terminal proton basically tells about functionallity that depends on protonation and deproatonation. Oppsite will happen in case of basic R group of amino acid that is why they possess positive charge.
The basic amino acids easily attract protons, as their proton affinity (PA) value is higher. Look for these values in the data bases, e.g. NIST. Arg (R) has the highest PA value comparing to all other amino acids. Thus a proton preferentially binds Arg. PA value of Lys (K) is comparable, but these of the others amino acids are much lower.In the singly charged ion the charge will be always on the Arg. Withour Arg and Lys a proton may select any amino acid as their values are quite similar. If you have a double charged ion of a peptide with one Arg, the first proton will be attached to Arg and the second will be mobile.
It is quite easy. A base is defined as a molecule or part of a molecule with a high tendency to attract protons. Therefore in an ionization equilibrium the protonized version of the molecule will be favored. So a base will be protonized i.e. positively charged at equilibrium conditions.
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