medicalchanel Posted August 5, 2015 Report Share Posted August 5, 2015 Hi! I'm just a little confused with respect to finding the pI of an amino acid with multiple charged groups. Which is correct? 1) The pI = the average of all the pKa values of each group (pka1+pka2+pka3/3) or 2) The pI = the average of the pKa values on either side of the zwitterion? If you could provide an example with the explanation I would REALLY appreciate it! Thanks! Link to comment Share on other sites More sharing options...
doc123 Posted August 5, 2015 Report Share Posted August 5, 2015 Hi! I'm just a little confused with respect to finding the pI of an amino acid with multiple charged groups. Which is correct? 1) The pI = the average of all the pKa values of each group (pka1+pka2+pka3/3) or 2) The pI = the average of the pKa values on either side of the zwitterion? If you could provide an example with the explanation I would REALLY appreciate it! Thanks! Firstly, pI is pKa value where the net charge on the amino acid is zero (zwitterion). For a non polar amino acid (for example alanine), there are two reactive groups (the amino group and the carboxyl group). The pKa for the carboxyl is group is ~ 2 and for the amino group it is ~9. So if you think about it, the formation of zwitterion depends on the pH of the environment the amino acid is in. At pH 1 (a really acidic conditions) H bonds do not want to dissociate from the carboxyl group let alone the amino group, so you will have COOH and NH3+. The net charge is +1 on the amino acid here. As you increase the pH say to 5, the H in COOH group dissociates while the amino group still has the H ( COO- and NH3+) <--- this has a net charge of zero and is known as a zwitterion. To find the pI of non polar aa you need to find the average pKa values of the two reactive groups (2 + 9/ 2 = ~5.5). This pI value will be the same for all non polar aa. This is made a little complicated with polar amino acids. Just know that for acidic aa the pI is reached when the H bond in COOH dissociates while the acidic R group retains its H bond and the amino group still has its H and thus has a positive charge on it (NH3+). To find the pI for an acidic aa, find the average of the pKa of the carboxyl group and the pka of the r group. In the case of glutamic acid, it will be pKa 2 for carboxyl group, pka of 4 for r group, and 9 for amino group. The pI will be 2 + 4/ 2 = 3. Exact same principle for basic aa. The only difference is that to the find the pI, average the pKa of the r group and the amino group. With lysine for example, pka for carboxyl group is 2, pka of r group is 10, and pka of 9 for the amino group. The pI will be 10 + 9/ 2 = 9.5 Hope that helps! Link to comment Share on other sites More sharing options...
medicalchanel Posted August 5, 2015 Author Report Share Posted August 5, 2015 Firstly, pI is pKa value where the net charge on the amino acid is zero (zwitterion). For a non polar amino acid (for example alanine), there are two reactive groups (the amino group and the carboxyl group). The pKa for the carboxyl is group is ~ 2 and for the amino group it is ~9. So if you think about it, the formation of zwitterion depends on the pH of the environment the amino acid is in. At pH 1 (a really acidic conditions) H bonds do not want to dissociate from the carboxyl group let alone the amino group, so you will have COOH and NH3+. The net charge is +1 on the amino acid here. As you increase the pH say to 5, the H in COOH group dissociates while the amino group still has the H ( COO- and NH3+) <--- this has a net charge of zero and is known as a zwitterion. To find the pI of non polar aa you need to find the average pKa values of the two reactive groups (2 + 9/ 2 = ~5.5). This pI value will be the same for all non polar aa. This is made a little complicated with polar amino acids. Just know that for acidic aa the pI is reached when the H bond in COOH dissociates while the acidic R group retains its H bond and the amino group still has its H and thus has a positive charge on it (NH3+). To find the pI for an acidic aa, find the average of the pKa of the carboxyl group and the pka of the r group. In the case of glutamic acid, it will be pKa 2 for carboxyl group, pka of 4 for r group, and 9 for amino group. The pI will be 2 + 4/ 2 = 3. Exact same principle for basic aa. The only difference is that to the find the pI, average the pKa of the r group and the amino group. With lysine for example, pka for carboxyl group is 2, pka of r group is 10, and pka of 9 for the amino group. The pI will be 10 + 9/ 2 = 9.5 Hope that helps! Thank you SO much for this!! Out of all the info I read, this made sense! Just a question about the non polar aa you talked about in the beginning..."As you increase the pH say to 5, the H in COOH group dissociates"...does the H in the COOH group dissociate at a ph above 2 and below 7? (and below 2 and above 7, it would not dissociate?) Thanks again! Link to comment Share on other sites More sharing options...
doc123 Posted August 5, 2015 Report Share Posted August 5, 2015 Thank you SO much for this!! Out of all the info I read, this made sense! Just a question about the non polar aa you talked about in the beginning..."As you increase the pH say to 5, the H in COOH group dissociates"...does the H in the COOH group dissociate at a ph above 2 and below 7? (and below 2 and above 7, it would not dissociate?) Thanks again! The COOH will dissociate at a pH above 2. Once its dissociated, it's dissociated. So any pH above 2 COOH will become COO-. The amino group will dissociate above pH 9. Any pH below 9 the amino group will be positive (NH3+) and any pH above 9 it will dissociate to be come NH2. At pH of 11, for example, you have both groups dissociated as the COOH dissociated at 2 and NH3+ at 9, so it becomes COO - and NH2 (net negative charge)! Link to comment Share on other sites More sharing options...
medicalchanel Posted August 5, 2015 Author Report Share Posted August 5, 2015 The COOH will dissociate at a pH above 2. Once its dissociated, it's dissociated. So any pH above 2 COOH will become COO-. The amino group will dissociate above pH 9. Any pH below 9 the amino group will be positive (NH3+) and any pH above 9 it will dissociate to be come NH2. At pH of 11, for example, you have both groups dissociated as the COOH dissociated at 2 and NH3+ at 9, so it becomes COO - and NH2 (net negative charge)! Thank you ! So for example, if I have Lysine at pH 11, the COOH group will be COO-, the NH3 will be deprotonated to NH2 and the lysine R group will make the pI will be 9.5. What would the charge be on the ion? Link to comment Share on other sites More sharing options...
thehead321 Posted August 6, 2015 Report Share Posted August 6, 2015 pI = average of the 2 closest pKa values (if there's >2 charged functional groups) you should do yourself a favour and figure out why that is though Link to comment Share on other sites More sharing options...
doc123 Posted August 6, 2015 Report Share Posted August 6, 2015 Thank you ! So for example, if I have Lysine at pH 11, the COOH group will be COO-, the NH3 will be deprotonated to NH2 and the lysine R group will make the pI will be 9.5. What would the charge be on the ion? pI is when the net charge is 0...so if the COOH is COO- and NH3+ is NH2 at 9.5, then your r group would need to have a positive charge on it to cancel out the COO- Link to comment Share on other sites More sharing options...
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