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I'm reading about Lysine and doing some calculations on it's charge under various $\ce{pH}$.

Depending on the source, Lysine is usually stated as a charged amino acid with a $\ce{NH3+}$ group. However the video I'm watching is calculating the charge at 5 pH and it writes Lysine out with $\ce{NH2}$ and goes on to say that because the solution is pH 5, then $\ce{NH2 -> NH3+}$ and arguments that THIS is why Lysine is charged.

Does the literature state Lysine as a charged acid, assuming it is at pH 7? Or is the video I am watching wrong and it should not gain a charge as $\ce{NH3}$ will not accept a hydrogen?

Bonus: Why are only SOME groups given a Pka value?

http://www.geneinfinity.org/images/aapks.jpg

http://www.cem.msu.edu/~cem252/sp97/ch24/ch24aa.html

How would I calculate the charge for Isoleucin for example?

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The side chain of lysine is charged at all pH lower than 10.53 (according to the table you linked), and so it would be charged at pH 7. What happens is $\ce{NH2}$ is more or less stable, but once you start to have any decent amount of hydrogen in your solution it will donate its lone pair to become $\ce{NH3+}$.

Bonus answer: only the amino acids with ionizable side chains are given pKa values, because, well, they're the only ones that are ionizable. In other words, they're the only groups that will accept or donate a proton at any reasonable pH (you could theoretically ionize glutamine, but the pH would be ridiculously low, and well outside of the world of biochemists who are only really concerned with pH levels inside the body).

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    $\begingroup$ Thank you. I wish I could select more "best answers" but unfortunately only one can be selected and this one was most fitting for my level. I also found a video that helped me understand the topic better if anyone finds this thread in the future: youtube.com/watch?v=WxNYfc98Iqw $\endgroup$ – Paze Feb 9 '15 at 14:14
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At pH 7 lysine has a net charge of very close to +1.

The carboxylic acid group is fully deprotonated (-1 charge).

The alpha amino group is about 99% protonated (+1 charge).

The side chain amino group is fully protonated (+1 charge).

You need to look at the pK of each ionizable group, consider what fraction of the group is in each ionization state (for example using the Henderson Hasselbach equation), and add the charges of each group to get the net charge.

For isoleucin, at pH 7, the net charge will be almost neutral, because 7 is well above the carboxylic acid pK of 2.32 and significantly below the amino pK of 9.76. There will be a small fractional negative charge because 7 is closer to the pK of 9.76 than to the pK of 2.32. Note in the first linked table in the question, there is a column for "pI". The pI will be the only pH where the amino acid has a net neutral charge.

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  • $\begingroup$ isoelectric point of Lysine is ~ pH 9.7; That clearly means at physiological pH 7.4, Lysine is acidic (N-terminus is deprotonated) with +1 charge? $\endgroup$ – bonCodigo Feb 11 '18 at 12:10
  • $\begingroup$ @bonCodigo The second pKa of lysine is 8.95. At pH 7.4 the ratio of protonated to deprotonated will be 10^(8.95-7.4) = 35. So about +0.97. $\endgroup$ – DavePhD Feb 12 '18 at 19:11
  • $\begingroup$ LOL @DavePhd, that's a precise calculation. I meant to confirm my understanding, that Lysine is in the acidic range in this case. Still, Isoelectric point is calculated using Ka1 and Ka2. So why do we care about Ka2 again here? $\endgroup$ – bonCodigo Feb 12 '18 at 23:08
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In aqueous solutions amino acids are usually considered as zwitterions. Even as solid salt they are charged. I can't really say, why usually it is drawn uncharged. It may confuse but it isn't important when you want to know which charge it really has. Just take a look at the pH and the pka values.

In a solution the charge depends on the pH of the solution. If there are additional groups which can protonate or deprotonate you have to take a look at their pka.

Since Lysin has to amino groups and one carboxylic acid group. The pka of the both aminogroups is much higher than your pH of 5, so both are protonated. You have two positive charges. The carboxylic acid is deprotonated at pH 5 because its pka is 2.18. So one negative charge here.

That means Lysin has in total one positive charges at pH 5.

In water you have always charges because you have a acid and base in one molecule, so they can react with each other. COOH protonates the $NH_2$ and $NH_2$ deprotonates the COOH.

The charge of Isoleucin is an easy example because you have no side chains, just COOH and $NH_2$. You can take a given pH (maybe 5) and then take a look at the pka of both functional groups as written above. Then add the charges. Or you can take a look at the pI. This works even with side chains. If the pH = pI you have a zwitterion with on positive and one negative charge, so the whole molecule is neutral. If your pH is higher than the pI it is mor basic and something will deprotonate so you have a negative charge. If pH < pI something is protonated und you have a positive charge. pI refers to that point there half of all

BONUS: Just take a close look at the functional groups of the side chains. Since most times pka is refered to aqueous solutions only those groups are given a pka value which can be protonated or deprotonated in water. A Methyl group for example $R-CH_3$ can't be deprotoned in water. so why should they give a pka value? It wouldn't be helpful.

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