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In my book it talks about amino acids. It says the general structure of an amino acid is as follows:

enter image description here

However, on the next page it lists specific amino acids such as glycine shown here:

enter image description here

My question is when comparing the first image to glycine, why does glycine or any of the other specific amino acids have an extra H atom as in "H3N+"?

Where does the extra H come from and why is it positively charged?

Also, on the general structure it shows the an amino should have a COOH but on glycine it is just C double bonded to an O and then another O- negative charge.

Does this have to do with the pH and ionization?

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The two forms of amino acids that your question asks about are called zwitterions (technically IUPAC says they should be called dipolar ions but the term zwitteron is pervasive).

Since amino acids contain both acidic (the carboxylic acid) and basic (the amine) moieties the molecule is able to undergo what almost appears to be an intramolecular acid-base reaction in which the acidic proton of the carboxylic acid protonates the amine, this is what gives rise to the species on the right of the image below.

enter image description here

Its worth pointing out the this property of the amino acids is valid at physiological pH for the naturally occurring amino acids, generally in aqueous medium (which living organisms have. Also as Jan pointed out in the comments, other polar solvents would also allow the amino acid to show this characteristic).

At other pH values, the molecules become singly ionised, favouring either the cationic or anionic forms. The range of pH values at which the amino acid is zwitterionic will also vary depending on which amino acid you're looking at (the pKa values are different for every amino acid, even if only subtly)

enter image description here

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    $\begingroup$ Thank you so much! Very helpful. What exactly causes this "protonation?" Im assuming the water or cytosol within the cell? Or is that a much more complex theory based question? Also, The arrows indicate that this reaction is a reversible reaction? If so, do you know how/why is this reversible? $\endgroup$ – Atticus283blink Aug 28 '16 at 20:59
  • $\begingroup$ Its not a 'reaction' so much as an equilibrium between the zwitterionic and the neutral forms- they are in constant flux but the amount of zwitterion at equilibrium remains constant (the equilibrium constant). The water assists with the proton transfer between the carboxylic acid and the amine, yes. I noticed your images were from the Campbell Biology, you'd be well advised to read it alongside something like Lehringer's Biochemistry- it explains the chemical concepts far better $\endgroup$ – NotEvans. Aug 28 '16 at 21:04
  • $\begingroup$ Thank you again, I will be sure to checkout that material as well. $\endgroup$ – Atticus283blink Aug 29 '16 at 0:17
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NotWoodward has answered it perfectly! The glycine which has both positive and negative (resulting neutral charge) is a zwitter ion form. This form is achieved at different pH for different amino acids depending on their R groups.

How does pH actually affect the amino acid? I always break it down when I explain it to my students as follows:

An amino acid in a very protonated solution (low pH) is going to be saturated with hydrogen ions, so all molecules that can take a proton will take it as they are abundant. Therefore, N will take them and become $\ce{NH3+}$ and the carboxyl group will take it and form COOH, but as you keep on adding a base (increasing the pH), the base would react with an available proton for neutralisation.

Therefore, N will easily give away its extra proton and as pH increases will become $\ce{NH2}$. If you continue adding a base, once all N has given away its extra proton, Carboxy group would then give away the proton, resulting in $\ce{COO-}$. So this results in different forms of the same molecule at different pH to attain equilibrium.

Certain amino acids also have different names based on their states, example: Glutamic acid (RCOOH) and Glutamate ($\ce{RCOO-}$).

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  • $\begingroup$ The amino acid is at its 'isoelectric point' in its zwitterionic form. $\endgroup$ – Technetium Aug 31 '16 at 6:38

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