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Predicting Structures of AAs at various pH levels
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Vasil_5264
#1 Posted : Tuesday, June 02, 2020 9:08:02 PM
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Hello,
I was wondering how would you predict which group on a Amino Acid such as Lysine would be deprotinated at which pH. I would expect from the proximity to the electron withdrawing NH3+ group the headgroup's COOH is first to leave, which it is. However, after it leaves, we are left with a negatively-charged electron rich COO- very close to the NH3+ on the head group, this would destabilize the conjuate base, since electron donating groups promote basicity not acidity. So I would expect the NH3+ group on the R group (farther away) to be deprotinated first, however this is not the case. I am wondering why that is and if we're expected to know this.
-Thanks, Vasko
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INSTR_Kailey_109
#2 Posted : Friday, June 05, 2020 6:59:37 PM
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Being familiar with protonation states of amino acids is a reasonable question to be asked on the MCAT. Often, knowing the rough pKa of each functional group on the amino acid and comparing those to the pH given will tell you the protonation state. For example, if your pH is higher than the pKa, your functional group will be deprotonated to its conjugate base form, if your pH is lower than your pKa, your functional group will be protonated as its conjugate acid form.

For the case of the alpha carboxylic acid, it is more acidic than a regular carboxylic acid because the proximity of the NH3 group allows a stabilizing hydrogen bond in a 5-member ring. This also makes the NH3 more basic than a regular NH3 group.



As a result, the general pKa of the amino acids are as follows:



pKa carboxylic acid = 2

pKa amine = 9.5

pKa Histidine N = 6

pKa Aspartate/Glutamate carboxylic acid = 4

pKa Lysine = 11

pKa Arginine= 12.5





This is what the range would look like for lysine. As you increase the pH, the groups get slowly deprotonated starting from the group with the lowest pKa towards the group with the highest pKa.

See the image here
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