@simrat_n I believe the current formula is correct as well as the formulas for calculating the pI of basic and neutral amino acids. The convention these cards are built on is that pka1 = a-carboxyl group, pka2 = a-ammonium group, and pka3 = side chain group. However, I see that Kaplan lists these rules (similarly to your suggestion) as:
and
and
which I do agree might be more intuitive and may be worth incorporating into the cards in some capacity whether it be the text or extra section. At the very least, I think it might be worth stating the convention above (pka1 = a-carboxyl group, pka2 = a-ammonium group, and pka3 = side chain group) in the extra section of these 3 cards. What do you think?
Without some source citation or corroboration that it’s somehow wrong I dunno that I feel like going down this rabbit hole.
I can see an argument for having an accompanying image to specify pka1 and pka3 for clarity, or alter the notation in some way, though arguably it’s preferable in some ways to what can become the excessively long ‘pkaNH3+group’ which can look like a mess in a formula or Mathjax.
I’ve also seen pkaCOOH and pkNH3 which might be something like a happy medium.
Kaplan uses the long-form notation (gross).
UWorld seems to dodge it entirely, by just explaining it out via text.
KA uses the pka1 form, etc.
@Brian_BH What do you think about listing the convention for naming pKas for these cards in the extra section. I can see how these cards are confusing if you don’t know the convention of naming pka1, pka2, and pka3. I’ve actually seen the pka’s numbered in terms of order in the reaction in other sources (though not primary) but commonly used in undergrad for chemistry such as here. I also think people (though incorrectly) will instintictually think that pka1-3 are simply in the order of which they appear in the reaction rather than corresponding to a specific part of an amino acid. Which would imply the pI for an acidic side chain is 1/2(pka1+pka2).
Given that Kaplan and UWorld skip explaining this convention I think it’s worth including because people may look this concept up online to clarify and see something like above and be confused.
Yeah, I agree broadly. I think the options are:
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Just use pkCOOH and pkNH3. This would be the simplest. However, I don’t remember off the top of my head which one AAMC will use, which leaves the potential that this isn’t the ideal notation and could lead to confusion down the line (clearly there’s not a uniform consensus anyway).
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Use an image to explain the convention of pka1, pka2. I think this is probably the middle road, but the safest option overall (and preserves notation).
Amino acids are also famously one of those things where a picture is hugely helpful (and should be readily easy to find in nearly all cases)
Just to make sure I’m following the options:
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Are you suggesting replacing pka1 in the formula with pkaCOOH and pka2 with pkaNH3? and keeping pka3 as pka3?
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An image already exists in this card (below) that with some reasoning you could understand the naming convention (but it would take some thought).
A slight improvement would be something like this:
But I still wonder if the easiest thing for everyone would be something like this:
- Keep card text as is
- Say in the extra section.
pKa1 = alpha-carboxyl group
pKa2 = alpha-amino group
pka3 = R group
- though the long notation isn’t the prettiest from Kaplan I think it is probably the most clear and maybe wouldn’t be so bad to include in the extra section.
- throw out existing image and use the slight improvement one I suggested.
I think this option kind of covers all our bases and leaves no room for confusion and potential that we are not using the ideal notation which could be a source of confusion on test day.
- Is an option. I don’t think it’s the best option.
- I think this is likely the better choice, though I’m open to disagreement if you feel strongly otherwise.
I think the best option is:
- Keep phrasing as-is.
Include an explanation as you mention, in the Extra field; pka1 = whatever. pka2 = other whatever, etc., etc. - Ideally, find a way to include an image with each group labeled as pka1, pka2, etc. Picture-worth-a-thousand-words, etc.
Great. Makes sense to me and I think it’s a big improvement. To be honest, when I was reviewing the card when I was responding to the suggestion it gave me pause for a second. I forgot this convention as well. I’ll work on finding an image and if I can’t get a good open source one I’ll just cook one up with chemdoodle.
I can’t recall if I mentioned it, but if you can keep a running list of images we/you add to the deck it’s helpful. This is our proof-of-progress for showing the improvements, for monthly posts as well as to argue to the owners.
I think the next update post will come out next week, possibly. I usually include just like 4-8 images, doesn’t have to be anything insane. Usually I pick whatever Openstax images were added, or anything I stole from the Step Deck, just anything that looks like pretty window dressing and attracts eyeballs.
I have a file with all the new ones I’ve personally made as well as the openstax images. LMK when you need them for the post!