How well do we need to know amino acids?

[FauxBlue]

I'm not really comfortable with amino acids, not at an intimate level at least. I know their structures inside and outside. But amino acids suffer bipolar disorder, sometimes being polar to even non-polar. But I know amino acids can be positive sometimes and flush out those negative feelings.

On a more serious note: how well do we need to know amino acids? Down to the every pKa of each substituent and the pIs?? How useful is that (especially those who have written the MCAT already)??

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[Bruskie_77]

I'm not really comfortable with amino acids, not at an intimate level at least. I know their structures inside and outside. But amino acids suffer bipolar disorder, sometimes being polar to even non-polar. But I know amino acids can be positive sometimes and flush out those negative feelings.

On a more serious note: how well do we need to know amino acids? Down to the every pKa of each substituent and the pIs?? How useful is that (especially those who have written the MCAT already)??

Took it on the 18th. Know EVERYTHING.

 

[tturchi51]

Which of the following AA is likely to be found inside the core of a micelle? Know them well enough to answer that.

 

[p0gono]

know every which way to name them, their categories, their properties, and their structures (recognition). if you're going that far, may as well memorize their side chain pKa's, but it's not necessary as long as you are comfortable with relative acidities of the acidic, basic, etc AAs.

 

[clathrin413]

I'm in the TBR class, and the instructors have all said that people who took the new exam have come back reporting a LOT of amino acid biochemistry on their exams. I don't think memorizing pI's is necessary, but structures/grouping/special properties (ex: proline causes turns, glycine is achiral, cysteine can form disulfide bonds) seem necessary. Oh, apparently we are expected to know three-letter and one-letter codes, according to TBR.

 

[OrdinaryDO]

I'm in the TBR class, and the instructors have all said that people who took the new exam have come back reporting a LOT of amino acid biochemistry on their exams. I don't think memorizing pI's is necessary, but structures/grouping/special properties (ex: proline causes turns, glycine is achiral, cysteine can form disulfide bonds) seem necessary. Oh, apparently we are expected to know three-letter and one-letter codes, according to TBR.

You should know HOW to calculate pI. You should also be familiar with acidity of each AA if given a pH to identify which AA would fit the characteristic charge.

 

[clathrin413]

Yeah, totally agree, definitely know how to calculate pI, especially for the acidic and basic amino acids.

 

[FauxBlue]

Yeah, totally agree, definitely know how to calculate pI, especially for the acidic and basic amino acids.

how do we do that again? I'm blanking out on this right now....

I know with two pKa values its just the average between the two, but with acidic and basic amino acids that's 3 pKas...

 

[clathrin413]

how do we do that again? I'm blanking out on this right now....

I know with two pKa values its just the average between the two, but with acidic and basic amino acids that's 3 pKas...

acidic amino acid: pI = avg(pKa1, pKa2).

basic amino acid: pI = avg(pKa2, pKa3).

Those shortcuts work but it's proly better to think of it in terms of averaging the two pKa values between which the amino acid exists as a neutral zwitterion.

A great tutorial: http://www.mhhe.com/physsci/chemistry/carey5e/Ch27/ch27-1-4.html. All pKa's and pI's are on the next page.

 

[radioactive15]

How do you find the pI of a chain of amino acids?

Suppose there's a peptide made with ADGKL

Where in the calculation of pI do you include the individual side chain pKa's? is it just guess and check by testing all of the multiple choice answers? Is there an efficient way to calculate pI in a sequence of AAs?

 

[ChrisMack390]

I plan to know all of the side chains, the 3 and 1 letter abbreviations, and anything unique about them (cysteine makes SH bridges, proline causes loops, etc). I don't think I will memorize the side chain pKa, but I will know roughly where the should fall, for example an acidic AA side chain is going to have a low pKa, so the PI for that AA is going to be somewhere near 3.

Most of the Kaplan questions just relate to which ones are hydrophobic/philic or which AA is most similar to _____.

 

[Dr. Trenb]

Know it as you know your name.

 

[chillbrolol]

.

 

[yeezuswest]

Does anyone know specifically what kind of structures to memorize for the amino acids? So for example, my textbook uses something like this:

Whereas the TPR review book uses this:

 

[ChrisMack390]

Know the side chains.

You really should know enough about orgo to realize that those are exactly the same thing. IE you should be comfortable drawing/picturing one if given the other.

 

[yeezuswest]

Okay yeah, I was just checking because I memorized all the sidechains using the first example but when it comes to the wedge-dash notation it takes me a little longer to visualize the amino acid for some reason.

 

[Dreamstoo]

Okay yeah, I was just checking because I memorized all the sidechains using the first example but when it comes to the wedge-dash notation it takes me a little longer to visualize the amino acid for some reason.

http://www.sporcle.com/games/sproutcm/amino-acids-from-structures

use this for practice. It helped a lot! I did this for 2-3 weeks in April on a daily basis alongside 1 letter and 3 letter code quizzes. Best way to memorize them is doing them twice a day and they only take 5 minutes to do alltogether.

 

[clathrin413]

Definitely remember that all the protein-composing amino acids are L-amino acids with (S) stereochemistry (except for cysteine). I feel like that is really easy to test, it's been on several TBR passages/questions.

 

[Moose A Moose]

Do you even lift?

 

[Ad2b]

http://adoc2be.blogspot.com/2015/08/amino-acids-101.html

Draw this. 3 or 4x and you'll have them. Plus you understand them. Which you need in medical school anyway.

 

[LakridsA]

How would you determine the pI of an "unknown amino acid" given its titration curve and from the curve you are able to deduce 3 different pka's? How do you know which two pka's to add

 

[StudyLater]

Which of the following AA is likely to be found inside the core of a micelle? Know them well enough to answer that.

So just know which are polar and nonpolar? Cool. On it.

I'm in the TBR class, and the instructors have all said that people who took the new exam have come back reporting a LOT of amino acid biochemistry on their exams. I don't think memorizing pI's is necessary, but structures/grouping/special properties (ex: proline causes turns, glycine is achiral, cysteine can form disulfide bonds) seem necessary. Oh, apparently we are expected to know three-letter and one-letter codes, according to TBR.

None of that should be surprising. Commonly mentioned in most texts. 3-letters are easy. 1-letters: quizlet flashcards and 20mins of your time. Most of those are pretty easy too, except N Q D E, but then you learn them and then they're fine.

Point is, amino acids aren't terrible, and you probably already know a lot about them already. Take an hour to memorize what you don't know and move on to other things.

 

[FauxBlue]

How would you determine the pI of an "unknown amino acid" given its titration curve and from the curve you are able to deduce 3 different pka's? How do you know which two pka's to add

I think the rule of thumb is that you take an average of the two pKa values that are the closest to each other. In the unknown amino acid, you'll already know that the alpha-carboxylic acid is around 2.5 and the alpha-amino group is around 10. Depending on the titration curve, I believe you'll be able to then spot out the pKa of the unknown R group and relate it to the rest.

Ex. If the unknown R group has an equivalence point at approximately 8. You know it's a basic side chain. The pI will approximately be 8+10/2 = ~9

 

[StudyLater]

If the unknown R group has an equivalence point at approximately 8. You know it's a basic side chain. The pI will approximately be 8+10/2 = ~9

pH = pKa at the half equivalence point. Did I miss something? He would have to look at the corresponding pH at the half equivalence point for the R group and the half equivalence point for the amino group (or just assume it's 10).

But also I don't get how you can say it's basic if just one of the equivalence points is 8. Do you base the basicity/acidity of the amino acid on just the middle curve (where we've got three successive curves as in a polyprotic H3PO4 titration)?

 

[FauxBlue]

pH = pKa at the half equivalence point. Did I miss something? He would have to look at the corresponding pH at the half equivalence point for the R group and the half equivalence point for the amino group (or just assume it's 10).

But also I don't get how you can say it's basic if just one of the equivalence points is 8. Do you base the basicity/acidity of the amino acid on just the middle curve (where we've got three successive curves as in a polyprotic H3PO4 titration)?

You're right I've mistaken the concept with acidic side chains. My understanding was that the only two acidic amino acids being aspartic acid and glutamic acid with side chain pKas of ~4 could be easily distinguishable since they are the only two amino acids with a side chain at that pKa.

With side chains with pKas > 7, there is the problem with cysteine and tyrosine which have side chain pKa values of ~8 and ~10, respectively. Both side chains are negatively charged at pH's below their pKa value unlike the basic side chains seen in (histidine/lysine/arginine).

I think this question would be easy to solve if it were an unknown amino acid with an acidic side chain (an equivalence point at ~4), but in terms of an amino acid with a side chain pKa above 7, it would definitely require more information to determine which pKa values to average.

What are your thoughts???

 

[tturchi51]

average the pkas above and below neutral form (aka 0 charge, thats zero not the letter o), and divide by 2.

You are making this way more difficult than you need to Faux.... If you know polar, nonpolar, basic, acidic, then you will get all the AA questions right, except possibly ONE calculation problem involving AAs. Remember, the question you are spending all this time fretting over is worth the same value as the other 58 questions in that section!

 

[FauxBlue]

average the pkas above and below neutral form (aka 0 charge, thats zero not the letter o), and divide by 2.

You are making this way more difficult than you need to Faux.... If you know polar, nonpolar, basic, acidic, then you will get all the AA questions right, except possibly ONE calculation problem involving AAs. Remember, the question you are spending all this time fretting over is worth the same value as the other 58 questions in that section!

Don't worry I won't focus on one question for the entire section! I'm attempting to answer the question with intent to get a better understanding of figuring out pIs (which may come up more often than you'd think!)

Referring to your method of averaging pKas above and below the "neutral form." How do you deduce whether the side chain group will be negatively or positively charged beyond or below a certain pH because tyrosine/cysteine/histidine/lysine have very similar pKa values for their side chains, but at a low pH, tyrosine/cysteine would be protonated and neutral while histidine/lysine would be protonated and positively charged... how do you distinguish between the two?

I'm becoming more confused as this goes on haha~! Help is appreciated~~~

 

[tturchi51]

They will give you the exact pka somewhere in the passage for each side chain. And if you happened to take my advice and learn the basic AAs, you would know that histidine and lysine are basic and carry a positive charge a physiological pH

 

[tturchi51]

memorize the polar AAs, nonpolar, Basic, and Acidic!!!!!! If the Basic ones you mentioned are + charged at that particular pH, what do you think the acidic AAs would be?

 

[fleur64]

How do you find the pI of a chain of amino acids?

Suppose there's a peptide made with ADGKL

Where in the calculation of pI do you include the individual side chain pKa's? is it just guess and check by testing all of the multiple choice answers? Is there an efficient way to calculate pI in a sequence of AAs?

Does anyone know the answer to this? I am a bit confused about how to find the PI of a peptide :/ I can figure it out when its just 2 AA and understand the concept but not sure how to apply it to a peptide.

 

[BerkReviewTeach]

Does anyone know the answer to this? I am a bit confused about how to find the PI of a peptide :/ I can figure it out when its just 2 AA and understand the concept but not sure how to apply it to a peptide.

A polypeptide is not much different than a dipeptide (or amino acid for that mater). You have the amino terminal (between 9 and 10), the carboxyl terminal (between 2 and 3), and the side chains of five amino acids to worry about (D, E, H, K, and R).

First you need to determine which pKas to average. When fully protonated, the polypeptide will have a (+) for the N-terminal and one (+) for every K, R, and H. In this protein, there is only a K to worry about, so the total charge at pH = 1 is +2. This means it must be deprotonated twice to make it neutral, so the two pKas that surround the zwitterion are pKa2 and pKa3.

You need to average pKa2 and pKa3. The pKas are sequential from smallest to largest, so pKa1 is the C-terminal (2-3), pKa2 is the COOH-sidechain of D (3-5), pKa3 is the N-terminal (9-10), and pKa4 is the NH3+-sidechain of K (10-11).

The average of 4 and 9.5 is 6.75.

This is a fairly easy question once you get practice. If you have any questions, then look at Page 188 of BR Organic Chemistry Book 2 for an explanation of the technique and then do the samples questions from pages 189-192. By the time you finish those questions, you'll be a master of pI.

 

[TheTao]

Med Biochem is the #1 failed class in med school. Learn it now.

 

[kel148]

I think a lot of people are approaching this the wrong way. Amino acids are so crucial to biochemical processes--amino acid chemistry is an integral component of physiology that you should appreciate rather than fear. You will need to understand how amino acids function in medical school-- so why wouldn't you do yourself a favor and master the concepts now? This is not like memorizing kinematics equations that you will never have to consider again in medical school/practice. The question of "what exactly needs to be memorized about amino acids for the MCAT" should be replaced with "how can I best understand amino acid chemistry?"

What I found on the May 2015 exam was that my overall understanding of amino acid chemistry tremendously assisted me in a way memorization could not. If you have a strong foundation in AAs and actually understand the way they function and why, you are setting yourself up for success on the exam.

 

[El-Rami]

how do we do that again? I'm blanking out on this right now....

I know with two pKa values its just the average between the two, but with acidic and basic amino acids that's 3 pKas...

Neutral AA: pI = (pKa Carboxyl group + pKa Amino group)/2
Basic AA: pI = (pKa R group + pKa Amino group)/2
Acidic AA: pI = (pKa R group + pKa Carboxyl group)/2

Acidic pI < 6
Basic pI > 6
Neutral pI ~6

In a peptide/protein, the more basic residues means a higher pI and vice-versa.

 

[BerkReviewTeach]

I think a lot of people are approaching this the wrong way. Amino acids are so crucial to biochemical processes--amino acid chemistry is an integral component of physiology that you should appreciate rather than fear. You will need to understand how amino acids function in medical school-- so why wouldn't you do yourself a favor and master the concepts now? This is not like memorizing kinematics equations that you will never have to consider again in medical school/practice. The question of "what exactly needs to be memorized about amino acids for the MCAT" should be replaced with "how can I best understand amino acid chemistry?"

What I found on the May 2015 exam was that my overall understanding of amino acid chemistry tremendously assisted me in a way memorization could not. If you have a strong foundation in AAs and actually understand the way they function and why, you are setting yourself up for success on the exam.

Absolutely perfect way to look at it!

The complaints about biochemistry are a bit high at the moment. This will probably change as the novelty of the exam wears off.

Truly understanding the material and how to apply it pays dividends on the MCAT! Your attitude, and the attitude of the 90% willing to work a little harder to get a better understanding, is exactly what you need not only for the amino acids section, but everywhere. Sure, there is some memorization, but if you can reason your way through questions, that's even better.

Thank you for your post.

 

[kanda1o]

Quick question... Was about to make a thread for this but this one is doing mighty fine!

For the AA, Arginine. Does the R group have one pKa? Or three? I'm really confused with this specific AA. And if only one pKa for the R group, which Nitrogen?

THANKS IN ADVANCE!

 

[BerkReviewTeach]

For the AA, Arginine. Does the R group have one pKa? Or three? I'm really confused with this specific AA. And if only one pKa for the R group, which Nitrogen?

THANKS IN ADVANCE!

Just one that that you care about, around 12.0. To remove another H from that group would be very difficult, resulting in a pKa so large, that it is impractical in biological systems.