Amino Acid Notations and Classifications

Notations

Amino acids are referred to in three different ways: by their full name (ex: Aspartate), by their three-letter abbreviation (ex: Asp), or by their one-letter abbreviation (ex: D).  You should know all three as the AAMC loves to ask questions and interchanges the different forms frequently.

Additionally, we will see protein or peptide-specific notations pop up often. While we haven’t discussed either of those biomolecules yet it is worth looking ahead at the notations since it contains amino acid content.

Strings

One of the most common types of amino acid notations present on the MCAT is the protein or peptide string. Basically, a list of amino acids in one-letter or three-letter notation that shows the order and potential positioning of different amino acids. This notation is most useful for net charge questions as well as determining what type of interactions a peptide or protein might have.

Positions

As seen above peptides or proteins are collections of amino acids all strung together. Since each contains multiple amino acids and often the same amino acid more than once it is helpful to be able to describe a specific amino acid in the chain. To do this you will often see the one-letter abbreviation of an amino acid followed by a number.

The one-letter abbreviation tells you what amino acid while the number tells you at what position. For example, E60 lets us know that there is a glutamate (E) at the 60th position in this protein.

Mutations

Another common notation is the mutation notation, which follows the form of position notation with an additional one-letter amino acid abbreviation as shown below.

Here the first amino acid represents the old, non-mutated amino acid while the second amino acid represents what it is changing to, The number in between tells you at what position along the protein or peptide this occurs. For example, the above notation E6V means that a glutamate at the 6th position is being switched out for a valine, which is the mutation that leads to the devastating disease sickle cell anemia.

Classifications

Now that we understand how the MCAT will refer to amino acids let’s take a look at how they are categorized. While there are a lot of different ways to slice up amino acids the biggest groups amino acids by polarity so we will begin there. As we go through we will also explore a couple of different question types that are relevant to each classification and have a chance to practice some MCAT style amino acid questions.

Hydrophobic

Hydrophobic or non-polar amino acids contain side chains filled with nonpolar carbon chains. Due to this amino acids in this classification will form regions of proteins that span the hydrophobic cell membrane, end up on the inner surface of a protein, or any other area in cells or our bodies where hydrophobic molecules predominate.

Hydrophilic

Polar amino acids by contrast have side chains containing substituents that are able to form hydrogen bonds such as -OH groups and -NH groups or they will have charged side chains. Hydrophilic residues will be exposed to the liquid environments in our cells and bodies. As a result, we often find these amino acids on the exposed surface side of a protein, lining the inside of an ion channel, or in any other polar environment.

Polar Versus Nonpolar Questions

Now that we have had a chance to go over the biggest amino acid classification let’s explore how we can use this information by looking at some sample questions.

• Which of the following amino acids would be found embedded on the outer surface of the cell membrane?
• Which of the following peptide strands would be in the transmembrane domain of an ion channel?

Here each question is asking us to determine what type of cellular environment is present and match it up with an appropriate amino acid. For example, the outer surface of the cell membrane is water exposed and thus polar. Therefore we would need to choose a polar or hydrophilic amino acid in order for it to be able to interact with the extracellular fluid.

In contrast, the transmembrane domain is largely hydrophobic so only hydrophobic or nonpolar amino acids would be found there. In either case, we must know whether an amino acid is polar or nonpolar and match that up to the environment in which it exists since like will interact will like when polarity is being considered.

Aromatic

There are also lots of smaller classifications that amino acids can fall into and we will look into those now starting with the aromatic amino acids. All of the aromatic amino acids contain a benzene ring making it the hallmark of the three residues in this category. By virtue of being aromatic, they can absorb light in the ultraviolet (UV) spectrum and form pi-stacking interactions with one another.

Don’t Be a DERK

Up next and one of the most tested classifications is grouping by charge. To remember the charged amino acids you can use the mnemonic DERK. With aspartate (D) and glutamate (E) being negatively charged and arginine (R) and lysine (K) being positively charged.

Why no histidine?

If you look up an amino acid sheet on the internet you are almost certainly going to see histidine listed as a basic and positively charged amino acid. So why isn’t it listed here? At neutral or physiological pH the majority of the histidine residues have a net zero charge. Since the MCAT almost always asks questions about the charge of amino acids at these pHs it is worth treating histidine as uncharged.

[histidine net charge based on pKa]

Net Charge Questions

Now that we have a handy way of remembering our charged amino acids let’s put this knowledge into practice by learning how to solve net charge problems.

Net charge questions are fairly common and tend to fall into two major categories, calculating the net charge straight up or determining the change in net charge. Here the key to answering either question is remembering DERK represents the charged amino acids. Then all you have to do is label each charged amino acid and tally up the total or the difference.

Let’s walk through two questions to see how this works.

• A peptide strand has the following sequence, GLKDYE, what is its net charge at a physiological pH (approx. 7.4)?
• What is the change in net charge for the following peptide variant H45E, L67I, K89T, R99D?

For the first question, we need to find the overall charge of the peptide GLKDYE. Since only DERK are charged we will only concern ourselves with those residues and forget the rest.

So the overall net charge of this peptide strand would be -1!

In the other question, we are concerned with the change in net charge and will need to focus on any of the listed mutations that contain DERK. Therefore we will only pay attention to H45E, K89T, and R99D omitting L67I since it doesn’t contain a charged amino acid.

When accounting for the change in net charge we will be focused on tracking a difference in charge for each mutated residue. To do this it is best if we write out what we start with and what we end up with that way we can determine how the overall charge changed. For example, when we change from 0 to -1 it is pretty clear that we gained one negative charge however when we go from +1 to -1 we gain two negative charges.

Now that we walk through both of those questions briefly try a couple more out on your own.

Yummy YST Bread

Phosphorylation radically changes the properties of an amino acid by adding negative charges to previously neutral amino acids. In this case, phosphorylation can act as a quick and easy way to control protein function. However, only three amino acids are phosphorylated and all of them have OH bonds in their sides chains. You can remember the three by using the mnemonic YST, which makes me think of yeast bread.

Interestingly and importantly (as far as the MCAT goes) phosphorylated residues are comparable in structure and function to glutamate and aspartate since both have negative charges they can play similar roles in protein structure.

Lose or Retain Function Question

Hopefully, the YST mnemonic will help you keep the phosphorylated residues straight. Since most of these amino acids play an important role in regulating various cellular functions let’s discuss the lose/retain function amino acid questions and try some on our own. Here are a couple of examples:

• Which of the following amino acid substitutions is LEAST likely to result in loss of function for the constituent protein?
• Which amino acid substitution is MOST likely to retain the protein’s original functionality?

Another common question type centers around retain or losing function in these cases we are looking for the biggest amino acid change or the smallest amino acid change. In almost all cases this means completely changing classification or staying within the same amino acid classification.

For example, in the loss of function question, we would look for a substitution that switches amino acid classifications drastically, such as D46K. In this example, the negatively charged residue aspartate becomes positively charged residue lysine. This would almost certainly wreak havoc on the interactions this protein forms and lead to loss of function.

On the contrary D46E wouldn’t change much at all since aspartate, a negatively charged residue, is converted into glutamate, another negatively charged residue. Although the glutamate is a bit longer than aspartate they share the same classification and as a result would function similarly.

Special Ones

Some amino acids don’t fall neatly into any other special categories, but do have unique and notable features we need to know.

Glycine, Gly, G

Glycine is notable as it is the only achiral amino acid. All other amino acids are chiral and as a result undergo stereoselective reactions.

Proline, Pro, P

Proline is notable because its side chain includes its amino end. This results in significant structural rigidity that disrupts secondary structural elements such as ⍺-helices and β-sheets. However, their overall structure and rigidity allow them to form the turns in protein structure.

Cysteine, Cys, C

Cysteine is unique due to its ability to form disulfide bonds that hold tertiary and quaternary structures together. These bonds form when two cysteine residues undergo oxidation and later break when these bonds are reduced. When answering questions about cysteine lookout for the following keywords: reducing, covalent bond, crosslinks, and disulfide. These are a key tip-off that cysteine is the correct or incorrect answer based on the question.

Relative Size

Another important consideration when looking at amino acids is their size. More importantly, we should have a general understanding of the amino acid’s relative sizes to others in the same classification. For example among the negatively charged residues, aspartate is smaller than glutamate. For the polar uncharged residues, asparagine is smaller glutamine. Finally, for our non-polar residues valine is smaller than either leucine or isoleucine.

It is fairly unlikely that relative size will come down to comparing a negatively charged residue to a positively charged residue because the biggest difference between them is their overall charge rather than their size. Below is a chart summing up the most important size comparisons to know.

Category	Size Ranking (Smallest to Largest)
Hydrophobic	Gly < Ala < Val < Leu = Ile
Polar Uncharged	Asn < Gln
Acidic/- Charge	Asp < Glu

More Amino Acid Questions

Throughout this lesson, we have explored some of the most common amino acid questions that show up on the exam. There are a few more worth noting so we will look at these question types in isolation and explore how to solve each.

Binding Pocket Versus Binds X Molecule

• The binding pocket of an enzyme is lined with anionic residues. Which of the following amino acids would you expect to find in the binding pocket?
• An enzyme binds anionic molecules. With this in mind what amino acid residues would you expect to find in the enzyme’s binding pocket?

In the first question, it states that anionic residues line the binding pocket this means that we will find negatively charged amino acids in the binding pocket. Thus we would choose our negatively charged amino acids as an answer.

However, in the second question, we are told the function of the amino acids, that they bind anionic molecules or negatively charged molecules. In this case, we have to determine what amino acid can bind negatively charged molecules. Since opposites attract we would look for positively charged residues as an answer.

Anytime you see a binding based question be careful to note whether the given information describes the binding pocket or the ligand that ends up binding since you can easily end up with the opposite answer if you switch this information up.

Structure

For structure-based questions, you will want to scan any given figures in a passage and find the amino acid present paying particular attention to identifying an amino acid’s side chain. The easiest way to find a side chain is to look for an amide functional group since this is how most amino acids are incorporated into other larger molecules.

Once you find the amide bond look one carbon away from the carbonyl to see if there is a recognizable side chain attached.

Other times amino acids will be modified and ultimately retain their overall configuration and shape but will not be attached to other molecules. In this case, looking for an amide group won’t be terribly helpful. Instead, focus on looking at the overall shape of the molecule and try and link it up to the overall shape of one of the amino acids.

Additionally, look to see if you can find the carboxylic acid end and the amino end since the side chain should originate on the carbon in between them. Unfortunately, both the N-terminus and the C-terminus of the amino acid might have been modified and therefore no longer easy to find. Don’t fret though just focus on the overall shape as discussed above.

In Conclusion

Phew!!! That was a big one. We are going to be constantly revisiting this material as we progress through the rest of this class it really is super important and we will have multiple chances to see how it is used. It is critical that we memorize every single amino acid’s general structure, one-letter abbreviation, three-letter abbreviation, general properties, and any special properties. This is a big task and might seem intimidating. To make it easier print out the amino acid cheat sheet and use it as you go through questions. Try to recall them first, but if you can’t look it up and you will start to learn as you go.