Amino Acid Properties

Amino acids are arguably the most important content material to understand on the MCAT. There is pretty much a 100% chance that whatever test you end up getting on test day it will have an amino acid question if not more than one. Since this is the case we are going to be taking a bit of a deep dive into this molecule type.

What Is It?

An amino acid is described pretty well by its name. An amine group attached to an acid, specifically a carboxylic acid. From a more general perspective, amino acids or residues as they are sometimes called are the building blocks of proteins and peptides as we will see later. Between the amino end called the N-terminus and the carboxylic acid called the C-terminus there is a variable side chain.

This side chain is the business end of an amino acid and determines its unique properties that later determine a protein’s shape, potential interactions, function, and other properties.

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We can think of it this way the side chain will determine an amino acid’s class. You can be a sword-wielding warrior, a valiant shieldmaiden, or a brigand ready to smash things up with your mace.


First up, all amino acids with the exception of glycine are chiral, that is they are optically active with a stereogenic center. The stereogenic center is located at the intersection of the side chain, carboxyl end, and amino end.

As we have seen previously chiral carbons can have a variety of different designations. However, in biological organisms, we predominately use the relative configuration notation of -L and -D. The L-version of amino acid is the most abundant in vivo however both the L and R versions of amino acids are utilized. This means that for the most part, all naturally occurring amino acids will end up having an S configuration with the exception of cysteine. Where despite being an L amino acid it has an R stereogenic center.

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Remember that the L- and D- designation is based on the configuration of glyceraldehyde. Here due to Sulfur having a higher priority than O L-Cysteine ends up with an S configuration.

This information might seem trivial, but in the biological world of stereoselective enzymes, the wrong stereochemistry means that the molecule is worthless to a cell. Imagine that your right hand is cold, but the only glove that you have is a left-handed one. It is really awkward to wear the left-handed glove and enzymes don’t tolerate awkwardness.

Not Gonna FIt!

Amphoteric and Zwitterionic

In addition to being chiral amino acids are amphoteric, which means that an amino acid can act as both an acid and a base. Given its functional groups, this makes sense. The amino end acts as a base while the carboxyl act as an acid. As a result at physiological pH (7.35-7.45) the amino end will be protonated and carry a 1+ charge while the carboxyl end will be deprotonated and carry a 1 charge.

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Overall most amino acids are neutral since the 1+ charged N-terminus and the 1 charged C-Terminus cancel out. However, since amino acids have both an internal positive and negative charge it is a Zwitterion. Strangely Zwitter is German for hermaphrodite so a hermaphroditic ion is one with both a positive and negative charge but an overall net neutral charge.

This means that if you want to know the net charge of an amino acid at neutral or physiological pH you only need to consider the side chain not the backbone portion.


Amino acids aren’t always zwitterions though. The charges on both ends are generated due to acid-base reactions therefore solution pH will determine an amino acid’s overall charge. The easiest way to think about whether or not an amino acid will be protonated or deprotonated is by considering the pKa of each hydrogen in an amino acid. By proxy, we can determine the amino acid’s charge from pKa values too!

As a refresher pKa values are like the personal pH of a specific hydrogen within a molecule. For example, an amino acid’s carboxylic acid end has a pKa of roughly 2, which means that specific hydrogen is pretty darn acidic, while the amine end has a pKa of 9 making it solidly basic.

Ultimately the external pH controls how a species behaves and defines whether its hydrogens are acidic or basic. We can determine this easily by comparing the pKa of interest to the environmental pH. Then by asking ourselves is the molecule more or less acidic we can decide that hydrogen’s behavior. Let’s continue on with our example to illustrate how this works.

Imagine we plopped our amino acid into three different solutions. One at pH = 1, a second at pH = 10, and a third at pH = 7. In each case, we need to compare the solution pH to both the amino pKa and the carboxyl pKa and define it as an acid or a base. If the solution pH = 1 then the carboxyl with a pKa of 2 is more basic than the solution and will act as a base. If the solution pH = 10 then the amino end with a pKa of 9 is more acidic and will act as an acid. Look at the chart below to see a summary of how all the different situations will play out.

Solution IdentitySolution pHAmino pKaBehaviorAmino ChargeCarboxyl pKaBehaviorCarboxyl ChargeOverall Charge
Solution 119Base+12Base0+1
Solution 2109Acid02Acid-1-1
Solution 379Base+12Acid-10

In summary when the pH > pKa the hydrogen acts as an acid and is donated to the environment. Vice versa when pH < pKa that specific site acts as a base and accepts hydrogens from the environment. When pH = pKa the molecule can’t decide which way to go and half of all the molecules present will act as bases while the other half will act as acids.


While pKa’s are focused on the individual acid and basic portions of a molecule pI is concerned with how the molecule as a whole will behave in acidic and basic conditions. Specifically, pI or isoelectric point defines the pH at which an amino acid is electrically neutral. If we want we can calculate the pI of an amino acid by averaging the pKa values of the N and C termini.

pI = \frac{pKa_{amino}+pKa_{carboxyl}}{2}

For amino acids with acidic and basic side chains, their pI will be heavily influenced by the pKa of their side chain. For example, aspartate has a carboxylic acid on its side chain which drastically lowers the pI of the molecule.

In order to calculate the pI of the charged amino acids we will also be averaging two pKas however instead of using the two termini we will use the side chain and one terminus. If the amino acid is basic we will average the side chain pKa and the N-terminus. In contrast, the pI of an acidic amino acid is calculated by averaging the side chain pKa and the C-terminus. I remember this by thinking that you have to match base with base and acid with acid so use the N-terminus for basic amino acids and the C-terminus for acidic amino acids.

pI_{acidic} = \frac{pKa_{side\;chain}+pKa_{carboxyl}}{2}
pI_{basic} = \frac{pKa_{amino}+pKa_{side\;chain}}{2}

The big takeaway from all of this is that the higher an amino acid’s pI the more positively charged it is and the lower an amino acid’s pI the more negatively charged it is.

This means that we can determine the pI of a protein as a whole from the individual amino acids present. To do this we need to determine the pI contributors of a protein. We find these by listing out the charges of each amino acid at neutral or physiological pH. To see how this works let’s look at the following peptide.

It is okay if you don’t know the exact classification of each amino acid in this peptide yet since you will learn that in the next lesson, but at physiological pH (~7.35), the amino acids in this peptide will have the charges shown above. Since we are looking for the isoelectric point or when this molecule will be net neutral we can begin by canceling out any opposite charges.

From here we consider which residue or residues need to change in or to get the molecule to be neutral. Since only lysine is charged in this scenario it is the only pI contributor. If other residues were charged we would consider them pI contributors too. Then we average up all of the pI contributors to get a total pI for the peptide sequence as a whole. While this method isn’t 100% accurate it’s good enough for the MCAT since the answers are usually far enough apart to make an educated and correct guess.


Since amino acids are all about the base, about the base they are excellent candidates for titrations and acts like any other polyprotic acid. We will explore this specific idea later when we get to acids and bases and will look at how to incorporate pI calculations into titrations. For now let’s turn towards learning about the specific amino acids and their properties.