MCAT

Amino Acids for the MCAT

WRITTEN BY
The Medistudents Team
June 6, 2022

Amino acids form part of the MCAT syllabus, so it is important you revise this area thoroughly when preparing for your MCAT exam.

Amino Acids are the functional building blocks of proteins. Proteins are essential to life: they carry out complex chemical reactions, provide structure, regulate osmolarity of fluids, and are important pharmacological targets. To be considered “living,” an organism must have proteins (called enzymes) carrying out these complex reactions. Without the amino acid backbone, this wouldn’t be possible.

Amino Acid Structure

Amino acids all share the same basic structure, depicted below

A picture containing text, clockDescription automatically generated
Figure 1: Amino Acid Structure 

As you can see, there are 4 important components bound to a central carbon, called the α (alpha) carbon. These groups are:

The Carboxyl group

The Amino group

A variable Side chain (depicted as R)

A Hydrogen molecule

These groups are rotated around the α carbon in particular ways that allow them to interact with other amino acids. Arguably the most important component of the amino acid is the side chain. Different side chains will give the Amino Acid a different property, allowing it to interact with its environment in different ways.

Amino Acid Configuration

When learning about Amino Acids for the MCAT, you also need to understand Amino Acid configurations. Although an amino acid may have the same functional components as another, the orientation of the side groups around the α carbon may change the overall properties of the molecule. These configurations are commonly classified as L- or D-conformation.

Graphical user interface, applicationDescription automatically generated
Figure 2: Amino Acid Configuration

L-Amino Acids are more commonly found in nature, and in the human body, and are typically the type that are found in proteins. D-Amino Acids occur much less often in nature and, as a result, aren’t commonly used as a component in proteins.

To determine the configuration of an Amino Acid, you must compare the priority of the side groups of Amino Acids (A step-by-step instruction on how to do this will be covered in organic chemistry and determine the R- and S-configuration of carbon molecules).

If the priority of the amino acid is NH2 > COOH > R, then an L-amino acid is the same as an S-amino acid and a D-amino acid is the same as a R-amino acid.

Similarly, if the priority of the amino acid is NH2 > R > COOH, then an L-amino acid is the same as an S-amino acid and a D-amino acid is the same as a S-amino acid.

A Common Misconception: L and D configurations of amino acids are different from R and S configurations of organic molecules. An L-amino acid will not always be S, and a D-amino acid is not always R. Take the time to learn how to do this and make sure you understand it.

What do I need to know about Amino Acid Classification for the MCAT?

While there are hundreds of different amino acids that exist, there are only 20 that are used by the human body for protein synthesis. Each of these will have a name, a 3-letter abbreviation, and a 1 letter abbreviation. This makes it convenient to write out long chains of amino acids – the protein Titin, for example, is a sequence of 27,000 amino acids.

The twenty amino acids you will need to know are listed below. Please note that we are not counting Selenocysteine (Sec, U), and you will not be expected to know it on the MCAT:

Diagram, schematicDescription automatically generated
Figure 3: Amino Acid Structure and abbreviations, Wikimedia Commons

Let’s walk through an example of the structure of one of these acids, Alanine (Ala, A)

In the image, the red circle represents the R group – in this case, CH. The blue circle indicates the central carbon. The purple circle represents the carboxyl group. Finally, the green circle represents the amino group.

There are multiple ways to group amino acids together into classifications, and Figure 3 has already done a nice job on one classification: acidic, basic, and neutral amino acids. To understand this, we need to first understand the concept of a zwitterion.

A Zwitterion is a molecule that, at physiological pH (7.4), will have both positive and negative charges. Physiologic pH is the pH that most living humans will maintain and allows the body to have optimal function. While there is slight variation, this is generally considered to be a pH of 7.4. 

All amino acids are zwitterionic; the carboxyl group is highly acidic (will give up a proton and has a negative net charge at physiologic pH), while the amino group is highly basic (will not give up a proton and has a positive net charge at physiologic pH). Because of this, the acidic or basic nature of amino acids at physiologic pH will largely be determined by the structure of the side chain.

A polar molecule can be uncharged (or at least extremely close to it) based on the pH of the environment it is in. The pH at which a polar molecule carries no net charge is known as the Isoelectric Point of the molecule, noted as pI. If the pH is less than the isoelectric point, the surrounding pH will not be enough to strip the extra proton from the functional group. Amino acids with a pI greater than 7.4 will be basic amino acids and will have a positive charge at physiologic pH. If the pH is greater than the isoelectric point, the surrounding pH will be enough to strip the extra proton from the functional group. Amino acids with a pI less than 7.4 will be acidic amino acids and will have a negative charge at physiologic pH. Look at Figure 4 (below) to see the pKa and isoelectric point of some selected amino acids.

Amino Acid Side Chain pKa Isoelectric Point (pI)
Arginine 12.5 10.8
Aspartic Acid (Aspartate) 3.9 3.0
Cysteine 8.3 5.0
Glutamic Acid 4.3 3.2
Histidine 6.0 7.6
Lysine 10.5 9.8
Tyrosine 10.1 5.7
Table 1: pKa Values of Amino Acids

With this information in hand, it’s easy to see which amino acids are acidic and which are basic.

The Acidic Amino Acids are Aspartic Acid (also called Aspartate) and Glutamic Acid (Also called Glutamate). Both amino acids will have negative charges at physiologic pH.

The Basic Amino Acids are Arginine, Lysine, and Histidine. All these amino acids will have positive charges at physiologic pH.

Note that the free amino and carboxyl groups in amino acids or peptides can also be protonated or deprotonated, depending on the pH. This can vary between amino acids, but as a general rule of thumb the carboxyl group will be protonated if the pH is below 2 and the amino group will be deprotonated if the pH is above 10.

Before we move on to further classification, it is worth mentioning that Histidine (His, H) is one of the more unique amino acids. The isoelectric point is 7.6, which is quite close to the physiological pH of 7.4. Many organisms will take advantage of this situation – they can manipulate their pH slightly, allowing Histidine to exist in either an acidic OR a basic state, depending on what Histidine will be used for.

The last two sources of classifications that are important for you to know when studying Amino Acids for the MCAT, have to do with Hydrophobic Amino Acids and Hydrophilic Amino Acids. If an R group contains an acid, base, amine, or alcohol, it will be hydrophilic. Any R groups that do not contain these groups will be considered hydrophobic. This has important implications in the structure of proteins, so it is important to know the structure of the various R groups and how they interact with the environment.

Peptide Bond

Proteins have complex structures, and the most basic form is the linkage between the carbon backbone of two or more amino acids. This is known as the Primary Structure of proteins. Understanding the formation and destruction of these bonds is important for the MCAT as well.

Proteins are linked together via a Condensation Reaction, also called Dehydration Synthesis, as diagrammed below in Figure 4.

Diagram, schematicDescription automatically generated
Figure 4: Formation of the Peptide Bond, Wikimedia Commons

This reaction occurs between the carboxyl group of one amino acid and the amino group of another amino acid. Through electron movement and transfer, a water molecule will be formed as a by-product. As a result, there will be a bond formed (the peptide bond) between the carbon and nitrogen of two adjacent amino acids. At this point, the amino group at the end of the peptide is called the N-terminus. The carboxyl group at the other end of the peptide is called the C-terminus.

The other important reaction in terms of peptide bonds has to do with breaking the bond, which is achieved by a Hydrolysis Reaction. The overall reaction is essentially the opposite of the condensation reaction – a water molecule is consumed by the reaction and the peptide bond will be broken, resulting in two distinct molecules.

We hope you have found this information helpful when revising Amino Acids for the MCAT exam. Good luck! 

References

Contents