Amino Acids Peptides Proteins on the MCAT

Table of Contents

Amino acids are the building blocks of all the proteins in your body. The body uses these proteins for growth, the breakdown of food, repair, and many other functions.

This guide will introduce amino acids and proteins, key terms and definitions, and things you should remember as you prepare for the MCAT

Let’s get started!

Amino Acid Peptides & Proteins on the MCAT: What You Need to Know?

Amino acid peptides and proteins are covered in the Biochemistry section of the MCAT

Introductory biochemistry accounts for 25% of the Biological and Biochemical Foundations of Living Systems section (Bio/Biochem) and 25% of the Chemical and Physical Foundations of Biological Systems section (Chem/Phys).

It’s hard to predict the exact number of questions about amino acids and proteins that will appear on the MCAT. However, you can expect it to appear in both the Bio/Biochem and Chem/Phys sections.

Important Sub-Topics – Amino Acids & Proteins

You might vaguely remember amino acids and their structure from your introductory biochemistry courses. There are precisely 20 necessary amino acids that exist!

Amino acids are very important as they are the building blocks of proteins. These organic molecules join together to create various peptide proteins, which carry out many complex chemical reactions essential for the proper functioning of the human body.

Amino acids and peptide proteins can be complicated, so let’s break them down into important sub-topics you can concentrate on.

1. Amino Acids Structure

Amino acids are fundamental building blocks for proteins. These amino acids can be categorized based on their characteristics, which come from their unique side chains. These side categories include:

  • Nonpolar, nonaromatic
  • Aromatic
  • Polar
  • Acidic (Negatively charged)
  • Basic (positively charged)

The pH of the solution can affect the protonation state of the amino acid’s functional group because certain functional groups have unique pKa values. Includes:

  • Amino Group (-NH3+): ~9
  • Carboxyl Group (-COO-): ~2
  • Side Chain: Depends on amino acid

With the exception of glycine, all the 𝛼-carbons on the amino acids are chiral, meaning they have 4 different substituents attached to it. Glycine is an exception because its sidechain is just another hydrogen atom. 

It is important to know that all the proteinogenic amino acids in eukaryotes are L-amino acids; likewise, all amino acids, with the exception of cysteine, all have an (S)-absolute configuration. 

This exception for cysteine, having an (R)-absolute configuration, is due to the priority of the -CH2SH over the -COOH group. 

For more in-depth content review on amino acids structure, check out these detailed lesson notes created by top MCAT scorers. 

2. Amino Acid Reactions

Amino acid reactions lead to the formation of peptide bonds, which serve as the backbone of protein synthesis.

There are 2 types of reactions that exist:

Type of Reaction


Condensation Reaction (Dehydration Synthesis)

This reaction allows for the formation of peptide bonds, which serve as the basis for protein synthesis. As the name implies, a water molecule is also generated as a product of the reaction.


The peptide bond formation via condensation reactions is an example of an organic nucleophilic substitution reaction.


This reaction is basically the opposite of the condensation reaction, which results in the breaking of peptide bonds yielding amino acids. Similarly, as the name implies, a water molecule is used as a reactant in order to allow for the peptide bond breakage.

For more in-depth content review on amino acids reactions, check out these detailed lesson notes created by top MCAT scorers. 

3. Protein Structure

Protein structure covers all aspects of what gives a protein its shape and oftentimes its function, including the sequence of amino acids all the way to their 3D folding.

There are 4 levels of protein structure:

Primary (1°) - Linear sequence/order of amino acids.

Secondary (2°) – Local interactions between amino acid backbone. For example, hydrogen bonds between amide groups.

Tertiary (3°) – 3D Folding & Structure

Quarternary (4°) – Interactions between peptide subunits

Proteins can then be modified via the attachment of other molecules/ligands via covalent bonds. These protein modifications can result in different physiological outcomes:

Type of Modification



Addition of a phosphate group (usually think activation!)


Addition of a ubiquitin group (usually think degradation!)


Addition of a carbohydrate group


Addition of a lipid group

The external environment can also have implications on protein structure and reverse the 3D folding. These include:

Environmental Aspect

Effect on Protein Structure


Increased temperature can cause disruption of hydrogen bonds due to an increase in kinetic energy


Increased concentration of solutes can affect salt bridges by disrupting electrostatic interactions


Changes in pH can lead to changes in protonation states, which can also affect amino acid charge

When proteins fold, typically they follow the hydrophobic effect. This means that the protein will fold in a way to minimize interactions between hydrophobic amino acids and water molecules. This depends on the location of where the protein will function. 

If the protein is cytosolic, the surface amino acids will be hydrophilic, meaning they are polar, both negatively charged (acidic) and positively charged (basic). The inner core amino acids will be hydrophobic and nonpolar.

However, if the protein is transmembrane, surface amino acids will be hydrophobic and nonpolar. The inner core amino acids are hydrophilic, polar, negatively charged (acidic), and positively charged (basic).  

For more in-depth content review on protein structure, check out these detailed lesson notes created by top MCAT scorers. 

Key Terms and Definitions – Amino Acids & Proteins

Here are some of the more important key terms and definitions to remember for this general guide to amino acids and proteins!



Amino Acid

Simple organic structure, identifiable by a unique side group

Alpha Carbon

The first carbon atom that attaches to a functional group, such as a carbonyl


The end of an amino acid containing the positively charged amino group


The end of an amino acid containing the negatively charged carbonyl group

Salt Bridge

Interactions with amino acids with opposite charges and hydrogen bonding


A functional group where nitrogen is bonded to a carbonyl carbon atom

Additional FAQs – Amino Acids & Proteins on the MCAT

Do I need to memorize amino acids for MCAT?

Unfortunately, you WILL need to memorize all 20 amino acids for the MCAT exam.

How do you remember the Amino Acids for the MCAT?

Remembering all 20 amino acids can be a daunting process. Thankfully, there are many tried and tested strategies out there that you can use! One example is mnemonics. This method connects newly learned material to previously learned knowledge using visual and auditory cues. Basic mnemonic strategies emphasize the use of abbreviations, keywords, or rhymes. At MCAT Mastery, our mentors have created a list of MCAT biochemistry mnemonics, which covers amino acids!

Are Amino Acids D or L MCAT?

Amino acids will most likely be presented in both D and L configurations on the MCAT. It is unclear whether one is preferred, however, it is known that the L configuration is more common in nature.

Which Amino Acids are on the MCAT?

We cannot confirm which exact amino acids will appear on your specific exam. Therefore, it is a safe bet to simply memorize all 20 amino acids. This way, you will recognize any amino acid that could possibly appear in one of your MCAT questions.

Do You Need to Memorize pKas for the MCAT?

Not only should you memorize the pKa values, but you should also understand what the value indicates and what causes each amino acid to have a certain pKa value.

What is the Relationship Between Amino Acids Peptides and Proteins MCAT?

Amino acids join together through peptide bonds to create both peptides and proteins. In the most basic terms, peptides are smaller chains of two or three amino acids, whereas proteins are larger chains of amino acids. Proteins typically consist of multiple peptide subunits.

Additional Reading Links – Study Notes for Amino Acids Peptides Proteins on the MCAT

For more in-depth content review about amino acids peptides proteins on the MCAT, check out these detailed lesson notes created by top MCAT scorers!

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