Proteins for the MCAT: Everything You Need to Know
/Learn key MCAT concepts about proteins, the structure and classification of amino acids, plus practice questions and answers
(Note: This guide is part of our MCAT Biochemistry series.)
Part 1: Introduction to proteins
Part 2: Amino acids
a) Structure of amino acids
b) Classifying amino acids
Part 3: Peptide bonds
a) Formation
b) Hydrolysis
Part 4: Protein structure
a) Primary, secondary, tertiary, and quaternary structures
b) Specialized amino acids
c) Stability and interactions
d) Protein folding
Part 5: High-yield terms
Part 6: Passage-based questions and answers
Part 7: Standalone questions and answers
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Part 1: Introduction to proteins
Proteins are an incredibly high-yield concept on the MCAT, but like a lot of biochemistry topics, they aren’t easily mastered without a great deal of practice. These topics are especially intimidating because there is virtually no limit to what you can learn about proteins, amino acids, and everything else.
This guide will serve as an introduction to amino acids, protein structure, and protein interactions. While it will not be a comprehensive handbook to everything about proteins, it will be a good place to start studying these basic principles of biochemistry. Be sure to refer to our other biochemistry guides for further information on proteins, enzymes, and other biological molecules.
Throughout the guide, you will encounter several bolded terms. Their definitions are particularly important and can also be found in Part 4 of this guide. At the end of this guide, you will also find several passage-based and standalone questions to sharpen your skills.
Let’s begin!
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Part 2: Amino acids
a) Structure of amino acids
Amino acids are the building blocks of all proteins. The structures of amino acids are an extremely high-yield topic to study.
The structure of each amino acid can be divided into three separate regions:
The amino group, or N-terminus
The carboxylic acid group, or C-terminus
A unique identifying side chain, or R-group
Figure: Each amino acid has an amino group, an R group, and a carboxylic acid group.
Recall that an amino group is a functional group composed of NH3+. It is similar to ammonium (NH4+), except that at one position, the nitrogen is attached to a carbon instead of a hydrogen (NH2C instead of NH3). Note that this results in one free electron pair on the nitrogen atom. At physiological pH (pH ~7), this free electron pair is able to accept a bond to a single hydrogen atom. This results in a positive charge on the functional group.
The acid on every amino acid is a carboxylic acid, a functional group composed of COOH. At physiological pH (pH ~7), this carboxylic acid is deprotonated, leaving a negative charge on the functional group.
Note that at physiological pH, amino acids are zwitterions; they contain both positive and negative charges on the same molecule. Most amino acids have a net charge of zero. Exceptions arise when accounting for charges on the R-group, or side chain, of the amino acid.
These R groups, or side chains, can be as simple as a single hydrogen atom or as complex as an imidazole ring. There are 20 different R groups—each of which you should commit to memory. We’ll discuss these side chains further in the next section.
The R group is connected to the central carbon, which is known as the alpha carbon. This carbon is connected to every constituent of the amino acid: the amino group (-NH3+), the carboxylic acid part (-COO-), the R group, and a hydrogen atom (H).
Note that for 19 of the 20 amino acids, the alpha carbon itself is chiral, or attached to four different constituent groups. (The exception happens to be glycine, as the R group is simply a hydrogen atom.) Chirality refers to right- or left-handedness, denoted as D- and L- molecules, respectively. The chirality of biological molecules becomes quite important, as only L-configuration (left-handed) amino acids can be used by the body. (D-amino acids are not naturally found in eukaryotic metabolic pathways.)
Daltons (Da) are the unit of mass used to describe the masses of amino acids and proteins. They are defined as equivalent to Atomic Mass Units and therefore, 1 Dalton = 1 AMU = 1 g/mol. The average mass of an amino acid is 110 Da - this is useful for estimating the mass of a protein based on the number of amino acids in its peptide chain. For example, a protein formed from 100 amino acids would have a mass of 11,000 Da or 11 kDa.
Furthermore, some questions might ask us how many grams are present for a mole of such a protein. In this case, we simply recall that each Dalton = 1 g/mol. Our 100 amino acid example has a mass of 11,000 Da, meaning each mole of protein of this protein weighs 11,000 grams! To recap, just keep in mind that each amino acid is 110 Daltons, or 110 g/mol. This should help tackle any questions related to Daltons. As a final note, it is often ok to round 110 to 100, to make calculations easier - just be sure to remember this estimation when checking for the right answer!
b) Classifying amino acids
Each amino acid has a characteristic side chain, and the properties of these side chains are essential for the function of proteins.
Figure: A table of amino acids, including three- and one-letter abbreviations, side chains (highlighted), and the pKa of any acidic or basic side chains.
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