MCAT Organic Chemistry

Amino Acids & Proteins

MCAT Organic Chemistry > Amino Acids and Proteins


Amino acids are the basic biological building blocks of all life. Each amino acid contains a carboxyl group, an amino group, hydrogen, and an R group attached to a central alpha carbon. There are 20 naturally occurring amino acids which all derived their function from their prosthetic groups (organic molecules or metal ions)

MCAT Amino Acids and Proteins - Amino Acids

Stereochemistry is extremely important in understanding amino acids. Amino acids are classified based on L and D configurations. This is different from R and S, however there are similarities. L-amino acids are found in proteins and are extremely common in nature. To contrast, D-amino acids are hardly ever found in protein structure.

Naturally occurring amino acids are all L enantiomers. Therefore, in all Fischer projections of amino acids on the MCAT, the amino acid will be drawn on the left. L amino acids will all have S configurations, except for cysteine, which will have an R configuration because sulfur causes a change in priority in stereochemistry.

If the molecule has the following priority configuration then L = S and D = R.

NH2 > COOH > R

If the molecule has the following priority configuration then L = R and D = S.

NH2 > R > COOH

Acidic or Basic

See Acids and Bases

Amino Acids are classified as amphoteric species meaning they can function as either a base or an acid depending on the presence of certain factors. This also means that amino acids are dipolar ions (zwitterion).

If the solution is acidic, the amino acid will act as a base and pick up a proton. If the solution is basic, the amino acid will act as an acid and give up a proton to the solution. Through this function, amino acids help draw it’s environment back into equilibrium, and is part of their role in cellular function.

All amino acids have at least two pkas and the isoelectric point (pI) is between those two values. When pH = PI, all of the species have been de-protonated and the pH changes drastically (vertical line). When pH = PI the amino acids are considered neutrally charged.

As a general rule, at low pH, amino acids will exist as cations, and as the solution’s pH increases, a point will be reached where the amino acid exists as a zwitterions, with both positive and negative charges on the molecule. As the pH increases more, the amino acid will exist as an anion.

At low pH, amino acids are found as cations

At high pH, amino acids are found as anions

If the amino acid R group contains an amine, it is classified as a basic amino acid. Basic amino acids include:

If the amino acid contains a carboxylic acid functional group, the amino acid is classified as acidic. Acidic amino acids include:

Hydrophobic or Hydrophilic

An amino acid is considered hydrophilic if it has any of the following bases:

Non-polar amino acids are hydrophobic so they are often found buried within protein molecules. All amino acids that contain other functional groups than the ones listed above are considered hydrophobic

Polar, acid and basic amino acids are all hydrophilic and are often found on the surface of a protein.

Protein Structure

See Protein Structure

Amino Acid Reactions

Peptide Linkage

A peptide is consists of an amide bond between an amino acid and another molecule. It is formed when the amine group on an amino acid attacks a carbonyl group (C=O) of another molecule.


See Hydrolysis

In order to hydrolyze a peptide bond, it must be reacted with a strong base, or the reaction must be catalyzed by an enzyme as it is very difficult to do so. Usually this process occurs in the human body in order to break down larger molecules into smaller molecules.

MCAT Organic Chemistry

Organic Chemistry Topics