Now, it is important to remember that most amino acids are zwitterions meaning they contain a positive charge and a negative charge that cancel one another out making the amino acid neutral. When an amino acid is in its zwitterion form, it is described as reaching its isoelectric point, or pI. Yet, when
determining the acidity or basicity of an amino acid, you must look at its respective pKa values.
The pKa represents the pH at which half of a chemical species is deprotonated. The carboxyl group of an amino acid is designated pKa1, the amino group has pKa2, and the R group has pKa3. When an amino acid enters an
environment with a pH below its pKa values, the species will be protonated and form an overall positive charge. Alternatively, when the amino acid enters an environment with a pH above its pKa values, the species will be deprotonated and form an overall negative charge.
Amino acids undergo dehydration reactions to connect via
peptide bonds and form chains. These peptide chains always start with a nitrogen atom called the N terminus and end with a carbon atom called the C terminus to form proteins. This is the result of the nucleophilic amino group of one amino acid attacking the electrophilic carbonyl group of another amino acid.
Amino acids linked via peptide bonds are referred to as residues. Thus, a dipeptide consists of two residues and a tripeptide consists of three residues. A chain of less than 20 residues is called an oligopeptide. A chain of more than 20 residues is called a polypeptide. These linear chains of peptide bonds make up primary protein structure and are broken only by proteases via hydrolysis reactions.
Next, linear peptide chains fold into their secondary protein structure via hydrogen bonds between amino groups and nonadjacent carboxyl groups. Secondary protein structures include alpha helices, which form clockwise coils around a central axis; and beta-sheets, which form parallel or
antiparallel ribbons.
In tertiary protein structure, peptide chains fold into three-dimensional shapes by way of R group interactions such as hydrogen bonding, disulfide bridge formation, and hydrophobic interactions. Hydrophobic interactions conform proteins into a shape that positions hydrophobic R groups interiorly
shielding them from the environment.
Last, but not least, quaternary protein structure results from two or more peptide chains interacting with one another. These interactions produce proteins with multiple subunits, like hemoglobin. Like nucleic acids, the non-covalent interactions that form secondary, tertiary, and quaternary protein
structure are broken down by the process of denaturation.
Again, we cannot stress enough the importance of memorizing the essential amino acids to MCAT success. Add on a solid knowledge of protein formation and structure and feel some of that MCAT anxiety melt away.
| 
