Amino Acid Classification – MCAT Biochemistry | MedSchoolCoach

Amino Acid Classification

MCAT Biochemistry Chapter 1 - Section 1.2 - Amino Acids - Amino Acid Classification
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Sample MCAT Question - Amino Acid Classification

Which of the following amino acid side chains does NOT have a pKa value above 5?

a) H

b) D

c) K

d) R

B is correct. D or aspartic acid.

Acidic amino acids have low side chain pKa values. Aspartic acid (one letter code: D) is an acidic amino acid and has a side chain pKa value of 3.7 (which is lower than 5). Answer choice A is incorrect because histidine (one letter code: H) is a basic amino acid and has a side chain pKa value of 6 (which is higher than 5). Answer choice C is incorrect because lysine (one letter code: K) is a basic amino acid and has a side chain pKa value of 10.7 (which is higher than 5). Answer choice D is incorrect because arginine (one letter code: R) is a basic amino acid and has a side chain pKa value of 12.1 (which is higher than 5).

Amino Acid Classification

Amino acid classification is a very high yield MCAT topic. You should know the structures of all 20 proteinogenic α-amino acids, their one and three-letter codes, and the pKa values of the R groups of acidic/basic amino acids. You should also be able to recognize the different amino acids by their side chains. Subtleties in their structures have significant implications for their behavior, and it is often beneficial to be completely familiar with them for this reason. To make this task less intimidating and more systematic, we will be dividing up the amino acids into several classes with highly similar properties. These classes include acidic, basic, polar, nonpolar, sulfur-containing, aromatic, and hydroxyl-containing.

 

(If you need a refresher on the basic structure of amino acids and their 3D configuration before we get started, visit this post.)

Acidic Amino Acids

Aspartic acid (D) and glutamic acid (E) are the only two amino acids with acidic side chains. Aspartic acid’s side chain has a pKa of 3.7 and glutamic acid’s side chain has a pKa of 4.2 When deprotonated, these amino acids are commonly referred to as aspartate and glutamate respectively, in reference to their anionic state.

 

(The fact that the side chains of certain amino acids — including acidic amino acids — can be protonated or deprotonated, and subsequently charged or uncharged, is relevant to the concept of isoelectric point, which is a high-yield MCAT topic. For more information on the protonation and deprotonation of side chains and the concept of isoelectric point, visit this post.)

Acidic Amino Acids - MCAT Biochemistry
Figure 1. Acidic Amino Acids

Basic Amino Acids

There are three basic amino acids: histidine, lysine, and arginine. Histidine has a side chain pKa 6, lysine has a side chain pKa of 10.7, and arginine has a side chain pKa of 12.1. These pKa values, it’s important to note, are those of the conjugate acid. This means that when the surrounding pH is above these pKa’s, these basic side chains will be deprotonated and thus charge-neutral. By contrast, when the pH is below these values, the basic side chains will be protonated and thus positively charged. (Again, amino acid protonation states, and the implication this has for the concept of isoelectric point, is discussed further in this post.)

 

Basic Amino Acids - MCAT Biochemistry
Figure 2: Basic Amino Acids

Polar Amino Acids

The polar amino acids that are relevant for the MCAT are serine (S), threonine (T), asparagine (N), glutamine (Q), tyrosine (Y) and cysteine (C). Notice that all of these amino acids have strong dipole moments in their side chains, but their side chains cannot be charged at any pH.

Polar Amino Acids - MCAT Biochemistry
Figure 3. Polar Amino Acids

Nonpolar Amino Acids

The nonpolar amino acids are alanine (A), glycine (G), isoleucine (I), leucine (L), proline (P), valine (V), phenylalanine (F), tryptophan (W), and methionine (M). All these have side chains that are nonpolar and hydrophobic. Because they tend to cluster together, away from the aqueous solvent present in most cellular environments, their hydrophobicity has a large influence on tertiary structure. 

Non-Polar Amino Acids - MCAT Biochemistry
Figure 4. Non-Polar Amino Acids

This concludes the brief overview of the main way we classify amino acids. The following classifications are additional ways the aforementioned amino acids can also be classified.

Sulfur-Containing Amino Acids

Cysteine (C) and methionine (M) are the two sulfur-containing amino acids. Having a sulfur atom in their structures is a property that has many implications of which the following posts will cover.

Sulfur-Containing Amino Acids - MCAT Biochemistry
Figure 5. Sulfur-Containing Amino Acids

Aromatic Amino Acids

Aromatic amino acids are of interest not only because they are bulky, but also because they serve as precursors for many neurotransmitters. The resonance stabilization present in aromatic rings is also of interest in various experimental techniques. The aromatic amino acids are tyrosine, phenylalanine and tryptophan.

Aromatic Amino Acids - MCAT Biochemistry
Figure 6. Aromatic Amino Acids

Hydroxylated Amino Acids

Amino acids containing hydroxyl groups in their side chains readily participate in phosphorylation reactions –. The three hydroxyl group-containing amino acids are: Tyrosine (Y), serine (S) and threonine (T).

Hydroxylated Amino Acids - MCAT Biochemistry
Figure 7. Hydroxylated Amino Acids

Amino Acids with Unique Properties

A few amino acids are so structurally distinct that they require separate discussion. These are glycine (G), cysteine (C) and proline (P). These amino acids are important because the nature of their structure has implications in peptide and protein structure. And because the structure of proteins correlates to their function, it is important to take a closer look at these three amino acids.

 

Glycine is the only achiral amino acid, as its functional group is a single hydrogen atom. This means that its α-carbon is achiral because it is bound to two identical hydrogen atom substituents. All 19 other amino acids covered in this section are chiral. Additionally, the lack of a bulky R-group allows for significantly easier rotation than any other amino acid. Therefore, glycine is responsible for the flexible regions of peptide chains.

Glycine and Pyrrole - MCAT Biochemistry
Figure 8. Glycine and Pyrrole

Glycine is also a precursor of pyrrole, an important structural component of porphyrins. Porphyrins are a group of extensively conjugated heterocyclic compounds that readily form coordinate covalent (dative) bonds to transition metal cations, such as ferrous ion (Fe2+). The most notable example of such a compound is heme, the prosthetic group of hemoglobin.

Heme - MCAT Biochemistry
Figure 9. Heme

Cysteine is a sulfur-containing amino acid with a thiol group that can form disulfide bonds with other cysteine residues. This allows it to do many things – most importantly, it contributes to the tertiary structure of proteins through the formation of disulfide bonds between non-adjacent amino acids within a protein or peptide. Additionally, because the formation of the disulfide bridge requires oxidation, such peptides can act as powerful reducing agents – a function it serves on a molecule called glutathione (GSH). When oxidized, two molecules of glutathione form a unit called a glutathione dimer (GSSG). Finally, breaking an existing disulfide bond within a protein requires adding a reducing agent such as β-mercaptoethanol – which is relevant in many experimental methods of protein analysis.

Cysteine and Cystine - MCAT Biochemistry
Figure 10. Cysteine and Cystine

Finally, proline is a fascinating amino acid. It is a cyclized amino acid, and as such is also the only amino acid with a secondary amine group (or tertiary when incorporated into a peptide bond). This disrupts common secondary structure motifs and has a significant effect on the secondary structure of proteins by introducing a forced change in angle, a kink, due to its far greater rigidity than most other amino acids.

Proline - MCAT Biochemistry
Figure 11. Proline

Finally, proline is a fascinating amino acid. It is a cyclized amino acid, and as such is also the only amino acid with a secondary amine group (or tertiary when incorporated into a peptide bond). This disrupts common secondary structure motifs and has a significant effect on the secondary structure of proteins by introducing a forced change in angle, a kink, due to its far greater rigidity than most other amino acids.

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