3.1 Structure and properties of amino acids

Amino Acid Structure

Basic Components and Zwitterionic Form

Every amino acid shares the same core architecture: an amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom, and a variable side chain (R-group), all attached to a central alpha carbon ($C_\alpha$).

At physiological pH (~7.4), amino acids don't exist in their neutral drawn form. Instead, they exist as zwitterions: the amino group picks up a proton to become $-NH_3^+$, and the carboxyl group loses a proton to become $-COO^-$. The molecule carries both a positive and a negative charge, but the overall net charge is zero.

• Glycine is the simplest amino acid, with just a hydrogen atom as its R-group
• Alanine has a methyl group ($-CH_3$) as its R-group

The zwitterionic form matters because it affects how amino acids behave in solution, how they migrate in an electric field, and how they interact with other molecules.

R-group Diversity and Chirality

The R-group (side chain) is what makes each of the 20 standard amino acids unique. It determines polarity, hydrophobicity, charge, size, and reactivity.

Because the alpha carbon has four different groups attached to it, amino acids are chiral molecules. Chirality means a molecule can't be superimposed on its mirror image, the same way your left hand can't perfectly overlap your right hand. The one exception is glycine, whose R-group is just a hydrogen, making two of the four substituents identical and eliminating chirality.

• The two mirror-image forms are called L-amino acids and D-amino acids
• In the Fischer projection, L-amino acids have the amino group on the left when the carboxyl group points up
• L-amino acids are the form found in virtually all proteins in living organisms
• D-amino acids are rare but do appear in some bacterial cell walls and certain antibiotics (e.g., gramicidin, valinomycin)
• Swapping from L to D configuration in a protein can drastically alter its structure and function because the spatial arrangement of atoms around the alpha carbon changes

Amino Acid Types

Essential and Nonessential Amino Acids

Of the 20 standard amino acids, nine are essential, meaning the human body cannot synthesize them. They must come from your diet:

Nonessential amino acids can be made by the body through metabolic pathways: alanine, asparagine, aspartic acid, glutamic acid, glutamine, glycine, proline, and serine.

A few amino acids are conditionally essential, meaning they become essential under specific physiological circumstances. For example, arginine is conditionally essential during periods of rapid growth, and cysteine becomes essential when methionine intake is low (since cysteine is synthesized from methionine). Tyrosine is similarly conditionally essential because it's synthesized from phenylalanine.

Amino Acid Properties

Isoelectric Point (pI)

The isoelectric point (pI) is the pH at which an amino acid carries a net charge of zero. At this pH, the positive and negative charges on its ionizable groups exactly balance out.

Here's how charge changes with pH:

• pH below pI → the amino acid has a net positive charge (excess protonation of the amino group and any basic side chains)
• pH equal to pI → net charge is zero
• pH above pI → the amino acid has a net negative charge (deprotonation of the carboxyl group and any acidic side chains)

For a simple amino acid with no ionizable side chain (like glycine or alanine), the pI is calculated as the average of the two $pK_a$ values:

$pI = \frac{pK_{a1} + pK_{a2}}{2}$

where $pK_{a1}$ is for the carboxyl group and $pK_{a2}$ is for the amino group.

For amino acids with ionizable side chains, you average the two $pK_a$ values that flank the zwitterionic (net-zero) species. For acidic amino acids like aspartic acid and glutamic acid, you average the two lower $pK_a$ values. For basic amino acids like lysine, arginine, and histidine, you average the two higher $pK_a$ values.

The pI has direct practical applications. In isoelectric focusing, proteins migrate through a pH gradient until they reach the pH matching their pI, where they stop (net charge = zero, no more movement in the electric field). In ion-exchange chromatography, knowing a protein's pI helps you predict whether it will bind to a positively or negatively charged resin at a given buffer pH.