Amino Acids

Amino acids are the fundamental building blocks of proteins, small organic molecules that share a common structural core: a central carbon atom (the α-carbon) bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen atom, and a distinctive side chain called the R-group. It is the identity of the R-group that distinguishes each of the 20 standard amino acids found in living organisms, giving them unique chemical properties such as polarity, charge, and reactivity. In aqueous solution at physiological pH (around 7.4), amino acids exist predominantly as zwitterions — molecules that carry both a positive and a negative charge simultaneously yet have no overall net charge. This dual-charged form arises because the carboxyl group donates a proton to the amino group: the –COOH becomes –COO⁻ (carboxylate) and the –NH₂ becomes –NH₃⁺ (ammonium). Understanding the zwitterionic form is essential for explaining the high water solubility, relatively high melting points, and the acid–base behaviour of amino acids. From a nutritional and biochemical standpoint, amino acids are classified as either essential or non-essential. Essential amino acids cannot be synthesised by the human body in sufficient quantities and must be obtained through dietary intake, whereas non-essential amino acids can be biosynthesised from metabolic intermediates. This classification has direct implications for human health, protein quality assessment in food science, and the design of clinical nutrition products.

Key takeaways
  • General Structure of an Amino Acid
  • Formation of the Zwitterion
  • Isoelectric Point (pI)
  • Essential vs Non-Essential Amino Acids
  • Acid–Base Titration and the Henderson–Hasselbalch Equation

General Structure of an Amino Acid

Every standard amino acid has the molecular formula H₂N–CHR–COOH, where R represents the side chain. The α-carbon is a chiral centre in all amino acids except glycine (where R = H), meaning they exist as L- and D-enantiomers. Almost all naturally occurring amino acids in proteins are the L-form. The R-groups range from a simple hydrogen (glycine) to complex aromatic rings (phenylalanine, tryptophan), sulfur-containing chains (cysteine, methionine), or charged ionic groups at physiological pH (lysine, aspartate).

Formation of the Zwitterion

In water, the carboxyl group of an amino acid is a weak acid (pKₐ ≈ 2.0–2.4) and the ammonium group is a weak acid (pKₐ ≈ 9.0–10.5). At neutral pH, which lies between these two pKₐ values, the carboxyl group is fully deprotonated (–COO⁻) and the amino group is fully protonated (–NH₃⁺). The resulting species carries a positive charge on nitrogen and a negative charge on oxygen; overall charge = 0. This is the zwitterionic form. If acid is added (low pH), the carboxylate picks up a proton to give –COOH and the molecule becomes cationic (+1). If base is added (high pH), the ammonium loses a proton to give –NH₂ and the molecule becomes anionic (−1).

Isoelectric Point (pI)

The isoelectric point (pI) is the specific pH at which an amino acid (or protein) carries zero net charge and therefore does not migrate in an electric field. For a simple amino acid with only two ionisable groups, pI is calculated as the arithmetic mean of the two flanking pKₐ values: pI = (pKₐ1 + pKₐ2) / 2. For example, alanine has pKₐ1 = 2.34 (–COOH) and pKₐ2 = 9.69 (–NH₃⁺), giving pI = (2.34 + 9.69) / 2 = 6.02. Amino acids with ionisable R-groups (e.g., aspartate, lysine, histidine) have three pKₐ values, and pI is calculated using the two pKₐ values that flank the neutral zwitterion. At its pI, an amino acid has minimum solubility and maximum aggregation tendency, which is exploited in isoelectric focusing — a laboratory technique used to separate proteins.

Essential vs Non-Essential Amino Acids

Of the 20 standard amino acids, nine are classified as essential for humans: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine (remembered by the mnemonic 'His ILe LeU LyS MeT PheT TrP Val' or 'PVT TIM HaLL'). These cannot be synthesised de novo by human metabolic pathways in adequate amounts. The remaining eleven — alanine, arginine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine — are non-essential under normal conditions, though some (arginine, cysteine, tyrosine) become conditionally essential during illness, growth spurts, or metabolic stress. A complete protein source (e.g., eggs, meat, soy) supplies all nine essential amino acids, while incomplete protein sources (e.g., most plant proteins) lack or are low in one or more.

Acid–Base Titration and the Henderson–Hasselbalch Equation

The protonation state of each ionisable group at any given pH can be predicted using the Henderson–Hasselbalch equation: pH = pKₐ + log([A⁻]/[HA]). When pH = pKₐ, the concentrations of protonated and deprotonated forms are equal. As pH rises above pKₐ, the deprotonated form dominates; as pH falls below pKₐ, the protonated form dominates. For a titration curve of glycine (pKₐ1 = 2.35, pKₐ2 = 9.78), there are two buffering regions centred at each pKₐ and a flat plateau at pI = 6.07 corresponding to the zwitterion form. This titration behaviour is the experimental basis for determining pI values.

The Key Equation

pI=pKa1+pKa22pI = \frac{pK_{a1} + pK_{a2}}{2}
  • pI — Isoelectric point (dimensionless (pH units)): The pH at which the amino acid carries zero net electrical charge and exists predominantly as the zwitterion.
  • pK_{a1} — First acid dissociation constant (log scale) (dimensionless): The pKₐ of the α-carboxyl group (–COOH), typically in the range 2.0–2.4 for standard amino acids.
  • pK_{a2} — Second acid dissociation constant (log scale) (dimensionless): The pKₐ of the α-ammonium group (–NH₃⁺), typically in the range 9.0–10.5 for standard amino acids.

Worked Example

Problem. Aspartate (aspartic acid) has three ionisable groups with the following pKₐ values: pKₐ1 = 1.88 (α-carboxyl), pKₐ2 = 3.65 (side-chain carboxyl), pKₐ3 = 9.60 (α-ammonium). (a) Identify which form of aspartate predominates at pH 7.4. (b) Calculate the isoelectric point of aspartate.

pI=pKa1+pKa22=1.88+3.652=2.77pI = \frac{pK_{a1} + pK_{a2}}{2} = \frac{1.88 + 3.65}{2} = 2.77

Answer. At pH 7.4, aspartate carries a net charge of −1 (anionic form). The isoelectric point of aspartate is pI = 2.77, meaning it is negatively charged at physiological pH and would migrate toward the anode in electrophoresis.

Figure
Diagram
Amino Acid Zwitterion Formation and pH-Dependent ChargepH < pKa1 (Cationic, +1)e.g. pH < 2H₃N⁺|H—C—R|COOHNet charge: +1Zwitterion at pI (Neutral, 0)e.g. pH ≈ 6 (alanine)H₃N⁺|H—C—R|COO⁻Net charge: 0pH > pKa2 (Anionic, −1)e.g. pH > 10H₂N|H—C—R|COO⁻Net charge: −1+H⁺ / −OH⁻−H⁺ / +OH⁻Titration Curve of Glycine (pKa1=2.35, pKa2=9.78, pI=6.07)1270pHEquivalents of OH⁻ added →pH 7pKa1=2.35pKa2=9.78pI=6.07
Origins · 1 minEmil Fischer and how this was discovered
EF
Emil Fischer
1852–1919 · German

Emil Fischer was awarded the Nobel Prize in Chemistry in 1902 for his pioneering work on sugars and purines, but he made equally transformative contributions to amino acid and protein chemistry. Fischer developed the concept of the peptide bond — the amide linkage between amino acids — and in 1907 synthesised the first polypeptide chain (an 18-amino-acid peptide), providing the first experimental evidence that proteins are linear polymers of amino acids joined by peptide bonds. His 'lock-and-key' model of enzyme–substrate specificity remains a foundational concept in biochemistry. Fischer deliberately avoided working on explosives research during World War I and reportedly said he preferred to die of the chemicals in his own laboratory than those on a battlefield. He suffered severe health problems later in life from chronic exposure to phenylhydrazine, one of the reagents he used extensively in his carbohydrate research.

  • Peptide Bonds and Primary Protein Structure — Amino acids are linked together by peptide bonds (–CO–NH–) through condensation reactions to form polypeptide chains. Understanding the chemical nature of this bond is the direct next step after mastering amino acid structure.
  • Protein Secondary, Tertiary, and Quaternary Structure — The R-group properties of individual amino acids (polarity, charge, size) directly determine how polypeptide chains fold into α-helices, β-sheets, and three-dimensional globular or fibrous structures.
  • Weak Acids, Bases, and Buffer Systems — The zwitterion concept and isoelectric point calculations rely directly on the Henderson–Hasselbalch equation and the behaviour of weak acid/conjugate base pairs, core topics in acid–base chemistry.
  • Enzyme Structure and Catalysis — Enzymes are proteins whose catalytic activity depends critically on specific amino acids in the active site. The charge states and nucleophilicity of R-groups such as serine, histidine, and aspartate drive catalytic mechanisms.