Amino Acid
An amino acid is an organic molecule that contains both an amino group (–NH2) and a carboxyl group (–COOH) attached to the same central (alpha) carbon, along with a variable side chain (R group) that determines the identity and properties of each amino acid. There are 20 standard amino acids encoded by the genetic code that serve as the building blocks of proteins. Amino acids differ in polarity, charge, size, and chemical reactivity, which directly determines protein structure and function.
Key Formula
H2N-CH(R)-COOH (general amino acid structure; R = variable side chain)
LaTeX: \text{H}_2\text{N}\text{-}\underset{\displaystyle|}{{\overset{\displaystyle R}{\text{C}}}\text{H}}\text{-COOH}
| Symbol | Meaning | Unit |
|---|---|---|
| R | Side chain (distinguishes each of the 20 amino acids) | — |
| –NH2 | Amino group (basic, accepts proton) | — |
| –COOH | Carboxyl group (acidic, donates proton) | — |
| Cα | Alpha carbon (chiral centre in all except glycine) | — |
Worked Example
Problem
Alanine has a pKa of 2.35 (–COOH) and 9.69 (–NH3+). Calculate the isoelectric point (pI) of alanine.
Solution
Step 1: The isoelectric point pI is the pH at which alanine has no net charge (zwitterion form is dominant). Step 2: For a simple amino acid (no ionisable side chain), pI = (pKa1 + pKa2) / 2. Step 3: pI = (2.35 + 9.69) / 2 = 12.04 / 2 = 6.02. Step 4: At pH 6.02, alanine exists predominantly as +H3N-CH(CH3)-COO– (the zwitterion).
Answer
pI of alanine = 6.02
Classification of the 20 Standard Amino Acids
| Category | Examples | Side Chain Character | Role in Proteins | pI Range |
|---|---|---|---|---|
| Nonpolar, aliphatic | Gly, Ala, Val, Leu, Ile | Hydrophobic | Core packing | 5.97–6.02 |
| Aromatic | Phe, Tyr, Trp | Hydrophobic/polar | Core packing, UV absorption | 5.48–5.89 |
| Polar, uncharged | Ser, Thr, Cys, Asn, Gln | Hydrophilic | H-bonding, active sites | 5.07–6.30 |
| Positively charged | Lys, Arg, His | Basic, cationic at pH 7 | Salt bridges, DNA binding | 7.59–10.76 |
| Negatively charged | Asp, Glu | Acidic, anionic at pH 7 | Salt bridges, enzyme catalysis | 2.77–3.22 |
| Special | Pro, Met | Cyclic/S-containing | Helix disruption, redox | 5.74–5.97 |
Interactive Tools
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Related Terms
Peptide Bond
A peptide bond is a covalent amide linkage formed between the carboxyl group (–COOH) of one amino acid and the amino group (–NH2) of another, with the elimination of a water molecule in a condensation reaction. The resulting –CO–NH– bond has partial double bond character due to resonance delocalisation of the nitrogen lone pair into the carbonyl, making it planar and restricting rotation around the C–N bond. Peptide bonds are the primary covalent linkages in all protein chains.
Protein Structure
Protein structure refers to the hierarchical three-dimensional arrangement of a protein, described at four levels: primary (sequence of amino acids), secondary (local folding into alpha helices and beta sheets), tertiary (overall 3D fold of a single polypeptide), and quaternary (assembly of multiple polypeptide subunits). The structure of a protein is intimately linked to its function, and alterations in structure — through mutation, denaturation, or misfolding — can lead to loss of function or disease. Determining and predicting protein structure is one of the central challenges of biochemistry and structural biology.
IUPAC Nomenclature
IUPAC nomenclature is the systematic method for naming chemical compounds, developed and maintained by the International Union of Pure and Applied Chemistry (IUPAC). For organic compounds, it provides an unambiguous, internationally recognised name based on the longest carbon chain (parent chain), substituents, and functional groups, enabling chemists worldwide to communicate compound structures without ambiguity. The rules cover alkanes, alkenes, alkynes, halides, alcohols, carboxylic acids, and all other organic functional groups.
The term combines 'amino' (from ammonia, NH3) and 'acid' (from Latin 'acidus', sour). The first amino acid, asparagine, was isolated in 1806 by French chemists Vauquelin and Robiquet from asparagus juice. The name 'amino acid' became standard in the late 19th century as the class of compounds was systematically characterised.