Deep-Dive Guides · Amino Acids, Peptides & Proteins
Amino Acids, Peptides & Proteins — the complete deep dive
This topic is where organic mechanism meets structural biochemistry.
Free extract — the opening section of the guide, in full.
0. How to use this guide — the map
An α-amino acid carries an amino group and a carboxyl group on the same (α) carbon, plus a side chain R that defines its properties. The 20 proteinogenic amino acids are grouped by side-chain character:
| Class | Members (examples) | What it controls |
|---|---|---|
| Nonpolar / hydrophobic | Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, Trp | buried in the protein core; drive folding |
| Polar uncharged | Ser, Thr, Cys, Asn, Gln, Tyr | H-bonding; Ser/Cys are nucleophilic active-site residues |
| Acidic (−) | Asp, Glu (side-chain COOH) | low pI; negative at pH 7 |
| Basic (+) | Lys, Arg, His (side-chain N) | high pI; Lys and Arg are net-positive at pH 7, but His (side-chain pKa ≈ 6.0) is only ~9% protonated there and so is essentially uncharged — which is exactly what makes it the body’s buffer and the acid/base catalyst in enzyme active sites |
The four questions to ask of any problem here: (1) What is the charge state at the given pH (compare pH to each pKa)? (2) What is the pI, and therefore which way does the molecule move in electrophoresis? (3) For synthesis: which C–C or C–N bond is being formed, and is the product racemic? (4) For peptides/proteins: which level of structure (primary sequence, secondary H-bond pattern, tertiary fold, quaternary assembly) is the question about? Answer these and the rest follows.
Read the rest of this guide
The remaining 10 sections — Structure, acid–base behaviour & pI, Synthesis of amino acids, The peptide bond & peptide synthesis, Sequencing — reading a peptide N→C and more — are part of ChemVidya Full Access, along with the other guides, the books, the study notes and 6,000+ practice questions with worked solutions.