Lysine (Lys, K) - Structure, pKa, pI, and Codons
What is lysine and what is its side chain?
Lysine (Lys, K) has the side chain -(CH₂)₄NH₂ - 4-aminobutyl; a primary amine at the epsilon carbon. It is classified as basic (positive at ph 7), carries a positive (+1) charge at pH 7, and has an isoelectric point of 9.74.
| Three-letter code | Lys |
| One-letter code | K |
| Molecular formula | C₆H₁₄N₂O₂ |
| Molecular weight | 146.19 g/mol |
| Residue mass | 128.17 Da |
| Side chain | -(CH₂)₄NH₂ - 4-aminobutyl; a primary amine at the epsilon carbon. |
| Classification | Basic (positive at pH 7) |
| pKa (alpha-COOH) | 2.18 |
| pKa (alpha-NH3+) | 8.95 |
| pKa (side chain NH3+) | 10.53 |
| Isoelectric point (pI) | 9.74 |
| Charge at pH 7 | positive (+1) |
| Essentiality | Essential |
| Hydropathy (Kyte-Doolittle) | -3.9 |
| Configuration | L-form is (S) |
| Codons | AAA, AAG (2) |
Side chain
The R group of lysine is -(CH₂)₄NH₂. 4-aminobutyl; a primary amine at the epsilon carbon. This is what distinguishes it from the other 19 amino acids, since all of them share the same backbone: an alpha carbon bonded to an amino group, a carboxyl group, and a hydrogen.
Ionization and isoelectric point
Lysine has 3 ionizable groups: alpha-COOH (pKa 2.18), alpha-NH3+ (pKa 8.95), side chain NH3+ (pKa 10.53). The isoelectric point is the pH at which the molecule carries no net charge, found by averaging the two pKa values that bracket the neutral species.
pI = (8.95 + 10.53) / 2 = 9.74
Note that this uses the side chain pKa rather than both alpha group values, because the side chain ionizes within the range that brackets the neutral form.
These values are for the free amino acid. Inside a folded protein, the local environment shifts them substantially.
Stereochemistry
The alpha carbon of L-lysine is (S).
Genetic code
2 codons encode lysine: AAA, AAG.
MCAT notes
- Positively charged at pH 7 (side chain pKa 10.53).
- The site of acetylation on histone tails - neutralizing the positive charge loosens DNA binding and activates transcription - as well as methylation and ubiquitination.
- Trypsin cleaves C-terminal to lysine and arginine.
- Purely ketogenic. Also hydroxylated in collagen in a vitamin C dependent step, forming cross-links.
Interactive 3D structure with the R group isolated, a titration curve with a live pH cursor, and flashcards for all 20 amino acids.
View lysine in 3D