Peptide bond formation template

Glycine + L-alanine → Gly-Ala + H₂O with the planar peptide bond highlighted; aminoacyl-tRNA synthetase activation (aminoacyl-AMP, aminoacyl-tRNA) and peptidyl transfer on the ribosome.

What the template shows

• Two amino acids condense to an amide; in the cell the carboxyl group is first activated on tRNA
• The new C–N bond is the peptide bond (amide)
• Gly-Ala (dipeptide)
• Activation by aminoacyl-tRNA synthetase
• ATP → AMP + PPᵢ: two high-energy bonds spent per amino acid; R = 5′-adenosyl, R′ = tRNA (3′ end)
• alanyl-AMP
• Ala-tRNA
• Peptidyl transfer on the ribosome
• The A-site amino group attacks the P-site ester carbonyl; R = R′ = tRNA
• Gly-tRNA (P site)
• Ala-tRNA (A site)
• Gly-Ala-tRNA (A site)
• tRNA (P site)
• Condensation: –COOH + H₂N– → –CO–NH– + H₂O. In water hydrolysis is favoured, so cells activate the carboxyl group first.
• The peptide bond has partial C=N character (amide resonance): the C(O)–NH unit is planar, C–N is short (≈ 1.32 Å) and almost always trans.
• Peptidyl transferase is the 23S rRNA of the large subunit (a ribozyme); the chain grows from the N- to the C-terminus.
• Cost per peptide bond: 2 ATP equivalents for aminoacylation + 2 GTP for elongation (EF-Tu, EF-G).

Drawn with 72 atoms, 4 arrows, 3 shapes – every one editable in MolDraw.

Sources

• Nelson & Cox, Lehninger Principles of Biochemistry, 8th ed., 2021, ch. 27 Textbook
• Berg, Tymoczko, Gatto & Stryer, Biochemistry, 9th ed., 2019 Textbook
• Voet & Voet, Biochemistry, 4th ed., Wiley 2011 Textbook