- Instructions: Use the mouse and the buttons to investigate and compare the structures of the two tri-peptides below.
- Nomenclature: The distinctions between "peptides," "polypeptides," and "proteins" are somewhat arbitrary. Usually, peptides refer to small peptide polymers containing one or at most a few peptide bonds. "Polypeptides" refer to longer peptide polymers with numerous peptide bonds. Generally, proteins refer to biologically functional molecules composed of one of more "polypeptide chains." Note that a "trii-peptide" contains 3 amino acid residues but only 2 composed of n amino acid residues contains only n-1 peptides. peptide bonds. Thus, the term "trii-peptide" is a little misleading. In general, a linear polypeptide
- Atom Colors: Atoms are color shaded according to a modified Corey, Pauling, Koltun (CPK) color scheme.
- Conventions: Because of the way polypeptides are synthesized in the ribosome, polypeptide
sequences are always written in the N-to-C direction, where the first amino acid residue in the sequence (AA1) has a free, N-terminal α-amino
group (i.,e. α-NH3+)
and the last amino acid residue in the sequence (AAn) has a free, C-terminal α-carboxyl
group (i.e., α-COO-).
- Chemistry of
peptide synthesis in biological systems: During translation of mRNA (see Translation
Animation) peptides are formed in the ribosome by a condensation reaction between two amino acids
(AA) where the carboxyl group (COO-)
of one AA forms a peptide bond with
the amino group (NH3+)
of a second AA, producing H2O as the leaving group. Once the amino acid is incorporated
into a polypeptide chain, it is referred to as an amino acid
residue.
- AA1 + AA2
 AA1--AA2 (dipeptide): NH3+-CH(R1)-COO- + NH3+-CH(R2)-COO- NH3+-CH(R1)-C(O)-N(H)-CH(R2)-COO- + H2O
|
