In naming polypeptides, if asparagine is the second peptide from the N terminal, would it be named asparagyl? Would aspartate be aspartyl if it is the second peptide from the N terminal of a polypeptide?
To determine the correct naming of amino acids in polypeptides, you need to consider the modification of the amino acid as it becomes a part of a peptide chain.
When an amino acid is incorporated into a polypeptide chain, its carboxyl group (-COOH) reacts with the amino group (-NH2) of the neighboring amino acid to form a peptide bond. This reaction leads to the formation of a dipeptide, with the loss of a water molecule.
In the process, the carboxyl group of the first amino acid becomes the C-terminal (-COOH) of the dipeptide, while the amino group of the second amino acid becomes the N-terminal (-NH2) of the dipeptide.
Now, concerning the specific amino acids you mentioned:
1. Asparagine:
When asparagine is part of a polypeptide chain, and it is the N-terminal amino acid, it would be named as N-Asparagine or asparagyl, as you correctly mentioned.
2. Aspartate:
In the case of aspartate, if it is the N-terminal amino acid, it would be named as N-Aspartate or aspartyl.
It is important to note that these naming conventions apply specifically to the N-terminal amino acids in a peptide chain. If asparagine or aspartate is present within the chain, not at the N-terminal position, its name will not change.
To summarize, the names would be:
- N-terminal asparagine: N-Asparagine or asparagyl
- N-terminal aspartate: N-Aspartate or aspartyl