Structure, primary carboxyl terminus

Closer examination of 124 shows that there is one carboxyl group on one end (the carboxyl terminus, or C-terminus) of the peptide and there is an amino group at the other end (the amino terminus, or N-terminus). In the case of 124, an alanine residue occupies the N-terminus and a histidine residue occupies the C-terminus. By convention, the N-terminus is always drawn on the left and the C-terminus is drawn on the right. This is an important convention because when ala-val-ser-leu-ala-phe-glu-met-his is read for 124, it indicates that alanine is the N-terminus and histidine is the C-terminus. The order in which the amino acids are connected together is called the primary structure of a peptide. 

The specific sequence of amino acids of which the polypeptide is made is called the primary structure, and its formation is controlled by that piece of deoxyribonucleic acid (DNA) (Chapter 14) that dictates, through the genetic code vide infra), which amino acid the machinery (e.g., the ribosome [about which more will be said later]) that joins them is to use and in what order the amino acids are to be combined. In principle, the ribosome could build a linear chain from right to left or left to right, so, by convention, peptides are written with the N-terminal amino acid to the left and the carboxylate terminus on the right. 

In a protein the amino acids are joined together in a linear order by amide linkages, also known as peptide bonds. The sequence of the covalently linked amino acids is referred to as the primary level of structure for the protein. In writing the sequence of amino acids in a chain, it is conventional to orient the chain so that the amino acid on the left is the one with a free amino group on its a-carbon, while the last amino acid on the right is the one whose a-carbon carboxylate is free. In other words, the amino- or N-terminus of the peptide chain is written on the left, and the carboxyl-or C-terminus is written on the right. One more convention the term backbone for a protein refers to the series of covalent bonds joining one a-carbon in a chain to the next a-carbon. 

The sequence of amino acids in the polymer, from the free amino- or N-terminus to the free carboxyl- or C-terminus, is called the primary (1°) structure of a protein. This sequence is dictated by the genetic code. 

The primary structure was assessed by peptide mapping and N- and C-terminal sequencing. N-terminal sequence analysis showed that a single sequence was detected, MKAIFVLNAA, which corresponds exactly to the first 10 amino acids at the N terminus of P40 as predicted from the DNA sequence. Reverse phase HPLC analysis of a digestion of P40 with a lysine-specific endopeptidase, i.e. endoproteinase Lys-C, was used for identification and primary structure confirmation (Fig. 9). Endoproteinase Lys-C hydolyzes peptide bonds at the carboxylic side of lysine residues. The seventeen peaks resolved were characterized by mass spectrometry, allowing the confirmation of 99 % of the primary sequence. 

An ordered list of the amino acids from the N-terminus (where an amino group remains) to the carboxylic acid terminus (where a carboxylate remains) that also includes bridges across the structure created by sulfur-sulfur bonds from cysteine to cysteine is called the primary structure. The secondary structure of a peptide usually refers to repeating units that give rise to coils or ribbons or other repeating structural variants, while the tertiary structure consists of all of the contributions to the three-dimensional representation. When two or more polypeptide subunits are present in the protein, their relationship is called a quaternary structure. 

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