Organic Chemistry: Concepts and Applications - Headley Allan D. 2020

Synthetic Polymers and Biopolymers
20.12 Primary Structure and Properties of Peptides

Amino acids are bonded to each other via peptide bonds (also called amide bonds) to form peptides. Shown below is a portion of a peptide that contains four amino acids, in which the peptide bonds are indicated.

Image

Often times, the three-letter abbreviation is used to indicate different amino acids of the peptide; the dash between the amino acids indicates the peptide bond. Thus, Ala-Cys-Gly represents a tripeptide containing the amino acids: alanine, cysteine, and glycine.

Problem 20.12

With the aid of Table 20.2, give the structure of the tripeptide: Ala-Cys-Gly.

The backbone of proteins consists of repeating units of amino acids. To determine the individual acid residues, two tasks must be accomplished: (i) identification of the amino acids that are present and (ii) identification of the sequence of the amino acids of the peptide.

20.12.1 Identification of Amino Acids of Peptides

To determine the type amino acids that are present in a peptide, hydrolysis of the amide bonds can be accomplished. Reaction (20-45) shows the hydrolysis of a dipeptide.

(20-45)Image

After the hydrolysis, the individual amino acids must be separated and identified. The mixture of amino acids can be separated by column chromatography. Once separated, the identification of the amino acids of the above dipeptide, for example, can be accomplished by spectroscopy as discussed in Chapter 13. The other challenge now becomes the determination of the sequence of the amino of the original peptide and will be covered in the next section.

20.12.2 Identification of the Amino Acid Sequence

Based on the two amino acids determined from the hydrolysis reaction of the peptide shown above, there are two possible peptides that could give the results shown for a hydrolysis reaction.

Image

The terminal amino acids of a peptide can be determined since they react differently due to the presence of the different functional groups, the amine and carboxylic acid functionalities. The N-terminal has an amino group, while the C-terminal has a carboxylic acid functionality. Frederick Sanger devised a method to detect the N-terminal amino acid of peptides. The reaction with peptide 1 is shown in Reaction (20-46).

(20-46)Image

The hydrolysis of the product of Reaction (20-46) is shown below in Reaction (20-47).

(20-47)Image

Whereas the reaction of the Sanger reagent with peptide 2 gives a different product, as shown in Reaction (20-48).

(20-48)Image

The hydrolysis of the product of Reaction (20-48) is shown in Reaction (20-49).

(20-49)Image

The resulting hydrolysis of the peptide that has the labeled dinitrobenzene will give an indication of the N-terminal amino acid.

The Edman's reagent is another reagent that is often used to determine the N-terminal amino acid of a peptide. This reaction is used to determine the terminal amino end of a peptide and was discovered by Pehr Victor Edman, a Swedish biochemist, in 1952. The reaction is shown in Reaction (20-50).

(20-50)Image

Note that the N-terminal of the dipeptide has a thiourea label attached. The reaction of the product thiourea with trifluoroacetic acid (TFA) and heat results in hydrolysis of the amide bond giving rise to a thiazolinone of the N-terminal amino acid and the other amino acid of the dipeptide as shown in Reaction (20-51).

(20-51)Image

The thiazolinone is then hydrolyzed in acidic aqueous solution and undergoes a rearrangement to give a phenylthiahydantoin (PTH) as shown in Reaction (20-52).

(20-52)Image

Identification of the PHT will indicate the structure of the N-terminal amino acid.

Problem 20.13

Give the structures of the products of the reaction of the tri-peptide from Problem 20.12 with the Edman's Reagent, followed by hydrolysis.

After the identification of the N-terminal amino acid, the other task is to determine the amino acid sequence of the peptide. There are certain chemicals and enzymes that will cleave specific peptide bonds depending on the amino acids that make up the peptide bond. For example, trypsin, which is an intestinal digestive enzyme, specifically hydrolyses polypeptides at the carbonyl end of arginine and lysine. With this method, a segment of a peptide that has these adjacent amino acid residues can be determined. There are other enzymes that will perform similar cleavages, but at peptide bonds that have different amino acid residues. With this information, scientists can determine the actual sequence and type of amino acid in each peptide, no matter how many amino acids that are present in the peptide.