Question

After undergoing complete hydrolysis, a polypeptide yields the following amino acids: Ala, Gly, Lys, Ser, Phe. Partial hydrolysis yields the following fragments: Ala-Lys-Ser, Gly-Phe-Gly, Ser-Gly, Gly-Phe, Lys-Ser-Gly. An experiment using a marker establishes that Ala is the N-terminal amino acid. (a) Establish the amino acid sequence in this polypeptide. (b) What is the name of the polypeptide?

Short answer

The amino acid sequence of the polypeptide is Ala-Lys-Ser-Gly-Phe-Gly.

Step-by-step solution

Determine the N-terminal

The experiment using a marker establishes that Ala is the N-terminal amino acid. Therefore, the sequence will start with Ala.

Identify the subsequent sequence

The partial hydrolysis suggests that Ala is followed by Lys and then Ser, giving us the following sequence: Ala-Lys-Ser. Note that the Lys-Ser-Gly fragment can be appended at the end based on only one fragment Ala-Lys-Ser containing Lys-Ser pair, and Ser is also succeeded by Gly in one of the fragments. Our sequence becomes Ala-Lys-Ser-Gly.

Complete the sequence

The remaining fragments Gly-Phe-Gly and Gly-Phe suggest that the next two amino acids will be Phe-Gly as Gly-Phe pair repeats twice. Therefore, the final amino acid sequence becomes: Ala-Lys-Ser-Gly-Phe-Gly.

Naming the Polypeptide

Polypeptides are usually referred to by their amino acid composition in the sequence, and are not typically given a distinct name. In this case, the polypeptide would be referred to by its amino acid composition sequence: Ala-Lys-Ser-Gly-Phe-Gly.

Key concepts

Polypeptide Hydrolysis

Polypeptide hydrolysis is a process that breaks down proteins into their constituent amino acids. This is achieved by cleaving the peptide bonds that hold the amino acids together.
During hydrolysis, polypeptides are treated with water, often in the presence of enzymes or acidic conditions, which leads the peptide bonds to break.
Complete hydrolysis results in the release of all amino acids present in the protein, providing a full profile of the amino acids contained in the original polypeptide.

• This method is crucial for establishing the overall amino acid composition of a protein.
• Understanding hydrolysis lets scientists sequence the amino acids, which helps in identifying functional properties of proteins.
• Hydrolysis is also a key step in studying protein structure and function, as it breaks down complex arrangements into simpler, more manageable fragments.

N-terminal Amino Acid Identification

The N-terminal amino acid is the first amino acid in a polypeptide chain, characterized by a free amino group (NH\(_2\)). Determining the N-terminal is essential in understanding the structure and sequencing of polypeptides.
In the exercise above, Ala is identified as the N-terminal amino acid.
This was established using a specific marker which typically reacts with the free amino group at the N-terminal.

• Finding the N-terminal provides a starting point for deducing the rest of the sequence.
• It helps in distinguishing between different possible sequences of amino acids in the polypeptide.
• Determining the N-terminal aids in aligning sequences when trying to reconstruct longer peptide chains from fragments.
• Accurate identification is crucial for experimental techniques that rely on sequence data, like protein synthesis and antibody production.

Fragment Analysis

Fragment analysis involves breaking down polypeptides into smaller sequences or fragments to deduce the overall sequence of amino acids. The partial hydrolysis of polypeptides provides these fragments that can be analyzed in a stepwise manner.
In the given problem, fragments obtained from partial hydrolysis such as Ala-Lys-Ser, Gly-Phe-Gly, and others were analyzed to determine the sequence order.

• This process involves matching overlapping sequences in different fragments to establish continuity in the sequence.
• It requires careful observation to ensure all fragments align correctly with one another based on shared pairs of amino acids.
• The repetition of specific amino acids or dipeptides in different fragments helps confirm the connectivity and sequence of amino acids.
• Analyzing fragments is essential for understanding not just the sequence but sometimes the specific function or characteristic properties of the polypeptide.