Question

A peptide with the primary structure Lys-Arg-Pro-Leu-Ile-Asp-Gly-Ala must be synthesized by the methods developed by Merrifield. Calculate the percentage of the peptides synthesized that will be full length and have the correct sequence if the addition of each amino acid residue is \(96 \%\) efficient. Do the calculation a second time but assume a \(99 \%\) efficiency for each cycle.

Short answer

At 96% efficiency, 80.5% of the peptides are full length; at 99% efficiency, 93.3% are full length.

Step-by-step solution

Understanding the Problem

The problem asks us to calculate the percentage of peptides synthesized that are complete and have the correct sequence. We are given the efficiency levels for each amino acid addition in two scenarios: once with 96% efficiency per step and again with 99% efficiency per step.

Identify the Number of Steps

The peptide sequence given is Lys-Arg-Pro-Leu-Ile-Asp-Gly-Ala, which consists of 8 amino acids. This means there will be 7 coupling steps in the synthesis process because the length of the peptide minus one equals the number of steps needed.

Calculate Overall Efficiency for 96%

The overall efficiency for synthesizing the full-length peptide is the efficiency of each step raised to the power of the number of steps. For a 96% step efficiency: \[(0.96)^7\]

Compute 96% Efficiency Result

Calculate \[(0.96)^7 = 0.805\] which corresponds to 80.5%. This means 80.5% of the synthesized peptides will be full length and have the correct sequence if each step is 96% efficient.

Calculate Overall Efficiency for 99%

Similarly, for a 99% step efficiency: \[(0.99)^7\]

Compute 99% Efficiency Result

Calculate \[(0.99)^7 = 0.933\] which corresponds to 93.3%. This means 93.3% of the synthesized peptides will be full length and have the correct sequence if each step is 99% efficient.

Key concepts

Merrifield synthesis

The Merrifield synthesis, named after its inventor, Bruce Merrifield, is a revolutionary method for synthesizing peptides. This method is often referred to as solid-phase peptide synthesis (SPPS). It involves anchoring the first amino acid of the peptide sequence to a solid support or resin. This allows one to easily remove excess reagents and byproducts by simple washing, which makes the technique highly efficient and scalable.

In Merrifield synthesis, amino acids are added sequentially in the correct order to construct the desired peptide chain. Each amino acid is protected at its amino group and activated at its carboxyl end to ensure precise coupling. After each coupling step, the amino-protecting group is removed to allow for the addition of the next amino acid. This cycle is repeated until the full peptide chain is synthesized.

Solid-phase synthesis has significantly improved the speed and yield of peptide synthesis compared to earlier methods, revolutionizing the production of peptides for research and therapeutic use.

Coupling efficiency

Coupling efficiency is a crucial parameter in peptide synthesis, as it determines the percentage of peptide chains that successfully incorporate the incoming amino acid at each step. It is a measure of how well the desired chemical reaction occurs during each coupling cycle.

A high coupling efficiency means that most of the peptide chains have successfully reacted and incorporated the new amino acid. Factors affecting coupling efficiency include the type of amino acid, the reagents used, and the synthesis conditions like temperature and solvent.

In practical terms, coupling efficiencies of around 99% are considered very high; however, even a slight drop in efficiency can significantly impact the overall yield of the full-length peptide. As seen in the exercise, an efficiency drop from 99% to 96% per step results in a decrease from 93.3% to 80.5% yield over seven cycles. It's important to optimize coupling conditions to achieve the highest possible efficiency, particularly in longer peptide sequences.

Amino acid sequence

An amino acid sequence is the unique order in which amino acids are linked together to form a peptide or protein. The sequence determines the structure and function of the protein, as even a single change in this sequence can drastically alter the protein's properties.

In the context of peptide synthesis, ensuring that the amino acid sequence is assembled correctly is critical. During Merrifield synthesis, each amino acid is added in a specific order, corresponding to its position in the desired peptide chain.

For example, in the peptide sequence Lys-Arg-Pro-Leu-Ile-Asp-Gly-Ala from the exercise, any mistake in the order of these amino acids would result in a peptide with different characteristics and properties. This precision is achieved by carefully planning the sequence of coupling steps and selecting suitable protecting groups and activation reagents to ensure correct assembly.

Biochemistry calculations

Biochemistry calculations play an important role in determining the success of peptide synthesis. These calculations can include determining the overall yield of the synthesis process, which is defined by the efficiency of each step of amino acid addition.

For example, calculating the overall efficiency involves raising the coupling efficiency of a single step to the power of the number of steps. In the exercise provided, with a 96% coupling efficiency for each of the 7 steps, the overall yield is calculated as \((0.96)^7 = 0.805\) or 80.5%. Similarly, with a 99% efficiency, the yield is \((0.99)^7 = 0.933\) or 93.3%.

These calculations help predict the percentage of peptide sequences which are both full-length and correctly sequenced, thus aiding in planning and optimizing synthetic strategies. Improving the efficiency of each step directly results in better yields and helps in the manufacture of peptides for various biochemical applications.