Question

A sample genetic code is given below: If an amino acid substitution matrix based on genetic code is derived for sequence alignment and analysis from evolutionary studies, which one of the following is TRUE?

1. Pro is most similar to His

2. Pro is most similar to Thr

3. Gly is most similar to Lys

4. Asp is most similar to Thr

Detailed Explanation

Amino acid substitution matrices are essential tools in sequence alignment, especially in bioinformatics, where they are used to quantify the similarity or dissimilarity between amino acids. These matrices are based on evolutionary studies, which observe how amino acids are substituted in various proteins across different species over time.

Let’s break down each option based on the known similarities and evolutionary relationships between the amino acids:

1. Pro is most similar to His

• Proline (Pro) is a non-polar amino acid with a unique cyclic structure, while Histidine (His) is a polar amino acid with an imidazole ring. Evolutionarily, their substitution is not commonly favored, as they have very different chemical properties, particularly in terms of their ability to form hydrogen bonds or participate in hydrophobic interactions. Therefore, they are not the most similar pair in terms of substitution.

2. Pro is most similar to Thr

• Threonine (Thr) is a polar amino acid, and Proline (Pro) is non-polar. The main similarity lies in their size and their influence on protein structure, especially in secondary structure formation. However, Proline and Threonine are quite different in terms of their side-chain properties. Proline has a unique rigid ring structure that limits its ability to form hydrogen bonds, while Threonine has a hydroxyl group that can form hydrogen bonds. While they might be somewhat similar due to size and structural constraints, they are not the most similar based on substitution matrices.

3. Gly is most similar to Lys

• Glycine (Gly) is the smallest amino acid with a single hydrogen atom as its side chain, while Lysine (Lys) is a basic, positively charged amino acid with a long aliphatic side chain. These two amino acids have very different sizes, charge properties, and structural roles in proteins. Their substitution is not commonly favored, making them not similar in terms of evolutionary substitution patterns.

4. Asp is most similar to Thr

• Aspartic acid (Asp) is a negatively charged amino acid, while Threonine (Thr) is a polar, uncharged amino acid. Both amino acids are relatively small, but they differ significantly in charge and the types of interactions they participate in. However, Aspartic acid and Threonine are sometimes found in similar structural environments in proteins due to their size and polarity. Asp and Thr are often involved in similar biochemical processes, and their substitution can be more tolerated in certain evolutionary contexts, especially in protein regions where charge may not play a central role.

Correct Answer: 4 (Asp is most similar to Thr)

Based on evolutionary studies and the amino acid substitution matrices, Aspartic acid (Asp) is considered most similar to Threonine (Thr). Although they differ in charge, their size and polar nature allow them to be more interchangeable in certain protein contexts. This makes them the most likely pair to be evolutionarily substituted for one another in some cases.

Conclusion

Amino acid substitution matrices derived from genetic code analysis reflect evolutionary similarities based on protein structure, function, and environmental contexts. In this case, Asp (Aspartic acid) and Thr (Threonine) show a higher degree of evolutionary similarity compared to other pairs.