You are performing site-directed mutagenesis to test predictions about which residues are essential for a protein's function. Which of each pair of amino acid substitutions listed below would you expect to disrupt protein function the most?

A. Val replaced by Ala or Phe
B. Lys replaced by Asp or Arg
C. Gln replaced by Glu or Asn
D. Pro replaced by His or Gly

A. Phe. Three of them are non polar. Phe is larger than others, introduce a greater sterical clash.

B. Asp. Lys and Arg are positively charged. Asp is negatively charged.
C. Glu. Gln and Asn are polar side chains. Glu is negatively charged.
D. His. Pro and Gly are non polar. His is basic.

A. Phe

B. Arg
C. Asn
D. His

A. Val replaced by Ala or Phe:

The substitution of Val with Ala would have the least disruptive effect since both amino acids are nonpolar and similar in size. On the other hand, the substitution of Val with Phe, an aromatic amino acid, may have a greater disruptive effect as it introduces a bulkier and aromatic side chain.

B. Lys replaced by Asp or Arg:
The substitution of Lys with Asp would be expected to have the most disruptive effect. Lysine is a positively charged amino acid, while aspartic acid (Asp) is negatively charged. This change in charge could significantly alter the protein's structure and function. On the other hand, replacing Lys with Arg, another positively charged amino acid, may have a less disruptive effect since the positive charge is maintained.

C. Gln replaced by Glu or Asn:
The substitution of Gln with Glu would be expected to have the most disruptive effect. Both amino acids are polar and have similar properties, but Glu carries a negatively charged side chain, which could alter the protein's structure and function. The substitution of Gln with Asn, a similar amino acid with an uncharged side chain, may have a less disruptive effect.

D. Pro replaced by His or Gly:
The substitution of Pro with His would be expected to have the most disruptive effect. Proline has a unique structure with a rigid cyclic side chain, while histidine (His) has a bulky and positively charged side chain. This change in structure and charge could significantly disrupt the protein's function. On the other hand, replacing Pro with Gly, a small and flexible amino acid, may have a less disruptive effect since Gly can accommodate various conformations.

To determine which amino acid substitutions would most likely disrupt protein function, you should consider the properties and characteristics of the amino acids involved. Here is an analysis of each pair:

A. Val (Valine) is a nonpolar, hydrophobic amino acid. Both Ala (Alanine) and Phe (Phenylalanine) are also nonpolar, with Ala being smaller and Phe being larger. Since they have similar properties, both substitutions are unlikely to have a significant impact on protein function. However, the substitution of Phe, being larger, might introduce steric hindrance and slightly affect protein structure.

B. Lys (Lysine) is a positively charged amino acid, whereas Asp (Aspartic acid) is negatively charged, and Arg (Arginine) is also positively charged. The substitution of Lys with Asp would greatly change the charge distribution and potentially disrupt protein function. On the other hand, replacing Lys with Arg, which has a similar charge and size, is less likely to have a major impact on protein function.

C. Gln (Glutamine) is polar, uncharged, and neutral. Replacing Gln with Glu (Glutamic acid), which is also polar but negatively charged, could lead to a significant change in the charge distribution and alter protein function. Substituting Gln with Asn (Asparagine), a polar, uncharged amino acid with similar properties, would have less impact on protein function.

D. Pro (Proline) is unique due to its rigid cyclic structure. Substituting it with His (Histidine), an aromatic amino acid with a basic side chain, could introduce conformational changes in the protein and potentially disrupt its structure and function. In contrast, substituting Pro with Gly (Glycine), the smallest and most flexible amino acid, is unlikely to have a significant effect on protein function.

In summary:

A. Val replaced by Ala: Not likely to disrupt function significantly
A. Val replaced by Phe: Might slightly affect protein structure due to steric hindrance
B. Lys replaced by Asp: Likely to disrupt function significantly
B. Lys replaced by Arg: Less likely to disrupt function significantly
C. Gln replaced by Glu: Likely to disrupt function significantly
C. Gln replaced by Asn: Less likely to disrupt function significantly
D. Pro replaced by His: Likely to disrupt function significantly
D. Pro replaced by Gly: Not likely to disrupt function significantly