Question

Consider the amino acids shown in Figure 20.2 Based on your knowledge of intermolecular forces, indicate which amino acids you would expect to be hydrophilic and which would be hydrophobic. Fxplain your reasoning for each of the amino acids.

Short answer

The hydrophilic amino acids are Asparagine, Aspartic Acid, Glutamine, Glutamic Acid, Histidine, Lysine, Serine, Threonine, Tyrosine, and Arginine. These amino acids have polar or charged groups in their side chains, allowing them to form favorable interactions with water. On the other hand, the hydrophobic amino acids are Alanine, Cysteine, Glycine, Isoleucine, Leucine, Methionine, Phenylalanine, Proline, Tryptophan, and Valine. These amino acids have nonpolar groups in their side chains, causing them to repel water or not interact with it.

Step-by-step solution

Understanding hydrophilic and hydrophobic amino acids

Hydrophilic amino acids are those that have a high affinity for water, due to the presence of polar groups or charged groups in their side chains. Hydrophobic amino acids are those that repel water or do not interact with water, due to the presence of nonpolar groups in their side chains.

Classifying amino acids based on intermolecular forces

Analyze the side chains of the 20 common amino acids and classify them as hydrophilic or hydrophobic. Amino Acids with Hydrophilic Side Chains: 1. Asparagine (Asn / N) – CONH2 (polar due to the amide group) 2. Aspartic Acid (Asp / D) – COOH (polar and acidic due to the carboxyl group) 3. Glutamine (Gln / Q) – CH2CONH2 (polar due to the amide group) 4. Glutamic Acid (Glu / E) – CH2COOH (polar and acidic due to the carboxyl group) 5. Histidine (His / H) – C3H3N2H (polar and basic due to the imidazole ring) 6. Lysine (Lys / K) – CH2CH2CH2CH2NH2 (polar and basic due to the amino group) 7. Serine (Ser / S) – CH2OH (polar due to the hydroxyl group) 8. Threonine (Thr / T) – CH(OH)CH3 (polar due to the hydroxyl group) 9. Tyrosine (Tyr / Y) – CH2C6H4OH (polar due to the phenolic hydroxyl group) 10. Arginine (Arg / R) – CH2CH2CH2NH2 (polar and basic due to the guanidino group) Amino Acids with Hydrophobic Side Chains: 1. Alanine (Ala / A) – CH3 2. Cysteine (Cys / C) – CH2SH 3. Glycine (Gly / G) – H 4. Isoleucine (Ile / I) – CH(CH3)CH2CH3 5. Leucine (Leu / L) – CH2CH(CH3)2 6. Methionine (Met / M) – CH2CH2SCH3 7. Phenylalanine (Phe / F) – CH2C6H5 8. Proline (Pro / P) – CH2CH2CH2NH 9. Tryptophan (Trp / W) – CH2C8H6N 10. Valine (Val / V) – CH(CH3)2 By understanding the nature of amino acids' side chains and their affinity for water or nonpolar environments, we can classify them as hydrophilic or hydrophobic amino acids.

Key concepts

Intermolecular Forces

Intermolecular forces are the forces that act between molecules, influencing their physical and chemical properties. These forces are critical in determining how molecules, like amino acids, interact with each other and with their environment. There are several types of intermolecular forces:

• Van der Waals forces (dispersion forces): These are weak attractions that occur between all molecules, particularly in nonpolar environments.


• Hydrogen bonds: These strong forces occur when hydrogen is bonded to electronegative atoms like oxygen or nitrogen, common in polar molecules.


• Ionic interactions: Occur between charged molecules or ions with opposite charges, playing a role in the structure and stability of proteins.

Understanding these forces helps us explain the behavior of amino acids, as they determine whether amino acids will seek out or repel water—a concept at the heart of classifying them as hydrophilic or hydrophobic.

Hydrophilic Amino Acids

Hydrophilic amino acids are those that have side chains with a strong affinity for water. This is because they typically contain polar or charged functional groups that can form hydrogen bonds or ionic interactions with water.
Here are some examples:

• Asparagine (Asn) and Glutamine (Gln): Both have amide groups that are polar.
• Aspartic Acid (Asp) and Glutamic Acid (Glu): These contain carboxyl groups, making them acidic and polar.


• Histidine (His): With an imidazole ring, it can pick up and release protons, making it polar and basic.

These amino acids are typically found on the exterior of proteins, interacting with the aqueous cellular environment and are crucial for forming stable structures through interactions with water molecules.

Hydrophobic Amino Acids

Hydrophobic amino acids have side chains that avoid water. This is generally due to the presence of nonpolar groups, which cannot interact favorably with water's polar molecules. Instead, they tend to associate with other nonpolar molecules or regions within a protein.
Some typical hydrophobic amino acids are:

• Leucine (Leu), Isoleucine (Ile), and Valine (Val): These have branched aliphatic side chains.


• Phenylalanine (Phe) and Tryptophan (Trp): Contain aromatic rings which are nonpolar.
• Alanine (Ala) and Glycine (Gly): Small, with nonpolar methyl and hydrogen side chains, respectively.

While hydrophobic amino acids are often embedded in the interior of proteins, shielding them from water, they are vital in maintaining protein stability and proper folding.

Side Chains

Amino acid side chains, also known as R groups, are vital for determining the chemical nature and reactivity of amino acids. They are the part of the amino acid structure that varies, giving each amino acid its unique characteristics. There are a variety of side chains:

• Nonpolar side chains: Characterized by hydrocarbons, making them hydrophobic, like those found in Leucine or Valine.


• Polar side chains: Often contain groups such as amides (Asn, Gln), hydroxyls (Ser, Thr, Tyr), which make them hydrophilic.
• Charged side chains: These can be acidic (Asp, Glu) or basic (Lys, Arg) and often participate in ionic interactions with opposite charges.

The characteristics of side chains influence protein folding and function, providing specificity and diversity necessary for myriad biological functions.

Polar and Nonpolar Interactions

The concept of polar and nonpolar interactions is fundamental in biochemistry, especially in understanding how proteins fold and interact with each other. Polar interactions occur when polar molecules or parts of molecules attract each other due to opposite charges.

• Polar interactions: Predominantly include hydrogen bonding and ionic interactions. They are crucial for forming secondary and tertiary structures of proteins.
• Nonpolar interactions: Also known as hydrophobic interactions, these occur when nonpolar molecules avoid aqueous environments, clustering together instead. This drives the formation of lipid bilayers and the folding of protein interiors.

The balance between these interactions influences protein structure and stability, dictating how they function. Understanding these interactions helps in predicting protein behaviors and reactivities in different environments.