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Chapter 6: Problem 3

Discuss the potential contributions to hydrophobic and van der Waals interactions and ionic and hydrogen bonds for the side chains of Asp, Leu, Tyr, and His in a protein.

Short Answer

Expert verified
Aspartate (Asp) can engage in ionic interactions due to its negative charge and form hydrogen bonds. Leucine (Leu) contributes to hydrophobic interactions due to its non-polar nature and to van der Waals interactions. Tyrosine (Tyr) can form hydrogen bonds due to its hydroxyl group, contribute to hydrophobic interactions, and participate in van der Waals interactions. Histidine (His) can engage in both ionic interactions and hydrogen bonds and participate in hydrophobic and van der Waals interactions.

Step by step solution

01

Identify the properties of Aspartate (Asp)

Aspartate is a polar and negatively charged (at physiological pH) amino acid due to its carboxyl side chain. Thus, Aspartate can form ionic interactions with positively charged side chains and can also form hydrogen bonds.
02

Identify the properties of Leucine (Leu)

Leucine, with its aliphatic side chain, is a non-polar and hydrophobic amino acid. It prefers to stay within the protein core, away from the aqueous environment, thus contributing to hydrophobic interactions. Also, this side chain can participate in van der Waals interactions.
03

Identify the properties of Tyrosine (Tyr)

Tyrosine, having a phenolic side chain, is a polar amino acid. The presence of a hydroxyl group on the phenolic ring allows it to form H-bonds, while the aromatic ring can contribute to hydrophobic interactions. Additionally, van der Waals interactions are possible due to the sizable aromatic ring.
04

Identify the properties of Histidine (His)

Histidine, having an aromatic imidazole side chain, is a polar and basic amino acid. It can form both ionic interactions due to its positive charge under physiological conditions and hydrogen bonds due to the presence of nitrogen atoms in the imidazole ring. Also, hydrophobic and van der Waals interactions are possible due to the bulkiness of the imidazole ring.

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Most popular questions from this chapter

Choose any three regions in the Ramachandran plot and discuss the likelihood of observing that combination of \(\phi\) and \(\psi\) in a peptide or protein. Defend your answer using suitable molecular models of a peptide.

Two polypeptides, \(A\) and \(B\), have similar tertiary structures, but \(A\) normally exists as a monomer, whereas \(\mathrm{B}\) exists as a tetramer, \(\mathrm{B}_{4}\) What differences might be expected in the amino acid composition of A versus B?

It is often observed that Gly residues are conserved in proteins to a greater degree than other amino acids. From what you have learned in this chapter, suggest a reason for this observation.

Imagine that the dimensions of the alpha helix were such that there were exactly 3.5 amino acids per turn, instead of \(3.6 .\) What would be the consequences for coiled-coil structures?

A new protein of unknown structure has been purified. Gel filtration chromatography reveals that the native protein has a molecular weight of 240,000 , Chromatography in the presence of \(6 M\) guanidine hydrochloride yields only a peak for a protein of \(M\) \(60,000 .\) Chromatography in the presence of \(6 \mathrm{M}\) guanidine hydrochloride and \(10 \mathrm{m}\) M \(\beta\) -mercaptoethanol yields peaks for proteins of \(M, 34,000\) and \(26,000 .\) Explain what can be determined about the structure of this protein from these data.
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