Chapter 6

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.

Pro is the amino acid least commonly found in \(\alpha\) -helices but most commonly found in \(\beta\) -turns, Discuss the reasons for this behavior.

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.

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.

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.

Which amino acids would be capable of forming H bonds with a lysine residue in a protein?

Poly-L-glutamate adopts an a-helical structure at low pH but becomes a random coil above pH \(5 .\) Explain this behavior.

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?