Question

1. For each polypeptide sequence listed, choose from the options given below to indicate which
secondary structure the sequence is most likely to form upon folding. The nonpolar amino acids
are italicized. Explain your choice(s).

A. Leu-Gly-Val-Leu-Ser-Leu-Phe-Ser-Gly-Leu-Met-Trp-Phe-Phe-Trp-Ile
B. Leu-Leu-Gln-Ser-Ile-Ala-Ser-Val-Leu-Gln-Ser-Leu-Leu-Cys-Ala-Ile
C. Thr-Leu-Asn-Ile-Ser-Phe-Gln-Met-Glu-Leu-Asp-Val-Ser-Ile-Arg-Trp

amphipathic α helix hydrophilic α helix
hydrophobic α helix amphipathic β sheet
hydrophilic β sheet

Answer 1

Look for patterns. These secondary structures are just that: patterns.

One key features of a beta sheet is that the side chains on successive amino acids poke out (very scientific terminology) on alternating sides of the beta sheet. If all the residues in the beta sheet are hydrophilic, you will get a hydrophilic beta sheet; if alternating residues are hydrophilic and hydrophobic and they stick out on alternating sides, then one side of the sheet will be made of entirely hydrophilic residues and the other side of the sheet will be made of entirely hydrophobic residues. So the sheet overall will be hydrophobic.

One key feature of the alpha helix is that it takes roughly seven residues to complete one winding of the sheet. So if three residues are hydrophobic they will wind up roughly on the same side of the helix. And if the next four residues are hydrophilic, they will end up on roughly the opposite side of the helix. So again you get an amphipathic molecule...

I leave it to you (or someone else) to work out out how to distinguish between how to tell alpha helices from beta sheets.