Final answer:
Alpha helices embed in a bilayer due to their amphipathic nature, with hydrophobic amino acid residues aligning within the membrane's core. Using hydropathy plots, hydrophobic alpha-helical domains can be predicted to form integral membrane proteins with functional structures.
Step-by-step explanation:
Alpha helices have the capacity to be embedded in a bilayer because of their amphipathic nature, meaning they possess both hydrophobic and hydrophilic characteristics. Hydrophobic amino acid residues tend to orient themselves towards the fatty acid core of the membrane, while hydrophilic residues face the aqueous environment. The alpha helix's structure, in which every turn has an arrangement of 3.6 amino acid residues, allows for the R groups to protrude outward from the helix chain. This facilitates the sorting of amino acid side chains, such that hydrophobic R groups can be isolated on one side of the helix, favoring their integration into the membrane. Moreover, integral membrane proteins can span the lipid bilayer multiple times with these alpha helices, and interact with other helices to form pores or channels that can transport polar molecules and ions. Ultimately, this leads to their significant role in forming the structure of cells and tissues.
Hydrophobic alpha-helical domains are a hallmark of membrane-spanning proteins, and can be predicted through analysis of a polypeptide's primary structure using a hydropathy plot. Tertiary protein structure and the orientation of alpha helices and beta sheets are influenced by their interactions, which allows the formation of functional protein structures within the cell membrane.