Practice question

Stabilization of transmembrane segments inside bilayer originates from hydrophobic effect plus van der Waals packing. Sec61 translocon provides aqueous pore laterally gated allowing nascent hydrophobic sequence to partition directly into lipid phase assessed by apparent free energy scale of Hessa and von Heijne measuring contribution per residue leucine minus zero point five six kilocalories, arginine positive two point five kilocalories. Burying non-polar side chains of leucine isoleucine valine phenylalanine methionine avoids forcing water to form ordered clathrate cages around them, releasing water to bulk increasing system entropy and providing favorable free energy. Once inserted, side chain interactions with surrounding acyl chains and annular shell lipids contribute additional stabilization minimizing hydrophobic mismatch where thickness adjusts locally via stretching or tilting. Flanking tryptophan tyrosine favor interfacial region aromatic belt via snorkeling, positively charged lysine arginine anchor cytosolic side following positive-inside rule. Ionic hydrogen bonding stabilizes extramembranous loops but not core insertion, covalent lipid anchors define separate class. Hydrophobic interactions therefore dominate stabilization.