Question

1). Where do the hydrophobic amino acid residues usually end up in a folded protein and why? How does hydrogen bonding play a role in stabilizing the beta-sheet structure? Where do the R groups then end up in this structural pattern?

2). Why is the alpha-helix so commonly found? Describe the structural basis of this conformation.

3). How do amyloid-beta peptides aggregate and eventually cause Alzheimer's disease? Where do the amyloid-beta peptides come form (what protein are they from and where is that protein normally found)?

Answer 1

1.The hydrophobic aminoacid residues are found buried inside in a folded protein.This is because hydrophobic aminoacids possess side chains that do not like to interact with water or aqueous environment and hence to avod water, they pack themselves on the interior of a folded protein.The beta sheet structure consists of beta strands and these beta strands are connected to each other laterally in different segmentsby two or three hydrogen bonds in which N-H of one strand forms hydrogen bond with C=O of another adjacent strand.The R groups end up in opposite directions.

2.Alpha helix is so commonly found as it is very stable with low energy states.The structure is in form of a coil with amino acid chains in it. The coiling is always in right-handed direction. In this structure, every partially-positive amino group associates with a partially-negative oxygen in the carboxyl group of the amino acid that is present four residues before on the chain. Also, this structure is tightly packed and the coiling and  twisting formation gives it the form of a rod.

3.Amyloid beta peptides consists of 36-43 aminoacids and are mostly beta peptides that form amyloid plaques in the brain resulting in Alzheimer's disease.They come from/derived from Amyloid Precursor Protein(APP) via  cleavage by beta secretase and gamma secretase.