Becker's World of the Cell 9th Edition by Lewis Kleinsmith, Jeff Hardin, Gregory Paul Bertoni

Exercise 10

Hydropathy: The Plot Thickens. A hydropathy plot can be used to predict the structure of a membrane protein based on its amino acid sequence and the hydrophobicity values of the amino acids. Hydrophobicity is measured as the standard free energy change, AG°', for the transfer of a given amino acid residue from a hydrophobic solvent into water, in kilojoules/mole (kj/mol). The hydropathy index is calculated by averaging the hydrophobicity values for a series of short segments of the polypeptide, with each segment displaced one amino acid further from the N-terminus. The hydropathy index of each successive segment is then plotted as a function of the location of that segment in the amino acid sequence, and the plot is examined for regions of high hydropathy index.
(a)Why do scientists try to predict the structure of a membrane protein by this indirect means when the technique of X-ray crystallography would reveal the structure directly
(b)Given the way it is defined, would you expect the hydrophobicity index of a hydrophobic residue such as valine or isoleucine to be positive or negative What about a hydrophilic residue such as aspartic acid or arginine
(c)Listed below are four amino acids and four hydrophobicity values. Match the hydrophobicity values with the correct amino acids, and explain your reasoning.
Amino acids: alanine; arginine; isoleucine; serine Hydrophobicity (in kj/mol): +3.1; +1.0; -1.1; -7.5
(d)Shown in Figure is a hydropathy plot for a specific integral membrane protein. Draw a horizontal bar over each transmembrane segment as identified by the plot. How long is the average transmembrane segment How well does that value compare with the number you calculated in Problem 7-6c How many transmembrane segments do you think the protein has Can you guess which protein this might be
FIGURE Hydropathy Plot for an Integral Membrane Protein.