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BIOCHEM GRE Subject Question

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You have been investigating a membrane protein that appears to have seven 24 residue transmembrane Alpha helices. Assume that each helix is perpendicular to the plane of the membrane and goes exactly from side of the membrane to the other. Also assume that each helix is linked to the next by a loop with a minimun of 12 amino acid residues.

A) From typical helix parameters and the information given, estimate the thickness of the membrane?

B) What is the minimum number of residues in this protein?

C) Using the result of B) estimate the molecular weight of this protein?

D) How many mainchain H-bonds are in each helix?

E) What types of amino acids residues do you expect to make up the bulk of each transmembrane helix?

F) What types of amino acids residues might you expect to find at the ends of each transmembrane helix?

G) Are the NH2-terminus and COOH terminus on the same side or opposite sides of the membrane?

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(A) In an average alpha helix, each amino acid residue advances by 0.15 nm along the helix axis. With each transmembrane helix being made up of 24 residues, the length of the helix would be 24 x 0.15 nm = 3.6 nm.

(B) The minimum number of residues would be (7 x 24) + (6 x 12) = 240

(C) Since the average molecular mass of an amino acid residue is 110, therefore the estimated MW would be 110 x 240 = 26.4 kd

(D) In an alpha helix, every carbonyl oxygen in the mainchain backbone is hydrogen bonded to an amide hydrogen three residues ...

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