Introductory Biochemistry class

1.   (2 marks) Name the amino acids which are:

➢   absent or rare in β-structures
➢   absent in the helical regions of protein
➢   present in high percentage in tropocollagen
➢    predominate in β-structures

2.   (3 marks) In which of the following solvents will a peptide having ten residues (a decapeptide) be most likely to form an α-helix? The least likely? Explain.

   DICHLOROMETHANE       DIMETHYLFORMAMIDE       WATER
      CH2Cl2            H-CO-N(CH3)2            H2O
3.   (2 marks) The synthetic polypeptide polyglutamate, or (Glu)n, forms regions of  α - helices in aqueous solutions below pH 3.0, but above pH 5.0 assumes an extended conformation. Why? At what pH would polylysine, or (Lys)n, be likely to form  α - helices? (pKa values for side chains are 4.1 and 10.5 for glutamate and lysine, respectively).

4.   (2 marks) The synthetic hexapeptide has the following primary structure : Lys - Glu - Lys - Glu - Lys - Glu. Calculate the pI value for this hexapeptide. Values of pKa  for carboxylate, amino group, and a side chain, respectively, are as follows : Glu - 2.1; 9.5; 4.1 (side chain); Lys - 2.2; 9.1; 10.5 (side chain). What would be the pI value if this hexapeptide has a cyclic structure?

5.   (1 mark) Name bonds stabilizing the quaternary structure of tropocollagen.