Question

After going through all the activities, conclude your write up by addressing these two questions.

A)interactions between what parts of the polypeptide chain are the most important for defining secondary structure?

B) Do you think that all amino acid sequences would have the same propensity for forming helices and/or sheets? Why/why not?

Activity 1:Thinking about Phi and Psi angles Make a four-residue peptide and switch atom numbering on. Can you identify the N-and C-termini?

Activity 2–Playing with alpha-helices After resetting, make a 10-residue peptide.

Activity 3 –Making some Beta-sheets After resetting, make two10-residue peptides. Show peptide planes and residue labels. Orient each so that they are running in opposite directions (ie, one will go 1to10 left to right, the other 10 to 1)

Activity 4 –Miscellaneous Explorations and Problems. These activities require to build on the experiences in Activities 1-3.

Answer 1

In a protein chain three dihedral angles are formed namely; phi, psi and omega. Dihedral angles are the angle between two intersecting planes.Secondary structure of protein is discussed in the images below.hgfrg