4.14: Chapter 4 Questions

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Section 1 Questions:

Q1) Newman projection

Q2) Explain what conformation peptide bonds predominately fall into, cis or trans. Can you think of a situation in which the nonpredominate form could be found in a biological system?
A2) Most peptide bonds are in the trans conformation which helps to reduce steric hindrance R-groups of the amino acids but also decreases the strain on the peptide linkage. The cis form can be found in peptides, but at a low percentage. As the cis form causes strain on the peptide backbone. Enzymes can utilize this bond strain to overcome the activation energy for catalysis.

Q3) Ramachandran Plot example (define the regions)

Section 2 Questions:

Q1) Which amino acid(s) is(are) considered to be alpha helix breaker(s)? Explain why this occurs.
A1) Proline is consider to be the amino acids that "breaks" the secondary structure of an alpha helix. This occurs due to the amine ring in the proline R-group. This R-group is unable to participate in H-bonding needed for helix stabilization, and also is sterically locked in one conformation. Glycine is also an alpha helix breaker. Glycine has only a hydrogen as its R-group and therefore has no constrains for its Φ and Ψ angles. This makes glycine too flexible to hold the structure needed for am alpha helix.

Q2) Helical wheel question

Q3) Beta sheet/alpha helix counting from PDB file

Q4)