Exam (elaborations)
BCMB 401 Exam 1 questions with verified solutions
- Course
- BCMB 401
- Institution
- South University
BCMB 401 Exam 1 questions with verified solutions
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BCMB 401 Exam 1How to determine the pI of an amino acid or peptide: - correct answer ✔✔Take the average of the two pKa values on either side of the zwitterion (charge = 0)
Peptide bond orientation - correct answer ✔✔Because of resonance stabilization, the peptide bond has partial double bond characer, resulting in a rigid planar geometry with no free rotation.
Because of the steric clash of R-groups, all peptide bonds are in trans orientation, except for proline which can be found in both
Peptide conformation angles - correct answer ✔✔phi - represents the bond between the amide-N and alpha-C
psi - represents bond between carbonyl-C and alpha-C
Ramachandran Plot - correct answer ✔✔Psi is vertical, phi is horizontal. Green shows favorable values with minimal R group steric clash
Secondary structure alpha helix - correct answer ✔✔The C=O from residue n is hydrogen bonded to the N-H from residue n+4
Secondary structure alpha helix residue preference - correct answer ✔✔Most preferred: Ala, Leu, Met, Glu, Gln, His, Lys, Arg
Less preferred: Tyr, Trp, Phe, Ile, Val, Thr, Cys (large and bulky)
Gly - H is small and flexible, entropically not favored
Pro - Side chain linked to alpha N, has no N-H to H-bond and restricted phi/psi angles
Asp, Asn, Ser - H-bonding side chains compete directly with backbone H-bonds
Parallel/antiparallel beta sheets - correct answer ✔✔R chains alternate on either side of the peptide backbone.
Antiparallel - hydrogen bonds are paired perpendicularly across
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