1. Draw the structure of a peptide bond between two amino acids. Why is it said that the C-N bond has a partial double bond structure. Draw the resonance states of the double bond.
Between each amino acid residue is a C=O and N-H bond. Due to the double bond that C=O has it is a good accepter for hydrogen bonding, while N-H is a good donor for hydrogen bonding. The C=O bonds and the N-H bonds both are used to stabilize the protein sequence.
2. Explain the reason why the six atoms that are involved in the peptide bond share a common geometric plane?
Due to the free electron pair on nitrogen there is a partial resonance structure between the C=O and the C=N causing the structure to have no freedom of rotation. All peptide bonds occur in this Trans conformation.
3. Explain the term “polypeptide backbone”.
Polypeptides are amino acids linked together by peptide bonds therefore creating a structure known as a polypeptide. A polypeptide backbone is a key contributor to the secondary structure of a protein due to the backbone to backbone hydrogen bonding interactions.
4. What are the only two covalent bonds along a polypeptide backbone that have freedom of rotation?
The two covalent bonds along a polypeptide backbone that have freedom of rotation are the amino to alpha carbon bond as well as the alpha carbon to the carbonyl group. The bond between the amino and the alpha carbon are called (phi bonds) whereas the bonds between the alpha carbon and the carbonyl group are called (psi bonds).
5. What are the φ and ψ angles? How are they measured? What are the possible values for each?
The bond between the amino and the alpha carbon are called (phi bonds) whereas the bonds between the alpha carbon and the carbonyl group are called (psi bonds). The (phi) and (psi) angles will range from 180 degrees to -180 degrees/ (180 degrees or -180 degrees) ***** When the first and fourth atoms are farthest apart. *****
6. What is the conformation when both the φ and ψ angles are zero?
The conformation when phi and psi angles are equal to 0 is non-favorable due to steric interactions. However is looks somewhat cyclic.
7. What is a Ramachandran plot?
A Ramachandran plot is used to determine the possible phi and psi angles in order to determine the conformation of the protein. Used to visualize backbone dihedral angle of amino acid residues. Most amino acid residues are located to the left of the 0 degree phi angle due to the fact that most amino acids/ peptide chains are l residues. Conformations that are shown in the ramachandran plot are those with little to no steric interference, based on vander walls radii. Branched residues have less allowed conformations. While straight chain amino acid residues have more allowed residues.
The reason for the limited conformation is due to the cyclic “r” side chain
Phi and psi angles range from -35 to -85 degrees.
8. Can a Ramachandran plot provide the entire information for a protein’s 3D structure, given that it contains the φψ information for all the alpha carbons in the polypeptide?
Yes, a ramachandran plot can also determine where the parallel beta pleated sheets are, where the antiparallel beta pleated sheets are, where the twists are, left and right handed alpha helices.
9. Describe what are primary, secondary, tertiary, and quaternary structures in proteins.
• Primary structure: unique sequence of amino acids in a protein (polypeptide)
• Secondary Structure: Local and main chain arrangements of its main chain atoms. Composed of alpha helices and beta pleated sheets. Defined by hydrogen bonding between the amino groups and the carboxyl groups. Secondary structure is generated when the phi and psi angles...