User:Eric Martz/Ramachandran Principle Quiz

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1. How many bonded atoms are required to constitute a dihedral (torsion) angle, such as phi or psi?

None
1
2
3
4
5
→
The phi angle is defined by (1) the carboxy carbon from the previous amino acid; (2) N in the amino acid containing the phi bond; (3) Cα in the amino acid containing the phi bond; and (4) the carboxy carbon of the amino acid containing the phi bond.

2. The number of phi and psi angles in an isolated amino acid (not in a polypeptide chain) is:

None
1
2
3
4
5
→The phi angle involves the carboxy carbon of the previous amino acid in a polypeptide chain. The psi angle involves the N of the subsequent amino acid. Therefore an isolated single amino acid has neither phi nor psi angles.

3. The number of atoms held into a geometric plane by a peptide bond is:

3
4
5
6
7
8
→

Questions below may have more than one correct answer.

4. Phi and psi angles directly determine

Primary structure.
Secondary structure.
Tertiary structure.
Quaternary structure.
→See Protein primary, secondary, tertiary and quaternary structure.

5. Alpha helices are compatible with

All possible phi-psi angle combinations.
A limited range of phi-psi angle combinations.
A limited range of phi angles with all possible psi angles.
A limited range of psi angles with all possible phi angles.
→See Protein primary, secondary, tertiary and quaternary structure.

6. Common secondary structures are energetically favored because

They optimize main-chain hydrogen bonds.
They represent all possible conformations.
They maximize clashes between atoms.
They minimize clashes between atoms.

7. Overlap of van der Waals radii

Between two non-bonded atoms is called a clash.
Between two covalently bonded atoms is called a clash.
Occurring between two non-bonded atoms in a molecular model signifies an energetically favorable interaction.
Is physically impossible between two non-bonded real atoms.

8. xxx

They optimize main-chain hydrogen bonds.
They represent all possible conformations.
They maximize clashes between atoms.
They minimize clashes between atoms.

9.

They optimize main-chain hydrogen bonds.
They represent all possible conformations.
They maximize clashes between atoms.
They minimize clashes between atoms.

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Eric Martz

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