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. In a Ramachandran plot, the dots cluster

Where clashes occur.
Where clashes do not occur.
Where alpha helices occur.
Where beta strands occur.
Where neither alpha helices nor beta strands occur.
Where the phi and psi angles are energetically favorable.

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Eric Martz

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