User:Eric Martz/Ramachandran Principle Quiz

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The nine-question quiz below is offered to accompany the interactive [[Tutorial:Ramachandran principle and phi psi angles]], which is also available as a [http://tinyurl.com/RamachandranPrinciple Slideshow] and a [http://tinyurl.com/RamachandranPrincipleYoutube YouTube video].
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<quiz display=simple>
<quiz display=simple>
- 
-
{The number of phi and psi bonds in each amino acid in a polypeptide chain is:
 
-
|type="[]"}
 
-
- None
 
-
- 1
 
-
+ 2
 
-
- 3
 
-
- 4
 
-
- 5
 
-
||The phi bond is between N and C<sub>&alpha;</sub>. The psi bond is between C<sub>&alpha;</sub> and the carbonyl carbon.
 
{How many bonded atoms are required to constitute a
{How many bonded atoms are required to constitute a
-
[http://biomodel.uah.es/model5/prot/diedros_en.htm dihedral (torsion) angle], such as phi or psi?
+
dihedral (torsion) angle, such as phi or psi?
-
|type="[]"}
+
|type="()"}
- None
- None
- 1
- 1
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+ 4
+ 4
- 5
- 5
-
||[[Image:Phi-angle.png|150px|right]]
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||[[Image:Phi-angle.png|150px|right]]The phi [http://biomodel.uah.es/model5/prot/diedros_en.htm dihedral (torsion) angle] is defined by (1) the carboxy carbon from the previous amino acid; (2) N in the amino acid containing the phi bond; (3) C<sub>&alpha;</sub> in the amino acid containing the phi bond; and (4) the carboxy carbon of the amino acid containing the phi bond.
-
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) C<sub>&alpha;</sub> in the amino acid containing the phi bond; and (4) the carboxy carbon of the amino acid containing the phi bond.
+
{The number of phi and psi angles in an isolated amino acid (not in a polypeptide chain) is:
{The number of phi and psi angles in an isolated amino acid (not in a polypeptide chain) is:
-
|type="[]"}
+
|type="()"}
-
- None
+
+ None
- 1
- 1
-
+ 2
+
- 2
- 3
- 3
- 4
- 4
- 5
- 5
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||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.
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{The number of atoms held into a geometric plane by a peptide bond is:
 +
|type="()"}
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- 3
 +
- 4
 +
- 5
 +
+ 6
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- 7
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- 8
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||[[Image:Peptide-bond-plane-6-atoms.png|150px]]
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{'''Questions below may have <font color="red">more than one</font> correct answer.'''}
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{Question
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{The peptide bond is unable to rotate because
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|type="[]" coef="2"}
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|type="[]"}
-
+ Correct answer.
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- It is a covalent bond.
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- Incorrect answer.
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- It is a non-covalent bond.
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+ Correct answer.
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- Rotation would cause clashes.
-
- Incorrect answer.
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+ It is a partially double bond.
-
||feedback
+
 
 +
{Phi and psi angles directly determine
 +
|type="[]"}
 +
- Primary structure.
 +
+ Secondary structure.
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+ Tertiary structure.
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- Quaternary structure.
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||See [[Protein primary, secondary, tertiary and quaternary structure]].
 +
 
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{Alpha helices are compatible with
 +
|type="[]"}
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- All possible phi-psi angle combinations.
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+ A limited range of phi-psi angle combinations.
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- A limited range of phi angles with all possible psi angles.
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- A limited range of psi angles with all possible phi angles.
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||See [http://bioinformatics.org/molvis/phipsi/index.htm#plot Ramachandran Plot].
 +
 
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{Common secondary structures are energetically favored because
 +
|type="[]"}
 +
+ They optimize main-chain hydrogen bonds.
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- They represent all possible conformations.
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- They maximize clashes between atoms.
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+ They minimize clashes between atoms.
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{Overlap of [https://en.wikipedia.org/wiki/Van_der_Waals_radius van der Waals radii]
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|type="[]"}
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+ Between two non-bonded atoms is called a ''clash''.
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- Between two covalently bonded atoms is called a ''clash''.
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- Occurring between two non-bonded atoms in a molecular model signifies an energetically favorable interaction.
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+ Is physically impossible between two non-bonded real atoms.
 +
 
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{In a Ramachandran plot, the dots cluster
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|type="[]"}
 +
- Where clashes occur.
 +
+ Where clashes do not occur.
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+ Where alpha helices occur.
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+ Where beta strands occur.
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- Where alpha helices, beta strands, and turns do not occur.
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+ Where the phi and psi angles are energetically favorable.
</quiz>
</quiz>
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[[Category:Pages with quizzes]]

Current revision

The nine-question quiz below is offered to accompany the interactive Tutorial:Ramachandran principle and phi psi angles, which is also available as a Slideshow and a YouTube video.

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 dihedral (torsion) 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. The peptide bond is unable to rotate because

It is a covalent bond.
It is a non-covalent bond.
Rotation would cause clashes.
It is a partially double bond.

5. Phi and psi angles directly determine

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

6. 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 Ramachandran Plot.

7. 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.

8. 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.

9. In a Ramachandran plot, the dots cluster

Where clashes occur.
Where clashes do not occur.
Where alpha helices occur.
Where beta strands occur.
Where alpha helices, beta strands, and turns do not occur.
Where the phi and psi angles are energetically favorable.

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Eric Martz

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