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Sandbox max quiz 2

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<applet load='2oau' size='400' frame='true' align='right' caption='Position of protein in relation to membrane bilayer (red represents periplasmic side while blue represents cytoplasmic layer) (2oau).'
<applet load='2oau' size='400' frame='true' align='right' caption='Position of protein in relation to membrane bilayer (red represents periplasmic side while blue represents cytoplasmic layer) (2oau).'
scene='User:Eric_Martz/Sandbox_0/2oau_opm/2' />
scene='User:Eric_Martz/Sandbox_0/2oau_opm/2' />
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{If the amino acid sequence of a protein is reversed (the primary structure is the same except from N to C it now reads C to N) the protein will fold to the same tertiary structure.
+
<applet size='400' frame='true' align='right' caption='Morph: 2oau to 2vv5.'
 +
scene='User:Eric_Martz/Sandbox_0/2oau_2vv5_morph_cao_pdb_gz/1' />
 +
 
 +
{Using the scene to the right showing the structure of E. coli McsS as well as the morph between the open and closed conformation, which side undergoes the most major conformational change.
|type="()"}
|type="()"}
-
- true
+
- Cytosolic
-
+ false
+
+ Periplasmic
-
|| The primary protein structure is directional because of the asymmetrical nature of amino acids. This causes potentially different molecular interactions depending on the order of the amino acid sequence and results in a different tertiary structure.
+
|| Why might the smaller periplasmic side be the site of conformational shifting? What other functions might the cytoplasmic domain serve?

Revision as of 17:00, 15 April 2010

This is a placeholder

1.

Position of protein in relation to membrane bilayer (red represents periplasmic side while blue represents cytoplasmic layer) (2oau).

Drag the structure with the mouse to rotate

Morph: 2oau to 2vv5.

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{Using the scene to the right showing the structure of E. coli McsS as well as the morph between the open and closed conformation, which side undergoes the most major conformational change.

Cytosolic
Periplasmic
→ Why might the smaller periplasmic side be the site of conformational shifting? What other functions might the cytoplasmic domain serve?

2. Which scene most likely highlights the hydrophobic sections of the protein:

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→ The first scene highlights a number of residues on the inner section of the protein. The location of these residues suggests they are hydrophobic

3.

Name an amino acid likely to be used in binding a metallic cationic cofactor.
→ The negative charge for some, while the electronegative components for others has the potential to bind to positively charged cations.

4. Some common techniques used by proteins to link hydrophobic and hydrophilic regions are

relying on dissolved amphipathic molecules to shield exposed hydrophobic residues from the cytosol.
stacking beta sheets with alternating hydrophobic and hydrophilic residues.
replacing the functional group on amino acid residues with more energetically favorable groups.
varying the order of hydrophobic and hydrophilic residues on an alpha helix so that the two types are segregated to opposite sides of the helix.

5. Which of these has a single domain?

[[

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]]
[[

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]]
[[

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]]
[[

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]]

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