User:J. Shaun Lott/BIOSCI 203: Difference between revisions

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~~</StructureSection>~~On the right-hand side of this page is a view of a protein structure shown using the Jmol viewer within [http://proteopedia.org/wiki/index.php/Main_Page Proteopedia]. [http://wiki.jmol.org:81/index.php/Main_Page Jmol] is an easy way to view protein structures. Use the left mouse button to rotate the protein model, the middle mouse button or scroll wheel to zoom in and out (option-click on a Mac), and the right mouse button for more options and information (control-click on a Mac). Try this out for yourself now ==>

On the right-hand side of this page is a view of a protein structure shown using the Jmol viewer within [http://proteopedia.org/wiki/index.php/Main_Page Proteopedia]. [http://wiki.jmol.org:81/index.php/Main_Page Jmol] is an easy way to view protein structures. Use the left mouse button to rotate the protein model, the middle mouse button or scroll wheel to zoom in and out (option-click on a Mac), and the right mouse button for more options and information (control-click on a Mac). Try this out for yourself now ==>

The [http://www.rcsb.org/pdb/explore/explore.do?structureId=1PRX protein][http://www.proteopedia.org/wiki/index.php/1prx structure] we will be looking at in this part of the lab is the N-terminal domain of the human 1-Cys peroxidase enzyme [http://www.nature.com.ezproxy.auckland.ac.nz/nsmb/journal/v5/n5/abs/nsb0598-400.html hORF6]. Click

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'''Q6: How many α-helices are there in this protein?'''

'''Q7: How many α-helices are there in this protein?'''

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'''Q7: How many β-strands make up the β-sheet?'''

'''Q8: How many β-strands make up the β-sheet?'''

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'''Q8: Is the topology of the β-sheet parallel, anti-parallel or mixed?'''

'''Q9: Is the topology of the β-sheet parallel, anti-parallel or mixed?'''

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Use the Henderson-Hasselbach equation to answer the questions below.

(The pKa of the –SH group of free cysteine is 8.5. The cytosol of human cells is normally at pH 7.3. The pKa of the active site cysteine in a 1-Cys Prx enzyme has been measured at 6.0.)

(The pKa of the –SH group of free cysteine is 8.35. The cytosol of human cells is normally at pH 7.35 The pKa of the active site cysteine in a 1-Cys Prx enzyme has been measured at 6.2.)

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'''Q9: What would be the % ionization of the –SH group of free cysteine in the cytosol?'''

'''Q10: What would be the % ionization of the –SH group of free cysteine in the cytosol?'''

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'''~~Q10~~: What would be the % ionization of the –SH group of the Prx active site cysteine in the cytosol?'''

'''Q11: What would be the % ionization of the –SH group of the Prx active site cysteine in the cytosol?'''

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'''~~Q11~~: ~~Which~~ residues have side chains ~~close to~~ Cys47? (Hint: try mousing over each of the displayed sidechains to identify them.)'''

'''Q12: Give the name and residue number for each of the amino acid residues that have side chains within 4Å of the sulfur atom in Cys47. (Hint: try mousing over each of the displayed sidechains to identify them.)'''

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'''~~Q12~~: What feature of the local environment around Cys47 might stabilize the existence of a thiolate ion?'''

'''Q13: What feature of the local environment around Cys47 might stabilize the existence of a thiolate ion?'''

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-</StructureSection>On the right-hand side of this page is a view of a protein structure shown using the Jmol viewer within [http://proteopedia.org/wiki/index.php/Main_Page Proteopedia]. [http://wiki.jmol.org:81/index.php/Main_Page Jmol] is an easy way to view protein structures. Use the left mouse button to rotate the protein model, the middle mouse button or scroll wheel to zoom in and out (option-click on a Mac), and the right mouse button for more options and information (control-click on a Mac). Try this out for yourself now ==>
+On the right-hand side of this page is a view of a protein structure shown using the Jmol viewer within [http://proteopedia.org/wiki/index.php/Main_Page Proteopedia]. [http://wiki.jmol.org:81/index.php/Main_Page Jmol] is an easy way to view protein structures. Use the left mouse button to rotate the protein model, the middle mouse button or scroll wheel to zoom in and out (option-click on a Mac), and the right mouse button for more options and information (control-click on a Mac). Try this out for yourself now ==>
 The [http://www.rcsb.org/pdb/explore/explore.do?structureId=1PRX protein][http://www.proteopedia.org/wiki/index.php/1prx structure] we will be looking at in this part of the lab is the N-terminal domain of the human 1-Cys peroxidase enzyme [http://www.nature.com.ezproxy.auckland.ac.nz/nsmb/journal/v5/n5/abs/nsb0598-400.html hORF6]. Click
@@ Line 19: / Line 19: @@
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-'''Q6: How many α-helices are there in this protein?'''
+'''Q7: How many α-helices are there in this protein?'''
 ----
-'''Q7: How many β-strands make up the β-sheet?'''
+'''Q8: How many β-strands make up the β-sheet?'''
 ----
-'''Q8: Is the topology of the β-sheet parallel, anti-parallel or mixed?'''
+'''Q9: Is the topology of the β-sheet parallel, anti-parallel or mixed?'''
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@@ Line 36: / Line 36: @@
 Use the Henderson-Hasselbach equation to answer the questions below.
-(The p<i>K</i><sub>a</sub> of the –SH group of free cysteine is 8.5. The cytosol of human cells is normally at pH 7.3. The p<i>K</i><sub>a</sub> of the active site cysteine in a 1-Cys Prx enzyme has been measured at 6.0.)
+(The p<i>K</i><sub>a</sub> of the –SH group of free cysteine is 8.35. The cytosol of human cells is normally at pH 7.35 The p<i>K</i><sub>a</sub> of the active site cysteine in a 1-Cys Prx enzyme has been measured at 6.2.)
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-'''Q9: What would be the % ionization of the –SH group of free cysteine in the cytosol?'''
+'''Q10: What would be the % ionization of the –SH group of free cysteine in the cytosol?'''
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-'''Q10: What would be the % ionization of the –SH group of the Prx active site cysteine in the cytosol?'''
+'''Q11: What would be the % ionization of the –SH group of the Prx active site cysteine in the cytosol?'''
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@@ Line 53: / Line 53: @@
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-'''Q11: Which residues have side chains close to Cys47? (Hint: try mousing over each of the displayed sidechains to identify them.)'''
+'''Q12: Give the name and residue number for each of the amino acid residues that have side chains within 4Å of the sulfur atom in Cys47. (Hint: try mousing over each of the displayed sidechains to identify them.)'''
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-'''Q12: What feature of the local environment around Cys47  might stabilize the existence of a thiolate ion?'''
+'''Q13: What feature of the local environment around Cys47 might stabilize the existence of a thiolate ion?'''
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