User:Michael Roberts/BIOL115 Myo: Difference between revisions

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~~'''MOLECULAR MODEL~~:~~'''~~

== Molecular model: ==

The initial view here is a ball-and-stick representation of the molecular structure of myoglobin.

'''SECONDARY STRUCTURE''':

'''SECONDARY STRUCTURE''': This next view simplifies things, and just shows a <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/9'>cartoon representation </scene>of the secondary structure of the protein.

This next view simplifies things, and just shows a <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/9'>cartoon representation </scene>of the secondary structure of the protein.

You see how the <scene name='User:Michael_Roberts/BIOL115_Myo/Hbonds/1'>hydrogen bonds</scene> (yellow) that maintain the main secondary structure of the protein are arranged in this next view.

Some amino acids have specific effects on secondary structure. This next view shows the locations of the <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/11'>PROLINE</scene> residues in myoglobin. You can see that they all fall at the end of a stretch of helix. This is bacause their large side chains do not fit within the straight run of α-helix.

'''THE GLOBIN FOLD''':

'''THE GLOBIN FOLD''': In this next view, the eight <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/3'>individual alpha-helices </scene>are each coloured differently. This gives you an impression of the classic globion fold. The α-helices pack together tightly, and there is very little space in the centre of the protein.

In this next view, the eight <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/3'>individual alpha-helices </scene>are each coloured differently. This gives you an impression of the classic globion fold. The α-helices pack together tightly, and there is very little space in the centre of the protein.

'''HYDROPHOBICITY''':

'''HYDROPHOBICITY''': Globular folds like this are characterised by a polar, <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/4'>hydrophilic exterior</scene>, which interacts with the aqueous solvent, and a hydrophobic core.

Globular folds like this are characterised by a polar, <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/4'>hydrophilic exterior</scene>, which interacts with the aqueous solvent, and a hydrophobic core.

{{Template:ColorKey_Hydrophobic}}, {{Template:ColorKey_Polar}}

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~~'''THE HEME GROUP''':~~

== The Heme Group ==

Now let's turn our attention to the main function of myoglobin - oxygen binding.

Oxygen is bound by a <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/1'>heme group</scene>, which sits in a hydrophobic pocket in the myoglobin protein.

@@ Line 13: / Line 13: @@
 <StructureSection load='1mbo' size='500' side='right' caption='Structure of Myoglobin (PDB entry [[1mbo]])' scene='User:Michael_Roberts/BIOL115_Myo/Start/1'>
-'''MOLECULAR MODEL:'''
+== Molecular model: ==
 The initial view here is a ball-and-stick representation of the molecular structure of myoglobin.
-'''SECONDARY STRUCTURE''':
+'''SECONDARY STRUCTURE''': This next view simplifies things, and just shows a <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/9'>cartoon representation </scene>of the secondary structure of the protein.
-This next view simplifies things, and just shows a <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/9'>cartoon representation </scene>of the secondary structure of the protein.
 You see how the <scene name='User:Michael_Roberts/BIOL115_Myo/Hbonds/1'>hydrogen bonds</scene> (yellow) that maintain the main secondary structure of the protein are arranged in this next view.
 Some amino acids have specific effects on secondary structure. This next view shows the locations of the <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/11'>PROLINE</scene> residues in myoglobin. You can see that they all fall at the end of a stretch of helix. This is bacause their large side chains do not fit within the straight run of α-helix.
-'''THE GLOBIN FOLD''':
+'''THE GLOBIN FOLD''': In this next view, the eight <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/3'>individual alpha-helices </scene>are each coloured differently. This gives you an impression of the classic globion fold. The α-helices pack together tightly, and there is very little space in the centre of the protein.
-In this next view, the eight <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/3'>individual alpha-helices </scene>are each coloured differently. This gives you an impression of the classic globion fold. The α-helices pack together tightly, and there is very little space in the centre of the protein.
-'''HYDROPHOBICITY''':
+'''HYDROPHOBICITY''': Globular folds like this are characterised by a polar, <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/4'>hydrophilic exterior</scene>, which interacts with the aqueous solvent, and a hydrophobic core.
-Globular folds like this are characterised by a polar, <scene name='User:Michael_Roberts/BIOL115_Myo/Secondary_structure/4'>hydrophilic exterior</scene>, which interacts with the aqueous solvent, and a hydrophobic core.
 {{Template:ColorKey_Hydrophobic}},  {{Template:ColorKey_Polar}}
@@ Line 37: / Line 32: @@
-'''THE HEME GROUP''':
+== The Heme Group ==
 Now let's turn our attention to the main function of myoglobin - oxygen binding.
 Oxygen is bound by a <scene name='User:Michael_Roberts/BIOL115_Myo/Heme/1'>heme group</scene>, which sits in a hydrophobic pocket in the myoglobin protein.