User:Michael Roberts/Open-Day Demo: Difference between revisions

(10 intermediate revisions by the same user not shown)

Line 4:

==Representing protein structures==

'''Spacefill model'''

The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.

The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called <scene name='70/703491/Basic_representations/1'>'spacefill'</scene> view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.

In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.

Line 22:

'''Amino acid trace'''

Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>~~traces~~ the ~~chains~~</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!

Here's a much more simplified view that <scene name='70/703491/Basic_representations/4'>shows a trace of the backbone</scene> of the amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!

One question this view does raise, is how the three separate chains are held together in the right way? The answer is the <scene name='70/703491/Basic_representations/5'>presence of disulphide bridges</scene> that link the chains together to form the correct overall structure.

Line 37:

Line 39:

'''Secondary Structure'''

The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta ~~sheet~~, a flat~~, sheet-like~~ arrangement of amino acids.

The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone. There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.

Line 48:

Line 50:

Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.

== Secondary Structure in chymotrypsin ==

Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look.

This time, we'll display a <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>cartoon representation</scene> indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, with only a small amount of α-helix.

''Colour key:''

{{Template:ColorKey_Helix}},

{{Template:ColorKey_Strand}}.

We can also see that the protein is organised into two structurally-similar domains. Each domain contains a group of beta strands arranged as anti-parallel sheets forming a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.

Finally, here's chymotrypsin with a molecule of <scene name='70/703491/Substrate/3'>substrate</scene> bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.

</StructureSection>

@@ Line 4: / Line 4: @@
-<StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'>
+<StructureSection load='1afq' size='600' side='right' caption=' ' scene='70/703491/Basic_representations/1'>
 ==Representing protein structures==
 '''Spacefill model'''
-The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.
+The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called <scene name='70/703491/Basic_representations/1'>'spacefill'</scene> view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.
 In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.
@@ Line 22: / Line 22: @@
 '''Amino acid trace'''
-Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!
+Here's a much more simplified view that <scene name='70/703491/Basic_representations/4'>shows a trace of the backbone</scene> of the amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!
+One question this view does raise, is how the three separate chains are held together in the right way? The answer is the <scene name='70/703491/Basic_representations/5'>presence of disulphide bridges</scene> that link the chains together to form the correct overall structure.
@@ Line 37: / Line 39: @@
 '''Secondary Structure'''
-The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances.  This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone.  There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta sheet, a flat, sheet-like arrangement of amino acids.
+The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances.  This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/1'>hydrogen bonds</scene> along the amino acid backbone.  There are only two main forms of secondary structure seen in proteins: alpha helix, which forms coiled cylinders of amino acids, as shown here, and beta strands, a planar (flat) arrangement of amino acids which often line up together to from so-called beta sheets.
@@ Line 48: / Line 50: @@
 Some proteins, such as the hemoglobin molecule displayed here, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.
+== Secondary Structure in chymotrypsin ==
+Now that we know something about the structural organisation of proteins, let's go back to our chymotrypsin molecule and have another look.
+This time, we'll display a <scene name='User:Michael_Roberts/BIOL115_Chymo/2ndry_structure/1'>cartoon representation</scene> indicating the main secondary structural elements. We can see that the main structural form in chymotrypsin is the beta strand, with only a small amount of α-helix.
+''Colour key:''
+{{Template:ColorKey_Helix}},
+{{Template:ColorKey_Strand}}.
+We can also see that the protein is organised into two structurally-similar domains. Each domain contains a group of beta strands arranged as anti-parallel sheets forming a circular structure known as a beta barrel. You can rotate the molecule so that you can see down through each of the two beta barrels in turn.
+Finally, here's chymotrypsin with a molecule of <scene name='70/703491/Substrate/3'>substrate</scene> bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.
 </StructureSection>