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

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== ~~Spacefill view~~ ==

==Representing protein structures==

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''.

'''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''.

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.

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== Ball-and-stick molecular model ==

'''Ball-and-stick molecular model'''

This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.

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== Amino acid trace ==

'''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!

What we really need to do next is to have a basic [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure ~~introduction~~ to protein structure]. This ~~link will take you~~ to ~~a page~~ that ~~introduces you~~ to the ~~basic concepts~~.

What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.

== Levels of Protein Structure ==

'''Primary structure'''

Proteins are polymers of amino acids joined together in linear chains. There are four recognised levels of structural organisation for proteins.

The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.

'''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.

'''Tertiary Structure'''

These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.

'''Quaternary Structure'''

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>.

</StructureSection>

@@ Line 5: / Line 5: @@
 <StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'>
-== Spacefill view ==
+==Representing protein structures==
-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''.
+'''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''.
 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 12: / Line 14: @@
-== Ball-and-stick molecular model ==
+'''Ball-and-stick molecular model'''
 This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.
@@ Line 19: / Line 21: @@
-== Amino acid trace ==
+'''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!
-What we really need to do next is to have a basic [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure introduction to protein structure]. This link will take you to a page that introduces you to the basic concepts.
+What we really need to do next is to have a basic introduction to protein structure. The section that follows is based on the [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure Introduction to Protein Structure] Proteopedia page.
+== Levels of Protein Structure ==
+'''Primary structure'''
+Proteins are polymers of amino acids joined together in linear chains.  There are four recognised levels of structural organisation for proteins.
+The first, referred to as the <scene name='57/575866/Primary_sequence/2'>primary structure</scene>, is simply the amino acid sequence, from the N terminus (start) to the C terminus (end) of the protein.
+'''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.
+'''Tertiary Structure'''
+These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>.
+'''Quaternary Structure'''
+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>.
 </StructureSection>