Introduction to protein structure: Difference between revisions
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<StructureSection load='1a3n' size='350' side='right' caption='Structure of Hemoglobin (PDB entry [[1a3n]])' scene=''> | <StructureSection load='1a3n' size='350' side='right' caption='Structure of Hemoglobin (PDB entry [[1a3n]])' scene=''> | ||
This tutorial illustrates some basic properties of protein structure and useful commands in Jmol and Proteopedia. Clicking the green links changes the view in the structure box to illustrate the principle described by the text. If the structure box has a puzzle piece in it, please make sure you have the latest version of [[Java]] installed and follow the directions to allow Proteopedia to run. | This tutorial illustrates some basic properties of protein structure and useful commands in Jmol and Proteopedia. Clicking the green links changes the view in the structure box to illustrate the principle described by the text. If the structure box has a puzzle piece in it, please make sure you have the latest version of [[Java]] installed and follow the directions to allow Proteopedia to run. To identify a particular atom, toggle off any rotation and hold the mouse button over the atom of interest. This indicates the amino acid residue, the position in the chain, which chain, what atom it is (CA means the alpha carbon), and the overall number of the atom. | ||
== Levels of Protein Structure == | == Levels of Protein Structure == | ||
Proteins are condensation polymers of amino acids. The <scene name='57/575866/Primary_sequence/2'>primary structure</scene> is the amino acid sequence, from the N terminus to the C terminus of the protein. 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/ | Proteins are condensation polymers of amino acids. The <scene name='57/575866/Primary_sequence/2'>primary structure</scene> is the amino acid sequence, from the N terminus to the C terminus of the protein. 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/3'>hydrogen bonds</scene> along the <scene name='57/575866/Backbone/2'>backbone</scene>. 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>. Some proteins, such as the displayed hemoglobin molecule, 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>. | ||
'''Questions based upon these scenes:''' | '''Questions based upon these scenes:''' | ||
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Next, we will look at two of the <scene name='57/575866/1cyo_20_32_transparent/1'>beta strands</scene>. The side chains have been faded out to make the backbone more obvious. | Next, we will look at two of the <scene name='57/575866/1cyo_20_32_transparent/1'>beta strands</scene>. The side chains have been faded out to make the backbone more obvious. | ||
Quest #20) Are these two strands are parallel or antiparallel | Quest #20) Are these two strands are parallel or antiparallel? | ||
Quest #21) Where are the side chains positioned, relative to the main direction of the strand? | Quest #21) Where are the side chains positioned, relative to the main direction of the strand? | ||
