User:Robert Dutnall/Chem331 Tutorial2a: Difference between revisions
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New page: == Biochemistry Tutorial #2 - Secondary Structure (Part 1) == The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are ... |
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Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end. | Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end. | ||
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===Hydrogen Bonding in α-helices=== | |||
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'/> | |||
I'll reset the structure for you. Now, look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis? | |||
<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence). | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence). | ||
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==The 3<sub>10</sub>-helix== | ==The 3<sub>10</sub>-helix== | ||
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<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain. | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain. | ||
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===Hydrogen Bonding in 3-10 Helices=== | |||
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'/> | |||
I've zoomed back out and turned on the hydrogen bonds for the mainchain. Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly. | |||
<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene> | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene> | ||
