Peptide: Difference between revisions

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Peptides are short chains of amino acids linked by peptide bonds. By convention, a '''peptide''' is not more than 30-50 amino acids in length. Longer chains of amino acids are called polypeptides or proteins. Wikipedia offers a good discussion of [http://en.wikipedia.org/wiki/Peptide peptides, with examples].

==Peptides & Backbones==

This is the '''<scene name='Peptide/Emartz_view1/7'>backbone</scene>''' of 1 amino acid. Adding to the backbone with an additional amino acid on each side gives a '''<scene name='Peptide/Emartz_view2/6'>tripeptide</scene>''' (3 amino acids). No side groups are shown, and most hydrogens are omitted. Now each amino acid has a 1 carbon side group so we have '''<scene name='Peptide/Emartz_view3/4'>Ala-Ala-Ala</scene>''' (tri-alanine). Adding a carbon chain plus an NH3 on the first amino acid gives '''<scene name='Peptide/Emartz_view4/5'>Lys-Ala-Ala</scene>'''. Adding '''<scene name='Peptide/Emartz_view5/4'> three more carbons </scene>''' to the 3rd amino acid gives isoleucine: Lys-Ala-Ile. The 4th amino acid is threonine with its hydroxyl, giving '''<scene name='Peptide/Emartz_view6/2'> Lys-Ala-Ile-Thr</scene>'''. Here is the shape of the '''<scene name='Peptide/Emartz_view7/2'>tetrapeptide</scene>''' (4 AAs). The stick representation has too much detail for larger proteins, so the α-carbons are connected with a line called the '''<scene name='Peptide/Emartz_view8/3'>backbone trace</scene>'''. Showing only the '''<scene name='Peptide/Emartz_view9/5'>backbone</scene>''' makes it easier to see the path of the protein chain (its secondary and tertiary structure).

This is the '''<scene name='Peptide/Emartz_view1/8'>backbone</scene>''' of 1 amino acid. Adding to the backbone with an additional amino acid on each side gives a '''<scene name='Peptide/Emartz_view2/6'>tripeptide</scene>''' (3 amino acids). No side groups are shown, and most hydrogens are omitted. Now each amino acid has a 1 carbon side group so we have '''<scene name='Peptide/Emartz_view3/4'>Ala-Ala-Ala</scene>''' (tri-alanine). Adding a carbon chain plus an NH3 on the first amino acid gives '''<scene name='Peptide/Emartz_view4/5'>Lys-Ala-Ala</scene>'''. Adding '''<scene name='Peptide/Emartz_view5/4'> three more carbons </scene>''' to the 3rd amino acid gives isoleucine: Lys-Ala-Ile. The 4th amino acid is threonine with its hydroxyl, giving '''<scene name='Peptide/Emartz_view6/2'> Lys-Ala-Ile-Thr</scene>'''. Here is the shape of the '''<scene name='Peptide/Emartz_view7/2'>tetrapeptide</scene>''' (4 AAs). The stick representation has too much detail for larger proteins, so the α-carbons are connected with a line called the '''<scene name='Peptide/Emartz_view8/3'>backbone trace</scene>'''. Showing only the '''<scene name='Peptide/Emartz_view9/5'>backbone</scene>''' makes it easier to see the path of the protein chain (its secondary and tertiary structure).

==Content Attribution==

The above scenes in Jmol were adapted from the chapter ''Peptides and Backbones'' in a tutorial on Hemoglobin first written by [[User:Eric Martz|Eric Martz]] as a ''RasMol Movie Script'' released in March, 1996, which was released as a [http://molviz.org/hemoglob Hemoglobin Tutorial] implemented with [[Chime]] in September, 1997, and a [http://molviz.org/hemoglobin Hemoglobin Tutorial] implemented with [[Jmol]] in July 2007.

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-<applet load="" scene="Peptide/Emartz_view1/6" size="500" color="white" frame="true" caption="Peptides, small chains of amino acids." align="right" />
+<applet load="" scene="Peptide/Emartz_view1/8" size="500" color="white" frame="true" caption="Peptides, small chains of amino acids." align="right" />
 Peptides are short chains of amino acids linked by peptide bonds. By convention, a '''peptide''' is not more than 30-50 amino acids in length.  Longer chains of amino acids are called polypeptides or proteins. Wikipedia offers a good discussion of [http://en.wikipedia.org/wiki/Peptide peptides, with examples].
 ==Peptides & Backbones==
-This is the '''<scene name='Peptide/Emartz_view1/7'>backbone</scene>''' of 1 amino acid.  Adding to the backbone with an additional amino acid on each side gives a '''<scene name='Peptide/Emartz_view2/6'>tripeptide</scene>''' (3 amino acids).  No side groups are shown, and most hydrogens are omitted.  Now each amino acid has a 1 carbon side group so we have '''<scene name='Peptide/Emartz_view3/4'>Ala-Ala-Ala</scene>''' (tri-alanine).  Adding a carbon chain plus an NH3 on the first amino acid gives '''<scene name='Peptide/Emartz_view4/5'>Lys-Ala-Ala</scene>'''.  Adding '''<scene name='Peptide/Emartz_view5/4'> three more carbons </scene>''' to the 3rd amino acid gives isoleucine: Lys-Ala-Ile.  The 4th amino acid is threonine with its hydroxyl, giving '''<scene name='Peptide/Emartz_view6/2'> Lys-Ala-Ile-Thr</scene>'''.  Here is the shape of the '''<scene name='Peptide/Emartz_view7/2'>tetrapeptide</scene>''' (4 AAs).  The stick representation has too much detail for larger proteins, so the α-carbons are connected with a line called the '''<scene name='Peptide/Emartz_view8/3'>backbone trace</scene>'''.  Showing only the '''<scene name='Peptide/Emartz_view9/5'>backbone</scene>''' makes it easier to see the path of the protein chain (its secondary and tertiary structure).
+This is the '''<scene name='Peptide/Emartz_view1/8'>backbone</scene>''' of 1 amino acid.  Adding to the backbone with an additional amino acid on each side gives a '''<scene name='Peptide/Emartz_view2/6'>tripeptide</scene>''' (3 amino acids).  No side groups are shown, and most hydrogens are omitted.  Now each amino acid has a 1 carbon side group so we have '''<scene name='Peptide/Emartz_view3/4'>Ala-Ala-Ala</scene>''' (tri-alanine).  Adding a carbon chain plus an NH3 on the first amino acid gives '''<scene name='Peptide/Emartz_view4/5'>Lys-Ala-Ala</scene>'''.  Adding '''<scene name='Peptide/Emartz_view5/4'> three more carbons </scene>''' to the 3rd amino acid gives isoleucine: Lys-Ala-Ile.  The 4th amino acid is threonine with its hydroxyl, giving '''<scene name='Peptide/Emartz_view6/2'> Lys-Ala-Ile-Thr</scene>'''.  Here is the shape of the '''<scene name='Peptide/Emartz_view7/2'>tetrapeptide</scene>''' (4 AAs).  The stick representation has too much detail for larger proteins, so the α-carbons are connected with a line called the '''<scene name='Peptide/Emartz_view8/3'>backbone trace</scene>'''.  Showing only the '''<scene name='Peptide/Emartz_view9/5'>backbone</scene>''' makes it easier to see the path of the protein chain (its secondary and tertiary structure).
 ==Content Attribution==
 The above scenes in Jmol were adapted from the chapter ''Peptides and Backbones'' in a tutorial on Hemoglobin first written by [[User:Eric Martz|Eric Martz]] as a ''RasMol Movie Script'' released in March, 1996, which was released as a [http://molviz.org/hemoglob Hemoglobin Tutorial] implemented with [[Chime]] in September, 1997, and a [http://molviz.org/hemoglobin Hemoglobin Tutorial] implemented with [[Jmol]] in July 2007.