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Revision as of 06:49, 25 July 2011
Biochemistry Tutorial #1 - Peptides Pt. 1Biochemistry Tutorial #1 - Peptides Pt. 1
The alpha amino acids polymerize, or bond, through the elimination of a water molecule. Polymers composed of two amino acid residues are known as dipeptides. Longer polymers are called oligopeptides (up to around 20 amino acids) or polypeptides (> 20 amino acids). Proteins can contain any number of amino acids linked together but each has a unique length (number of amino acids) and sequence (the identity and order of amino acids in the polymer).
In this excercise, you will identify amino acids, the amino and carboxy groups involved in the peptide bond, look at peptide bonds and oligopeptide structure and finally also examine disulfide bonds.
Which amino acid is this?Which amino acid is this?
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Scroll down when you know what it is.
You can rotate the amino acid by holding down the right mouse button and dragging.
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This is Arginine (Arg, R) and amino acid with a positively charged side chain.
Identify the α-amino and α-carboxy groups involved in peptide bond formation.
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Name the new amino acid.
Scroll down to get the answer
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This is Tyrosine (Tyr, Y), an aromatic amino acid
Again, identify the amino and carboxy groups involved in peptide bond formation.
Click to have the N and C groups labeled.
Alpha CarbonsAlpha Carbons
Now here are both structures. Identify the α-carbons on each amino acid.
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Click to label the α-carbon on Arginine
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Click to label the α-carbon on Tyrosine
DipeptidesDipeptides
Identify the main chain groups and side chains of this dipeptide.
Distinguish which end is the amino terminus and which amino acid is at the carboxyl terminus?
Which amino acid is at the N terminus? Which is at the C terminus?
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Click to label the N and C termini.
Click to label the two amino acids.
Scroll down for more.
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Notice that the Arginine is on the amino terminal end and the Tyrosine is on the carboxy terminal end.
The short way to name this dipeptide is: Arg-Tyr or RY
Identify the atoms involved in the peptide bond between Tyrosine and Arginine
Click to change the color of those atoms to white.
Peptide bonds almost always assume the trans conformation: that in which successive alpha carbon atoms are on opposite sides of the peptide (C-N) bond joining them. Click to show this trans bond. The exception are peptide bonds involving proline (when P is on the C-terminal side of the bond) - these can be trans or cis.
Backbone AtomsBackbone Atoms
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If the R groups (side chains) of the amino acids are no longer displayed, then you will be looking at the backbone of the dipeptide.
This dipeptide has a completely extended conformation.
Rotate the molecule and you should notice how planar the peptide bond is.