User:Stephen Mills/Peptide tutorial 1

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Biochemistry 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?

Scroll down when you know what it is.


Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.


You can rotate the amino acid by holding down the right mouse button and dragging.

Other things you can do:

To rotate: left drag
To Zoom: scroll button or shift + left drag
To Translate: ctrl + right drag
Right click to bring up an options menu




















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.













Name the new amino acid.


Scroll down to get the answer






















This is Tyrosine (Tyr, Y), an aromatic amino acid

Again, identify the amino and carboxy groups involved in peptide bond formation.




















Alpha Carbons

Now here are both structures. Identify the α-carbons on each amino acid.


Arginine

to label the α-carbon on Arginine.

Tyrosine

to label the α-carbon on Tyrosine.



















Dipeptides

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?







Scroll down for more.














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



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. 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 Atoms


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.





Click here to go on to the next part of this tutorial.

Click here to go back to the main Tutorial page.

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Stephen Mills

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