|MadSci Network: Biochemistry|
I am afraid I don't have a very good answer. I dug out all of my graduate biochemistry books and they all said the same thing. Triple bonded carbons are not common in biological systems. Of course they provided no references.
For a very brief overview of alkynes and what their orbitals look like visit http://www.chemhelper.com/ alkynetutorial.html.
There are some examples of alkynes in biological systems such as antibiotics and some poisons produced by frogs(1).
(1) http://www.chm.bris.ac.uk/motm/ htx/htx.htm
So here is my take on this, which more than likely will not be a complete answer. Triple bonds are very strong and stiff. These bonds do not bend or twist. I would guess that this is not a favorable thing for a biomolecule. Generally you want your biomolecule to be able to bend and twist so they can fit together to carry out a reaction.
Proteins and enzymes are fairly floppy and this allows them to adapt to their environments. If these molecules were composed of triple bonds they would be quite rigid and would lack the ability to adapt to changing conditions.
I hope that helps a little.
Try the links in the MadSci Library for more information on Biochemistry.