Naked Science Forum
Non Life Sciences => Chemistry => Topic started by: sebology on 19/02/2014 12:41:17
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In A Level chemistry we do a lot on polymerisation, especially in amino acids. The definition of an amino acid is it has an amine and a carboxylic functional group at each end; which makes me think of 3 questions:
"what stops these two groups from reacting with each other?"
"How long does a molecule have to be to double back on itself like much longer proteins do all the time"
"and if molecules can fold like this, does that mean there's an inherent 'stretchiness' to σ and π bonds?"
[diagram=699_0]
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Amines and carboxylic acids react very quickly, to form amonium and carboxylate ions (acid-base proton transfer), so amino acids usually exist as zwitterions in neutral aqueous solution.
Amines and carboxylic acids don't condense to form amides at any appreciable rate unless there is a catalyst or an enzyme around to help the reaction.
If an alpha amino acid can cyclize to form a 3-membered ring, it would be pretty strained. (2-aziridinone is a known compound, even commercially available, but not necessarily representative)
But I know amino acids can form very stable cyclodimers (2 amino acids, 6 member rings)
sigma and pi bonds are somewhat "stretchy" but it takes energy to to build tension in a molecule, just as it would any spring.
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Small rings of amino acids would be rather inflexible, both mechanically, and in terms of providing active sites for biochemical reactions.
In biological systems, enzymes constructed from amino acids catalyse many reactions. They do this by forming pockets of charge to hold metallic ions, or to match the surface charges of a biological substrate. They are able to cleave molecules by introducing reactants at just the right position, and mechanically changing their shape.
Biological proteins have large and complex shapes, and are constructed from one or more linear segments; having the end join up with the start imposes some fairly severe constraints on their construction - constraints which are apparently unnecessary for their operation.
One area where rings are seen is in circular DNA (http://en.wikipedia.org/wiki/Circular_DNA), as seen in mitochondrial DNA, some bacteria, viruses & plasmids.