Interesting Molecules of Life: Porphyrins—Part I


What is a Porphyrin? The term porphyrin denotes a class of molecules utilized in respiration and sensory processes (i.e. heme, chlorophyll, and similar molecules associated with bacteria). The purpose of the upcoming posts will be to familiarize one with patterns that seemingly meander from primitive life through the complexities associated in the oxygenation of blood and photosynthesis. At first glance, one may not readily associate a hemoglobin molecule with a chlorophyll molecule—but their molecular structures are eerily similar. The nature of life bears a common molecular machinery throughout—or otherwise: life’s atoms, molecules, and their geometric relationships have a commonality.

Much of the geometric commonality is based upon the dynamics in quantum mechanics (chemical bonding). The important aspect to why nature chose porphyrin-like structures for heme or chlorophyll is the nebulous point of bio-organic chemistry. Organic chemistry, as we know it, is said to have a potential (bio) molecular database numbering in the millions. That “glib” statement is portentous to the nature of evolution, itself! The subtle permutations which molecular evolution may “pursue” is dictated (in part) by the most energetically, stable organic species.

The geometric commonality of the porphyrin molecule is not lost to biologists or to biochemists—however it is not discussed as fully as amino acids or DNA/RNA in common popularization. Perhaps one reason is its overall complexity and lack of “a quick payoff” (or otherwise termed as the money-maker). DNA/RNA and amino acids are readily understood by most of the scientific literate public. However, ask about the common geometry of the three molecules (illustrated below), and a few may be apt to shrug their shoulders and walk away.

Hope to see you through the end of the series of posts on life’s molecules.

The Figures in this first post are obtained at the National Institutes of Health website:

(URL) http://www.ncbi.nlm.nih.gov/ 

Fig. 1 Heme molecule (part Hemoglobin molecule which is responsible for blood pigmentation) There are four heme molecules per hemoglobin protein—two of which are directly bound to an oxygen molecule

Source URL
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=54708752



Fig. 2 Deoxygenated Human Hemoglobin—(without oxygen)—structure determined through neutron diffraction of hemoglobin—without atom labeling or individual bonding. Resolution at 2 Angstrom. (Source citation at end of post)

Source URL

http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=81550


 

Source URL 
 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5496853
				

 
Fig. 4 Molecular Structure Surrounding single Chlorophyll molecule

Source URL
				http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=25750

 
Fig. 5 Factor F430—molecule associated Methanogenic bacteria

Source URL 

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=24892763&loc=ec_rcs
			
 __

REFERENCES (the references should be available behind a paywall)

Deoxygenated Hemoglobin citation reference: (Source citation: Direct determination of protonation states of histidine residues in a 2 a neutron structure of deoxy-human normal adult hemoglobin and implications for the bohr effect.  Kovalevsky AY, Chatake T, Shibayama N, Park SY, Ishikawa T, Mustyakimov M, Fisher Z, Langan P, Morimoto Y.  J.Mol.Biol. (2010) 398 p.276)

Chlorophyll with Surrounding Molecular Architecture: (Source citation: Crystal structure of plant photosystem I. Ben-Shem A, Frolow F, Nelson N.

Nature (2003) 426 p.630)

Factor  F430: (Source citation: Structure of an F430 variant from archaea associated with anaerobic oxidation of methane. Mayr S, Latkoczy C, Krüger M, Günther D, Shima S, Thauer RK, Widdel F, Jaun B.
		J. Am. Chem. Soc.. (2008) Aug 13;130(32):10758-67
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