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chem331:phosphorus_biochemistry

This article was Under Review by Daniel and was edited by Michael. Ready for publishing.

Phosphorus Biochemistry

by Cameron Kubota

Phosphorus is an important chemical element that can be found in practically everything from its natural, rock formations to the fertilizer we use in our yards. Extensive research has been done on the many forms of phosphorus, but one of the most important places in which phosphorus plays a vital role is in our own body.

Phosphorus Overview

Phosphate Molecule (C. Ophardt, 2003)

Phosphorus itself has five valence electrons and therefore is most stable when it forms three bonds to other elements, resulting in a trigonal pyramidal configuration. However, one of its most stable and important forms is phosphate. Phosphate is the inorganic salt of phosphoric acid that has tetrahedral molecular geometry and is formed when four oxygen atoms form bonds with the phosphorus atom. Three of the oxygen atoms are singly bonded to the phosphorus atom, each with a formal charge of -1. The other oxygen has a double bond to the phosphorus atom. Both the double bonded oxygen and phosphorus atoms have formal charges of 0.1)

Phosphorus in Biological Systems

Nucleic Phosphorus

Representation of DNA Helix. Note the amount of phosphorus/phosphate present (Licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license)

In the human body, one of the most essential uses of phosphorus as a part of phosphate is in DNA and RNA. The backbone of the DNA double helix strand is comprised of mainly carbons, hydrogens, and nitrogens. However, the phosphate unit acts as a bridge, connecting each sugar unit to form the polynucleotide strand (polynucleotide is the name given to the chain consisting of nucleobase, sugar, phosphate units).2)3) These covalent bonds between the 5-carbon ring sugars and phosphates are called phosphodiester bonds and they occur at each 3' and 5' carbon terminals of the sugar. 4) Phosphorus becomes an integral element in DNA and RNA because of these phosphodiester bonds. Without phosphorus, the bonds couldn't be made that link the sugar residues, causing the DNA and RNA strands to fall apart. The idea that phosphorus is crucial in the structure of DNA was discovered by Watson and Crick in 1953 when the first structure of DNA was proposed, the same structure we adhere to today. 5) However, in 2010, Wolfe-Simon and her team found an extremophile strain of bacteria in Mono Lake, California referred to as GFAJ-1 that they claimed could exist under phosphorus-free conditions by substituting arsenic for phosphorus. However, further studies must be done to determine whether or not this breakthrough discovery holds true for other strains of DNA.6)

Phospholipids

Structure of a generic phospholipid(David P. Chynoweth MSPH, Ph.D, 2006)

Phospholipid Bilayer(Licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license)

The phospholipid, the most common being the glycerophospholipids, is a class of lipids that form the lipid bilayer in the cell membrane. An individual phospholipid is composed of elements such as carbon, phosphorus, and nitrogen, and it is because of the electronegativity difference between these atoms that gives the phospholipid its amphipathic nature, the ability of having both hydrophobic and hydrophilic properties.7) The individual phospholipids naturally line up parallel to each other with all the polar, hydrophilic “heads”, the component in which the phosphorus lies, in a line on the outside of the bilayer and all the nonpolar, hydrophobic tails on the inside of the bilayer. This specific structure gives the lipid bilayer its functions, one of which is acting as a mediator that, based on properties such as size, fluidity, and polarity, allows certain molecules and proteins to be transported across the membrane.8)

The phospholipid bilayer also houses integral transmembrane proteins that transmit and transport signals in and out of the cell. These proteins act as messengers across the cell membrane and are retained in the membrane due to long hydrophobic segments that are buried in the nonpolar membrane. The polar lengths of the proteins are attracted to the polar head of the phospholipids and stick out on both sides of the bilayer. The nature of these proteins can be summed up in a hydropathy plot.9)

Phospholipids aren't only key in lipid bilayers, but can also be found in other parts of the body. Disphosphotidylglycerol, also known as cardiolipin, was first observed in heart tissue, phosphatidylcholine and phosphatidylethanolamine were both determined to be major components of lecithin, even a calcium-activated, phospholipid-dependent protein kinase was extracted from a rat's brain proving that glycerophospholipids also regulate systems in the brain.10)11)

Energetic Phosphorus

Diagram of ATP conversion to ADP and then to AMP. Also shows release in energy(C. Kubota, 2012)

Phosphorus is crucial in energy exchange through adenosine triphosphate and adenosine diphosphate (ATP and ADP respectively).12) The body needs energy and in order to do work and through mechanisms such as the TCA cycle and Glycolysis, ATP can be formed by creating a triphosphate group on an adenine, ribose structure. In order to use this energy, one of the phosphates from this high-energy ATP molecule can be transferred to a specific substrate through kinases. Or the high energy bond can be cleaved that in turn releases the phosphate as inorganic phosphate. Either way, by cleaving the high-energy bond, our body now has energy to use. In dire cases, these enzymes can even cleave another high energy bond formed between the phosphate groups to form adenosine monophosphate which often acts as a regulator, activating the cycles needed to produce more energy rich ATP molecules.In ATP and ADP, the phosphate units create bonds that are not resonance stabilized, though it was found that magnesium interacts with the triphosphate or diphosphate group by semi-stabilizing the strongly negative charged phosphate units. The reason the phosphate bonds are considered high-energy bonds is not because the actual cleavage of the bonds releases energy, but because by cleaving the bond, the molecule can be better resonance stabilized, resulting in more stable products than reactants, a favorable reaction.13)

1) Lide, David R (2004). “CRC Handbook of Chemistry and Physics”
2) Ghosh A, Bansal M (2003). “A glossary of DNA structures from A to Z”
3) , 4) , 12) Paytan, Adina et.al. (2007). “The Oceanic Phosphorus Cycle”
5) Watson, J.D. and Crick, F.H.C. (1953). “The Structure of DNA”
6) Wolfe-Simon, Felisa et al. (2010-12-02). “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”
7) Singer, S.J. and Nicolson, Garth (1972). “The Fluid Mosaic Model of the Structure of Cell Membranes”
8) , 9) , 10) , 13) Garrett, Reginald and Grisham, Charles (2010). Biochemistry
11) Kikkawa, U. et.al. (1982). “Calcium-Activated, Phospholipid-Dependent Protein Kinase from Rat Brain”
chem331/phosphorus_biochemistry.txt · Last modified: 2016/06/07 09:53 (external edit)