The phosphodiester bonds are the covalent bonds that occur between two of the oxygen atoms of a phosphate group and the hydroxyl groups of two other different molecules. In this type of bond, the phosphate group acts as a stable bonding "bridge" between the two molecules through their oxygen atoms..
The fundamental role of phosphodiester bonds in nature is that of the formation of chains of nucleic acids, both DNA and RNA. Together with pentose sugars (deoxyribose or ribose, as the case may be), phosphate groups are part of the supporting structure of these important biomolecules..
The nucleotide chains of DNA or RNA, like proteins, can assume different three-dimensional conformations that are stabilized by non-covalent bonds, such as hydrogen bonds between complementary bases..
However, the primary structure is given by the linear sequence of nucleotides covalently linked through phosphodiester bonds..
Article index
Like peptide bonds in proteins and glycosidic bonds between monosaccharides, phosphodiester bonds result from dehydration reactions in which a water molecule is lost. Here is the general scheme of one of these dehydration reactions:
H-X1-OH + H-Xtwo-OH → H-X1-Xtwo-OH + HtwoOR
Phosphate ions correspond to the completely deprotonated conjugate base of phosphoric acid and are called inorganic phosphates, abbreviated as Pi. When two phosphate groups are linked together, an anhydrous phosphate bond is formed, and a molecule known as inorganic pyrophosphate or PPi is obtained..
When a phosphate ion is attached to a carbon atom in an organic molecule, the chemical bond is called a phosphate ester, and the resulting species is an organic monophosphate. If the organic molecule binds to more than one phosphate group, organic diphosphates or triphosphates are formed.
When a single inorganic phosphate molecule is attached to two organic groups, a phosphodiester or "phosphate diester" bond is employed. It is important not to confuse the phosphodiester bonds with the high energy phosphoanhydro bonds between the phosphate groups of molecules such as ATP, for example..
Phosphodiester bonds between adjacent nucleotides consist of two phosphoester bonds that occur between the hydroxyl at the 5 'position of one nucleotide and the hydroxyl at the 3' position of the next nucleotide in a DNA or RNA strand.
Depending on the conditions of the environment, these bonds can be hydrolyzed both enzymatically and non-enzymatically.
The formation and breaking of chemical bonds is crucial for all vital processes as we know them, and the case of phosphodiester bonds is no exception..
Among the most important enzymes that can form these bonds are DNA or RNA polymerases and ribozymes. Phosphodiesterase enzymes are capable of enzymatically hydrolyzing them.
During replication, a crucial process for cell proliferation, in each reaction cycle a dNTP (deoxynucleotide triphosphate) complementary to the template base is incorporated into the DNA through a nucleotide transfer reaction..
The polymerase is responsible for forming a new bond between the 3'-OH of the template strand and the α-phosphate of the dNTP, thanks to the energy released from the breaking of the bonds between the α and β phosphates of the dNTP, which are linked by phosphoanhydro bonds.
The result is the extension of the chain by one nucleotide and the release of a molecule of pyrophosphate (PPi) s. These reactions have been determined to merit two divalent magnesium ions (Mgtwo+), whose presence allows the electrostatic stabilization of the nucleophile OH- to get the approximation to the active site of the enzyme.
The pKto of a phosphodiester bond is close to 0, so in an aqueous solution these bonds are completely ionized, negatively charged.
This gives nucleic acid molecules a negative charge, which is neutralized thanks to ionic interactions with the positive charges of protein amino acid residues, electrostatic bonding with metal ions, or association with polyamines..
In an aqueous solution the phosphodiester bonds in DNA molecules are much more stable than in RNA molecules. In an alkaline solution, these bonds in RNA molecules are cleaved by intramolecular displacement of the nucleoside at the 5 'end by a 2' oxyanion..
As mentioned, the most relevant role of these bonds is their participation in the formation of the skeleton of nucleic acid molecules, which are one of the most important molecules in the cellular world..
The activity of topoisomerase enzymes, which actively participate in DNA replication and protein synthesis, depends on the interaction of the phosphodiester bonds at the 5 'end of DNA with the side chain of tyrosine residues in the active site of these enzymes.
Molecules that participate as second messengers, such as cyclic adenosine monophosphate (cAMP) or cyclic guanosine triphosphate (cGTP), possess phosphodiester bonds that are hydrolyzed by specific enzymes known as phosphodiesterases, whose participation is of utmost importance for many signaling processes mobile.
Glycerophospholipids, fundamental components in biological membranes, are composed of a glycerol molecule that is attached through phosphodiester bonds to the polar “head” groups that constitute the hydrophilic region of the molecule..
Yet No Comments