Phosphodiester bond
Encyclopedia
A phosphodiester bond is a group of strong covalent bond
s between a phosphate group and two 5-carbon ring carbohydrate
s (pentose
s) over two ester
bonds. Phosphodiester bonds are central to all known life, as they make up the backbone of each helical strand of DNA
. In DNA and RNA
, the phosphodiester bond is the linkage between the 3' carbon atom
of one sugar molecule and the 5' carbon atom
of another; the sugar molecules being deoxyribose
in DNA and ribose
in RNA. Phosphodiester bonds are also found in O-phosphonolipids (phospholipids) .
The phosphate groups in the phosphodiester bond are negatively-charged. Because the phosphate groups have a pKa near 0, they are negatively-charged at pH 7. This repulsion forces the phosphates to take opposite sides of the DNA strands and is neutralized by proteins (histones), metal ions such as magnesium, and polyamine
s.
In order for the phosphodiester bond to be formed and the nucleotide
s to be joined, the tri-phosphate or di-phosphate forms of the nucleotide building blocks are broken apart to give off energy required to drive the enzyme-catalyzed
reaction. When a single phosphate or two phosphates known as pyrophosphate
s break away and catalyze the reaction, the phosphodiester bond is formed.
Hydrolysis of phosphodiester bonds can be catalyzed by the action of phosphodiesterase
s which play an important role in repairing DNA sequences.
In biological systems, the phosphodiester bond between two ribonucleotide
s can be broken by alkaline hydrolysis because of the free 2' hydroxyl group
.
An enzyme that plays an important role in the repair of oxidative DNA damage is the 3'-phosphodiesterase.
During the replication of DNA, there is a hole between the phosphates in the backbone left by DNA polymerase I. DNA ligase is able to form a phosphodiester bond between the nucleotides.
Covalent bond
A covalent bond is a form of chemical bonding that is characterized by the sharing of pairs of electrons between atoms. The stable balance of attractive and repulsive forces between atoms when they share electrons is known as covalent bonding....
s between a phosphate group and two 5-carbon ring carbohydrate
Carbohydrate
A carbohydrate is an organic compound with the empirical formula ; that is, consists only of carbon, hydrogen, and oxygen, with a hydrogen:oxygen atom ratio of 2:1 . However, there are exceptions to this. One common example would be deoxyribose, a component of DNA, which has the empirical...
s (pentose
Pentose
A pentose is a monosaccharide with five carbon atoms. Pentoses are organized into two groups. Aldopentoses have an aldehyde functional group at position 1...
s) over two ester
Ester
Esters are chemical compounds derived by reacting an oxoacid with a hydroxyl compound such as an alcohol or phenol. Esters are usually derived from an inorganic acid or organic acid in which at least one -OH group is replaced by an -O-alkyl group, and most commonly from carboxylic acids and...
bonds. Phosphodiester bonds are central to all known life, as they make up the backbone of each helical strand of DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
. In DNA and RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
, the phosphodiester bond is the linkage between the 3' carbon atom
Directionality (molecular biology)
Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. The chemical convention of naming carbon atoms in the nucleotide sugar-ring numerically gives rise to a 5′-end and a 3′-end...
of one sugar molecule and the 5' carbon atom
Directionality (molecular biology)
Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. The chemical convention of naming carbon atoms in the nucleotide sugar-ring numerically gives rise to a 5′-end and a 3′-end...
of another; the sugar molecules being deoxyribose
Deoxyribose
Deoxyribose, more, precisely 2-deoxyribose, is a monosaccharide with idealized formula H---3-H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of an oxygen atom...
in DNA and ribose
Ribose
Ribose is an organic compound with the formula C5H10O5; specifically, a monosaccharide with linear form H––4–H, which has all the hydroxyl groups on the same side in the Fischer projection....
in RNA. Phosphodiester bonds are also found in O-phosphonolipids (phospholipids) .
The phosphate groups in the phosphodiester bond are negatively-charged. Because the phosphate groups have a pKa near 0, they are negatively-charged at pH 7. This repulsion forces the phosphates to take opposite sides of the DNA strands and is neutralized by proteins (histones), metal ions such as magnesium, and polyamine
Polyamine
A polyamine is an organic compound having two or more primary amino groups .This class of compounds includes several synthetic substances that are important feedstocks for the chemical industry, such as ethylene diamine , 1,3-diaminopropane , and hexamethylenediamine...
s.
In order for the phosphodiester bond to be formed and the nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s to be joined, the tri-phosphate or di-phosphate forms of the nucleotide building blocks are broken apart to give off energy required to drive the enzyme-catalyzed
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
reaction. When a single phosphate or two phosphates known as pyrophosphate
Pyrophosphate
In chemistry, the anion, the salts, and the esters of pyrophosphoric acid are called pyrophosphates. Any salt or ester containing two phosphate groups is called a diphosphate. As a food additive, diphosphates are known as E450.- Chemistry :...
s break away and catalyze the reaction, the phosphodiester bond is formed.
Hydrolysis of phosphodiester bonds can be catalyzed by the action of phosphodiesterase
Phosphodiesterase
A phosphodiesterase is any enzyme that breaks a phosphodiester bond. Usually, people speaking of phosphodiesterase are referring to cyclic nucleotide phosphodiesterases, which have great clinical significance and are described below...
s which play an important role in repairing DNA sequences.
In biological systems, the phosphodiester bond between two ribonucleotide
Ribonucleotide
A ribonucleotide or ribotide is a nucleotide in which a purine or pyrimidine base is linked to a ribose molecule and exactly one phosphate group. In living organisms the most common bases for ribonucleotides are adenine , guanine , cytosine , or uracil ....
s can be broken by alkaline hydrolysis because of the free 2' hydroxyl group
Hydroxyl
A hydroxyl is a chemical group containing an oxygen atom covalently bonded with a hydrogen atom. In inorganic chemistry, the hydroxyl group is known as the hydroxide ion, and scientists and reference works generally use these different terms though they refer to the same chemical structure in...
.
Enzyme activity
A phosphodiesterase is an enzyme that catalyzes the hydrolysis of phosphodiester bonds, for instance a bond in a molecule of cyclic AMP or cyclic GMP.An enzyme that plays an important role in the repair of oxidative DNA damage is the 3'-phosphodiesterase.
During the replication of DNA, there is a hole between the phosphates in the backbone left by DNA polymerase I. DNA ligase is able to form a phosphodiester bond between the nucleotides.
See also
- PhosphodiesterasePhosphodiesteraseA phosphodiesterase is any enzyme that breaks a phosphodiester bond. Usually, people speaking of phosphodiesterase are referring to cyclic nucleotide phosphodiesterases, which have great clinical significance and are described below...
- Phosphodiesterase inhibitorPhosphodiesterase inhibitorA phosphodiesterase inhibitor is a drug that blocks one or more of the five subtypes of the enzyme phosphodiesterase , therefore preventing the inactivation of the intracellular second messengers cyclic adenosine monophosphate and cyclic guanosine monophosphate by the respective PDE...
- DNA replicationDNA replicationDNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts with one double-stranded DNA molecule and produces two identical copies of the molecule...
, DNADNADeoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
, ATPAdenosine triphosphateAdenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism... - Teichoic acidTeichoic acidTeichoic acids are bacterial polysaccharides of glycerol phosphate or ribitol phosphate linked via phosphodiester bonds.-Location and structure:...
, DNase I - PDE5
- Nick (DNA)Nick (DNA)A nick is a discontinuity in a double stranded DNA molecule where there is no phosphodiester bond between adjacent nucleotides of one strand typically through damage or enzyme action. Nick allows for much needed release of torsion in the strand....