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Phosphodiester bond
 
 
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A phosphodiester bond is a group of strong covalent bonds
Covalent bond

A covalent bond is a form of chemical bonding that is characterized by the sharing of pairs of electrons between atoms, or between atoms and other covalent bonds....
 between the phosphorus atom
Phosphorus

Phosphorus is the chemical element that has the symbol P and atomic number 15. The name comes from the and . A Valency nonmetal of the nitrogen group, phosphorus is commonly found in inorganic phosphate minerals....
 in a phosphate group and two other molecule
Molecule

In chemistry, a molecule is defined as a sufficiently stable, electric charge neutral group of at least two atoms in a definite arrangement held together by very strong chemical bonds....
s over two ester
Ester

An ester is an often Aroma compound organic chemistry or partially organic compound formed by the reaction between an acid and an alcohol or aromatic alcohol with the elimination of water....
 bonds. Phosphodiester bonds are central to all life on Earth
Earth

Earth is the third planet from the Sun. Earth is the largest of the terrestrial planets in the Solar System in diameter, mass and density. It is also referred to as the World and Wiktionary:Terra.Note that by International Astronomical Union convention, the term "Terra" is used for naming extensive land masses, rather...
, as they make up the backbone of the strands of DNA
DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetics instructions used in the development and functioning of all known living organisms and some viruses....
.






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Phosphodiesterbonddiagram
A phosphodiester bond is a group of strong covalent bonds
Covalent bond

A covalent bond is a form of chemical bonding that is characterized by the sharing of pairs of electrons between atoms, or between atoms and other covalent bonds....
 between the phosphorus atom
Phosphorus

Phosphorus is the chemical element that has the symbol P and atomic number 15. The name comes from the and . A Valency nonmetal of the nitrogen group, phosphorus is commonly found in inorganic phosphate minerals....
 in a phosphate group and two other molecule
Molecule

In chemistry, a molecule is defined as a sufficiently stable, electric charge neutral group of at least two atoms in a definite arrangement held together by very strong chemical bonds....
s over two ester
Ester

An ester is an often Aroma compound organic chemistry or partially organic compound formed by the reaction between an acid and an alcohol or aromatic alcohol with the elimination of water....
 bonds. Phosphodiester bonds are central to all life on Earth
Earth

Earth is the third planet from the Sun. Earth is the largest of the terrestrial planets in the Solar System in diameter, mass and density. It is also referred to as the World and Wiktionary:Terra.Note that by International Astronomical Union convention, the term "Terra" is used for naming extensive land masses, rather...
, as they make up the backbone of the strands of DNA
DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetics instructions used in the development and functioning of all known living organisms and some viruses....
. In DNA and RNA
RNA

Ribonucleic acid is a type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nucleobase, a ribose sugar, and a phosphate....
, the phosphodiester bond is the linkage between the 3' carbon
Carbon

Carbon is a chemical element with chemical symbol C and atomic number 6. As a member of group 14 on the periodic table, it is nonmetallic and tetravalence?making four electrons available to form covalent bond chemical bonds....
 atom
Atom

|-! bgcolor=gray | Properties|-||}The atom is a basic unit of matter consisting of a dense, central atomic nucleus surrounded by a electron cloud of electric charge electrons....
 and the 5' carbon of the sugar deoxyribose
Deoxyribose

Deoxyribose, also known as D-Deoxyribose and 2-deoxyribose, is an aldopentose — a monosaccharide containing five carbon atoms, and including an aldehyde functional group in its linear structure....
 (in DNA) or ribose
Ribose

Ribose, primarily occurring as D-ribose, is an organic compound that occurs widely in nature. It is an aldopentose, that is a monosaccharide containing five carbon atoms that, in its acyclic form, has an aldehyde functional group at one end....
 (in RNA).

The phosphate groups in the phosphodiester bond are negatively-charged. Because the phosphate groups have a pKa
Equilibrium constant

For a general chemical equilibriumthe equilibrium constant can be defined bywhere is the activity of the chemical species A etc . It is conventional to put the activities of the products in the numerator and those of the reactants in the denominator....
 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
Magnesium in biology

Magnesium is an essential element in biological systems. Magnesium occurs typically as the Mg2+ ion. It is an essential mineral nutrient for life and is present in every cell type in every organism....
, and polyamines
Polyamine

The polyamines are organic compounds having two or more primary amino groups - such as putrescine, cadaverine, spermidine, and spermine - that are essential molecules in both eukaryotic and prokaryotic cells....
.

In order for the phosphodiester bond to be formed and the nucleotide
Nucleotide

Nucleotides are molecules that comprise the structural units of RNA and DNA. Additionally, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy , participate in cell 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 biomolecules that catalysis chemical reactions. Almost all enzymes are proteins. In enzymatic reactions, the molecules at the beginning of the process are called Substrate , and the enzyme converts them into different molecules, the products....
 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. Pyrophosphates were originally prepared by heating phosphates: the prefix pyro- derived from Greek, means "fire" in this context....
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 is a nucleotide in which a purine or pyrimidine base is linked to a ribose molecule. The base may be adenine , guanine , cytosine , or uracil ....
s can be broken by alkaline hydrolysis because of the free 2' hydroxyl group
Hydroxyl

Hydroxyl in chemistry stands for a molecule consisting of an oxygen atom and a hydrogen atom connected by a covalent bond. The neutral form is a hydroxyl Radical and the hydroxyl anion is called a hydroxide....
.

Enzyme activity

A 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....
 is an enzyme
Enzyme

Enzymes are biomolecules that catalysis chemical reactions. Almost all enzymes are proteins. In enzymatic reactions, the molecules at the beginning of the process are called Substrate , and the enzyme converts them into different molecules, the products....
 that catalyzes the hydrolysis
Hydrolysis

Hydrolysis is a chemical reaction during which one or more water are split into hydrogen and hydroxide ions which may go on to participate in further reactions....
 of phosphodiester bonds, for instance a bond in a molecule of cyclic AMP
Cyclic adenosine monophosphate

Cyclic adenosine monophosphate is a second messenger that is important in many biological processes. cAMP is derived from adenosine triphosphate and used for intracellular signal transduction in many different organisms....
 or cyclic GMP
Cyclic guanosine monophosphate

Cyclic guanosine monophosphate is a cyclic nucleotide derived from guanosine triphosphate . cGMP acts as a second messenger much like cyclic AMP, most notably by activating intracellular protein kinases in response to the binding of cell membrane-impermeable peptide hormones to the external cell surface....
.

An enzyme that plays an important role in the repair of oxidative DNA damage
DNA repair

DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolism activities and environmental factors such as UV light and Radiation can cause DNA damage, resulting in as many as 1 million individual molecular lesions per cell pe...
 is the 3'-phosphodiesterase.

During the replication of DNA
DNA replication

DNA replication, the basis for heredity, is a fundamental process occurring in all living organisms to copy their DNA. This process is "semiconservative replication" in that each strand of the original double-stranded DNA molecule serves as template for the reproduction of the complementary strand....
, there is a hole between the phosphates in the backbone left by DNA polymerase I
DNA polymerase I

DNA Polymerase I is an enzyme that participates in the process of DNA replication in prokaryotes. It is composed of 928 amino acids, and is an example of a Processivity enzyme - it can sequentially catalyze multiple polymerisations....
. DNA ligase
DNA ligase

In molecular biology, DNA ligase is a special type of ligase that can link together two DNA strands that have double-strand break . The alternative, a single-strand break, is fixed by a different type of DNA ligase using the Complementary DNA as a template but still requires DNA ligase to create the final phosphodiester bond to fully repair...
 is able to form a phosphodiester bond between the nucleotide
Nucleotide

Nucleotides are molecules that comprise the structural units of RNA and DNA. Additionally, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy , participate in cell signaling , and are incorporated into important cofactors of enzymatic reactions ....
s.

See also

  • 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....
  • Phosphodiesterase inhibitor
    Phosphodiesterase inhibitor

    A phosphodiesterase inhibitor is a medication 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 subtype....
  • DNA replication
    DNA replication

    DNA replication, the basis for heredity, is a fundamental process occurring in all living organisms to copy their DNA. This process is "semiconservative replication" in that each strand of the original double-stranded DNA molecule serves as template for the reproduction of the complementary strand....
    , DNA
    DNA

    Deoxyribonucleic acid is a nucleic acid that contains the genetics instructions used in the development and functioning of all known living organisms and some viruses....
    , ATP
    Adenosine triphosphate

    This article is about the chemical used by cells as an energy carrier. For other uses, see ATP .Adenosine-5'-triphosphate is a multifunctional nucleotide, and plays an important role in cell biology as a coenzyme that is the "molecule unit of currency" of intracellular energy transfer....
  • Teichoic acid
    Teichoic acid

    Teichoic acids are polysaccharides of glycerol phosphate or ribitol phospate linked via phosphodiester bonds....
    , DNase I
  • PDE5