Phosphodiester bond: Difference between revisions
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{{Short description|–O– linkage between phosphoric acid and two other compounds}} |
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[[Image:Phosphodiester Bond Diagram.svg|thumb|200px|Diagram of phosphodiester bonds (PO<sub>4</sub><sup>3−</sup>) between three nucleotides.]] |
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[[Image:Phosphodiester Bond Diagram.svg|thumb|200px|Diagram of phosphodiester bonds ({{chem2|PO4(3-)}}) between three [[nucleotide]]s. The 5' end has a 5' carbon attached to a phosphate, and the other end, the 3' end, has a 3' carbon attached to a hydroxyl group.]] |
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In [[chemistry]], a '''phosphodiester bond''' occurs when exactly two of the [[hydroxyl group]]s ({{chem2|\sOH}}) in [[phosphoric acid]] react with hydroxyl groups on other molecules to form two [[ester]] bonds. The "bond" involves this linkage {{chem2|C\sO\sPO2-O\sC}}.<ref>{{cite web|url=https://teaching.ncl.ac.uk/bms/wiki/index.php/Phosphodiester_bond|title=Phosphodiester bond|website=School of BioMedical Sciences Wiki}}</ref> Discussion of phosphodiesters is dominated by their prevalence in [[DNA]] and [[RNA]], but phosphodiesters occur in other biomolecules, e.g. [[acyl carrier protein]]s, [[Phospholipid|phospholipids]] and the cyclic forms of GMP and AMP (cGMP and cAMP).<ref name=":03" /> |
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== Phosphodiester Backbone of DNA and RNA == |
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Phosphodiester bonds make up the backbones of DNA and RNA. Specifically, the phosphodiester bond links the [[Directionality (molecular biology)|3' carbon atom]] of one sugar molecule and the [[Directionality (molecular biology)|5' carbon atom]] of another. These saccharide groups are derived from [[deoxyribose]] in DNA and [[ribose]] in RNA. Phosphodiesters are negatively charged at pH 7.<ref>{{cite book |last1=Plaisance, Laplace |title=Fundamental Biochemistry |date=2007 |publisher=McGraf Educational |pages=331–334 |edition=3}}</ref> Repulsion between these negative charges influences the conformation of the polynucleic acids. The negative charge attracts [[histones]], metal cations such as [[Magnesium in biology#Nucleic acids|magnesium]], and [[polyamine]]s. |
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Phosphodiester bonds make up the [[Polymer backbone|backbones]] of [[DNA]] and [[RNA]]. In the phosphodiester bonds of nucleic acids, a phosphate is attached to the 5' carbon of one nucleoside and to the 3' carbon of the adjacent nucleoside. Specifically, it is the phosphodiester bonds that link the [[Directionality (molecular biology)|3' carbon atom]] of one sugar molecule and the 5' carbon atom of another (hence the name 3', 5' phosphodiester linkage used with reference to this kind of bond in DNA and RNA chains).<ref name=":1">{{Cite book |last=Nelson |first=David L. |title=Lehninger Principles of Biochemistry |last2=Cox |first2=Michael M. |publisher=W.H. Freeman and Company |year=2013 |isbn=978-1-4292-3414-6 |edition=6th |location=New York |pages=284-286, 1014-1018}}</ref> The involved saccharide groups are [[deoxyribose]] in DNA and [[ribose]] in RNA. In order for the phosphodiester bond to form''',''' joining the [[Nucleoside|nucleosides]], 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.<ref>{{cite book |last1=Kulkarni |title=Biochemistry |date=2008 |publisher=Pragati Books |pages=57–60 |display-authors=etal}}</ref> In DNA replication, for example, formation of the phosphodiester bonds is catalyzed by a [[DNA polymerase]] [[enzyme]], using a pair of [[magnesium]] [[Ion|cations]] and other supporting structures.<ref name=":1" /> Formation of the bond occurs not only in DNA and RNA replication, but also in the repair and recombination of nucleic acids, and may require the involvement of various polymerases, primers, and/or ligases. During the replication of DNA, for example, the [[DNA polymerase I]] leaves behind a hole between the phosphates in the newly formed backbone. [[DNA ligase]] is able to form a phosphodiester bond between the nucleotides on each side of the gap.<ref name=":03">{{Cite book |last=Miesfeld |first=Roger L. |title=Biochemistry |last2=McEvoy |first2=Megan M. |publisher=W.W. Norton & Company |year=2021 |isbn=9780393690453 |edition=2nd |location=New York |pages=110, 397, 941, 1034-1058}}</ref> |
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Phosphodiesters are negatively charged at [[pH]] 7.<ref>{{cite book |last1=Plaisance, Laplace |title=Fundamental Biochemistry |date=2007 |publisher=McGraf Educational |edition=3 |pages=331–334}}</ref> The negative charge attracts [[histones]], metal cations such as [[Magnesium in biology#Nucleic acids|magnesium]], and [[Polyamine|polyamines]] [needs citation]. Repulsion between these negative charges influences the conformation of the polynucleic acids. |
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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|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.<ref>{{cite book |last1=Kulkarni|display-authors=etal|title=Biochemistry |date=2008 |publisher=Pragati Books |pages=57–60}}</ref> |
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== Breaking the Phosphodiester Bond == |
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Hydrolysis of phosphodiester bonds is catalyzed by [[phosphodiesterase]]s, which are involved in repairing DNA sequences.<ref>{{cite book |last1=Alberts|display-authors=etal|title=Molecular Biology of the Cell |date=2017 |publisher=Garland Science |page=240 |edition=6}}</ref> |
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[[Hydrolysis]] (breaking) of phosphodiester bonds can be promoted in several ways. [[Phosphodiesterase|Phosphodiesterases]] are enzymes that catalyze the hydrolysis of the phosphodiester bond. These enzymes are involved in repairing DNA and RNA sequences, nucleotide salvage, and in the conversion of cGMP and cAMP to GMP and AMP, respectively.<ref name=":03" /> Hydrolysis of the phosphodiester bond also occurs chemically and spontaneously, without the aid of enzymes. For example, simple [[ribose]] (in RNA) has one more [[hydroxyl group]] than [[deoxyribose]] (in DNA), making the former less stable and more susceptible to [[alkaline hydrolysis]], wherein relatively high pH conditions induce the breaking of the phosphodiester linkage between two [[Ribonucleotide|ribonucleotides]]. The relative instability of RNA under hydroxyl attack of its phosphodiester bonds makes it inadequate for the storage of genomic information, but contributes to its usefulness in [[Transcription (biology)|transcription]] and [[Translation (biology)|translation]]. <ref name=":03" /> |
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The phosphodiester linkage between two [[ribonucleotide]]s can be broken by [[alkaline hydrolysis]], whereas the linkage between two [[deoxyribonucleotide]]s is more stable under these conditions. The relative ease of [[RNA hydrolysis]] is an effect of the presence of the 2' [[hydroxyl|hydroxyl group]]. |
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== Enzyme activity == |
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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]]. |
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An enzyme that plays an important role in the repair of oxidative DNA damage is the 3'-phosphodiesterase. |
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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. |
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== See also == |
== See also == |
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Latest revision as of 14:02, 13 January 2024
In chemistry, a phosphodiester bond occurs when exactly two of the hydroxyl groups (−OH) in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds. The "bond" involves this linkage C−O−PO−2O−C.[1] Discussion of phosphodiesters is dominated by their prevalence in DNA and RNA, but phosphodiesters occur in other biomolecules, e.g. acyl carrier proteins, phospholipids and the cyclic forms of GMP and AMP (cGMP and cAMP).[2]
Phosphodiester Backbone of DNA and RNA
[edit]Phosphodiester bonds make up the backbones of DNA and RNA. In the phosphodiester bonds of nucleic acids, a phosphate is attached to the 5' carbon of one nucleoside and to the 3' carbon of the adjacent nucleoside. Specifically, it is the phosphodiester bonds that link the 3' carbon atom of one sugar molecule and the 5' carbon atom of another (hence the name 3', 5' phosphodiester linkage used with reference to this kind of bond in DNA and RNA chains).[3] The involved saccharide groups are deoxyribose in DNA and ribose in RNA. In order for the phosphodiester bond to form, joining the nucleosides, 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.[4] In DNA replication, for example, formation of the phosphodiester bonds is catalyzed by a DNA polymerase enzyme, using a pair of magnesium cations and other supporting structures.[3] Formation of the bond occurs not only in DNA and RNA replication, but also in the repair and recombination of nucleic acids, and may require the involvement of various polymerases, primers, and/or ligases. During the replication of DNA, for example, the DNA polymerase I leaves behind a hole between the phosphates in the newly formed backbone. DNA ligase is able to form a phosphodiester bond between the nucleotides on each side of the gap.[2]
Phosphodiesters are negatively charged at pH 7.[5] The negative charge attracts histones, metal cations such as magnesium, and polyamines [needs citation]. Repulsion between these negative charges influences the conformation of the polynucleic acids.
Breaking the Phosphodiester Bond
[edit]Hydrolysis (breaking) of phosphodiester bonds can be promoted in several ways. Phosphodiesterases are enzymes that catalyze the hydrolysis of the phosphodiester bond. These enzymes are involved in repairing DNA and RNA sequences, nucleotide salvage, and in the conversion of cGMP and cAMP to GMP and AMP, respectively.[2] Hydrolysis of the phosphodiester bond also occurs chemically and spontaneously, without the aid of enzymes. For example, simple ribose (in RNA) has one more hydroxyl group than deoxyribose (in DNA), making the former less stable and more susceptible to alkaline hydrolysis, wherein relatively high pH conditions induce the breaking of the phosphodiester linkage between two ribonucleotides. The relative instability of RNA under hydroxyl attack of its phosphodiester bonds makes it inadequate for the storage of genomic information, but contributes to its usefulness in transcription and translation. [2]
See also
[edit]- Phosphodiesterase
- Phosphodiesterase inhibitor
- DNA replication, DNA, ATP
- Teichoic acid, DNase I
- PDE5
- Nick (DNA)
References
[edit]- ^ "Phosphodiester bond". School of BioMedical Sciences Wiki.
- ^ a b c d Miesfeld, Roger L.; McEvoy, Megan M. (2021). Biochemistry (2nd ed.). New York: W.W. Norton & Company. pp. 110, 397, 941, 1034–1058. ISBN 9780393690453.
- ^ a b Nelson, David L.; Cox, Michael M. (2013). Lehninger Principles of Biochemistry (6th ed.). New York: W.H. Freeman and Company. pp. 284–286, 1014–1018. ISBN 978-1-4292-3414-6.
- ^ Kulkarni; et al. (2008). Biochemistry. Pragati Books. pp. 57–60.
- ^ Plaisance, Laplace (2007). Fundamental Biochemistry (3 ed.). McGraf Educational. pp. 331–334.