Difference between revisions of "Uracil" - New World Encyclopedia

From New World Encyclopedia
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! {{chembox header}} | General
 
! {{chembox header}} | General
 
|-  
 
|-  
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| [[IUPAC nomenclature|Systematic name]]
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| [[IUPAC nomenclature|Systematic name]]*
 
| Pyrimidine-2,4(1''H'',3''H'')-dione
 
| Pyrimidine-2,4(1''H'',3''H'')-dione
 
|-
 
|-
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| Uracil, 2-oxy-4-oxy pyrimidine, <br/>2,4(1H,3H)-pyrimidinedione, <br/>2,4-dihydroxypryimidine, <br /> 2,4-pyrimidinediol
 
| Uracil, 2-oxy-4-oxy pyrimidine, <br/>2,4(1H,3H)-pyrimidinedione, <br/>2,4-dihydroxypryimidine, <br /> 2,4-pyrimidinediol
 
|-
 
|-
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| [[Chemical formula|Molecular formula]]
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| [[Chemical formula|Molecular formula]]*
 
| C<sub>4</sub>H<sub>4</sub>N<sub>2</sub>O<sub>2</sub>
 
| C<sub>4</sub>H<sub>4</sub>N<sub>2</sub>O<sub>2</sub>
 
|-
 
|-
−
| [[Molar mass]]
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| [[Molar mass]]*
 
| 112.08676 g/mol
 
| 112.08676 g/mol
 
|-
 
|-
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| Solid
 
| Solid
 
|-
 
|-
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| [[CAS registry number|CAS number]]
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| [[CAS registry number|CAS number]]*
 
| [66-22-8]
 
| [66-22-8]
 
|-
 
|-
 
! {{chembox header}} | Properties
 
! {{chembox header}} | Properties
 
|-
 
|-
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| [[Density]] and [[Phase (matter)|phase]]
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| [[Density]]* and [[Phase (matter)|phase]]*
 
|  <!-- NO reference for this source anyone? //—>
 
|  <!-- NO reference for this source anyone? //—>
 
|-
 
|-
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| [[Solubility]] in [[Water (molecule)|water]]
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| [[Solubility]]* in [[Water (molecule)|water]]
 
| Soluble.
 
| Soluble.
 
|-
 
|-
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<!-- | solubility info on other solvents —>
 
<!-- | solubility info on other solvents —>
 
<!-- |- —>
 
<!-- |- —>
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| [[Melting point]]
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| [[Melting point]]*
 
| 335 °C (608 K)
 
| 335 °C (608 K)
 
|-
 
|-
−
| [[Boiling point]]
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| [[Boiling point]]*
 
| N/A
 
| N/A
 
|-
 
|-
−
| [[Acid dissociation constant|Acidity]] (p''K''<sub>a</sub>)  
+
| [[Acid dissociation constant|Acidity]]* (p''K''<sub>a</sub>)  
 
| basic pK<sub>a</sub> = -3.4,<br/>acidic pK<sub>a</sub> = 9.38<sub>9</sup>.
 
| basic pK<sub>a</sub> = -3.4,<br/>acidic pK<sub>a</sub> = 9.38<sub>9</sup>.
 
|-
 
|-
 
! {{chembox header}} | Structure
 
! {{chembox header}} | Structure
 
|-
 
|-
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| [[Orbital hybridisation#Molecule shape|Molecular shape]]  
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| [[Orbital hybridisation#Molecule shape|Molecular shape]]*
 
| pyrimidine <!-- e.g. trigonal bipyramidal —>
 
| pyrimidine <!-- e.g. trigonal bipyramidal —>
 
|-
 
|-
 
! {{chembox header}} | Hazards <!--  Summary only- MSDS entry provides more complete information —>
 
! {{chembox header}} | Hazards <!--  Summary only- MSDS entry provides more complete information —>
 
|-
 
|-
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| [[Material safety data sheet|MSDS]]
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| [[Material safety data sheet|MSDS]]*
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| [[Uracil (data page)#Material Safety Data Sheet|External MSDS]]
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| [[Uracil (data page)#Material Safety Data Sheet|External MSDS]]*
 
|-
 
|-
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| Main [[Worker safety and health|hazard]]s
+
| Main [[Worker safety and health|hazard]]*s
 
| carcinogen & tetratogen <br /> with chronic exposure
 
| carcinogen & tetratogen <br /> with chronic exposure
 
|-
 
|-
−
| [[NFPA 704]]
+
| [[NFPA 704]]*
 
| {{NFPA 704 | Health=1 | Flammability=1 }}
 
| {{NFPA 704 | Health=1 | Flammability=1 }}
 
|-
 
|-
−
| [[Flash point]]
+
| [[Flash point]]*
 
| non flammable
 
| non flammable
 
|-
 
|-
−
| [[Risk and Safety Statements|R/S statement]]
+
| [[Risk and Safety Statements|R/S statement]]*
 
| [[List of R-phrases|R]]
 
| [[List of R-phrases|R]]
 
|-
 
|-
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| [[RTECS]] number
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| [[RTECS]]* number
 
| YQ8650000
 
| YQ8650000
 
|-
 
|-
−
! {{chembox header}} | [[Uracil (data page)|Supplementary data page]]
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! {{chembox header}} | [[Uracil (data page)|Supplementary data page]]*
 
|-
 
|-
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| [[Uracil (data page)#Structure and properties|Structure and<br />properties]]  
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| [[Uracil (data page)#Structure and properties|Structure and<br />properties]]*
−
| [[Refractive index|''n'']], [[Dielectric constant|ε<sub>r</sub>]], etc.  
+
| [[Refractive index|''n'']], [[Dielectric constant|ε<sub>r</sub>]]*, etc.  
 
|-
 
|-
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| [[Uracil (data page)#Thermodynamic properties|Thermodynamic<br />data]]  
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| [[Uracil (data page)#Thermodynamic properties|Thermodynamic<br />data]]*
 
| Phase behaviour<br />Solid, liquid, gas  
 
| Phase behaviour<br />Solid, liquid, gas  
 
|-
 
|-
−
| [[Uracil (data page)#Spectral data|Spectral data]]
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| [[Uracil (data page)#Spectral data|Spectral data]]*
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| [[UV/VIS spectroscopy|UV]], [[Infrared spectroscopy|IR]], [[nuclear magnetic resonance spectroscopy|NMR]], [[Mass spectrometry|MS]]
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| [[UV/VIS spectroscopy|UV]]*, [[Infrared spectroscopy|IR]]*, [[nuclear magnetic resonance spectroscopy|NMR]]*, [[Mass spectrometry|MS]]*
 
|-
 
|-
 
! {{chembox header}} | Related compounds
 
! {{chembox header}} | Related compounds
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| [[Thymine]]
 
| [[Thymine]]
 
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|-
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| {{chembox header}} | <small>Except where noted otherwise, data are given for<br /> materials in their [[standard state|standard state (at 25°C, 100 kPa)]]<br />[[wikipedia:Chemical infobox|Infobox disclaimer and references]]</small>
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| {{chembox header}} | <small>Except where noted otherwise, data are given for<br /> materials in their [[standard state|standard state (at 25°C, 100 kPa)]]*<br> </small>
 
|-
 
|-
 
|}
 
|}
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'''Uracil''' is a [[pyrimidine]] which is common and naturally occurring.<ref name="Garrett1">Garrett, Reginald H.; Grisham, Charles M. Principals of Biochemistry  with a Human Focus. United States: Brooks/Cole Thomson Learning, 1997.</ref>  Uracil was originally discovered in 1900 and it was isolated by [[hydrolysis]] of [[yeast]] [[nuclein]] that was found in [[bovine]] [[thymus]] and [[spleen]], [[herring]] [[sperm]], and [[wheat]] [[germ]].<ref name="brown1">Brown, D.J. Heterocyclic Compounds: Thy Pyrimidines. Vol 52. New York: Interscience, 1994.</ref> Uracil is a planar, unsaturated compound that has the ability to absorb light<ref name="Horton1">Horton, Robert H.; ''et al.''Principles of Biochemistry. 3rd ed. Upper Saddle River, NJ: Prentice Hall, 2002.</ref>
+
'''Uracil''' is one of the five main [[nucleotide#Chemical structure and nomenclature|nucleobase]]s found in the [[nucleic acid]]s [[DNA]] and [[RNA]]. The others are [[adenine]], [[cytosine]], [[guanine]], and [[thymine]]. However, while the other four are found in DNA, Uracil is usually only found in RNA. Uracil, thymine, and cytosine are [[pyrimidine]] derivatives, and guanine and adenine are [[purine]] derivatives.
 +
 
 +
In DNA, thymine and cytosine form hydrogen bonds with their complementary purine derivatives, adenine and cytosine, respectively. In RNA, uracil replaces thymine as the usual complement of adenine. Thus, thymine is usually seen only in DNA and uracil only in RNA.
 +
 
 +
Uracil is common and naturally occurring (Garrett et al. 1997). Uracil was originally discovered in 1900 and it was isolated by [[hydrolysis]]* of [[yeast]] nuclein that was found in [[bovine]] [[thymus]] and [[spleen]], [[herring]] [[sperm]], and [[wheat]] germ (Brown 1994).  
 +
 
 +
 
  
 
==Properties==
 
==Properties==
 +
As a [[pyrimidine]] nucleobase, thymine is a [[heterocyclic]]* [[aromatic]]* [[organic compound]]*. ''Heterocyclic'' compounds are organic compounds (those containing [[carbon]]) that contain a ring structure containing atoms in addition to carbon, such as [[sulfur]], [[oxygen]], or [[nitrogen]], as part of the ring. ''Aromaticity'' is a chemical property in which a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone.
 +
 +
Uracil is a planar, unsaturated compound that has the ability to absorb light (Horton 2002).
 +
 +
 +
 +
 
Found in [[RNA]], it [[base pair]]s with [[adenine]] and is replaced by [[thymine]] in [[DNA]]. Methylation of uracil produces [[thymine]].<ref name="madsci1">www.madsci.org</ref> It turns into thymine to protect the DNA and to improve the efficiency of [[DNA replication]]. Uracil can base pair with any of the bases depending on how the molecule arranges itself on the [[helix]], but readily pairs with [[adenine]] because the methyl group is repelled into a fixed position.<ref name="madsci1">www.madsci.org</ref> As stated, uracil pairs with adenosine through [[hydrogen bonding]].  Uracil is the [[hydrogen bond acceptor]] and can form up to three hydrogen bonds. Uracil can also bind with a [[ribose]] sugar to form a [[ribonucleoside]], [[uridine]].  When a [[phosphate]] attaches to uridine, uridine 5'-monophosphate is produced.<ref name="Horton1">Horton, Robert H.; ''et al.''Principles of Biochemistry. 3rd ed. Upper Saddle River, NJ: Prentice Hall, 2002.</ref>  
 
Found in [[RNA]], it [[base pair]]s with [[adenine]] and is replaced by [[thymine]] in [[DNA]]. Methylation of uracil produces [[thymine]].<ref name="madsci1">www.madsci.org</ref> It turns into thymine to protect the DNA and to improve the efficiency of [[DNA replication]]. Uracil can base pair with any of the bases depending on how the molecule arranges itself on the [[helix]], but readily pairs with [[adenine]] because the methyl group is repelled into a fixed position.<ref name="madsci1">www.madsci.org</ref> As stated, uracil pairs with adenosine through [[hydrogen bonding]].  Uracil is the [[hydrogen bond acceptor]] and can form up to three hydrogen bonds. Uracil can also bind with a [[ribose]] sugar to form a [[ribonucleoside]], [[uridine]].  When a [[phosphate]] attaches to uridine, uridine 5'-monophosphate is produced.<ref name="Horton1">Horton, Robert H.; ''et al.''Principles of Biochemistry. 3rd ed. Upper Saddle River, NJ: Prentice Hall, 2002.</ref>  
  
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==External links==
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ref name="Garrett1">Garrett, Reginald H.; Grisham, Charles M. Principals of Biochemistry  with a Human Focus. United States: Brooks/Cole Thomson Learning, 1997.</ref> 
 +
 
 +
<ref name="Horton1">Horton, Robert H.; ''et al.''Principles of Biochemistry. 3rd ed. Upper Saddle River, NJ: Prentice Hall, 2002.</ref>
 +
 
 +
.<ref name="brown1">Brown, D.J. Heterocyclic Compounds: Thy Pyrimidines. Vol 52. New York: Interscience, 1994.</ref>
  
 
{{Nucleic acids}}
 
{{Nucleic acids}}
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[[Category:Life sciences]]
 
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{{credit|Uracil|95452158|Heterocyclic_compound|93187808|Aromaticity|93907113}}

Revision as of 01:32, 31 December 2006

Uracil
Chemical structure of uracil
General
Systematic name Pyrimidine-2,4(1H,3H)-dione
Other names Uracil, 2-oxy-4-oxy pyrimidine,
2,4(1H,3H)-pyrimidinedione,
2,4-dihydroxypryimidine,
2,4-pyrimidinediol
Molecular formula C4H4N2O2
Molar mass 112.08676 g/mol
Appearance Solid
CAS number [66-22-8]
Properties
Density and phase
Solubility in water Soluble.
Melting point 335 °C (608 K)
Boiling point N/A
Acidity (pKa) basic pKa = -3.4,
acidic pKa = 9.389.
Structure
Molecular shape pyrimidine
Hazards
MSDS External MSDS
Main hazards carcinogen & tetratogen
with chronic exposure
NFPA 704

NFPA 704.svg

1
1
0
 
Flash point non flammable
R/S statement R
RTECS number YQ8650000
Supplementary data page
Structure and
properties 		n, εr, etc.
Thermodynamic
data 		Phase behaviour
Solid, liquid, gas
Spectral data UV, IR, NMR, MS
Related compounds
Other cations
Related compounds Thymine
Except where noted otherwise, data are given for
materials in their standard state (at 25°C, 100 kPa)

Uracil is one of the five main nucleobases found in the nucleic acids DNA and RNA. The others are adenine, cytosine, guanine, and thymine. However, while the other four are found in DNA, Uracil is usually only found in RNA. Uracil, thymine, and cytosine are pyrimidine derivatives, and guanine and adenine are purine derivatives.

In DNA, thymine and cytosine form hydrogen bonds with their complementary purine derivatives, adenine and cytosine, respectively. In RNA, uracil replaces thymine as the usual complement of adenine. Thus, thymine is usually seen only in DNA and uracil only in RNA.

Uracil is common and naturally occurring (Garrett et al. 1997). Uracil was originally discovered in 1900 and it was isolated by hydrolysis of yeast nuclein that was found in bovine thymus and spleen, herring sperm, and wheat germ (Brown 1994).


Properties

As a pyrimidine nucleobase, thymine is a heterocyclic aromatic organic compound. Heterocyclic compounds are organic compounds (those containing carbon) that contain a ring structure containing atoms in addition to carbon, such as sulfur, oxygen, or nitrogen, as part of the ring. Aromaticity is a chemical property in which a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone.

Uracil is a planar, unsaturated compound that has the ability to absorb light (Horton 2002).



Found in RNA, it base pairs with adenine and is replaced by thymine in DNA. Methylation of uracil produces thymine.[1] It turns into thymine to protect the DNA and to improve the efficiency of DNA replication. Uracil can base pair with any of the bases depending on how the molecule arranges itself on the helix, but readily pairs with adenine because the methyl group is repelled into a fixed position.[1] As stated, uracil pairs with adenosine through hydrogen bonding. Uracil is the hydrogen bond acceptor and can form up to three hydrogen bonds. Uracil can also bind with a ribose sugar to form a ribonucleoside, uridine. When a phosphate attaches to uridine, uridine 5'-monophosphate is produced.[2]

Uracil, U, undergoes keto-enol tautomeric shifts because of its resonance structures due to the NH2 substitutents and OH substitutents. Also because any nuclear instability the molecule may have from the lack of formal aromaticity is compensated by the cyclic-amidic stability.[3] The keto tautomer is referred to the lactam structure, while the enol tautomer is referred to as the lactim structure. These tautomeric forms are predominant at pH=7. The lactam structure is the most common form of uracil.


Uracil also recycles itself to form nucleotides by undergoing a series of phophoribosyltransferase reactions.[4] Degradation of uracil produces substrates, aspartate, carbon dioxide, and ammonia.[4]

C4H4N2O2 → H3NCH2CH2COO- + NH4 + CO2

Oxidative degradation of uracil produces urea and maleic acid in the presence of H2O2 and Fe2+ or in the presence of diatomic oxygen and Fe2+.

Uracil is a weak acid, the first site of ionization of uracil is not known.[5] The negative charge is placed on the oxygen anion and produces a pKa of less than or equal to 12. The basic pKa = -3.4, while the acidic pKa = 9.389. In the gas phase, uracil has 4 sites that are more acidic than water.[6]

Synthesis

There are many laboratory syntheses of uracil available. The first reaction is the simplest of the syntheses, by adding water to cytosine to produce uracil and ammonia.[4] The most common way to synthesize uracil is by the condensation of maleic acid with urea in fuming sulfuric acid[3] as seen below also. Uracil can also be synthesized by a double decomposition of thiouracil in aqueous chloroacetic acid.[3]

C4H5N3O + H2O → C4H4N2O2 + NH3
C4H4O4 + CH4N2O → C4H4N2O2 + 2 H2O + CO

Photodehydrogenation of 5,6-diuracil, which is synthesized by beta-alanine reacting with urea, produces uracil.[7]

Reactions

Uracil readily undergoes regular reactions including oxidation, nitration, and alkylation. While in the presence of PhOH/NaOCl, uracil can be visualized in the blue region of UV light.[3] Uracil also has the capability to react with elemental halogens because of the presence of more than one strongly electron donating group.[3]

File:Bromorxn.gif

Uracil readily undergoes addition to ribose sugars and phosphates to partake in synthesis and further reactions in the body. Uracil becomes Uridine-monophosphate (UMP), uridine-diphosphate (UDP), uridine-triphosphate (UTP), and uracil-diphosphate glucose (UDP-glucose). Each one of these molecules in synthesized in the body and has specific functions.

File:Uridine.gif

When uracil reactes with anhydrous hydrazine a first order kinetic reacion occurs and the ring of uracil opens up.[8] If the pH of the reaction increases to >10.5 the uracil anion forms making the reaction go much slower, the same slowing of the reaction occurs if the pH decreases because of the protonation of the hydrazine.[8] The reactivity of uracil is unchanged even if the temperature changes.[8]

File:Hydrazine.gif

Uses

Uracil can be used for drug delivery and as a pharmaceutical. When elemental fluorine is reacted with uracil, 5-fluorouracil is produced. 5-Fluorouracil is an anticancer drug (antimetabolite) used to masquerade as uracil during the nucleic acid replication process.[4] The drug molecule also fools the enzymes that help in this process to incorporate this compound in the replication and not uracil, this causes the biological polymer (cancer) not to continue synthesizing.[4]

Uracil's use in the body is to help carry out the synthesis of many enzymes necessary for cell function through bonding with riboses and phosphates.[4] Uracil serves as allosteric regulator and coenzyme for reactions in the human body and in plants.[9] UMP controls the activity of carbamoyl phosphate synthetase and aspartate transcarbamoylase in plants, while UDP and UTP requlate CPSase II activity in animals. UDP-glucose regulates the conversion of glucose to galactose int he liver and other tissues in the process of carbohydrate metabolism.[9] Uracil is also involved in the biosynthesis of polysaccharides and the transportation of sugars containing aldehydes.[9]

It can also increase the risk for cancer in cases where the body is extremely deficient in folate.[10] The defiency in folate leads to increased ratio of deoxyuracilmonophosphates (dUMP)/deoxythyminemonophosphates (dTMP) and uracil misincorporation into DNA and eventually low production of DNA.[10]

Uracil can be used to determine microbial contamination of tomatoes. Only after lactic acid bacteria have contaminated the fruit, uracil appears.[11] Uracil's derivatives, that contain a diazine ring, are used in pesticides.[12] More often used as antiphotosynthetic herbicides and destroy weeds in cotton, sugar beet, turnips, soya, peas, sunflower crops, vineyards, berry plantations, and orchards.[12]

References
ISBN links support NWE through referral fees

  1. ↑ 1.0 1.1 www.madsci.org
  2. ↑ Horton, Robert H.; et al.Principles of Biochemistry. 3rd ed. Upper Saddle River, NJ: Prentice Hall, 2002.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 Brown, D.J. Heterocyclic Compounds: Thy Pyrimidines. Vol 52. New York: Interscience, 1994. Cite error: Invalid <ref> tag; name "brown1" defined multiple times with different content
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 Garrett, Reginald H.; Grisham, Charles M. Principles of Biochemistry with a Human Focus. United States: Brooks/Cole Thomson Learning, 1997.
  5. ↑ Zorbach, W.W. Synthetic Procedures in Nucleic Acid Chemistry: Physical and Physicochemical Aids in Determination of Structure. Vol 2. New York: Wiley-Interscience, 1973.
  6. ↑ Lee,J.K.; Kurinovich, Ma. J Am Soc Mass Spectrom.13(8), 2005, 985-95.
  7. ↑ Chittenden, G.J.F.; Schwartz, Alan W. Nature.263,(5575), 350-1.
  8. ↑ 8.0 8.1 8.2 Kochetkov, N.K. and Budovskii, E.I. Organic Chemistry of Nucleic Acids Part B. New York: Plenum Press, 1972.
  9. ↑ 9.0 9.1 9.2 Brown, E.G. Ring Nitrogen and Key Biomolecules: The Biochemistry of N-Heterocycles. Boston: Lluwer Academic Publishers, 1998.
  10. ↑ 10.0 10.1 Mashiyama, S.T; et al.'Anal Biochem. 330(1),2004, 58-69.
  11. ↑ Hildalgo, A; et al.'J Agric Food Chem.53(2),2005, 349-55.
  12. ↑ 12.0 12.1 Pozharskii, A.F.; et al.Heterocycles in Life and Society: An Introduction to Heterocyclic Chemistry and Biochemistry and the Role of Heterocycles in Science, Technology, Medicine, and Agriculture. New York: John Wiley and Sons, 1997.

ref name="Garrett1">Garrett, Reginald H.; Grisham, Charles M. Principals of Biochemistry with a Human Focus. United States: Brooks/Cole Thomson Learning, 1997.</ref>

[1]

.[2]

Nucleic acids edit
Nucleobases: Adenine - Thymine - Uracil - Guanine - Cytosine - Purine - Pyrimidine
Nucleosides: Adenosine - Uridine - Guanosine - Cytidine - Deoxyadenosine - Thymidine - Deoxyguanosine - Deoxycytidine
Nucleotides: AMP - UMP - GMP - CMP - ADP - UDP - GDP - CDP - ATP - UTP - GTP - CTP - cAMP - cGMP
Deoxynucleotides: dAMP - dTMP - dUMP - dGMP - dCMP - dADP - dTDP - dUDP - dGDP - dCDP - dATP - dTTP - dUTP - dGTP - dCTP
Nucleic acids: DNA - RNA - LNA - PNA - mRNA - ncRNA - miRNA - rRNA - siRNA - tRNA - mtDNA - Oligonucleotide

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  1. ↑ Horton, Robert H.; et al.Principles of Biochemistry. 3rd ed. Upper Saddle River, NJ: Prentice Hall, 2002.
  2. ↑ Brown, D.J. Heterocyclic Compounds: Thy Pyrimidines. Vol 52. New York: Interscience, 1994.
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