View source for Degenerate nucleotide gene transcriptions

'''Editor-In-Chief:''' Henry A. Hoff
[[Image:Nucleotides.gif|thumb|right|300px|This diagram indicates the components of a nucleotide. Credit: [[b:User:Calibuon|Calibuon]].]]
A '''degenerate nucleotide''' is a nucleotide that can perform the same function or yield the same output as a structurally different nucleotide.

Within the nucleotide is a nitrogenous base derived from either purine (Pu) or pyrimidine (Py).
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==Pyrimidines==
{{main|Chemicals/Bio-organics/Pyrimidines|Pyrimidines}}
{{Chembox
| Name = Pyrimidine
| ImageFileL1 = Pyrimidine 2D aromatic full.svg
| ImageFileR1 = Pyrimidine 2D numbers.svg
| ImageFileL2 = Pyrimidine-3D-balls-2.png
| ImageAltL2 = Pyrimidine molecule
| ImageFileR2 = Pyrimidine-3D-spacefill.png
| ImageAltR2 = Pyrimidine molecule
| IUPACName = Pyrimidine
| OtherNames = 1,3-Diazine, m-Diazine
}}

'''Def.''' any "six-membered aromatic heterocycle containing four carbon atoms, two nitrogen atoms and three double bonds"<ref name=DiazineWikt>{{ cite book
|author=[[wikt:User:SemperBlotto|SemperBlotto]]
|title=diazine
|publisher=Wikimedia Foundation, Inc
|location=San Francisco, California
|date=30 March 2008
|url=https://en.wiktionary.org/wiki/diazine
|accessdate=2014-06-04 }}</ref> is called a '''diazine'''.

The diazines have the two nitrogens at the one and two positions (1,2-diazine, pyridazine), one and three (1,3-diazine, pyrimidine), and one and four (1,4-diazine, purazine).

'''Def.''' a "diazine in which the two nitrogen atoms are in the meta-positions"<ref name=PyrimidineWikt>{{ cite book
|author=[[wikt:User:SemperBlotto|SemperBlotto]]
|title=pyrimidine
|publisher=Wikimedia Foundation, Inc
|location=San Francisco, California
|date=30 March 2008
|url=https://en.wiktionary.org/wiki/pyrimidine
|accessdate=2014-06-04 }}</ref> is called a '''pyrimidine'''.
{{clear}}

==Purines==
{{main|Chemicals/Bio-organics/Purines|Purines}}
[[Image:Purin num2.svg|thumb|right|250px|The diagram shows the structure of 9H-purine with position numbers. Credit: [[commons:User:NEUROtiker|NEUROtiker]].]]
'''Def.''' any "of a class of organic heterocyclic compounds composed of fused pyrimidine and imidazole rings"<ref name=PurineWikt>{{ cite book
|author=[[wikt:User:SemperBlotto|SemperBlotto]]
|title=purine
|publisher=Wikimedia Foundation, Inc
|location=San Francisco, California
|date=23 June 2006
|url=https://en.wiktionary.org/wiki/purine
|accessdate=2014-06-04 }}</ref> is called a '''purine'''.

The hydrogen occurring at the purine seven (7) position is called '''7H-purine'''.
{{clear}}

==Nitrogenous bases==
{{main|Chemicals/Bio-organics/Nitrogenous bases|Nitrogenous bases}}
[[Image:Adenine_chemical_structure.png|thumb|40px|left|Adenine]]
[[Image:Cytosine_chemical_structure.png|thumb|40px|right|Cytosine]]
[[Image:Guanine_chemical_structure.png|thumb|60px|left|Guanine]]
[[Image:Thymine_chemical_structure.png|thumb|40px|right|Thymine]]
A '''nitrogenous (nitrogen-containing) base''' is a nitrogen-containing molecule having the chemical properties of a base. It is an organic compound that owes its property as a base to the lone pair of [[electron]]s of a nitrogen atom.

Adenine (A, Ade) is a nucleobase that is a purine derivative. The shape of adenine is complementary to thymine.

Cytosine (C, Cyt) is a nucleobase that is a pyrimidine derivative. In Watson-Crick base pairing, it forms three hydrogen bonds with guanine.

Guanine (G, Gua) is a nucleobase that is a purine derivative. In DNA, guanine is paired with cytosine.

Thymine (T, Thy) is a nucleobase that is a pyrimidine derivative. In DNA, thymine (T) binds to adenine (A) via two hydrogen bonds, thus stabilizing the nucleic acid structures.
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==Pentoses==
{{main|Chemicals/Bio-organics/Pentoses|Pentoses}}
[[Image:Alpha-D-Ribulofuranose.svg|thumb|right|100px|This diagram shows alpha-D-ribulofuranose. Credit: [[commons:User:NEUROtiker|NEUROtiker]].]]
'''Def.''' a "sugar or saccharide containing five carbon atoms"<ref name=PentoseWikt>{{ cite book
|author=[[wikt:User:Jag123|Jag123]]
|title=pentose
|publisher=Wikimedia Foundation, Inc
|location=San Francisco, California
|date=11 March 2005
|url=https://en.wiktionary.org/wiki/pentose
|accessdate=2014-06-04 }}</ref> (usually as a furanose, five-membered ring, or pyranose, six-membered ring) is called a '''pentose'''.

'''Def.''' a "pentose that is also a ketose"<ref name=KetopentoseWikt>{{ cite book
|author=[[wikt:User:SemperBlotto|SemperBlotto]]
|title=ketopentose
|publisher=Wikimedia Foundation, Inc
|location=San Francisco, California
|date=10 August 2006
|url=https://en.wiktionary.org/wiki/ketopentose
|accessdate=2014-06-04 }}</ref> [having an oxygen atom joined to a carbon atom by a double bond] is called a '''ketopentose'''.

'''Def.''' a pentose that is also a aldose having an H-C=O carbonyl functional group attached to a hydrocarbon radical and a hydrogen atom is called an '''aldopentose'''.
{{clear}}

==Nucleosides==
{{main|Chemicals/Bio-organics/Nucleosides|Nucleosides}}
'''Def.''' an organic molecule in which a nitrogenous heterocyclic base (or nucleobase), which can be either a double-ringed purine or a single-ringed pyrimidine, is covalently attached to a five-carbon pentose sugar (deoxyribose in DNA or ribose in RNA) is called a '''nucleoside'''.

==Nucleotides==
{{main|Gene transcriptions/Nucleotides|Nucleotides}}
[[Image:Inosine diphosphate.png|thumb|right|250px|This diagram shows the component structure of a diphosphate nucleotide, inosine diphosphate. Credit: [[commons:User:MiPe|MiPe]].]]
[[Image:Inosine triphosphate.PNG|thumb|left|250px|Here are the components of inosine triphosphate. Credit: [[commons:User:MiPe|MiPe]].]]
'''Def.''' the monomer that consists of a nitrogenous heterocyclic base (or nucleobase), which can be either a double-ringed purine or a single-ringed pyrimidine; a five-carbon pentose sugar (deoxyribose in DNA or ribose in RNA); and a phosphate group is called a '''nucleotide'''.

At the top right is a diagram which shows the components that make up inosine diphosphate.

The image at the left shows the components for inosine triphosphate.
{{clear}}

==Degeneracies==
{{main|Gene transcriptions/Degeneracies|Degeneracies}}
"Within biological systems, '''degeneracy''' refers to circumstances where structurally dissimilar components/modules/pathways can perform similar functions (i.e. are effectively interchangeable) under certain conditions, but perform distinct functions in other conditions.<ref name=Edelman>{{ cite journal
|  author = Edelman and Gally
| title =  Degeneracy and complexity in biological systems
|  journal = Proceedings of the National Academy of Sciences, USA
| year = 2001
| volume = 98
| issue = 24
| pages = 13763–13768
| accessdate = 2011-03-11
|  doi = 10.1073/pnas.231499798 }}</ref> Degeneracy is thus a relational property that requires comparing the behaviour of two or more components. In particular, if degeneracy is present in a pair of components then there will exist conditions where the pair will appear functionally redundant but other conditions where they will appear functionally distinct.<ref name=Edelman/><ref name=Whitacre>{{ cite journal
|  author = Whitacre
| title =  Degeneracy: a link between evolvability, robustness and complexity in biological systems
|  journal = Theoretical Biology and Medical Modelling
| year = 2010
| volume = 7
| issue = 6
| url = http://www.tbiomed.com/content/7/1/6
| accessdate = 2011-03-11
|  doi = 10.1186/1742-4682-7-6 |  pages = 6 }}</ref>

Degeneracy contributes to the robustness of biological traits through several mechanisms. Degenerate components compensate for one another under conditions where they are functionally redundant, thus providing robustness against component or pathway failure. Because degenerate components are somewhat different, they tend to harbour unique sensitivities so that a targeted attack such as a specific inhibitor is less likely to present a risk to all components at once.<ref name=Whitacre/> There are numerous biological examples where degeneracy contributes to robustness in this way. For instance, gene families can encode for diverse proteins with many distinctive roles yet sometimes these proteins can compensate for each other during lost or suppressed gene expression, as seen in the developmental roles of the adhesins gene family in Saccharomyces.<ref name=Guo>{{ cite journal
|  author = Guo et al.
| title =  A Saccharomyces gene family involved in invasive growth, cell-cell adhesion, and mating
|  journal = Proceedings of the National Academy of Sciences, USA
| year = 2000
| volume = 97
| issue = 22
| pages = 12158–63
| accessdate = 2011-03-11
|  doi = 10.1073/pnas.220420397 }}</ref> Nutrients can be metabolized by distinct metabolic pathways that are effectively interchangeable for certain metabolites even though the total effects of each pathway are not identical.<ref name=Kitano>{{ cite journal
|  author = Kitano
| title =  Biological robustness
|  journal = Nature Reviews Genetics
| year = 2004
| volume = 5
| issue = 11
| pages = 826–37
| accessdate = 2011-03-11
|  doi = 10.1038/nrg1471
|  pmid = 15520792 }}</ref><ref name=Ma>{{ cite journal
|  author = Ma and AP Zeng
| title =  The connectivity structure, giant strong component and centrality of metabolic networks
|  journal = Bioinformatics
| year = 2003
| volume = 19
| issue = 11
| pages = 1423–30
| accessdate = 2011-03-11
|  doi = 10.1093/bioinformatics/btg177
|  pmid = 12874056 }}</ref> In cancer, therapies targeting the EGF receptor are thwarted by the co-activation of alternate receptor tyrosine kinases (RTK) that have partial functional overlap with the EGF receptor (and are therefore degenerate), but are not targeted by the same specific EGF receptor inhibitor.<ref name=Huang>{{ cite journal
|  author = Huang et al.
| title =  Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma
|  journal = Proceedings of the National Academy of Sciences
| year = 2007
| volume = 104
| issue = 31
| pages = 12867
| url =
| accessdate = 2011-03-11
|  doi = 10.1073/pnas.0705158104 |  last2 = Mukasa |  first2 = A. |  last3 = Bonavia |  first3 = R. |  last4 = Flynn |  first4 = R. A. |  last5 = Brewer |  first5 = Z. E. |  last6 = Cavenee |  first6 = W. K. |  last7 = Furnari |  first7 = F. B. |  last8 = White |  first8 = F. M. }}</ref><ref name=Stommel>{{ cite journal
|  author = Stommel et al.
| title =  Coactivation of receptor tyrosine kinases affects the response of tumor cells to targeted therapies
|  journal = Science
| year = 2007
| volume = 318
| issue = 5848
| pages = 287
| accessdate = 2011-03-11
|  doi = 10.1126/science.1142946
|  pmid = 17872411 |  last2 = Kimmelman |  first2 = AC |  last3 = Ying |  first3 = H |  last4 = Nabioullin |  first4 = R |  last5 = Ponugoti |  first5 = AH |  last6 = Wiedemeyer |  first6 = R |  last7 = Stegh |  first7 = AH |  last8 = Bradner |  first8 = JE |  last9 = Ligon |  first9 = KL }}</ref> Other examples from various levels of biological organization can be found in.<ref name=Edelman/>

==Codons==
{{main|Gene transcriptions/Codons|Codons}}
A position of a codon is said to be a fourfold degenerate site if any nucleotide at this position specifies the same amino acid. For example, the third position of the glycine codons (GGA, GGG, GGC, GGU) is a fourfold degenerate site, because all nucleotide substitutions at this site are synonymous; i.e., they do not change the amino acid.

There is only one threefold degenerate site where changing to three of the four nucleotides may have no effect on the amino acid (depending on what it is changed to), while changing to the fourth possible nucleotide always results in an amino acid substitution. This is the third position of an isoleucine codon: AUU, AUC, or AUA all encode isoleucine, but AUG encodes methionine.

A position of a codon is said to be a twofold degenerate site if only two of four possible nucleotides at this position specify the same amino acid. For example, the third position of the glutamic acid codons (GAA, GAG) is a twofold degenerate site. In twofold degenerate sites, the equivalent nucleotides are always either two purines (A/G) or two pyrimidines (C/U), so only transversional substitutions (purine to pyrimidine or pyrimidine to purine) in twofold degenerate sites are nonsynonymous.<ref name=Watson>{{ cite book
| author = Watson JD, Baker TA, Bell SP, Gann A, Levine M, Oosick R
| title = Molecular Biology of the Gene
| edition =
| publisher = Pearson/Benjamin Cummings
| location = San Francisco
| year = 2008
| pages =
| isbn = 0-8053-9592-X }}</ref>

A position of a codon is said to be a non-degenerate site if any mutation at this position results in amino acid substitution.

==Notations==
{{main|Notations}}
Alphabetically,

{| class="wikitable"
|-
! IUPAC nucleotide code
! Base
|-
| A
| Adenine
|-
| B
| C or G or T (U) [not A]
|-
| C
| Cytosine
|-
| D
| A or G or T (U) [not C]
|-
| G
| Guanine
|-
| H
| A or C or T (U) [not G]
|-
| K
| G or T (U) [Keto]
|-
| M
| A or C [aMine]
|-
| N
| aNy base
|-
| R
| A or G [puRine]
|-
| S
| G or C [Strong]
|-
| T (or U in [[RNA]])
| Thymine (or Uracil)
|-
| V
| A or C or G [not T]
|-
| W
| A or T (U) [Weak]
|-
| X<ref name=Moss>{{ cite book
|author=G. P. Moss
|title=Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences
|publisher=Nomenclature Committee of the International Union of Biochemistry (NC-IUB)
|location=Department of Chemistry, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
|date= 1992
|url=http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html#400
|accessdate=2017-09-02 }}</ref>
| N, aNy base
|-
| Y
| C or T (U) [pYrimidine]
|-
|}

The International Union of Pure and Applied Chemistry (IUPAC) is an international federation of National Adhering Organizations that represents chemists in individual countries. IUPAC's Inter-divisional Committee on Nomenclature and Symbols (IUPAC nomenclature) is the recognized world authority in developing standards for the naming of the [[chemical element]]s and compounds. Some important work IUPAC has done in these fields includes standardizing nucleotide base sequence code names.

{| class="wikitable" style="margin-left:25px; margin-top:0px; float:right; text-align:center;"
|-
! Symbol<ref name="iupac"/> !! Description !!colspan=5| Bases represented
|-
| '''A''' ||align=left| '''a'''denosine || A || || || ||rowspan=5| 1
|-
| '''C''' ||align=left| '''c'''ytidine || || C || || 
|-
| '''G''' ||align=left| '''g'''uanosine || || || G || 
|-
| '''T''' ||align=left| '''t'''hymidine || || || || T 
|- 
| '''U''' ||align=left| '''u'''ridine || || || || U
|- bgcolor=#e8e8e8
| '''W''' ||align=left| '''w'''eak || A || || || T ||rowspan=6| 2
|- bgcolor=#e8e8e8
| '''S''' ||align=left| '''s'''trong || || C || G || 
|- bgcolor=#e8e8e8
| '''M''' ||align=left| [Amine] a'''m'''ino || A || C || || 
|- bgcolor=#e8e8e8
| '''K''' ||align=left| [Ketone] '''k'''eto || || || G || T 
|- bgcolor=#e8e8e8
| '''R''' ||align=left| [Purine] pu'''r'''ine || A || || G || 
|- bgcolor=#e8e8e8
| '''Y''' ||align=left| [Pyrimidine] p'''y'''rimidine || || C || || T
|- 
| '''B''' ||align=left|  not A ('''B''' comes after A) || || C || G || T  ||rowspan=4| 3
|- 
| '''D''' ||align=left|  not C ('''D''' comes after C) || A || || G || T
|- 
| '''H''' ||align=left| not G ('''H''' comes after G)|| A || C || || T
|- 
| '''V''' ||align=left| not T ('''V''' comes after T and U) || A || C || G ||
|- bgcolor=#e8e8e8
| '''N''' or '''-''' ||align=left|  a'''n'''y base (not a gap) || A || C || G || T || 4
|}

These nucleotide notations are an International Union of Pure and Applied Chemistry (IUPAC)<ref name="iupac">{{ cite book
|url=http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
|author=Nomenclature Committee of the International Union of Biochemistry (NC-IUB)
|title=Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences 1984
|accessdate=2008-02-04}}</ref> representation for a position on a DNA sequence that can be have multiple possible alternatives.

An alternative way of writing the degenerate bases has, e.g., B: (C/G/T).
{{clear}}

==Hypotheses==
{{main|Hypotheses}}
# No promoters for the transcription of A1BG use degenerate nucleotides.

==Acknowledgements==

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from [http://www.wikiversity.org Wikiversity].

==See also==
{{div col|colwidth=12em}}
* [[Action potentials]]
* [[Biomembrane Transport]]
* [[Core promoter]]
* [[Homocysteine]]
* [[Methionine]]
* [[Transporter Kinetics]]
{{Div col end}}

==References==
{{reflist|2}}

==External links==
* [http://www.bing.com/search?q=&go=&qs=n&sk=&sc=8-15&qb=1&FORM=AXRE Bing Advanced search]
* [http://www.genome.jp/ GenomeNet KEGG database]
* [http://books.google.com/ Google Books]
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google scholar Advanced Scholar Search]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Home - Gene - NCBI]
* [http://www.jstor.org/ JSTOR]
* [http://www.lycos.com/ Lycos search]
* [http://nssdc.gsfc.nasa.gov/ NASA's National Space Science Data Center]
* [http://www.ncbi.nlm.nih.gov/sites/gquery NCBI All Databases Search]
* [http://www.osti.gov/ Office of Scientific & Technical Information]
* [http://www.ncbi.nlm.nih.gov/pccompound PubChem Public Chemical Database]
* [http://www.questia.com/ Questia - The Online Library of Books and Journals]
* [http://online.sagepub.com/ SAGE journals online]
* [http://www.adsabs.harvard.edu/ The SAO/NASA Astrophysics Data System]
* [http://www.scirus.com/srsapp/advanced/index.jsp?q1= Scirus for scientific information only advanced search]
* [http://www.springerlink.com/ SpringerLink]
* [http://www.tandfonline.com/ Taylor & Francis Online]
* [http://www.wikidoc.org/index.php/Main_Page WikiDoc The Living Textbook of Medicine]
* [http://onlinelibrary.wiley.com/advanced/search Wiley Online Library Advanced Search]
* [http://search.yahoo.com/web/advanced Yahoo Advanced Web Search]

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