Record Information
Version2.0
Creation Date2012-05-31 10:27:35 -0600
Update Date2015-09-13 12:56:08 -0600
Secondary Accession Numbers
  • ECMDB00595
Identification
Name:Hydrogen carbonate
Description:Bicarbonate is a simple single carbon molecule that plays surprisingly important roles in diverse biological processes. It is an anion that consists of one central carbon atom surrounded by three oxygen atoms in a trigonal planar arrangement, with a hydrogen atom attached to one of the oxygens. The bicarbonate ion carries a negative one formal charge and is the conjugate base of carbonic acid, H2CO3. The carbonate radical is an elusive and strong one-electron oxidant. Bicarbonate in equilibrium with carbon dioxide constitutes the main physiological buffer in cells. The bicarbonate-carbon dioxide pair stimulates the oxidation, peroxidation and nitration of several biological targets. The carbonate radical has also been proposed to be responsible for the stimulatory effects of the bicarbonate-carbon dioxide pair on oxidations mediated by hydrogen peroxide/transition metal ions. The ultimate precursor of the carbonate radical anion being bicarbonate, carbon dioxide, peroxymonocarbonate or complexes of transition metal ions with bicarbonate-derived species remains a matter of debate.
Structure
Thumb
Synonyms:
  • Bicarbonate
  • Bicarbonate (HCO3-)
  • Bicarbonate anion
  • Bicarbonate ion
  • Bicarbonate ion (HCO31-)
  • Bicarbonate ions
  • Bicarbonic acid
  • Bicarbonic acid (HCO3-)
  • Bicarbonic acid anion
  • Bicarbonic acid ion
  • Bicarbonic acid ion (HCO31-)
  • Bicarbonic acid ions
  • Carbonate
  • Carbonate (HCO31-)
  • Carbonate ion (HCO31-)
  • Carbonic acid
  • Carbonic acid (HCO31-)
  • Carbonic acid ion (HCO31-)
  • CO3-2
  • CO32-
  • CO3-2
  • CO32-
  • HCO3
  • HCO3-
  • HCO3
  • HCO3-
  • Hydrocarbonate(1-)
  • Hydrocarbonic acid(1-)
  • Hydrogen carbonate
  • Hydrogen carbonate (HCO3-)
  • Hydrogen carbonate anion
  • Hydrogen carbonate ion
  • Hydrogen carbonate ion (HCO3-)
  • Hydrogen carbonic acid
  • Hydrogen carbonic acid (HCO3-)
  • Hydrogen carbonic acid anion
  • Hydrogen carbonic acid ion
  • Hydrogen carbonic acid ion (HCO3-)
  • Hydrogencarbonate
  • Hydrogencarbonic acid
  • Hydrogentrioxocarbonate
  • Hydrogentrioxocarbonic acid
  • Monohydrogen carbonate
  • Monohydrogen carbonic acid
Chemical Formula:CHO3
Weight:Average: 61.0168
Monoisotopic: 60.992568898
InChI Key:BVKZGUZCCUSVTD-UHFFFAOYSA-M
InChI:InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-1
CAS number:71-52-3
IUPAC Name:carbonic acid
Traditional IUPAC Name:carbonic acid
SMILES:OC([O-])=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as organic carbonic acids. Organic carbonic acids are compounds comprising the carbonic acid functional group.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic carbonic acids and derivatives
Sub ClassOrganic carbonic acids
Direct ParentOrganic carbonic acids
Alternative Parents
Substituents
  • Carbonic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-1
Melting point:720 °C
Experimental Properties:
PropertyValueSource
Water Solubility:12.8 mg/mL [MERCK INDEX (1996); cold water]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility231 g/LALOGPS
logP0.6ALOGPS
logP0.25ChemAxon
logS0.57ALOGPS
pKa (Strongest Acidic)6.05ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity9.5 m³·mol⁻¹ChemAxon
Polarizability4.23 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
2 Adenosine triphosphate + L-Glutamine + Water + Hydrogen carbonate >2 ADP + Carbamoylphosphate + L-Glutamate +2 Hydrogen ion + Phosphate
Carbon dioxide + Water <> Hydrogen ion + Hydrogen carbonate
Acetyl-CoA + Adenosine triphosphate + Hydrogen carbonate <> ADP + Hydrogen ion + Malonyl-CoA + Phosphate
Cyanate + 3 Hydrogen ion + Hydrogen carbonate >2 Carbon dioxide + Ammonium
5-Aminoimidazole ribonucleotide + Adenosine triphosphate + Hydrogen carbonate > 5-Phosphoribosyl-5-carboxyaminoimidazole + ADP + Hydrogen ion + Phosphate
Carbon dioxide + Water + Phosphoenolpyruvic acid <> Hydrogen ion + Oxalacetic acid + Phosphate + Hydrogen carbonate
2 Adenosine triphosphate + L-Glutamine + Hydrogen carbonate + Water <>2 ADP + Phosphate + L-Glutamate + Carbamoylphosphate
Adenosine triphosphate + Acetyl-CoA + Hydrogen carbonate <> ADP + Phosphate + Malonyl-CoA
Cyanate + Hydrogen ion + Hydrogen carbonate <> Carbon dioxide + Carbamic acid
Adenosine triphosphate + Holo-[carboxylase] + Hydrogen carbonate + Holo-[carboxylase] <> ADP + Phosphate + Carboxybiotin-carboxyl-carrier protein + Carboxybiotin-carboxyl-carrier protein
Adenosine triphosphate + 5-Aminoimidazole ribonucleotide + Hydrogen carbonate <> ADP + Phosphate + 5-Carboxyamino-1-(5-phospho-D-ribosyl)imidazole + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
Adenosine triphosphate + Acetyl-CoA + Hydrogen carbonate > Hydrogen ion + Malonyl-CoA + Phosphate + ADP
Adenosine triphosphate + L-Glutamine + Hydrogen carbonate + Water > Hydrogen ion + Carbamoylphosphate + L-Glutamate + Phosphate + ADP
Phosphate + Oxalacetic acid <> Phosphoenolpyruvic acid + Hydrogen carbonate
Adenosine triphosphate + Hydrogen carbonate + Propionyl-CoA > Hydrogen ion + ADP + Phosphate + (S)-Methylmalonyl-CoA
Cyanate + Hydrogen carbonate + Hydrogen ion > Carbamic acid + Carbon dioxide
Adenosine triphosphate + Hydrogen carbonate + Ammonia > ADP + Phosphate + Carbamoylphosphate + Hydrogen ion
Hydrogen carbonate + Hydrogen ion <> Carbon dioxide + Water
5-Aminoimidazole ribonucleotide + Adenosine triphosphate + Hydrogen carbonate > Hydrogen ion + N5-Carboxyaminoimidazole ribonucleotide + ADP + Phosphate
2 Adenosine triphosphate + L-Glutamine + Hydrogen carbonate + Water + Ammonia + Carbamic acid + Carboxyphosphate <>2 ADP + Phosphate + L-Glutamate + Carbamoylphosphate
Cyanate + Hydrogen carbonate + 2 Hydrogen ion + Carbamic acid <> Ammonia +2 Carbon dioxide
L-Threonine + Adenosine triphosphate + Hydrogen carbonate <> L-Threonylcarbamoyladenylate + Pyrophosphate + Water
Carbon dioxide + Water > Hydrogen carbonate
Hydrogen carbonate + Cyanate + Hydrogen ion + Cyanate > Carbamic acid
Adenosine triphosphate + Pyruvic acid + Hydrogen carbonate > Adenosine diphosphate + Phosphate + Oxalacetic acid + ADP

SMPDB Pathways:
Fatty acid biosynthesisPW000900 ThumbThumb?image type=greyscaleThumb?image type=simple
Nitrogen metabolismPW000755 ThumbThumb?image type=greyscaleThumb?image type=simple
Propanoate metabolismPW000940 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyrimidine metabolismPW000942 ThumbThumb?image type=greyscaleThumb?image type=simple
arginine metabolismPW000790 ThumbThumb?image type=greyscaleThumb?image type=simple
biotin-carboxyl carrier protein assemblyPW002067 ThumbThumb?image type=greyscaleThumb?image type=simple
cyanate degradationPW002099 ThumbThumb?image type=greyscaleThumb?image type=simple
fatty acid elongation -- saturatedPW000798 ThumbThumb?image type=greyscaleThumb?image type=simple
palmitate biosynthesisPW000797 ThumbThumb?image type=greyscaleThumb?image type=simple
palmitate biosynthesis 2PW002044 ThumbThumb?image type=greyscaleThumb?image type=simple
propanoyl CoA degradationPW002057 ThumbThumb?image type=greyscaleThumb?image type=simple
purine nucleotides de novo biosynthesisPW000910 ThumbThumb?image type=greyscaleThumb?image type=simple
purine nucleotides de novo biosynthesis 1435709748PW000960 ThumbThumb?image type=greyscaleThumb?image type=simple
purine nucleotides de novo biosynthesis 2PW002033 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-9000000000-310dbbc64fba7d9c667eView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00du-9300000000-b9ab1da5629a3dfff55fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-9000000000-53429210d3161a8e792fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-9000000000-65bbb10c2768f3746b62View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-9000000000-b6afca3e3ac002546879View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-9000000000-0ef3797aeb5276c64c90View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03di-9000000000-5b50453541e6f14e35beView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-03di-9000000000-5b50453541e6f14e35beView in MoNA
References
References:
  • Casey JR: Why bicarbonate? Biochem Cell Biol. 2006 Dec;84(6):930-9. Pubmed: 17215880
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Medinas DB, Cerchiaro G, Trindade DF, Augusto O: The carbonate radical and related oxidants derived from bicarbonate buffer. IUBMB Life. 2007 Apr-May;59(4-5):255-62. Pubmed: 17505962
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Nakajima, Fumiaki; Arima, Toshikazu; Kikuchi, Shintaro; Hirano, Hachiro. Production of alkaline hydrogen carbonate. Jpn. Kokai Tokkyo Koho (2005), 15 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID6504
HMDB IDHMDB00595
Pubchem Compound ID769
Kegg IDC00288
ChemSpider ID749
WikipediaBicarbonate
BioCyc IDHCO3
EcoCyc IDHCO3

Enzymes

General function:
Involved in cyanate hydratase activity
Specific function:
Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide
Gene Name:
cynS
Uniprot ID:
P00816
Molecular weight:
17049
Reactions
Cyanate + HCO(3)(-) + 2 H(+) = NH(3) + 2 CO(2).
General function:
Involved in ATP binding
Specific function:
2 ATP + L-glutamine + HCO(3)(-) + H(2)O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate
Gene Name:
carB
Uniprot ID:
P00968
Molecular weight:
117841
Reactions
2 ATP + L-glutamine + HCO(3)(-) + H(2)O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate.
General function:
Involved in phosphoribosylaminoimidazole carboxylase activity
Specific function:
Possesses an ATPase activity that is dependent on the presence of AIR (aminoimidazole ribonucleotide). The association of purK and purE produces an enzyme complex capable of converting AIR to CAIR efficiently under physiological condition
Gene Name:
purK
Uniprot ID:
P09029
Molecular weight:
39461
Reactions
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO(3)(-) = ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole.
General function:
Involved in glutamine catabolic process
Specific function:
2 ATP + L-glutamine + HCO(3)(-) + H(2)O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate
Gene Name:
carA
Uniprot ID:
P0A6F1
Molecular weight:
41431
Reactions
2 ATP + L-glutamine + HCO(3)(-) + H(2)O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate.
General function:
Involved in acetyl-CoA carboxylase activity
Specific function:
Controls translation of mRNA for both itself and the alpha-subunit (accA) by binding to a probable hairpin in the 5' of the mRNA. Binding to mRNA inhibits translation; this is partially relieved by acetyl-CoA. Increasing amounts of mRNA also inhibit enzyme activity
Gene Name:
accD
Uniprot ID:
P0A9Q5
Molecular weight:
33322
Reactions
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA.
General function:
Involved in acetyl-CoA carboxylase activity
Specific function:
Component of the acetyl coenzyme A carboxylase (ACC) complex. First, biotin carboxylase catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the carboxyltransferase to acetyl-CoA to form malonyl-CoA
Gene Name:
accA
Uniprot ID:
P0ABD5
Molecular weight:
35241
Reactions
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA.
General function:
Involved in acetyl-CoA carboxylase activity
Specific function:
This protein is a component of the acetyl coenzyme A carboxylase complex; first, biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA
Gene Name:
accB
Uniprot ID:
P0ABD8
Molecular weight:
16687
General function:
Involved in carbonate dehydratase activity
Specific function:
Reversible hydration of carbon dioxide. Carbon dioxide formed in the bicarbonate-dependent decomposition of cyanate by cyanase (cynS) diffuses out of the cell faster than it would be hydrated to bicarbonate, so the apparent function of this enzyme is to catalyze the hydration of carbon dioxide and thus prevent depletion of cellular bicarbonate
Gene Name:
cynT
Uniprot ID:
P0ABE9
Molecular weight:
23764
Reactions
H(2)CO(3) = CO(2) + H(2)O.
General function:
Involved in ligase activity
Specific function:
This protein is a component of the acetyl coenzyme A carboxylase complex; first, biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA
Gene Name:
accC
Uniprot ID:
P24182
Molecular weight:
49320
Reactions
ATP + biotin-[carboxyl-carrier-protein] + CO(2) = ADP + phosphate + carboxy-biotin-[carboxyl-carrier-protein].
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA.
General function:
Involved in carbonate dehydratase activity
Specific function:
H(2)CO(3) = CO(2) + H(2)O
Gene Name:
can
Uniprot ID:
P61517
Molecular weight:
25097
Reactions
H(2)CO(3) = CO(2) + H(2)O.
General function:
threonylcarbamoyladenosine biosynthetic process
Specific function:
Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Catalyzes the conversion of L-threonine, bicarbonate/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of pyrophosphate. Is also able to catalyze the reverse reaction in vitro, i.e. the formation of ATP from TC-AMP and PPi. Shows higher affinity for the full-length tRNA(Thr) lacking only the t(6)A37 modification than for its fully modified counterpart. Could also be required for the maturation of 16S rRNA. Binds to double-stranded RNA but does not interact tightly with either of the ribosomal subunits, or the 70S particles.
Gene Name:
tsaC
Uniprot ID:
P45748
Molecular weight:
20767
Reactions
L-threonine + ATP + bicarbonate = L-threonylcarbamoyladenylate + diphosphate + H(2)O

Transporters

General function:
Involved in secondary active sulfate transmembrane transporter activity
Specific function:
Possible sulfate transporter
Gene Name:
ychM
Uniprot ID:
P0AFR2
Molecular weight:
59428