Amino acids

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Lysine has its carbon atoms labeled by position. Credit: YassineMrabet.

An amphoteric organic acid containing the amino group is an amino acid. Amino acids make up proteins.

Biochemistry[edit]

Def. a compound that releases at least one hydrogen ion (H+), or donates a proton, accepts an electron in reactions, when dissolved in water is called an acid.

Def. capable of reacting chemically either as an acid or a base is called amphoteric.

Organic chemistry[edit]

Def. any of various compounds derived from ammonia (NH3) by replacement of hydrogen (H) by one or more univalent hydrocarbon radicals is called an amine.

Def. a compound derived from ammonia by replacement of a hydrogen by a metal, containing the anion NH2- is called an amide.

Def. containing the group NH2 or a substituted group NHR or NR2 united to a radical group (R) other than an acid radical is called amino.

Most organic acids (carboxylic or fatty acids) contain the carboxyl group (-COOH).

Theoretical amino acids[edit]

Def. a simple organic compound containing both a carboxyl (-COOH) and an amino (-NH2) group is called an amino acid.

Electromagnetics[edit]

The diagram shows the structures and charging of the 21 essential amino acids. Credit: Dancojocari.

Chemistry[edit]

Main sources: Chemicals/Chemistry and Chemistry
The Fischer diagrams show L-serine (on the left) and D-serine (on the right). Credit: Armin Kübelbeck.

One way amino acids are classified is dextro (D) versus levo (L). This refers to the arrangement of certain radicals relative to the COOH portion.

Dextro has NH2 or the charged NH3+ on the right or on the bottom when the double bonded oxygen is on top.

Compounds[edit]

Main sources: Chemicals/Compounds and Compounds

Def. 2-aminopropanoic acid with the chemical formula: CH3 CH(NH2)COOH is called alanine.

Def. 3-aminopropanoic acid, (NH2)CH2 CH2 COOH, is called β-alanine.

Def. 2-aminobutanedioic acid, COOHCH2 CH(NH2)COOH, or symmetrically HOOCCH(NH2)CH2COOH, is called aspartic acid.

Def. 2-aminopentanedioic acid, HOOC(CH2)2 (NH2)COOH, is called glutamic acid.

Def. 2,6-Diaminohexanoic acid, CH2OH CH (NH2)COOH, is called lysine.

Def. 2-amino-3-hydroxypropanic acid, HO2CCH(NH2)CH2OH, is called serine.

Lysine anabolisms[edit]

These enzymes are involved in the biosynthesis of lysine. Credit: Calvero.

Lysine (Lys or K),[1] is an α-amino acid that contains an α-amino group (−NH3+ protonated under physiologicl conditions), an α-carboxylic acid group (which is in the deprotonated −COO form under biological conditions), and a side chain lysyl ((CH2)4NH2), classifying it as a charged (at physiological pH), aliphatic amino acid.

Lysine is an essential amino acid, with an element formula of C6H14N2O2.

In plants and most bacteria, lysine is synthesized from aspartic acid (aspartate):[2]

Lysine is a base. The ε-amino group often participates in hydrogen bonding and as a general base in catalysis. The ε-ammonium group (NH3+) is attached to the fourth carbon from the α-carbon, which is attached to the carboxyl (C=OOH) group.[3]

Enzymes involved in this biosynthesis include:[2]

  1. Aspartokinase
  2. Aspartate-semialdehyde dehydrogenase
  3. 4-hydroxy-tetrahydrodipicolinate synthase
  4. dihydrodipicolinate reductase or 4-hydroxy-tetrahydrodipicolinate reductase
  5. 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
  6. Succinyldiaminopimelate transaminase
  7. Succinyl-diaminopimelate desuccinylase
  8. Diaminopimelate epimerase
  9. Diaminopimelate decarboxylase
  • L-aspartate is first converted to L-aspartyl-4-phosphate by aspartokinase (or aspartate kinase). Adenosine triphosphate (ATP) is needed as an energy source for this step.
  • β-Aspartate semialdehyde dehydrogenase converts this into β-aspartyl-4-semialdehyde (or β-aspartate-4-semialdehyde). Energy from Nicotinamide adenine dinucleotide phosphate (NADPH) is used in this conversion.
  • 4-hydroxy-tetrahydrodipicolinate synthase adds a pyruvate group to the β-aspartyl-4-semialdehyde, and a water molecule is removed. This causes cyclization and gives rise to (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate.
  • This product is reduced to 2,3,4,5-tetrahydrodipicolinate (or Δ1-piperidine-2,6-dicarboxylate, in the figure: (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate) by dihydrodipicolinate reductase or 4-hydroxy-tetrahydrodipicolinate reductase. This reaction consumes an NADPH molecule and releases a second water molecule.
  • Tetrahydrodipicolinate N-acetyltransferase opens this ring and gives rise to N-succinyl-L-2-amino-6-oxoheptanedionate (or N-acyl-2-amino-6-oxopimelate). Two water molecules and one acyl-CoA (succinyl-CoA) enzyme are used in this reaction.
  • N-succinyl-L-2-amino-6-oxoheptanedionate is converted into N-succinyl-LL-2,6-diaminoheptanedionate (N-acyl-2,6-diaminopimelate). This reaction is catalyzed by the enzyme succinyl diaminopimelate aminotransferase. A glutamic acid molecule is used in this reaction and an oxoacid is produced as a byproduct.
  • N-succinyl-LL-2,6-diaminoheptanedionate (N-acyl-2,6-diaminopimelate) is converted into LL-2,6-diaminoheptanedionate (L,L-2,6-diaminopimelate) by succinyl diaminopimelate desuccinylase (acyldiaminopimelate deacylase). A water molecule is consumed in this reaction and a succinate is produced as a by-product.
  • LL-2,6-diaminoheptanedionate is converted by diaminopimelate epimerase into meso-2,6-diamino-heptanedionate (meso-2,6-diaminopimelate).
  • Finally, meso-2,6-diamino-heptanedionate is converted into L-lysine by diaminopimelate decarboxylase.

In fungi, euglenoids and some prokaryotes lysine is synthesized via the alpha-aminoadipate pathway.

Homocitrate is initially synthesised from acetyl-CoA and 2-oxoglutarate by homocitrate synthase. This is then converted to homoaconitate by homoaconitate hydratase (homoaconitase) and then to homoisocitrate by homoisocitrate dehydrogenase. A nitrogen atom is added from glutamate by[aminoadipate aminotransferase to form the alpha-aminoadipic acid (α-aminoadipate) from which this pathway gets its name. This is then reduced by L-aminoadipate-semialdehyde dehydrogenase (aminoadipate reductase) via an acyl-enzyme intermediate to a semialdehyde. Reaction with glutamate by one class of saccharopine dehydrogenase yields saccharopine which is then cleaved by a second saccharopine dehydrogenase to yield lysine and oxoglutarate.[4]

Metallosphaera cuprina[edit]

This is the Kegg diagram for Lysine biosynthesis - Metallosphaera cuprina. Credit: Kanelusa Laboratories.{{fairuse}}

"The genome of the metal sulfide-oxidizing, thermoacidophilic strain Metallosphaera cuprina Ar-4 has been completely sequenced and annotated."[5]

Lysine biosynthesis enzymes are

  1. Aspartokinase Gene ID: 10492721.
  2. Aspartate-semialdehyde dehydrogenase Gene ID: 10492720.
  3. 4-hydroxy-tetrahydrodipicolinate synthase Gene ID: 10492422.
  4. dihydrodipicolinate reductase or 4-hydroxy-tetrahydrodipicolinate reductase [EC 1.17.1.18]
  5. 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
  6. Succinyldiaminopimelate transaminase
  7. Succinyl-diaminopimelate desuccinylase
  8. Diaminopimelate epimerase
  9. Diaminopimelate decarboxylase

E.C. numbers can be searched using KEGG Enzyme.

  1. Gene ID: 10492201 is MCUP_RS00020 nicotinamide-nucleotide adenylyltransferase Mcup_0004.
  2. Gene ID: 10492208 is MCUP_RS00055 threonine ammonia-lyase Mcup_0011.
  3. Gene ID: 10492243 is MCUP_RS00245 riboflavin synthase Mcup_0046.
  4. Gene ID: 10492422 is MCUP_RS01150 dihydrodipicolinate synthase family protein or 4-hydroxy-tetrahydrodipicolinate synthase Mcup_0227 [EC:4.3.3.7].
  5. Gene ID: 10492489 is MCUP_RS01510 lysine biosynthesis enzyme LysX Mcup_0295.
  6. Gene ID: 10492603 is aroE shikimate dehydrogenase Mcup_0409.
  7. Gene ID: 10492720 is MCUP_RS02695 aspartate-semialdehyde dehydrogenase Mcup_0527 [EC:1.2.1.11]; PRK08664 Location:1 → 348: PRK08664; aspartate-semialdehyde dehydrogenase; Reviewed.
  8. Gene ID: 10492721 is MCUP_RS02700 aspartate kinase Mcup_0528 [EC:2.7.2.4]; COG0527 Location:1 → 438: LysC; Aspartokinase [Amino acid transport and metabolism].
  9. Gene ID: 10492728 is MCUP_RS02735 acylphosphatase Mcup_0535.
  10. Gene ID: 10492734 is MCUP_RS02765 anthranilate synthase component I Mcup_0541.
  11. Gene ID: 10492755 is MCUP_RS02865 S26 family signal peptidase Mcup_0562.
  12. Gene ID: 10492838 is MCUP_RS03335 threonine--tRNA ligase Mcup_0647.
  13. Gene ID: 10493454 is fabG 3-ketoacyl-ACP reductase Mcup_1263.
  14. Gene ID: 10493616 is MCUP_RS06695 aspartate-semialdehyde dehydrogenase Mcup_1427 [EC:1.2.1.75] malonyl-CoA reductase (malonate semialdehyde-forming) 1.2.1.76 succinate-semialdehyde dehydrogenase (acylating); PRK08664 Location:2 → 354: PRK08664; aspartate-semialdehyde dehydrogenase; Reviewed.
  15. Gene ID: 10493694 is MCUP_RS07065 DNA polymerase IV Mcup_1505.
  16. Gene ID: 10493881 is MCUP_RS07975 enoyl-CoA hydratase Mcup_1692.
  17. Gene ID: 10493946 is MCUP_RS08300 2-ketoisovalerate ferredoxin oxidoreductase Mcup_1758.
  18. Gene ID: 10494014 is MCUP_RS08605 nucleotide pyrophosphohydrolase Mcup_1826.
  19. Gene ID: 10494032 is pyrG CTP synthetase Mcup_1844.
  20. Gene ID: 10494054 is MCUP_RS08800 peptidyl-tRNA hydrolase Mcup_1866.
  21. Gene ID: 10494093 is MCUP_RS09005 lysine biosynthesis enzyme LysX Mcup_1905.
  22. Gene ID: 10494094 is MCUP_RS09010 sulfonate ABC transporter Mcup_1906.
  23. Gene ID: 32167125 is MCUP_RS09805 DNA-directed RNA polymerase subunit P Mcup_0095.

Hypotheses[edit]

Main source: Hypotheses
  1. Genes are used to produce amino acids.
  2. Archaea have a different pathway to produce lysine than bacteria, fungi, or plants.

See also[edit]

References[edit]

  1. IUPAC-IUBMB Joint Commission on Biochemical Nomenclature. Nomenclature and Symbolism for Amino Acids and Peptides, In: Recommendations on Organic & Biochemical Nomenclature, Symbols & Terminology etc. http://www.chem.qmul.ac.uk/iupac/AminoAcid/. Retrieved 2007-05-17. 
  2. 2.0 2.1 MetaCyc: L-lysine biosynthesis I. http://metacyc.org/META/NEW-IMAGE?type=PATHWAY&object=DAPLYSINESYN-PWY. 
  3. Lysine. The Biology Project, Department of Biochemistry and Molecular Biophysics, University of Arizona.
  4. Xu H, Andi B, Qian J, West AH, Cook PF (2006). "The α-aminoadipate pathway for lysine biosynthesis in fungi". Cell Biochemistry and Biophysics 46 (1): 43–64. doi:10.1385/CBB:46:1:43. PMID 16943623. 
  5. Li-Jun Liu, Xiao-Yan You, Huajun Zheng, Shengyue Wang, Cheng-Ying Jiang, and Shuang-Jiang Liu (July 2011). "Complete genome sequence of 'Metallosphaera cuprina', a metal sulfide-oxidizing archaeon from a hot spring". Journal of Bacteriology 193 (13): 3387-8. doi:10.1128/JB.05038-11. http://jb.asm.org/content/193/13/3387.full. Retrieved 2018-1-09. 

External links[edit]

{{Anthropology resources}}{{Gene project}}{{Phosphate biochemistry}}