Amino acids
An amphoteric organic acid containing the amino group is an amino acid.
Amino acids make up proteins.
Amino acids and proteins are the building blocks of life.
Amino acid, any of a group of organic molecules that consist of a basic amino group (NH2), an acidic carboxyl group (COOH), and an organic R group (or side chain) that is unique to each amino acid. The term amino acid is short for -amino  carboxylic acid. Each molecule contains a central carbon (C) atom, called the -carbon, to which both an amino and a carboxyl group are attached. The remaining two bonds of the -carbon atom are generally satisfied by a hydrogen (H) atom and the R group.
When proteins are digested or broken down, amino acids are left. The human body uses amino acids to make proteins to help the body:
Proteins are of primary importance to the continuing functioning of life on Earth. Proteins catalyze the vast majority of chemical reactions that occur in the cell. They provide many of the structural elements of a cell, and they help to bind cells together into tissues. Some proteins act as contractile elements to make movement possible. Others are responsible for the transport of vital materials from the outside of the cell (extracellular) to its inside (intracellular). Proteins, in the form of antibodies, protect animals from disease and, in the form of interferon, mount an intracellular attack against viruses that have eluded destruction by the antibodies and other immune system defenses. Many hormones are proteins. Last but certainly not least, proteins control the activity of genes (gene expression).
This plethora of vital tasks is reflected in the incredible spectrum of known proteins that vary markedly in their overall size, shape, and charge. By the end of the 19th century, scientists appreciated that, although there exist many different kinds of proteins in nature, all proteins upon their hydrolysis yield a class of simpler compounds, the building blocks of proteins, called amino acids. The simplest amino acid is called glycine, named for its sweet taste (glyco, sugar). It was one of the first amino acids to be identified, having been isolated from the protein gelatin in 1820. In the mid-1950s scientists involved in elucidating the relationship between proteins and genes agreed that 20 amino acids (called standard or common amino acids) were to be considered the essential building blocks of all proteins. The last of these to be discovered, threonine, had been identified in 1935.
Amino acids are classified into three groups:
Essential amino acids cannot be made by the body. As a result, they must come from food.
The 9 essential amino acids are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.
Nonessential means that our bodies produce an amino acid, even if we do not get it from the food we eat.
Nonessential amino acids include: alanine, asparagine, aspartic acid, and glutamic acid.
Conditional amino acids are usually not essential, except in times of illness and stress.
Conditional amino acids include: arginine, cysteine, glutamine, tyrosine, glycine, ornithine, proline, and serine.
You do not need to eat essential and nonessential amino acids at every meal, but getting a balance of them over the whole day is important. A diet based on a single plant item will not be adequate, but we no longer worry about pairing proteins (such as beans with rice) at a single meal. Instead we look at the adequacy of the diet overall throughout the day.
Standard Amino Acids:
Group I: Nonpolar amino acids,
Isoleucine is an isomer of leucine, and it contains two chiral carbon atoms. Proline is unique among the standard amino acids in that it does not have both free -amino and free -carboxyl groups. Instead, its side chain forms a cyclic structure as the nitrogen atom of proline is linked to two carbon atoms. (Strictly speaking, this means that proline is not an amino acid but rather an -imino acid.) Phenylalanine, as the name implies, consists of a phenyl group attached to alanine. Methionine is one of the two amino acids that possess a sulfur atom. Methionine plays a central role in protein biosynthesis (translation) as it is almost always the initiating amino acid. Methionine also provides methyl groups for metabolism. Tryptophan contains an indole ring attached to the alanyl side chain.
Group II: Polar, uncharged amino acids
Two amino acids, serine and threonine, contain aliphatic hydroxyl groups (that is, an oxygen atom bonded to a hydrogen atom, represented as OH). Tyrosine possesses a hydroxyl group in the aromatic ring, making it a phenol derivative. The hydroxyl groups in these three amino acids are subject to an important type of posttranslational modification: phosphorylation (see below Nonstandard amino acids). Like methionine, cysteine contains a sulfur atom. Unlike methionines sulfur atom, however, cysteines sulfur is very chemically reactive (see below Cysteine oxidation). Asparagine, first isolated from asparagus, and glutamine both contain amide R groups. The carbonyl group can function as a hydrogen bond acceptor, and the amino group (NH2) can function as a hydrogen bond donor.
Group III: Acidic amino acids
The side chains of aspartate and glutamate can form ionic bonds (salt bridges), and they can also function as hydrogen bond acceptors. Many proteins that bind metal ions (metalloproteins) for structural or functional purposes possess metal-binding sites containing aspartate or glutamate side chains or both. Free glutamate and glutamine play a central role in amino acid metabolism. Glutamate is the most abundant excitatory neurotransmitter in the central nervous system.
Group IV: Basic amino acids
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The imidazole side chain of histidine allows it to function in both acid and base catalysis near physiological pH values. None of the other standard amino acids possesses this important chemical property. Therefore, histidine is an amino acid that most often makes up the active sites of protein enzymes.
The majority of amino acids in Groups II, III, and IV are hydrophilic (water loving). As a result, they are often found clustered on the surface of globular proteins in aqueous solutions.
Amino Acid Reactions:
Peptide bond:
Amino acids joined by a series of peptide bonds are said to constitute a peptide. After they are incorporated into a peptide, the individual amino acids are referred to as amino acid residues. Small polymers of amino acids (fewer than 50) are called oligopeptides, while larger ones (more than 50) are referred to as polypeptides. Hence, a protein molecule is a polypeptide chain composed of many amino acid residues, with each residue joined to the next by a peptide bond. The lengths for different proteins range from a few dozen to thousands of amino acids, and each protein contains different relative proportions of the 20 standard amino acids.
Condensation reaction in which three molecules of the amino acid glycine produce a tripeptide chain, with the elimination of two molecules of water (H2O).
Condensation reaction in which three molecules of the amino acid glycine produce a tripeptide chain, with the elimination of two molecules of water (H2O).
Encyclopdia Britannica, Inc.
Cysteine oxidation:

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

# Electromagnetics

# Chemistry
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
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 -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
Lysine (Lys or K), is an -amino acid that contains an -amino group (NH3+ protonated under physiologicl conditions), an -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):
Lysine is a base. The -amino group often participates in hydrogen bonding and as a general base in catalysis. The -ammonium group (NH3+) is attached to the fourth carbon from the -carbon, which is attached to the carboxyl (C=OOH) group.
Enzymes involved in this biosynthesis include:
- Aspartokinase
- Aspartate-semialdehyde dehydrogenase
- 4-hydroxy-tetrahydrodipicolinate synthase
- dihydrodipicolinate reductase or 4-hydroxy-tetrahydrodipicolinate reductase
- 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
- Succinyldiaminopimelate transaminase
- Succinyl-diaminopimelate desuccinylase
- Diaminopimelate epimerase
- 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.
- -Aspartate semialdehyde dehydrogenase converts this into -aspartyl-4-semialdehyde (or -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 -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 1-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 (-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.

# Metallosphaera cuprina
"The genome of the metal sulfide-oxidizing, thermoacidophilic strain Metallosphaera cuprina Ar-4 has been completely sequenced and annotated."
Lysine biosynthesis enzymes are
- Aspartokinase Gene ID: 10492721.
- Aspartate-semialdehyde dehydrogenase Gene ID: 10492720.
- 4-hydroxy-tetrahydrodipicolinate synthase Gene ID: 10492422.
- dihydrodipicolinate reductase or 4-hydroxy-tetrahydrodipicolinate reductase 
- 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase 
- Succinyldiaminopimelate transaminase 
- Succinyl-diaminopimelate desuccinylase 
- Diaminopimelate epimerase 
- Diaminopimelate decarboxylase 

# Metallosphaera cuprina gene to enzyme match-up
E.C. numbers can be searched using KEGG Enzyme.
- Gene ID: 10492201 is MCUP_RS00020 nicotinamide-nucleotide adenylyltransferase Mcup_0004 .
- Gene ID: 10492208 is MCUP_RS00055 threonine ammonia-lyase Mcup_0011 .
- Gene ID: 10492218 is MCUP_RS00115 diaminohydroxyphosphoribosylaminopyrimidine reductase Mcup_0021 .
- Gene ID: 10492243 is MCUP_RS00245 riboflavin synthase Mcup_0046 .
- Gene ID: 10492277 is MCUP_RS00425 aldo/keto reductase Mcup_0081.
- Gene ID: 10492364 is MCUP_RS00875 alcohol dehydrogenase Mcup_0169 (NADP+) .
- Gene ID: 10492386 is MCUP_RS00980 hypothetical protein Mcup_0191.
- Gene ID: 10492404 is MCUP_RS01065 CoA-disulfide reductase Mcup_0209 .
- Gene ID: 10492412 is MCUP_RS01105 3-oxoacyl-ACP reductase Mcup_0217 .
- Gene ID: 10492422 is MCUP_RS01150 dihydrodipicolinate synthase family protein or 4-hydroxy-tetrahydrodipicolinate synthase Mcup_0227 .
- Gene ID: 10492489 is MCUP_RS01510 lysine biosynthesis enzyme LysX Mcup_0295 .
- Gene ID: 10492516 is MCUP_RS01655 2-polyprenylphenol hydroxylase Mcup_0322 .
- Gene ID: 10492603 is aroE shikimate dehydrogenase Mcup_0409 .
- Gene ID: 10492647 is MCUP_RS02325 3-oxoacyl-ACP reductase Mcup_0453 .
- Gene ID: 10492660 is MCUP_RS02390 3-oxoacyl-ACP reductase Mcup_0467 .
- Gene ID: 10492705 is MCUP_RS02610 ribonucleoside-diphosphate reductase , adenosylcobalamin-dependent  Mcup_0512.
- Gene ID: 10492720 is MCUP_RS02695 aspartate-semialdehyde dehydrogenase Mcup_0527 ; PRK08664 Location:1  348: PRK08664; aspartate-semialdehyde dehydrogenase; Reviewed.
- Gene ID: 10492721 is MCUP_RS02700 aspartate kinase Mcup_0528 ; COG0527 Location:1  438: LysC; Aspartokinase .
- Gene ID: 10492728 is MCUP_RS02735 acylphosphatase Mcup_0535 .
- Gene ID: 10492734 is MCUP_RS02765 anthranilate synthase component I Mcup_0541 .
- Gene ID: 10492739 is MCUP_RS02790 dehydrogenase Mcup_0546.
- Gene ID: 10492755 is MCUP_RS02865 S26 family signal peptidase Mcup_0562 .
- Gene ID: 10492771 is MCUP_RS02970 hydroxymethylglutaryl-CoA reductase (NADPH) Mcup_0580 .
- Gene ID: 10492799 is MCUP_RS03115 hypothetical protein Mcup_0608.
- Gene ID: 10492806 is MCUP_RS03150 thiol reductase thioredoxin Mcup_0615 .
- Gene ID: 10492838 is MCUP_RS03335 threonine--tRNA ligase Mcup_0647 .
- Gene ID: 10492872 is MCUP_RS03505 DsrE family protein Mcup_0681.
- Gene ID: 10492875 is MCUP_RS03520 heterodisulfide reductase Mcup_0684 .
- Gene ID: 10492876 is MCUP_RS03525 heterodisulfide reductase subunit B Mcup_0685 .
- Gene ID: 10492879 is MCUP_RS03540 heterodisulfide reductase subunit C Mcup_0688 .
- Gene ID: 10492880 is MCUP_RS03545 disulfide reductase Mcup_0689.
- Gene ID: 10492918 is MCUP_RS03695 oxidoreductase Mcup_0727.
- Gene ID: 10493002 is MCUP_RS04100 succinate-semialdehyde dehydrogenase Mcup_0811 .
- Gene ID: 10493114 is MCUP_RS04635 NAD(P)-dependent oxidoreductase Mcup_0923 .
- Gene ID: 10493216 is MCUP_RS05050 FAD-dependent oxidoreductase Mcup_1025 .
- Gene ID: 10493261 is MCUP_RS05240 pyridine nucleotide-disulfide oxidoreductase Mcup_1070 .
- Gene ID: 10493372 is MCUP_RS05540 beta-ketoacyl-ACP reductase Mcup_1181 .
- Gene ID: 10493374 is MCUP_RS05550 rubredoxin Mcup_1183 .
- Gene ID: 10493379 is MCUP_RS05575 flavin reductase Mcup_1188 .
- Gene ID: 10493392 is MCUP_RS05635 pyrroline-5-carboxylate reductase Mcup_1201 .
- Gene ID: 10493407 is MCUP_RS05700 alcohol dehydrogenase Mcup_1216 (NADP+) .
- Gene ID: 10493417 is MCUP_RS05750 thiol reductase thioredoxin Mcup_1226 .
- Gene ID: 10493454 is fabG 3-ketoacyl-ACP reductase Mcup_1263 .
- Gene ID: 10493470 is MCUP_RS06010 vitamin K epoxide reductase Mcup_1279 .
- Gene ID: 10493478 is MCUP_RS06050 nitrite reductase Mcup_1288 .
- Gene ID: 10493482 is MCUP_RS06070 component of anaerobic dehydrogenase Mcup_1292.
- Gene ID: 10493515 is MCUP_RS06215 mercury(II) reductase Mcup_1326 .
- Gene ID: 10493544 is MCUP_RS06335 ferredoxin--NADP(+) reductase Mcup_1355 .
- Gene ID: 10493553 is MCUP_RS06375 dTDP-4-dehydrorhamnose reductase Mcup_1364 .
- Gene ID: 10493582 is MCUP_RS06525 disulfide reductase Mcup_1393 .
- Gene ID: 10493583 is MCUP_RS06530 succinate dehydrogenase Mcup_1394 .
- Gene ID: 10493584 is MCUP_RS06535 succinate dehydrogenase flavoprotein subunit Mcup_1395 .
- Gene ID: 10493616 is MCUP_RS06695 aspartate-semialdehyde dehydrogenase Mcup_1427  malonyl-CoA reductase (malonate semialdehyde-forming) 1.2.1.76 succinate-semialdehyde dehydrogenase (acylating); PRK08664 Location:2  354: PRK08664; aspartate-semialdehyde dehydrogenase; Reviewed.
- Gene ID: 10493619 is MCUP_RS06710 peptide-methionine (S)-S-oxide reductase Mcup_1430 .
- Gene ID: 10493642 is MCUP_RS06820 DNA-binding protein Mcup_1453.
- Gene ID: 10493691 is MCUP_RS07050 alcohol dehydrogenase Mcup_1502 (NADP+) .
- Gene ID: 10493694 is MCUP_RS07065 DNA polymerase IV Mcup_1505 .
- Gene ID: 10493700 is MCUP_RS07095 thioredoxin-disulfide reductase Mcup_1511 .
- Gene ID: 10493802 is MCUP_RS07585 FAD-dependent oxidoreductase Mcup_1613 .
- Gene ID: 10493824 is MCUP_RS07690 aldo/keto reductase Mcup_1635.
- Gene ID: 10493838 is MCUP_RS07760 alcohol dehydrogenase (NADP+) Mcup_1649 .
- Gene ID: 10493847 is MCUP_RS07805 flavoprotein Mcup_1658 .
- Gene ID: 10493859 is MCUP_RS07865 NADH oxidase Mcup_1670 .
- Gene ID: 10493870 is MCUP_RS07920 alcohol dehydrogenase Mcup_1681 (NADP+) .
- Gene ID: 10493881 is MCUP_RS07975 enoyl-CoA hydratase Mcup_1692 .
- Gene ID: 10493903 is MCUP_RS08085 oxidoreductase Mcup_1714 .
- Gene ID: 10493920 is MCUP_RS08170 hypothetical protein Mcup_1731.
- Gene ID: 10493946 is MCUP_RS08300 2-ketoisovalerate ferredoxin oxidoreductase Mcup_1758 .
- Gene ID: 10493950 is MCUP_RS08320 4Fe-4S ferredoxin Mcup_1762 .
- Gene ID: 10494003 is MCUP_RS08555 D-glycerate dehydrogenase Mcup_1815.
- Gene ID: 10494014 is MCUP_RS08605 nucleotide pyrophosphohydrolase Mcup_1826 .
- Gene ID: 10494032 is pyrG CTP synthetase Mcup_1844 .
- Gene ID: 10494046 is MCUP_RS08765 glutamyl-tRNA reductase Mcup_1858 .
- Gene ID: 10494054 is MCUP_RS08800 peptidyl-tRNA hydrolase Mcup_1866 .
- Gene ID: 10494093 is MCUP_RS09005 lysine biosynthesis enzyme LysX Mcup_1905 .
- Gene ID: 10494094 is MCUP_RS09010 sulfonate ABC transporter Mcup_1906 .
- Gene ID: 10494097 is MCUP_RS09025 N-acetyl-gamma-glutamyl-phosphate reductase Mcup_1909 .
- Gene ID: 10494159 is MCUP_RS09350 hypothetical protein Mcup_1971.
- Gene ID: 32167125 is MCUP_RS09805 DNA-directed RNA polymerase subunit P Mcup_0095 .
- Gene ID: 32167145 is MCUP_RS09905 YHS domain-containing protein Mcup_1601.
- Gene ID: 32167149 is MCUP_RS09925 30S ribosomal protein S14 Mcup_1953.
- Gene ID: 32167150 is MCUP_RS09930 50S ribosomal protein L37e Mcup_1997.

# Hypotheses
- Genes are used to produce amino acids.
- Archaea have a different pathway to produce lysine than bacteria, fungi, or plants.

# Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
Initial content for this page in some instances came from Wikiversity.