Information

2.7: Amino Acids - Biology


Amino acids are the building blocks (monomers) of proteins. The shape and other properties of each protein is dictated by the precise sequence of amino acids in it.

Each amino acid consists of an alpha carbon atom to which is attached

  • a hydrogen atom
  • an amino group (hence "amino" acid)
  • a carboxyl group (-COOH). This gives up a proton and is thus an acid (hence amino "acid")
  • one of 20 different "R" groups. It is the structure of the R group that determines which of the 20 it is and its special properties. The amino acid shown here is Alanine
Table 2.7.1: Types of Amino Acids. For each amino acid both three-letter and single letter codes are given
AlanineAlaAhydrophobic
ArginineArgRfree amino group makes it basic and hydrophilic
AsparagineAsnNcarbohydrate can be covalently linked ("N-linked) to its -NH
Aspartic acidAspDfree carboxyl group makes it acidic and hydrophilic
CysteineCysCoxidation of their sulfhydryl (-SH) groups link 2 Cys (S-S)
Glutamic acidGluEfree carboxyl group makes it acidic and hydrophilic
GlutamineGlnQmoderately hydrophilic
GlycineGlyGso small it is amphiphilic (can exist in any surroundings)
HistidineHisHbasic and hydrophilic
IsoleucineIleIhydrophobic
LeucineLeuLhydrophobic
LysineLysKstrongly basic and hydrophilic
MethionineMetMhydrophobic
PhenylalaninePheFvery hydrophobic
ProlineProPcauses kinks in the chain
SerineSerScarbohydrate can be covalently linked ("O-linked") to its -OH
ThreonineThrTcarbohydrate can be covalently linked ("O-linked") to its -OH
TryptophanTrpWscarce in most plant proteins
TyrosineTyrYa phosphate or sulfate group can be covalently attached to its -OH
ValineValVhydrophobic

The Essential Amino Acids

Humans must include adequate amounts of 9 amino acids in their diet.

  • Histidine
  • Isoleucine
  • Leucine
  • Lysine
  • Methionine (and/or cysteine)
  • Phenylalanine (and/or tyrosine)
  • Threonine
  • Tryptophan
  • Valine

These "essential" amino acids cannot be synthesized from other precursors. However, cysteine can partially meet the need for methionine (they both contain sulfur), and tyrosine can partially substitute for phenylalanine. Two of the essential amino acids, lysine and tryptophan, are poorly represented in most plant proteins. Thus strict vegetarians should ensure that their diet contains sufficient amounts of these two amino acids. 19 of the 20 amino acids listed above can exist in two forms in three dimensions.


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Contents

The first few amino acids were discovered in the early 19th century. [17] [18] In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named asparagine, the first amino acid to be discovered. [19] [20] Cystine was discovered in 1810, [21] although its monomer, cysteine, remained undiscovered until 1884. [20] [22] Glycine and leucine were discovered in 1820. [23] The last of the 20 common amino acids to be discovered was threonine in 1935 by William Cumming Rose, who also determined the essential amino acids and established the minimum daily requirements of all amino acids for optimal growth. [24] [25]

The unity of the chemical category was recognized by Wurtz in 1865, but he gave no particular name to it. [26] The first use of the term "amino acid" in the English language dates from 1898, [27] while the German term, Aminosäure, was used earlier. [28] Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis. In 1902, Emil Fischer and Franz Hofmeister independently proposed that proteins are formed from many amino acids, whereby bonds are formed between the amino group of one amino acid with the carboxyl group of another, resulting in a linear structure that Fischer termed "peptide". [29]

In the structure shown at the top of the page, R represents a side chain specific to each amino acid. The carbon atom next to the carboxyl group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as alpha amino acids. [30] These include amino acids such as proline which contain secondary amines, which used to be often referred to as "imino acids". [31] [32] [33]

Isomerism Edit

Alpha-amino acids are the common natural forms of amino acids. With the exception of glycine, other natural amino acids adopt the L configuration. [34] While L-amino acids represent all of the amino acids found in proteins during translation in the ribosome.

The L and D convention for amino acid configuration refers not to the optical activity of the amino acid itself but rather to the optical activity of the isomer of glyceraldehyde from which that amino acid can, in theory, be synthesized (D-glyceraldehyde is dextrorotatory L-glyceraldehyde is levorotatory). In alternative fashion, the (S) and (R) designators are used to indicate the absolute configuration. Almost all of the amino acids in proteins are (S) at the α carbon, with cysteine being (R) and glycine non-chiral. [35] Cysteine has its side chain in the same geometric location as the other amino acids, but the R/S terminology is reversed because sulfur has higher atomic number compared to the carboxyl oxygen which gives the side chain a higher priority by the Cahn-Ingold-Prelog sequence rules, whereas the atoms in most other side chains give them lower priority compared to the carboxyl group. [ citation needed ]

D-amino acid residues are found in some proteins, but they are rare.

Side chains Edit

Amino acids are designated as α- when the nitrogen atom is attached to the carbon atom adjacent to the carboxyl group: in this case the compound contains the substructure N–C–CO2. Amino acids with the sub-structure N–C–C–CO2 are classified as β- amino acids. γ-Amino acids contain the substructure N–C–C–C–CO2, and so on. [36]

Amino acids are usually classified by the properties of their side chain into four groups. The side chain can make an amino acid a weak acid or a weak base, and a hydrophile if the side chain is polar or a hydrophobe if it is nonpolar. [34] The phrase "branched-chain amino acids" or BCAA refers to the amino acids having aliphatic side chains that are linear these are leucine, isoleucine, and valine. Proline is the only proteinogenic amino acid whose side-group links to the α-amino group and, thus, is also the only proteinogenic amino acid containing a secondary amine at this position. [34] In chemical terms, proline is, therefore, an imino acid, since it lacks a primary amino group, [37] although it is still classed as an amino acid in the current biochemical nomenclature [38] and may also be called an "N-alkylated alpha-amino acid". [39]

Zwitterions Edit

In aqueous solution amino acids exist in two forms (as illustrated at the right), the molecular form and the zwitterion form in equilibrium with each other. The two forms coexist over the pH range pK1 − 2 to pK2 + 2 , which for glycine is pH 0–12. The ratio of the concentrations of the two isomers is independent of pH. The value of this ratio cannot be determined experimentally.

Because all amino acids contain amine and carboxylic acid functional groups, they are amphiprotic. [34] At pH = pK1 (approximately 2.2) there will be equal concentration of the species NH +
3 CH(R)CO
2 H and NH +
3 CH(R)CO −
2 and at pH = pK2 (approximately 10) there will be equal concentration of the species NH +
3 CH(R)CO −
2 and NH
2 CH(R)CO −
2 . It follows that the neutral molecule and the zwitterion are effectively the only species present at biological pH. [40]

It is generally assumed that the concentration of the zwitterion is much greater than the concentration of the neutral molecule on the basis of comparisons with the known pK values of amines and carboxylic acids.

Isoelectric point Edit

Proteinogenic amino acids Edit

Amino acids are the structural units (monomers) that make up proteins. They join together to form short polymer chains called peptides or longer chains called either polypeptides or proteins. These chains are linear and unbranched, with each amino acid residue within the chain attached to two neighboring amino acids. The process of making proteins encoded by DNA/RNA genetic material is called translation and involves the step-by-step addition of amino acids to a growing protein chain by a ribozyme that is called a ribosome. [42] The order in which the amino acids are added is read through the genetic code from an mRNA template, which is an RNA copy of one of the organism's genes.

Twenty-two amino acids are naturally incorporated into polypeptides and are called proteinogenic or natural amino acids. [34] Of these, 20 are encoded by the universal genetic code. The remaining 2, selenocysteine and pyrrolysine, are incorporated into proteins by unique synthetic mechanisms. Selenocysteine is incorporated when the mRNA being translated includes a SECIS element, which causes the UGA codon to encode selenocysteine instead of a stop codon. [43] Pyrrolysine is used by some methanogenic archaea in enzymes that they use to produce methane. It is coded for with the codon UAG, which is normally a stop codon in other organisms. [44] This UAG codon is followed by a PYLIS downstream sequence. [45]

Several independent evolutionary studies, using different types of data, have suggested that Gly, Ala, Asp, Val, Ser, Pro, Glu, Leu, Thr (i.e. G, A, D, V, S, P, E, L, T) may belong to a group of amino acids that constituted the early genetic code, whereas Cys, Met, Tyr, Trp, His, Phe (i.e. C, M, Y, W, H, F) may belong to a group of amino acids that constituted later additions of the genetic code. [46] [47] [48] [49]

Non-proteinogenic amino acids Edit

Aside from the 22 proteinogenic amino acids, many non-proteinogenic amino acids are known. Those either are not found in proteins (for example carnitine, GABA, levothyroxine) or are not produced directly and in isolation by standard cellular machinery (for example, hydroxyproline and selenomethionine).

Non-proteinogenic amino acids that are found in proteins are formed by post-translational modification, which is modification after translation during protein synthesis. These modifications are often essential for the function or regulation of a protein. For example, the carboxylation of glutamate allows for better binding of calcium cations, [50] and collagen contains hydroxyproline, generated by hydroxylation of proline. [51] Another example is the formation of hypusine in the translation initiation factor EIF5A, through modification of a lysine residue. [52] Such modifications can also determine the localization of the protein, e.g., the addition of long hydrophobic groups can cause a protein to bind to a phospholipid membrane. [53]

Some non-proteinogenic amino acids are not found in proteins. Examples include 2-aminoisobutyric acid and the neurotransmitter gamma-aminobutyric acid. Non-proteinogenic amino acids often occur as intermediates in the metabolic pathways for standard amino acids – for example, ornithine and citrulline occur in the urea cycle, part of amino acid catabolism (see below). [54] A rare exception to the dominance of α-amino acids in biology is the β-amino acid beta alanine (3-aminopropanoic acid), which is used in plants and microorganisms in the synthesis of pantothenic acid (vitamin B5), a component of coenzyme A. [55]

Nonstandard amino acids Edit

The 20 amino acids that are encoded directly by the codons of the universal genetic code are called standard or canonical amino acids. A modified form of methionine (N-formylmethionine) is often incorporated in place of methionine as the initial amino acid of proteins in bacteria, mitochondria and chloroplasts. Other amino acids are called nonstandard or non-canonical. Most of the nonstandard amino acids are also non-proteinogenic (i.e. they cannot be incorporated into proteins during translation), but two of them are proteinogenic, as they can be incorporated translationally into proteins by exploiting information not encoded in the universal genetic code.

The two nonstandard proteinogenic amino acids are selenocysteine (present in many non-eukaryotes as well as most eukaryotes, but not coded directly by DNA) and pyrrolysine (found only in some archaea and at least one bacterium). The incorporation of these nonstandard amino acids is rare. For example, 25 human proteins include selenocysteine in their primary structure, [56] and the structurally characterized enzymes (selenoenzymes) employ selenocysteine as the catalytic moiety in their active sites. [57] Pyrrolysine and selenocysteine are encoded via variant codons. For example, selenocysteine is encoded by stop codon and SECIS element. [10] [11] [12]

In human nutrition Edit

When taken up into the human body from the diet, the 20 standard amino acids either are used to synthesize proteins, other biomolecules, or are oxidized to urea and carbon dioxide as a source of energy. [58] The oxidation pathway starts with the removal of the amino group by a transaminase the amino group is then fed into the urea cycle. The other product of transamidation is a keto acid that enters the citric acid cycle. [59] Glucogenic amino acids can also be converted into glucose, through gluconeogenesis. [60] Of the 20 standard amino acids, nine (His, Ile, Leu, Lys, Met, Phe, Thr, Trp and Val) are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food. [61] [62] [63] In addition, cysteine, tyrosine, and arginine are considered semiessential amino acids, and taurine a semiessential aminosulfonic acid in children. The metabolic pathways that synthesize these monomers are not fully developed. [64] [65] The amounts required also depend on the age and health of the individual, so it is hard to make general statements about the dietary requirement for some amino acids. Dietary exposure to the nonstandard amino acid BMAA has been linked to human neurodegenerative diseases, including ALS. [66] [67]

Non-protein functions Edit

In humans, non-protein amino acids also have important roles as metabolic intermediates, such as in the biosynthesis of the neurotransmitter gamma-aminobutyric acid (GABA). Many amino acids are used to synthesize other molecules, for example:

    is a precursor of the neurotransmitter serotonin. [74] (and its precursor phenylalanine) are precursors of the catecholamineneurotransmittersdopamine, epinephrine and norepinephrine and various trace amines. is a precursor of phenethylamine and tyrosine in humans. In plants, it is a precursor of various phenylpropanoids, which are important in plant metabolism. is a precursor of porphyrins such as heme. [75] is a precursor of nitric oxide. [76] and S-adenosylmethionine are precursors of polyamines. [77] , glycine, and glutamine are precursors of nucleotides. [78] However, not all of the functions of other abundant nonstandard amino acids are known.

Some nonstandard amino acids are used as defenses against herbivores in plants. [79] For example, canavanine is an analogue of arginine that is found in many legumes, [80] and in particularly large amounts in Canavalia gladiata (sword bean). [81] This amino acid protects the plants from predators such as insects and can cause illness in people if some types of legumes are eaten without processing. [82] The non-protein amino acid mimosine is found in other species of legume, in particular Leucaena leucocephala. [83] This compound is an analogue of tyrosine and can poison animals that graze on these plants.

Amino acids are used for a variety of applications in industry, but their main use is as additives to animal feed. This is necessary, since many of the bulk components of these feeds, such as soybeans, either have low levels or lack some of the essential amino acids: lysine, methionine, threonine, and tryptophan are most important in the production of these feeds. [84] In this industry, amino acids are also used to chelate metal cations in order to improve the absorption of minerals from supplements, which may be required to improve the health or production of these animals. [85]

The food industry is also a major consumer of amino acids, in particular, glutamic acid, which is used as a flavor enhancer, [86] and aspartame (aspartylphenylalanine 1-methyl ester) as a low-calorie artificial sweetener. [87] Similar technology to that used for animal nutrition is employed in the human nutrition industry to alleviate symptoms of mineral deficiencies, such as anemia, by improving mineral absorption and reducing negative side effects from inorganic mineral supplementation. [88]

The chelating ability of amino acids has been used in fertilizers for agriculture to facilitate the delivery of minerals to plants in order to correct mineral deficiencies, such as iron chlorosis. These fertilizers are also used to prevent deficiencies from occurring and improving the overall health of the plants. [89] The remaining production of amino acids is used in the synthesis of drugs and cosmetics. [84]

Similarly, some amino acids derivatives are used in pharmaceutical industry. They include 5-HTP (5-hydroxytryptophan) used for experimental treatment of depression, [90] L-DOPA (L-dihydroxyphenylalanine) for Parkinson's treatment, [91] and eflornithine drug that inhibits ornithine decarboxylase and used in the treatment of sleeping sickness. [92]

Expanded genetic code Edit

Since 2001, 40 non-natural amino acids have been added into protein by creating a unique codon (recoding) and a corresponding transfer-RNA:aminoacyl – tRNA-synthetase pair to encode it with diverse physicochemical and biological properties in order to be used as a tool to exploring protein structure and function or to create novel or enhanced proteins. [13] [14]

Nullomers Edit

Nullomers are codons that in theory code for an amino acid, however in nature there is a selective bias against using this codon in favor of another, for example bacteria prefer to use CGA instead of AGA to code for arginine. [93] This creates some sequences that do not appear in the genome. This characteristic can be taken advantage of and used to create new selective cancer-fighting drugs [94] and to prevent cross-contamination of DNA samples from crime-scene investigations. [95]

Chemical building blocks Edit

Amino acids are important as low-cost feedstocks. These compounds are used in chiral pool synthesis as enantiomerically pure building blocks. [96]

Amino acids have been investigated as precursors chiral catalysts, such as for asymmetric hydrogenation reactions, although no commercial applications exist. [97]

Biodegradable plastics Edit

Amino acids have been considered as components of biodegradable polymers, which have applications as environmentally friendly packaging and in medicine in drug delivery and the construction of prosthetic implants. [98] An interesting example of such materials is polyaspartate, a water-soluble biodegradable polymer that may have applications in disposable diapers and agriculture. [99] Due to its solubility and ability to chelate metal ions, polyaspartate is also being used as a biodegradeable antiscaling agent and a corrosion inhibitor. [100] [101] In addition, the aromatic amino acid tyrosine has been considered as a possible replacement for phenols such as bisphenol A in the manufacture of polycarbonates. [102]

Chemical synthesis Edit

The commercial production of amino acids usually relies on mutant bacteria that overproduce individual amino acids using glucose as a carbon source. Some amino acids are produced by enzymatic conversions of synthetic intermediates. 2-Aminothiazoline-4-carboxylic acid is an intermediate in one industrial synthesis of L-cysteine for example. Aspartic acid is produced by the addition of ammonia to fumarate using a lyase. [103]

Biosynthesis Edit

In plants, nitrogen is first assimilated into organic compounds in the form of glutamate, formed from alpha-ketoglutarate and ammonia in the mitochondrion. For other amino acids, plants use transaminases to move the amino group from glutamate to another alpha-keto acid. For example, aspartate aminotransferase converts glutamate and oxaloacetate to alpha-ketoglutarate and aspartate. [104] Other organisms use transaminases for amino acid synthesis, too.

Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, homocysteine is formed through the transsulfuration pathway or by the demethylation of methionine via the intermediate metabolite S-adenosylmethionine, [105] while hydroxyproline is made by a post translational modification of proline. [106]

Microorganisms and plants synthesize many uncommon amino acids. For example, some microbes make 2-aminoisobutyric acid and lanthionine, which is a sulfide-bridged derivative of alanine. Both of these amino acids are found in peptidic lantibiotics such as alamethicin. [107] However, in plants, 1-aminocyclopropane-1-carboxylic acid is a small disubstituted cyclic amino acid that is an intermediate in the production of the plant hormone ethylene. [108]

Amino acids undergo the reactions expected of the constituent functional groups. [109] [110]

Peptide bond formation Edit

As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water. In cells, this reaction does not occur directly instead, the amino acid is first activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase. [111] This aminoacyl-tRNA is then a substrate for the ribosome, which catalyzes the attack of the amino group of the elongating protein chain on the ester bond. [112] As a result of this mechanism, all proteins made by ribosomes are synthesized starting at their N-terminus and moving toward their C-terminus.

However, not all peptide bonds are formed in this way. In a few cases, peptides are synthesized by specific enzymes. For example, the tripeptide glutathione is an essential part of the defenses of cells against oxidative stress. This peptide is synthesized in two steps from free amino acids. [113] In the first step, gamma-glutamylcysteine synthetase condenses cysteine and glutamic acid through a peptide bond formed between the side chain carboxyl of the glutamate (the gamma carbon of this side chain) and the amino group of the cysteine. This dipeptide is then condensed with glycine by glutathione synthetase to form glutathione. [114]

In chemistry, peptides are synthesized by a variety of reactions. One of the most-used in solid-phase peptide synthesis uses the aromatic oxime derivatives of amino acids as activated units. These are added in sequence onto the growing peptide chain, which is attached to a solid resin support. [115] Libraries of peptides are used in drug discovery through high-throughput screening. [116]

The combination of functional groups allow amino acids to be effective polydentate ligands for metal–amino acid chelates. [117] The multiple side chains of amino acids can also undergo chemical reactions.

Catabolism Edit

Degradation of an amino acid often involves deamination by moving its amino group to alpha-ketoglutarate, forming glutamate. This process involves transaminases, often the same as those used in amination during synthesis. In many vertebrates, the amino group is then removed through the urea cycle and is excreted in the form of urea. However, amino acid degradation can produce uric acid or ammonia instead. For example, serine dehydratase converts serine to pyruvate and ammonia. [78] After removal of one or more amino groups, the remainder of the molecule can sometimes be used to synthesize new amino acids, or it can be used for energy by entering glycolysis or the citric acid cycle, as detailed in image at right.

Complexation Edit

The ca. 20 canonical amino acids can be classified according to their properties. Important factors are charge, hydrophilicity or hydrophobicity, size, and functional groups. [34] These properties influence protein structure and protein–protein interactions. The water-soluble proteins tend to have their hydrophobic residues (Leu, Ile, Val, Phe, and Trp) buried in the middle of the protein, whereas hydrophilic side chains are exposed to the aqueous solvent. (Note that in biochemistry, a residue refers to a specific monomer within the polymeric chain of a polysaccharide, protein or nucleic acid.) The integral membrane proteins tend to have outer rings of exposed hydrophobic amino acids that anchor them into the lipid bilayer. Some peripheral membrane proteins have a patch of hydrophobic amino acids on their surface that locks onto the membrane. In similar fashion, proteins that have to bind to positively charged molecules have surfaces rich with negatively charged amino acids like glutamate and aspartate, while proteins binding to negatively charged molecules have surfaces rich with positively charged chains like lysine and arginine. For example, lysine and arginine are highly enriched in low complexity regions of nucleic-acid binding proteins. [49] There are various hydrophobicity scales of amino acid residues. [120]

Some amino acids have special properties such as cysteine, that can form covalent disulfide bonds to other cysteine residues, proline that forms a cycle to the polypeptide backbone, and glycine that is more flexible than other amino acids.

Furthermore, glycine and proline are highly enriched within low complexity regions of eukaryotic and prokaryotic proteins, whereas the opposite (under-represented) has been observed for highly reactive, or complex, or hydrophobic amino acids, such as cysteine, phenylalanine, tryptophan, methionine, valine, leucine, isoleucine. [49] [121] [122]

Many proteins undergo a range of posttranslational modifications, whereby additional chemical groups are attached to the amino acid side chains. Some modifications can produce hydrophobic lipoproteins, [123] or hydrophilic glycoproteins. [124] These type of modification allow the reversible targeting of a protein to a membrane. For example, the addition and removal of the fatty acid palmitic acid to cysteine residues in some signaling proteins causes the proteins to attach and then detach from cell membranes. [125]

Table of standard amino acid abbreviations and properties Edit

Amino acid Letter code Side chain Hydropathy
index [126]
Molar absorptivity [127] Molecular mass Abundance in proteins (%) [128] Standard genetic coding, IUPAC notation
3 1 Class Polarity [129] Charge, at pH 7.4 [129] Wavelength, λmax (nm) Coefficient, ε (mM −1 ·cm −1 )
Alanine Ala A Aliphatic Nonpolar Neutral 1.8 89.094 8.76 GCN
Arginine Arg R Basic Basic polar Positive −4.5 174.203 5.78 MGR, CGY (coding codons can also be expressed by: CGN, AGR)
Asparagine Asn N Amide Polar Neutral −3.5 132.119 3.93 AAY
Aspartic acid Asp D Acid Acidic polar Negative −3.5 133.104 5.49 GAY
Cysteine Cys C Sulfuric Nonpolar Neutral 2.5 250 0.3 121.154 1.38 UGY
Glutamine Gln Q Amide Polar Neutral −3.5 146.146 3.9 CAR
Glutamic acid Glu E Acid Acidic polar Negative −3.5 147.131 6.32 GAR
Glycine Gly G Aliphatic Nonpolar Neutral −0.4 75.067 7.03 GGN
Histidine His H Basic aromatic Basic polar Positive, 10%
Neutral, 90%
−3.2 211 5.9 155.156 2.26 CAY
Isoleucine Ile I Aliphatic Nonpolar Neutral 4.5 131.175 5.49 AUH
Leucine Leu L Aliphatic Nonpolar Neutral 3.8 131.175 9.68 YUR, CUY (coding codons can also be expressed by: CUN, UUR)
Lysine Lys K Basic Basic polar Positive −3.9 146.189 5.19 AAR
Methionine Met M Sulfuric Nonpolar Neutral 1.9 149.208 2.32 AUG
Phenylalanine Phe F Aromatic Nonpolar Neutral 2.8 257, 206, 188 0.2, 9.3, 60.0 165.192 3.87 UUY
Proline Pro P Cyclic Nonpolar Neutral −1.6 115.132 5.02 CCN
Serine Ser S Hydroxylic Polar Neutral −0.8 105.093 7.14 UCN, AGY
Threonine Thr T Hydroxylic Polar Neutral −0.7 119.119 5.53 ACN
Tryptophan Trp W Aromatic Nonpolar Neutral −0.9 280, 219 5.6, 47.0 204.228 1.25 UGG
Tyrosine Tyr Y Aromatic Polar Neutral −1.3 274, 222, 193 1.4, 8.0, 48.0 181.191 2.91 UAY
Valine Val V Aliphatic Nonpolar Neutral 4.2 117.148 6.73 GUN

Two additional amino acids are in some species coded for by codons that are usually interpreted as stop codons:

21st and 22nd amino acids 3-letter 1-letter Molecular mass
Selenocysteine Sec U 168.064
Pyrrolysine Pyl O 255.313

In addition to the specific amino acid codes, placeholders are used in cases where chemical or crystallographic analysis of a peptide or protein cannot conclusively determine the identity of a residue. They are also used to summarise conserved protein sequence motifs. The use of single letters to indicate sets of similar residues is similar to the use of abbreviation codes for degenerate bases. [130] [131]

Ambiguous amino acids 3-letter 1-letter Amino acids included Codons included
Any / unknown Xaa X All NNN
Asparagine or aspartic acid Asx B D, N RAY
Glutamine or glutamic acid Glx Z E, Q SAR
Leucine or isoleucine Xle J I, L YTR, ATH, CTY (coding codons can also be expressed by: CTN, ATH, TTR MTY, YTR, ATA MTY, HTA, YTG)
Hydrophobic Φ V, I, L, F, W, Y, M NTN, TAY, TGG
Aromatic Ω F, W, Y, H YWY, TTY, TGG (coding codons can also be expressed by: TWY, CAY, TGG)
Aliphatic (non-aromatic) Ψ V, I, L, M VTN, TTR (coding codons can also be expressed by: NTR, VTY)
Small π P, G, A, S BCN, RGY, GGR
Hydrophilic ζ S, T, H, N, Q, E, D, K, R VAN, WCN, CGN, AGY (coding codons can also be expressed by: VAN, WCN, MGY, CGP)
Positively-charged + K, R, H ARR, CRY, CGR
Negatively-charged D, E GAN

Unk is sometimes used instead of Xaa, but is less standard.

In addition, many nonstandard amino acids have a specific code. For example, several peptide drugs, such as Bortezomib and MG132, are artificially synthesized and retain their protecting groups, which have specific codes. Bortezomib is Pyz–Phe–boroLeu, and MG132 is Z–Leu–Leu–Leu–al. To aid in the analysis of protein structure, photo-reactive amino acid analogs are available. These include photoleucine (pLeu) and photomethionine (pMet). [132]

The total nitrogen content of organic matter is mainly formed by the amino groups in proteins. The Total Kjeldahl Nitrogen (TKN) is a measure of nitrogen widely used in the analysis of (waste) water, soil, food, feed and organic matter in general. As the name suggests, the Kjeldahl method is applied. More sensitive methods are available. [133] [134]

  1. ^Proline is an exception to this general formula. It lacks the NH2 group because of the cyclization of the side chain and is known as an imino acid it falls under the category of special structured amino acids.
  2. ^ For example, ruminants such as cows obtain a number of amino acids via microbes in the first two stomach chambers.
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Amino Acids with Acid or Base R-groups

Amino acids are organic compounds which contain both an amino group and a carboxyl group. They are distinguished by the attached functional group R.

Of the twenty amino acids that make up proteins, six of them have acid or base R-groups . Compare with the simplest of the amino acids, glycine, which has only H as an R-group.

* Amino acids which are essential amino acids which cannot be made by the human body and, therefore, must be obtained in the diet.


Amino Acid Codon Table

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Codon Table

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Codon Chart Table – The Nucleotides Within DNA And RNA

"Mono dibase codon amino acid" logic Order of hits from

From lab to table boosting plants with biochemistry Curious

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The standard codon table The table orders the 64 codons

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Table of codons


1 Answer 1

You are right in your reasoning: at any pH for any titratable group, there is a distribution between the protonated and deprotonated species. We can calculate this distribution and therefore the average charge of the species with the Henderson-Hasselbalch equation:

Where A is the conjugate acid and B is the conjugate base. For carboxyls and primary amines, this can also be written as $ce<[COOH]>>$ and $ce<[NH3+]>>$, respectively. As a simple example, if the pH was 2.28, the ratio between the protonated and deprotonated form of the carboxyl group (pKa = 2.28) would be $ce = 10^0 = 1>$. This means $ce<[COO-] = [COOH]>$ and the average charge of the carboxyl is thus -0.5.

Now, for cases where $mathrm$, we need to determine the mole fraction, $chi$, for each charged species. Given that $mathrm <[A]>= frac>$ and $ce$, we can derive these equations:

Plugging in the numbers, we get:

99.9981% of the carboxyl groups are in the deprotonated (negative) state and

99.3872% of the amino groups are in the protonated (positive) state. The average charge of methionine at pH 7 is simply the sum of these mole fractions, accounting for the charge of each species, and is approximately equal to -0.006109. I assume your textbook is rounding.


Carbohydrates as Energy

Carbohydrates are the preferred source of energy for most of the tissues in the body, including the nervous system and the heart. Carbohydrates from the diet are converted into glucose, which can either be immediately used as a source of energy or stored in the form of glycogen. The body cannot digest all carbohydrates in the diet, however indigestible carbohydrates, also known as fiber, travel through the intestines and can help maintain proper digestive health.


2.7: Amino Acids - Biology

Introduction:

Metabolic reprogramming by cancer cells to allow proliferation and survival suggests targeting of relatively cancer cell-specific metabolic processes as a potential cancer therapy. The amino acid (aa) glutamine (GLN) functions as an exchange factor to facilitate cell import of essential amino acids (EAA), which positively regulate translation by the mTORC1 pathway (via phosphorylation of S70K and 4EBP1), allowing proliferation. Most cancer cells also rely on GLN, rather than glucose for citric acid cycle (TCA) anaplerosis, and as a source of energy, anti-oxidants and components for protein synthesis.

L-asparaginase (L-Ase), an enzyme that breaks down extracellular asparagine (ASN, the least prevalent intracellular aa), is used in the treatment of ALL. L-Ase is also glutaminolytic, resulting in GLN depletion and apoptosis that is suppressed by ASN repletion, which modulates the cell stress responses (ISR, upregulatingATF4, CHOP, aa transporters, and asparagine synthetase (ASNS)). Thus, (i) ASN is a critical signal preventing cell death from GLN depletion (ii) ASN repletion (via ASNS) may be the important function of GLN within cancer cells, and (iii) mechanisms that deplete bothkey aa may be synergistic in implementing cancer cell death

Apart from non-EAA synthesis and aa uptake (#1 in Fig. 1A), there are two major pathways of cellular aa repletion: (i) autophagy, a process whereby damaged proteins are delivered to the lysosome for degradation (#2), and (ii) the ubiquitin-proteasome system (UPS, #3), which also degrades damaged or misfolded cell proteins, allowing aa recycling. Notably, UPS inhibition significantly decreases ASN (andcystine) levels.

The aim of our studies is to explore mechanisms of depleting intracellular GLN and ASN levels in cancer cells, firstinvestigating the potential synergistic effects of combining L-Ase, with Chloroquine (CQ, autophagy inhibition) and Bortezomib (BTZ, proteasome inhibition), and then analyzing cancer cell counter mechanisms.

We performed kill-curves with individual drugs, and then combinations of L-ase, CQ and BTZ in REH (ALL) cells. Notably, inhibitory effects on aarepletion pathways, as determined by western blot analysis of cell lysates at 12h (Fig. 1B), were seen with a combination of significantly lowered doses of each drug [BTZ 2nM (40% of LD50) L-Ase 0.2IU (15%) CQ 100mM (50%)]. The mTORC1 pathway is especially susceptible to inhibition by drug combination-mediated aa depletion (decreased phosphorylation of 4EBP1 and S6K1 compare lanes 2-4 & 5-8), while autophagy (monitored by increasing levels of LC3-II) is also inhibited. Cell viability was assessed after 48h. Although the low doses of each drug used has a minimal impact on viability (range 75-130% of control), the combination above (2nM0.2IU100mM) results in synergistic cell death [55% (n = 1)]. We will examine further the effects of this drug combination on normal CD34+ cells, prior to studies of efficacy inxeno-transplant models.

Most tumors are metabolically flexible, e.g., they can use glucose if deprived of GLN to replenish TCA, and, via TCA intermediates, increase GLN levels, and thereby ASN, via pyruvate carboxylase (PC), transaminases (GOT1, 2), glutaminesynthetases(GDH, GS) and ASNS (see Fig. 1 pathways). Thus, we interrogated, byqPCR, potentially relevant pathways that may be used to evade glutamine and asparagine depletion-induced apoptosis (Fig. 1C). Of 12 genes tested, GLN deprivation significantlyupregulatesGLS1, GOT1, and ASNS to increase ASN levels, while the ISR is activated (CHOP), and SLC7A11, a cysteine importer upregulated in tumors (for glutathione production) is also significantly upregulated. Preliminary studies of REH and A549 (lung cancer) cells suggest a common theme in metabolic responses to GLN depletion in diverse cancer cells is ASN synthesis through GOT1 and ASNS upregulation, and likely ROS production throughcystineuptake.

Conclusions: Commonly, inhibition of one metabolic pathway results in upregulation of another. Our studies indicate that combination therapy, using low doses of available, well-studied drugs depletes keyaa ASN and GLN, and prevents their repletion, causing cancer cell death. In addition, our studies of the cellular responses to GLN depletion alone indicate additional targets that should be considered to prevent ASN-mediated inhibition of cell death in diverse cancer types.


Placental Amino Acid Transporters

The substrate specificity, distribution, and kinetic characteristics of the primary amino acid transporters shown to be present in the human syncytiotrophoblast are presented in Tables 1 and 2.

Transport systems for neutral amino acids.

At least five different transport systems for neutral amino acids have been identified in the human syncytiotrophoblast using villous tissue fragments (12), in vitro perfused placenta (13–15), and cultured trophoblast cells (16) and cell lines (17) as well as in plasma membrane vesicles (Table 1). System A mediates the transport of zwitterionic amino acids with small side chains and has not yet been characterized at the molecular level (6). System A activity is present both in the syncytiotrophoblast MVM and BM, however, the maximal transport capacity of the transporters is much higher in MVM (18, 19). Another Na + -dependent transporter for neutral amino acids is system ASC, a transporter that appears to be localized in BM (19), although ASC activity has been demonstrated in MVM in some studies (20) but not in all (18, 21). At the molecular level, transporters with ASC-like activity are members of a superfamily of sodium-dependent transporters for anionic and neutral amino acids (6). The clone ASCT1 is likely to represent the relevant cDNA for the human ASC transporter (22), however the expression of this gene appears to be very low in placenta (23). Therefore, it has been suggested that an as yet undefined ASC-like transporter might be responsible for the ASC activity in the placenta and liver (6). In contrast, the human transcript ATB 0 , coding for the broad scope Na + -dependent transporter B 0 , is highly expressed in the placenta (24). Cell lines of choriocarcinoma origin exhibit B 0 -like activity (25), but whether this activity is present in syncytiotrophoblast plasma membranes has not been addressed in detail (21, 26). The Na + -dependent N system has recently been cloned and is primarily expressed in the liver (27). Some evidence suggests that system N-like activity might be present in human placental MVM (28), whereas other studies have failed to demonstrate this activity (29).

Taurine is a β-amino acid with a multitude of important physiologic functions, although it is not incorporated into proteins. The tissue concentration of taurine in human placenta is 100- to 200-fold higher than the concentration in maternal blood (1), suggesting the presence of a highly efficient active transport of taurine across MVM. The transport system for β-amino acids in MVM has been studied thoroughly (30–32). The Na + -dependent taurine uptake in BM is only 6% of that of MVM (33), demonstrating that system β is almost exclusively polarized to MVM. The human taurine transporter, TAUT, has been cloned from thyroid cells (34) and placenta (35) and has been found to be a member of the superfamily of sodium- and chloride-dependent neurotransmitter transporters (6).

System L is a Na + -independent transport system for neutral amino acids found in most mammalian cells, including syncytiotrophoblast MVM (18, 36) and BM (19, 26). Recently, two isoforms, LAT-1 (37) and LAT-2 (38, 39), of a subunit of the L transporter have been cloned and characterized. LAT form a heterodimeric complex with 4F2hc, a protein implicated in cationic amino acid transport. This heterodimer appears to be responsible for the L-type of transport activity. Both LAT-1 and LAT-2 mRNA are highly expressed in the placenta (37–39).

In addition to the transport systems for neutral amino acids discussed here, other transporters may be present in the syncytiotrophoblast as well. For example, the glycine transporter GLY might be present in MVM (40). Furthermore, evidence from Kudo et al. suggest that several other amino acid transporters, yet to be fully characterized, are present in both MVM (21) and BM (26).

Transport systems for cationic amino acids.

At least five different systems mediate transport of cationic amino acids in mammalian cells, three of which have been characterized at the molecular level (6). Some controversy exists regarding which of these transporters are present in the syncytiotrophoblast membranes. However, it is well established that system y + is the main transporter for cationic amino acids in MVM (41–44) whereas y + L represents the principal transport pathway across BM (43–45). Furthermore, y + L is also present in the MVM (41–44). System y + is a Na + -independent electrogenic transporter, which interacts only weakly with neutral amino acids and therefore is specific for cationic amino acids. In contrast, y + L binds and transports neutral amino acids in the presence of sodium. The ecotropic murine leukemia virus receptor has been cloned and characterized as a cationic amino acid transporter (CAT-1) with y + -like activity and widespread expression in human tissues, including the placenta (44, 46, 47). Additional human y + -like transporters have been cloned (CAT-2–4) and of these CAT-4 appears to be expressed on the mRNA level in the placenta (6) and might therefore contribute to placental y + activity. Recently it was shown that CAT-1, -2B, and -4 is expressed in cultured trophoblast cells and in the BeWo choriocarcinoma cell line (48), supporting the possibility that multiple members of the CAT family are expressed in the placenta in vivo. Expression of the gene for the heavy chain of the cell surface antigens (4F2hc) in oocytes results in a y + L-like transport activity (49, 50), and it was suggested that 4F2hc is a subunit or a regulator of the y + L transporter. Indeed, 4F2hc mRNA is present in the human placenta and the protein appears to be expressed in MVM but not in BM (44). More recently, y + LAT, a membrane protein that associates with 4F2hc and mediates y + L-like amino acid transport activity, was identified and characterized (51, 52).

Some functional evidence has indicated that b, 0,+ activity is present in BM (45), in contrast to the findings of other investigators (44). In addition, Ayuk et al. were unable to demonstrate placental mRNA expression of rBAT (44), the gene coding for b, 0,+ (53). Another question that remains to be resolved is whether system y + is present (41, 43) or not (44) in the syncytiotrophoblast basal membrane. When CAT-1 cRNA was injected into oocytes, the resulting y + transport activity resembled the activity found in BM but not in MVM (48), giving some support to the view that y + activity is present in BM.

Transport systems for anionic amino acids.

The anionic amino acids glutamate and aspartate are not transferred from mother to fetus in the perfused placenta in vitro(54). Pioneer work in the sheep fetus has demonstrated that glutamate is produced from glutamine in the fetal liver (55) and subsequently taken up and metabolized by the placenta (56). Indirect evidence such as a high degree of oxidation of glutamate to CO2 in human trophoblast (57) and lack of net transfer of glutamate into the umbilical circulation from the placenta (58) suggest that anionic amino acids are handled in a similar fashion by the human placenta. Indeed, X - AG, a Na + - and K + -dependent transport system for anionic amino acids, is present in both plasma membranes of the syncytiotrophoblast (59–61). A family of five anionic amino acid transporters (EAAT1–5) have been cloned and, of these, EAAT 1–4 have been shown to be expressed on the mRNA level in the human placenta (62, 63).

Mechanisms for Net Materno-Fetal Transfer

This review concerns the primary amino acid transporter systems identified in the syncytiotrophoblast plasma membranes, and this information is clearly insufficient to completely analyze transplacental transport. Such analysis would require detailed information about transporter density per unit membrane area, surface areas of MVM and BM, concentrations of amino acids and ions in maternal, placental, and fetal compartments, placental metabolism of amino acids, and electrical driving forces in vivo. Furthermore, apart from the indirect evidence referred to in the introduction, the possible role of the endothelium in the transplacental transfer of amino acids remains to be elucidated. Some of this information is available. For example, MVM surface area has been estimated to be approximately sixfold larger than the area of BM (64), amino acid concentrations are quite well established (1), and membrane potentials have been measured in vitro(65). In membrane transport literature, the denominator mg membrane protein is assumed to represent membrane area. Although the validity of this assumption is difficult to test with certainty, MVM and BM isolated from human syncytiotrophoblast have similar phospholipid/protein ratio (66), lending some support for the validity of roughly comparing MVM and BM. Nevertheless, the following discussion on mechanisms of amino acid transport across the placenta will not take all these factors into account and will therefore represent a simplified model of in vivo processes.

There is no net transfer of aspartate and glutamate across the human placenta (54). Furthermore, there is a net uptake of serine by the placenta from the umbilical circulation in the fetal lamb (67) and it is possible that this apply also to human pregnancy. For most other amino acids there is a net transfer from the maternal to the fetal circulation. The mechanisms by which this vectorial transport is achieved remain to be fully established. However, available information is sufficient to allow the formulation of some general principles. First, by analogy with the intestinal epithelium (68), the unequal distribution of amino acid transporters to the two polarized plasma membranes of the syncytiotrophoblast represents the basic mechanism accounting for net transfer of amino acids to the fetus (9). Second, for most amino acids, placental concentrations are higher, sometimes much higher, than fetal plasma concentrations, which in turn are higher than maternal concentrations (1). This strongly suggests that the transport across MVM represents the active step in transplacental transfer, the nature of the driving force differing among different classes of amino acids. After being concentrated in the syncytiotrophoblast cell, amino acids diffuse down their concentration gradient into the fetal circulation as well as back to the mother. Net transport to the fetal compartment will result if the influx in greater than efflux in MVM and efflux is greater than influx across the BM.

For most neutral amino acids, Na + -dependent transporter systems are available in the MVM (Table 1), and the driving force for the accumulation of these amino acids in the syncytiotrophoblast cell is the Na + -gradient across the MVM, ultimately dependent on the activity of Na + /K + -ATPase. Systems A and β, in particular, are highly polarized toward the MVM, providing the basis for net flux of neutral amino acids from the mother to the fetus (Fig. 1). A strong candidate for exit pathway across the BM is system L, the broad-scope Na + -independent transporter. The unspecific permeability of the basal membrane in vitro to neutral amino acids is not insignificant (19, 26, 43) probably due to high fluidity of this membrane (69). It is therefore possible that nonmediated transport across the lipid bilayer of the BM might contribute to the exit of neutral amino acids from the syncytiotrophoblast cell. A Na + -independent pathway for taurine transport has been identified in BM (33), however the exact nature of this pathway remains to be established. Taurine is not only an essential amino acid for normal fetal development but also plays an important role in syncytiotrophoblast volume regulation (70). In response to a hyposmotic challenge, taurine is rapidly released from the cell through volume-activated channels. Whether these pathways also represent an exit pathway across BM and therefore are involved in transplacental taurine transport is currently unknown.

Mechanisms for transplacental transport: system A. Glycine is an example of a neutral amino acid transported by the Na + -dependent system A and is concentrated in the syncytiotrophoblast energized by the Na + gradient. Subsequently, glycine diffuses into the fetal circulation as well as back to the mother mediated by system L. The strong polarization of the system A transporter to MVM provides the basis for net transport to the fetus. Glycine concentrations in maternal and fetal plasma as well as in placental tissue were obtained from Boyd and Yudilevich (77).

Some neutral amino acids appear not to be transported across the MVM by Na + -dependent systems. This is particularly true for leucine, an amino acid that is transported mainly by the L system (43). Therefore it is not immediately apparent what represents the driving force for uphill transport of leucine across the MVM. However, the L system exhibits strong trans-stimulation, i.e. the uptake of leucine is stimulated by a high intracellular concentration of another neutral amino acid (4). A possible candidate for driving the uptake of leucine is glycine (Fig. 2), which is transported by system A and found in high concentrations in the placenta (1). Interestingly, in vivo studies suggest that although glycine is rapidly taken up by the placenta from the maternal circulation, transfer of this amino acid to the fetus is limited (71). Although some of the glycine taken up by the placenta may be metabolized, the study of Cetin et al. also raises the possibility that glycine diffuses back into the maternal circulation. Because glycine is also accepted by the L system, glycine efflux might drive an uphill transport of leucine across MVM, a hypothesis that is supported by in vitro data (43). The mechanisms responsible for the preferential efflux of leucine into the fetal circulation remain to be established but might be related to a substantial nonmediated transport of leucine across BM or a higher sensitivity of the MVM system L transporter for trans-stimulation.

Mechanisms for transplacental transport: system L. Leucine appears to be transported almost exclusively by system L, a transporter that exhibits strong trans-stimulation by other neutral amino acids such as glycine. The steep, outwardly directed glycine gradient represents a possible driving force for the uphill accumulation of leucine into the syncytiotrophoblast. The mechanisms underlying the preferential efflux of leucine across BM remain to be established (see text). Glycine and leucine concentrations in maternal and fetal plasma as well as in placental tissue were obtained from Boyd and Yudilevich (77).

The syncytiotrophoblast cell interior is negative in relation to the outside, and potential difference has to be taken into account in the analysis of transport processes carrying net charge (i.e. electrogenic transporters). System A represents such a transporter carrying a net positive charge into the cell, the sodium gradient and the electrical potential both constituting the driving forces for uphill amino acid transport. The main transporter for cationic amino acids in the MVM is system y + , a Na + independent transporter carrying net positive charge. Therefore, the electrical potential difference provides the driving force for the transport of cationic amino acids against a concentration gradient across MVM (Fig. 3). On the fetal-facing side of the syncytiotrophoblast cell, two driving forces with opposite directions will influence the flux of positively charged amino acids across BM: an outwardly directed concentration gradient and an inwardly directed electrical gradient. The basis for a net efflux of cationic amino acids under these conditions is the polarization of the y + L transporter to the BM. This transporter is not electrogenic because it binds Na + and a neutral amino acid on one side of the plasma membrane and mediates exchange with a cationic amino acid (7). Because extracellular Na + concentrations are 10-fold higher than intracellular concentrations, the net transport of Na + /neutral amino acid will be into the cell and direction of transport for cationic amino acid will be out of the cell.

Mechanisms for transplacental transport: cationic amino acids. The uphill transport across MVM is driven by the negative charge inside the syncytium, mediated by system y + , which is an electrogenic transporter. In contrast, the electroneutral system y + L is the main transporter for cationic amino acids in BM. This transporter binds Na + and a neutral amino acid mainly on the outside of the cell and performs exchange with cationic amino acids, thereby providing the driving force for efflux of cationic amino acids across BM. Lysine concentrations in maternal and fetal plasma as well as in placental tissue were obtained from Boyd and Yudilevich (77). The transtrophoblast potential difference given in the figure was measured in mature intermediate villi by Greenwood et al.(65) and the actual value might therefore be somewhat different at the level of the exchange area.

Placental Amino Acid Transport in Regulating Fetal Growth

Some evidence suggests that placental amino acid transport systems are specifically altered in pregnancy complications associated with restricted fetal growth (IUGR) (72). IUGR remains an important obstetric and pediatric problem characterized in utero by a reduced fetal plasma concentration of a number of amino acids (58). This pregnancy complication is associated with a marked decrease in the activity of system A in MVM (73–75), whereas information about BM is less abundant (75). Leucine uptake was shown to be decreased in both MVM and BM, whereas the uptake of lysine was reduced in BM only (43). Furthermore, the activity of the taurine transporter is reduced in MVM in association with IUGR (33). In contrast to the effect of IUGR on these amino acid transporters, the activity and expression of syncytiotrophoblast glucose transporters remains unaltered (66).

Insulin stimulates fetal growth and is secreted from the fetal endocrine pancreas in response to amino acids and glucose, providing a direct and efficient coupling between plasma concentrations of major nutrients and growth. It may be speculated that the down-regulation of placental amino acid transporter systems in IUGR results in decreased fetal plasma concentrations of certain amino acids, thereby contributing to the restricted fetal growth (33, 43). However, whether the observed changes in placental amino acid transporters represent a primary event in the pathophysiology of IUGR or is secondary to the growth restriction remains to be established.

Note added in proof: Due to the rapid development in this area some additional amino acid transporters have been cloned and characterized since the preparation of this manuscript. Of particular interest to the field of placental amino acid transport is the recent molecular identification of two isoforms of the system A transporter in the rat (78, 79) and in the human (80, 81). Both these isoforms, ATA1 and ATA2, have been shown to be expressed in the human placenta (80, 81).


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