Amino acids and nitrogen

Digestion and absorption

Digestion cuts food proteins into amino acids and chains of two or three, which the small intestine absorbs ¹².

The pancreas secretes its proteases as inactive zymogens ¹. Mutations in SLC6A19, which encodes the neutral amino acid transporter B0AT1, cause Hartnup disorder ³.

Essential and non-essential amino acids

The body cannot make nine of the twenty amino acids in proteins, so they must come from food ¹.

They are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine ¹.

Transamination and pyridoxal phosphate

Before most amino acids are broken down, enzymes that depend on a form of vitamin B6 move the amino group onto another molecule ¹.

Aminotransferases transfer the α-amino group to 2-oxoglutarate, forming glutamate and the corresponding 2-oxo acid ¹. Their cofactor is pyridoxal 5′-phosphate (PLP) ².

Glutamate dehydrogenase

In mitochondria, one enzyme releases the collected amino groups from glutamate as ammonium ².

Leucine stimulates insulin secretion in beta cells by allosterically activating this enzyme, GLUD1 ⁵. Eight children with the hyperinsulinism–hyperammonaemia syndrome each had a heterozygous GLUD1 variant in the allosteric domain ⁵.

The urea cycle

The liver converts ammonium, which is toxic to the brain, into urea, which is excreted ².

Urea cycleLiver; OTC in the mitochondrial matrix; ASS1, ASL and ARG1 in the cytosol

OrnithineCitrullineOrnithine transcarbamylase (OTC)Carbamoyl phosphateMatrix; carbamoyl phosphate comes from CPS1, activated by N-acetylglutamate
CitrullineArgininosuccinateArgininosuccinate synthase 1 (ASS1)Aspartate, ATPCytosol; citrulline leaves the matrix via ORNT1; ATP yields AMP and diphosphate
ArgininosuccinateArginineArgininosuccinate lyase (ASL)Releases fumarate, which links the cycle to the citric acid cycle
ArginineOrnithineArginase 1 (ARG1)H2O, Mn2+ (2 per subunit)Releases urea; ornithine re-enters the matrix via ORNT1 (SLC25A15)

Inherited urea cycle disorders occur in at least 1 in 35,000 to 1 in 51,946 live births ⁶. Sodium benzoate, sodium phenylacetate and sodium phenylbutyrate allow excretion of nitrogen by alternative pathways ⁶.

Phenylketonuria and newborn screening

In phenylketonuria, the enzyme that turns phenylalanine into tyrosine is deficient ⁷.

Untreated, the phenylalanine that accumulates causes lasting brain damage ⁷. Global prevalence is estimated at 1 in 23,930 live births ⁸. Newborn screening measures phenylalanine in dried blood spots collected 24 to 72 hours after birth ⁷. Treatment combines a phenylalanine-restricted diet with phenylalanine-free protein supplements ⁷. Between 25% and 50% of patients respond to sapropterin, synthetic tetrahydrobiopterin ⁷. Aspartame is hydrolysed in the gut to phenylalanine ⁹. Its acceptable daily intake of 40 mg/kg body weight does not apply to people with phenylketonuria ⁹. When maternal blood phenylalanine stays above 360 µmol/L during pregnancy, more than 90% of the children have intellectual disability ⁷.

Carbon skeletons: glucose and ketone bodies

Without its nitrogen, the rest of an amino acid can become glucose or ketone bodies, or be oxidised for energy ¹.

Skeletons that yield pyruvate, 2-oxoglutarate, succinyl-CoA, fumarate or oxaloacetate can supply gluconeogenesis ¹. From acetyl-CoA and acetoacetyl-CoA, mammals make ketone bodies but no net glucose ¹. Only leucine and lysine are exclusively ketogenic ¹.

Gluconeogenesis from pyruvateMitochondrial matrix, cytosol and endoplasmic reticulum of liver and kidney cortex

Pyruvate
Pyruvate carboxylase (PC), mitochondrialATP to ADP, HCO3−, BiotinAcetyl-CoA activates allosterically; two pyruvate enter per glucose
Oxaloacetate
Malate dehydrogenase 2 (MDH2), mitochondrialNADH to NAD+Malate then crosses the inner mitochondrial membrane
Malate
Malate dehydrogenase 1 (MDH1), cytosolicNAD+ to NADHSupplies the cytosolic NADH used by GAPDH
Oxaloacetate
Phosphoenolpyruvate carboxykinase 1 (PCK1), cytosolicGTP to GDPReleases CO2; PCK2 catalyses the same reaction in mitochondria
Phosphoenolpyruvate
Enolase 1 (ENO1)H2O
2-Phosphoglycerate
Phosphoglycerate mutase 1 (PGAM1)
3-Phosphoglycerate
Phosphoglycerate kinase 1 (PGK1)ATP to ADP
1,3-Bisphosphoglycerate
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)NADH to NAD+Releases phosphate
Glyceraldehyde 3-phosphate
Aldolase B (ALDOB)Dihydroxyacetone phosphateDHAP comes from a second triose by triose-phosphate isomerase (TPI1)
Fructose 1,6-bisphosphate
Fructose-1,6-bisphosphatase 1 (FBP1)H2OFructose 2,6-bisphosphateAMPReleases phosphate; glucagon lowers fructose 2,6-bisphosphate
Fructose 6-phosphate
Glucose-6-phosphate isomerase (GPI)
Glucose 6-phosphate
Glucose-6-phosphatase (G6PC1), endoplasmic reticulumH2OSLC37A4 moves the substrate into the ER lumen; releases phosphate
Glucose

KetogenesisMitochondrial matrix of hepatocytes

Long-chain acyl-CoA
several stepsMalonyl-CoAEntry through the CPT1A carnitine shuttle, then β-oxidation
Acetyl-CoA
Acetyl-CoA acetyltransferase 1 (ACAT1)Acetyl-CoAMitochondrial thiolase; condenses two acetyl-CoA and releases CoA
Acetoacetyl-CoA
HMG-CoA synthase 2 (HMGCS2), mitochondrialAcetyl-CoA, H2OCommitted step; releases CoA; deficiency impairs ketogenesis in fasting
HMG-CoA
HMG-CoA lyase (HMGCL)Releases acetyl-CoA; acetoacetate decarboxylates spontaneously to acetone
Acetoacetate
3-Hydroxybutyrate dehydrogenase 1 (BDH1)NADH to NAD+Near equilibrium; the product ratio follows mitochondrial NADH/NAD+
D-3-Hydroxybutyrate

References

Textbook or database
Berg JM, Tymoczko JL, Gatto GJ Jr, Stryer L. Biochemistry W. H. Freeman, 9th edition, 2019.
https://isbnsearch.org/isbn/9781319114671
Funding and finding
Funding
not stated
Finding
Textbook, ISBN 978-1-319-11467-1. Pepsin begins proteolysis in the stomach and pancreatic proteases are secreted as zymogens. Nine amino acids are essential for humans: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine; tyrosine is formed from phenylalanine and the sulfur of cysteine comes from methionine. Aminotransferases transfer alpha-amino groups to 2-oxoglutarate through a pyridoxal phosphate Schiff base, an external aldimine and pyridoxamine phosphate in a ping-pong mechanism. One nitrogen of urea comes from ammonium and the other from aspartate; one urea costs four phosphoanhydride bonds. Benzoate is excreted as hippurate after conjugation with glycine and phenylacetate as phenylacetylglutamine after conjugation with glutamine. The carbon skeletons of the 20 amino acids are converted into pyruvate, 2-oxoglutarate, succinyl-CoA, fumarate, oxaloacetate, acetyl-CoA and acetoacetyl-CoA; mammals make no net glucose from acetyl-CoA or acetoacetyl-CoA; leucine and lysine are solely ketogenic, and isoleucine, phenylalanine, tryptophan and tyrosine are both ketogenic and glucogenic. Alanine formed by transamination in muscle reaches the liver, where its carbon forms glucose and its nitrogen urea, in the glucose-alanine cycle.
Textbook or database
UniProt Consortium. UniProt: the Universal Protein Knowledgebase in 2025 Nucleic Acids Research, 2025.
doi:10.1093/nar/gkae1010 PubMed 39552041
Funding and finding
Funding
National Human Genome Research Institute (NHGRI) [HG002273]; Office of the Director, NIH OD [U24HG007822]; National Institute of Allergy and Infectious Diseases (NIAID); National Institute on Aging (NIA); National Institute of General Medical Sciences (NIGMS) [R35GM141873]; National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK); National Eye Institute (NEI); National Cancer Institute (NCI); National Heart, Lung, and Blood Institute (NHLBI); Biotechnology and Biological Sciences Research Council (BBSRC) [BB/T015608/1]; National Science Foundation's Directorate for Biological Sciences [BB/X002179/1]; Open Targets; Horizon 2020 - Research and Innovation Framework Programme [825575]; State Secretariat for Education, Research and Innovation (SERI); European Molecular Biology Laboratory (EMBL) Australia. Funding for open access charge: National Institutes of Health.
Finding
Reviewed human entries read 2026-10-21. PNLIP (P16233) preferentially splits the esters of long-chain fatty acids at positions 1 and 3, producing mainly 2-monoacylglycerol and free fatty acids. CLPS (P04118) is a cofactor that anchors pancreatic lipase at the lipid-water interface; without it bile salts wash the enzyme off. MOGAT2 (Q3SYC2) transfers an acyl chain from acyl-CoA to monoacylglycerol, forming diacylglycerol. DGAT1 (O75907) catalyses the terminal and only committed step of triacylglycerol synthesis, is highly expressed in small-intestinal epithelial cells and is essential for absorption of dietary fats. MTTP (P55157) transports triglyceride, cholesteryl ester and phospholipid between phospholipid surfaces and is required for assembly and secretion of apolipoprotein B-containing lipoproteins. APOB (P04114): apo B-48 is a major protein of chylomicrons. SCD (O00767) inserts a cis double bond at the delta-9 position of fatty acyl-CoA substrates including stearoyl-CoA, using O2 and electrons from reduced cytochrome b5. FDFT1 (P37268) condenses two farnesyl diphosphates to squalene, the first committed step of sterol biosynthesis. SQLE (Q14534) oxidises squalene to (S)-2,3-epoxysqualene and is considered rate-limiting in steroid biosynthesis. COMT (P21964) catalyses catechol + S-adenosyl-L-methionine = guaiacol + S-adenosyl-L-homocysteine; the Val158Met variant results in a 3- to 4-fold difference in activity. LCT (P09848), lactase/phlorizin hydrolase, a homodimer of the apical membrane of small-intestinal enterocytes, hydrolyses lactose to beta-D-galactose and D-glucose (EC 3.2.1.108). SLC5A1 (P13866, SGLT1) transports D-glucose or D-galactose across the apical membrane of enterocytes with 2 Na+ per sugar; basolateral exit is provided by GLUT2. SLC2A2 (P11168, GLUT2) is a facilitative transporter of glucose, fructose and galactose. GALM (Q96C23), GALK1 (P51570), GALT (P07902) and GALE (Q14376) constitute the Leloir pathway that converts beta-D-galactose to glucose 1-phosphate in the liver; GALM interconverts beta- and alpha-D-galactose, GALK1 phosphorylates alpha-D-galactose with ATP in the first committed step, GALT converts alpha-D-galactose 1-phosphate and UDP-glucose to alpha-D-glucose 1-phosphate and UDP-galactose, GALE interconverts UDP-glucose and UDP-galactose. PGM1 (P36871) isomerises alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate via glucose 1,6-bisphosphate. TRPV6 (Q9H1D0) is a calcium-selective channel that mediates Ca2+ uptake in tissues including the intestine. S100G (P29377) is calbindin-D9k, the intestinal vitamin D-dependent calcium-binding protein. ATP2B1 (P20020, PMCA1) transports calcium from the cytoplasm to the extracellular space, is located in the basolateral membrane and promotes intestinal calcium absorption.
Independent research
Kleta R, Romeo E, Ristic Z, Ohura T, Stuart C, Arcos-Burgos M, et al. Mutations in SLC6A19, encoding B0AT1, cause Hartnup disorder Nature Genetics, 2004.
doi:10.1038/ng1405 PubMed 15286787
Funding and finding
Funding
Grants-in-aid from the Japanese Government to A.K. and Swiss National Science Foundation grants to F.V.
Finding
Hartnup disorder, autosomal recessive, results from impaired neutral amino acid transport across epithelial cells of renal proximal tubules and intestinal mucosa; symptoms include transient pellagra-like rashes, cerebellar ataxia and psychosis. Mutations in SLC6A19 were identified in the original 1956 family and in three Japanese families; its product B0AT1 is expressed mainly in intestine and renal proximal tubule and functions as a neutral amino acid transporter.
Expert consensus
Joint WHO/FAO/UNU Expert Consultation. Protein and amino acid requirements in human nutrition World Health Organization Technical Report Series, No. 935, 2007.
PubMed 18330140
Funding and finding
Funding
Joint WHO/FAO/UNU Expert Consultation held at WHO headquarters, Geneva, 9-16 April 2002; the report states no other source of funding.
Finding
Nutritionally indispensable amino acids: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine; conditionally indispensable: e.g. cysteine, tyrosine, taurine, glycine, arginine, glutamine and proline. Adult average protein requirement 0.66 g/kg per day; safe level 0.83 g/kg per day for protein with a protein digestibility-corrected amino acid score of 1.0, expected to meet the needs of 97.5% of healthy adults. Mean adult indispensable amino acid requirements (mg/kg per day): histidine 10, isoleucine 20, leucine 39, lysine 30, methionine plus cysteine 15, phenylalanine plus tyrosine 25, threonine 15, tryptophan 4, valine 26.
Independent research
Stanley CA, Lieu YK, Hsu BY, Burlina AB, Greenberg CR, Hopwood NJ, et al. Hyperinsulinism and hyperammonemia in infants with regulatory mutations of the glutamate dehydrogenase gene New England Journal of Medicine, 1998.
doi:10.1056/NEJM199805073381904 PubMed 9571255
Funding and finding
Participants
8
Funding
Supported in part by grants from the National Institutes of Health (RR-00240) and the American Diabetes Association.
Finding
All eight children were heterozygous for a GLUD1 variant altering one of four residues between 446 and 454, in the proposed allosteric domain. The IC50 of GTP for glutamate dehydrogenase in lymphoblasts was nearly four times normal in sporadic cases and twice normal in familial cases; basal and ADP-stimulated activity was normal in sporadic cases. Plasma ammonium was 80 to 200 umol/L (normal below 40) without symptoms of hyperammonaemia. Leucine stimulates insulin secretion by allosterically activating glutamate dehydrogenase.
Textbook or database
Simpson KL, MacLeod EL, Kakajiwala A, Gropman AL, Ah Mew N. Urea Cycle Disorders Overview GeneReviews, University of Washington, Seattle, 2025.
PubMed 20301396
Funding and finding
Funding
not stated in the chapter
Finding
Expert-authored, peer-reviewed chapter, first posted 2003, comprehensive update 3 July 2025. The urea cycle comprises CPS1, OTC, ASS1, ASL and ARG1, the cofactor-producing enzyme NAGS and the transporters ORNT1 (SLC25A15) and citrin (SLC25A13); CPS1, NAGS and OTC act in mitochondria, ASS1, ASL and ARG1 in the cytosol. Incidence of urea cycle disorders at least 1 in 35,000 to 1 in 51,946 live births; OTC deficiency, the most common, about 1 in 56,500, X-linked; all others autosomal recessive. Urinary orotic acid is markedly raised in OTC deficiency and normal or low in CPS1 and NAGS deficiency; excess carbamoyl phosphate enters pyrimidine synthesis. N-carbamylglutamate (carglumic acid), an analogue of N-acetylglutamate, essentially normalises urea cycle function in NAGS deficiency. Sodium phenylacetate, sodium benzoate and sodium phenylbutyrate allow alternative-pathway excretion of nitrogen.
Textbook or database
Arnold G, Vockley J. Phenylalanine Hydroxylase Deficiency GeneReviews, University of Washington, Seattle, 2025.
PubMed 20301677
Funding and finding
Funding
not stated in the chapter
Finding
Expert-authored, peer-reviewed chapter, first posted 2000, comprehensive update 13 March 2025, revised 20 November 2025. Autosomal recessive; biallelic PAH variants; PAH at 12q23.2. Phenylketonuria denotes untreated plasma phenylalanine above 1,000 umol/L; untreated or late-diagnosed disease causes irreversible intellectual disability, seizures and microcephaly. Defects of tetrahydrobiopterin synthesis or recycling (GCH1, PTS, QDPR, PCBD1) account for about 2% of raised blood phenylalanine. Newborn screening uses dried blood spots collected 24 to 72 hours after birth, with phenylalanine and tyrosine measured by tandem mass spectrometry; biochemical diagnosis requires blood phenylalanine above 120 umol/L and a phenylalanine-to-tyrosine ratio of 3 or more. Treatment: phenylalanine-restricted diet with phenylalanine-free protein supplements based on amino acids or glycomacropeptide; 25% to 50% respond to sapropterin, a synthetic form of tetrahydrobiopterin; pegvaliase, a PEGylated phenylalanine ammonia lyase given subcutaneously, is approved in the US for adults with phenylalanine above 600 umol/L. Aspartame is metabolised in the gut to phenylalanine and aspartate. Maternal phenylalanine consistently above 360 umol/L in pregnancy causes intellectual disability in more than 90% of offspring. The chapter attributes brain toxicity to phenylacetic, phenylpyruvic and phenyllactic acids and to tyrosine and neurotransmitter deficiency.
Independent research
Hillert A, Anikster Y, Belanger-Quintana A, Burlina A, Burton BK, Carducci C, et al. The Genetic Landscape and Epidemiology of Phenylketonuria American Journal of Human Genetics, 2020.
doi:10.1016/j.ajhg.2020.06.006 PubMed 32668217
Funding and finding
Participants
16,092
Funding
Funded in part by the Fundacion Isabel Gemio-Fundacion La Caixa (LCF/PR/PR16/11110018), the Regional Government of Madrid (B2017/BMD3721) and NIH grants R01DK117916 and R01NR016991; Murdoch Children's Research Institute work supported by the Victorian Government's Operational Infrastructure Support Program; newborn-screening work of G.F.H. supported by the Dietmar Hopp Foundation. Manuscript editing funded by the corresponding author's institution.
Finding
Estimated global prevalence 1 in 23,930 live births, about 0.45 million affected people; prevalence highest in European and certain Middle Eastern populations and 1 in 125,000 in Japan. Phenotype distribution among 16,092 affected people: 62% classic PKU, 22% mild PKU, 16% mild hyperphenylalaninaemia.
Regulator
EFSA Panel on Food Additives and Nutrient Sources added to Food (ANS). Scientific Opinion on the re-evaluation of aspartame (E 951) as a food additive EFSA Journal, 2013.
doi:10.2903/j.efsa.2013.3496
Funding and finding
Funding
European Food Safety Authority; on request from the European Commission (question number EFSA-Q-2011-00406).
Finding
Aspartame is rapidly and completely hydrolysed in the gastrointestinal tract to phenylalanine, aspartic acid and methanol. Developmental toxicity in animals was attributed to phenylalanine. The acceptable daily intake of 40 mg/kg bw per day was retained; in normal people and PKU heterozygotes, intakes up to the ADI in addition to dietary phenylalanine would not raise peak plasma phenylalanine above the clinical guideline for preventing adverse effects in fetuses. The ADI is not applicable to PKU patients.
Expert consensus
Smith WE, Berry SA, Bloom K, Brown C, Burton BK, Demarest OM, et al. Phenylalanine hydroxylase deficiency diagnosis and management: A 2023 evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG) Genetics in Medicine, 2025.
doi:10.1016/j.gim.2024.101289 PubMed 39630157
Funding and finding
Funding
Funding for this guideline was provided internally through staff support by ACMG; workgroup members were uncompensated. Crossref funder metadata lists BioMarin Pharmaceutical and the National PKU Alliance; the article text does not state their role.
Finding
Treatment should be lifelong for individuals with untreated phenylalanine above 360 umol/L, and phenylalanine should be maintained at or below 360 umol/L for life (strong recommendations, high certainty). In 14 meta-analysed studies, mean IQ was 106.38 (95% CI 101.38 to 111.39) with mean lifetime phenylalanine at or below 360 umol/L and 101.95 (100.75 to 103.15) above it.
Industry-funded
Levy HL, Milanowski A, Chakrapani A, Cleary M, Lee P, Trefz FK, et al. Efficacy of sapropterin dihydrochloride (tetrahydrobiopterin, 6R-BH4) for reduction of phenylalanine concentration in patients with phenylketonuria: a phase III randomised placebo-controlled study Lancet, 2007.
doi:10.1016/S0140-6736(07)61234-3 PubMed 17693179
Funding and finding
Registration
NCT00104247
Participants
89
Follow-up
6 weeks
Funding
Lead sponsor BioMarin Pharmaceutical (ClinicalTrials.gov NCT00104247). The funding statement of the article was not readable; the archived article page showed only the summary and affiliations.
Finding
42 patients were assigned sapropterin 10 mg/kg once daily and 47 placebo. After 6 weeks mean blood phenylalanine fell by 236 (SD 257) umol/L with sapropterin and rose by 3 (SD 240) umol/L with placebo (p<0.0001). A reduction of 30% or more occurred in 18 of 41 (44%) versus 4 of 47 (9%): absolute difference 35 percentage points, number needed to treat about 3 over 6 weeks.
Expert consensus
van Wegberg AMJ, MacDonald A, Ahring K, Bélanger-Quintana A, Blau N, Bosch AM, et al. The complete European guidelines on phenylketonuria: diagnosis and treatment Orphanet Journal of Rare Diseases, 2017.
doi:10.1186/s13023-017-0685-2 PubMed 29025426
Funding and finding
Funding
A grant from the European Society for Phenylketonuria and Allied Disorders (ESPKU) funded a project assistant; the ESPKU had no opportunity to influence the writing process. One group meeting and one plenary meeting were supported by Excemed.
Finding
Treat untreated blood phenylalanine above 600 umol/L; treat 360 to 600 umol/L during the first 12 years of life; patients aged 12 years or more with untreated phenylalanine below 600 umol/L do not require treatment; upper target 360 umol/L before 12 years and 600 umol/L from 12 years, lower target 120 umol/L; treatment for life recommended. The precise pathogenesis of brain dysfunction is still unclear; existing treatments aim at decreasing blood phenylalanine because high concentrations are strongly related to neurocognitive outcome.
Funding unknown
Edgar AJ. The human L-threonine 3-dehydrogenase gene is an expressed pseudogene BMC Genetics, 2002.
doi:10.1186/1471-2156-3-18 PubMed 12361482
Funding and finding
Funding
not stated
Finding
Threonine is degraded either by L-threonine 3-dehydrogenase to 2-amino-3-ketobutyrate, which with CoA yields glycine and acetyl-CoA, or by serine/threonine dehydratase to NH4+ and 2-ketobutyrate. The human TDH gene at 8p23-22 has a premature stop codon in exon 6 (codon of arginine-214) and lacks the splice acceptor before exon 6 in all individuals examined (23 genotyped, 20 sequenced); its transcripts encode truncated proteins of 157 to 230 residues. The author suggests that the dehydratase pathway may be the only route of threonine catabolism in humans, asks which enzyme forms the small fraction of glycine from threonine, and notes that absence of threonine dehydrogenase activity in human liver has not been demonstrated directly.
Independent research
Darling PB, Grunow J, Rafii M, Brookes S, Ball RO, Pencharz PB. Threonine dehydrogenase is a minor degradative pathway of threonine catabolism in adult humans American Journal of Physiology. Endocrinology and Metabolism, 2000.
doi:10.1152/ajpendo.2000.278.5.E877 PubMed 10780944
Funding and finding
Participants
6
Funding
Medical Research Council (MRC) of Canada Grant MT-12928; P. B. Darling held an MRC studentship.
Finding
Threonine conversion to glycine, the threonine dehydrogenase pathway, accounted for 10% of total threonine catabolism on the control diet and 7% on both threonine-supplemented diets (7-11% in the abstract); oxidation to CO2 accounted for 90% to 93%.

Updated 2026-10-21