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Biochemistry, Amino Acid Synthesis and Degradation

Editor: Consolato Sergi Updated: 1/11/2023 3:51:33 PM


Amino acids are organic compounds that consist of alpha carbon in the center, hydrogen (H), amino (-NH2), carboxyl (-COOH), and specific R (side chain) groups. One linear chain of amino acids is called a polypeptide, and one or more polypeptides make up a protein. There are 20 major types of amino acids found in proteins, of which the differences are the side chains (R groups) that contain various chemical structures. This R group gives each amino acid and, finally, each protein-specific characteristic. These features include size, shape, hydrophilicity, hydrophobicity, interactions, polarity, and pH level. Each of these characteristics is crucial for the stability of the proteins in the human body and environment.[1]

Issues of Concern

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Issues of Concern

As building blocks of proteins, amino acids are essential for multiple biological processes, including cell growth, division, and metabolic signaling pathways.[2] Amino acid synthesis and degradation are tightly controlled via a plethora of mechanisms in physiological conditions. However, the dysregulation of pathways involved in amino acid biogenesis and catabolism have been characterized in multiple inborn metabolic disorders such as phenylketonuria (PKU), alkaptonuria, and maple syrup urine disease (MSUD).[3]

Molecular Level

The amino acids with nonpolar R groups include glycine (G, Gly, NH2-CH2-COOH), alanine (A, Ala, CH3-CH(NH2)-COOH), valine (V, Val, (CH3)2-CH-CH(NH2)-COOH), leucine (L, Leu, (CH3)2-CH-CH2-CH(NH2)-COOH), methionine (M, Met, CH3-S-(CH2)2-CH(NH2)-COOH ), isoleucine (I, Ile, CH3-CH2-CH(CH3)-CH(NH2)-COOH), phenylalanine (F, Phe, Ph-CH2-CH(NH2)-COOH), tyrosine (Y, Tyr, HO-Ph-CH2-CH(NH2)-COOH), and tryptophan (W, Trp, Ph-NH-CH=C-CH2-CH(NH2)-COOH). Gly, Ala, Val, Leu, Met, and Ile have aliphatic R groups, and Phe, Tyr, and Trp have aromatic R groups. The aliphatic or aromatic group makes the amino acids hydrophobic (also called "water fear") or group with no tendency to be close to aqueous solutions. The globular proteins will opportunistically bury the hydrophobic side chains inside the protein interior by folding into a three-dimensional shape in aqueous solutions.[4]

The amino acids with polar uncharged R groups are serine (S, Ser, HO-CH2-CH(NH2)-COOH), threonine (T, Thr, CH3-CH(OH)-CH(NH2)-COOH), cysteine (C, Cys, HS-CH2-CH(NH2)-COOH), proline (P, Pro, NH-(CH2)3-CH-COOH), asparagine (N, Asn, H2N-CO-CH2-CH(NH2)-COOH) and glutamine (Q, Gln, H2N-CO-(CH2)2-CH(NH2)-COOH). The side chains of these amino acids possess functional spectrum groups. Most have one or more atoms, such as oxygen, nitrogen, or sulfur, with electron pairs, allowing hydrogen bonding to water or other molecules.[5]

Also, aspartate (D, Asp, HOOC-CH2-CH(NH2)-COOH) and glutamate (E, Glu, HOOC-(CH2)2-CH(NH2)-COOH) are amino acids with negatively charged R groups. On the contrary, lysine (K, H2N-(CH2)4-CH(NH2)-COOH), arginine (R, Arg, HN=C(NH2)-NH-(CH2)3-CH(NH2)-COOH), and histidine (H, His, NH-CH=N-CH=C-CH2-CH(NH2)-COOH) are amino acids with positively charged R groups.[6][7]

The amino acids are linked with their neighbors in a specific order by covalent bonds, also known as peptide bonds. These particular bonds are the amide linkages that form when the amino group reacts with the carboxylate carbon connecting two amino acids. The free amino group at one end of the polypeptide is typically called the amino-terminal or N-terminal. In contrast, the open carboxyl group at the other end is labeled as the carboxyl-terminal or C-terminal. Protein sequences are written or read from the N-to-C terminal direction. The chains of the amino acids or progression of the amino acids distinguish exquisitely one protein from another. The organism's DNA is specific in coding a particular sequence of amino acids. Each protein consists of one or more polypeptide chains. Proteins are polymers of 50 or more amino acids, while peptides are shorter amino acid polymers. A protease, which is also known as peptidase or proteinase, is an enzyme that catalyzes proteolysis. This phenomenon is constituted by the breakdown of proteins into smaller polypeptides and, eventually, single amino acids. Proteases cleave the peptide bonds within proteins by hydrolysis, which is a chemical reaction where the water breaks bonds. Acids, alkalis, or enzymes may be employed to determine protein hydrolysis.[8][9]


The general functions of amino acids include the involvement in protein synthesis, biosynthetic products, and metabolic energy. Essentially, there is a crucial difference between positive and negative nitrogen balance, which is critical for understanding amino acid metabolism. In a positive balance, the nitrogen consumed is more considerable than the nitrogen excreted, while in a negative balance, the nitrogen consumed is less than the nitrogen excreted. A positive balance denotes net protein synthesis. It occurs when the organism is recovering from starvation, growth, and pregnancy. In contrast, a negative balance entails mobilization of the amino acids, tissue necrosis, or a poor-quality condition of the human body as a consequence of 3rd-degree burns or significant surgical operations. [10][11]

The amino acids subdivide into essential and non-essential. There are amino acids that need to be obtained directly (diet) and amino acids that can be synthesized by the organism. The amino acids the human body cannot produce are called essential amino acids, which contain His, Ile, Leu, Lys, Met, Val, Phe, Thr, and Trp. The human body gets these nine essential amino acids from food or nutritional supplement. In specific medical conditions or at different ages, the other amino acids may be conditionally essential for the human body.[12]

Glutamate is a non-essential amino acid that can be synthesized from alpha-ketoglutaric acid in the Krebs or citric acid cycle. In the brain and spinal cord, glutamate is synthesized from glutamine as part of the glutamate-glutamine cycle by the enzyme glutaminase. Glutamate cannot cross the blood-brain barrier unaided and serves as a metabolic precursor for the neurotransmitter gamma-aminobutyric acid (GABA) via the action of glutamate decarboxylase.[13]

Methionine is converted to S-adenosylmethionine (SAM) by methionine adenosyltransferase. Loss of methionine has correlated with an accumulation of hydrogen peroxide (H2O2) in hair follicles, a decrease in tyrosinase effectiveness, and a gradual loss of the natural hair color.[14] Methionine is crucial for the increase in the intracellular concentration of glutathione (GSH). GSH is an antioxidant found in animals, plants, fungi, bacteria, and archaea. Promoting antioxidant-mediated cell defense and redox regulation is critical in protecting cells against dopamine-induced nigral cell loss by oxidative binding metabolites.[15] Methionine is an amino acid, an intermediate component for the biosynthesis of some amino acids. These amino acids are cysteine, carnitine, taurine, lecithin, and phosphatidylcholine. Also, methionine is medium in the biosynthesis of additional phospholipids. Improper transformation of methionine can lead to atherosclerosis due to the accumulation of homocysteine. Moreover, this amino acid is essential to reversing the damaging methylation of the glucocorticoid receptor gene caused by repeated stress exposures, with implications for depression.[16]

Glycine is considered to be not essential to the human diet. The body can synthesize this amino acid from the amino acid serine. However, the metabolic capacity for glycine biosynthesis does not satisfy the need for collagen synthesis in several organisms. In the liver of some of them at the vertebrate level, glycine synthesis is catalyzed by glycine synthase, which is also known as glycine cleavage enzyme. Glycine is integral to the creation of alpha-helices in secondary protein structure, and, mainly, it is the most copious amino acid in collagen harboring triple-helices. Glycine is also an inhibitory neurotransmitter. The interference of its release within the central nervous system (spinal cord) can induce spastic paralysis due to uninhibited muscle contraction.[17]


Amino acids are synthesized through different pathways. Cys is synthesized from Met, while Tyr synthesis can occur using Phe, considering that the amino acid precursors can be available in the body. The amino acid Arg, which arises from the urea cycle, is considered "semi-essential" because the synthetic capacity of the human body is limited. Non-essential amino acids need their precursors, which must be available in the organism. Specifically, Ala and Gly's amino acids need pyruvate to be synthesized, while aspartic acid and Asn rely on oxaloacetic acid (OAA). Thus, six essential amino acids and three non-essential are integrated from oxaloacetate and pyruvate.[18]

The transamination from Glu is vital in forming Asp and Ala from OAA and pyruvate. Asp is crucial in synthesizing Asn, Met, Lys, and Thr. OAA is critical because no Asp would form without it. The alpha-ketoglutaric acid or 2-oxoglutaric acid is one of two ketone derivatives of glutaric acid. Its anion, alpha-ketoglutarate (alpha-KG), also known as 2-oxoglutarate, is a biological compound of paramount importance. It is the keto acid produced by the deamination of Glu and is an intermediate compound in the urea or Krebs cycle. The amino acids glutamic acid and Gln arise from alpha-KG.[19]

Finally, the amino acid Pro derives from Glu, while Ser is from 3-phosphoglyceric acid (3PG). The 3PG is the conjugate acid of glycerate 3-phosphate. It is a biochemically significant metabolic intermediate in glycolysis and the Calvin cycle. In the Calvin cycle or photosynthetic carbon reduction (PCR) cycle of photosynthesis, 3PG is vital. It is the product of the spontaneous scission of an unstable 6-carbon intermediate formed upon CO fixation. Thus, glycerate 3-phosphate is a precursor for Ser, which, in turn, can create Cys and Gly through the homocysteine cycle. Therefore, Pro arises from Glu, while Ser is from 3PG. In the transamination reaction, an amino acid (Ala or Asp) exchanges its amine group for the oxy group in alpha-KG. The products are Glu and pyruvate or OAA (from Ala or Asp, accordingly).[19][20]

Different proteases can degrade proteins into many small peptides or amino acids by hydrolyzing their peptide bonds. The unused amino acids may degrade further to join several metabolic processes. At first, the amino acids deaminate to their metabolic intermediates. This process is helpful for the excretion of an excessive amount of nitrogen. Subsequently, they can transform into the remaining carbon skeleton. In particular, this deamination process contains two steps. The first part uses deamination. In this step, the aminotransferase catalyzes the -NH2 group of the amino acid to alpha-KG. After that, it produces Glu and a novel alpha-keto acid of the specific amino acid. The Glu -NH2 group could then be transferred to OAA to form alpha-KG and Asp. This trans-amination series only degrade the primary amino acid, while the -NH2 group nitrogen does not exclude. There is an alternative pathway, using NADP or NAD+ as the oxidizing agent, and Glu dehydrogenase deaminates Glu. Then, it produces ammonia and alpha-KG.

In the evaluation of the biochemistry of the amino acids, seven metabolic intermediates of the aminoacidic degradation platform are paramount. They include acetyl-CoA, pyruvate, alpha-KG, acetoacetate, fumarate, succinyl-CoA, and OAA. In the most updated classification, Leu, Ile, Thr, and Lys degrade to acetyl-CoA, while Cys, Ala, Thr, Gly, Trp, and Ser degrade to pyruvate. Glu, Arg, His, Pro, and Gln degrade to alpha-KG, while Lys, Leu, Trp, Tyr, and Phe break down to acetoacetate. Finally, Tyr, Phe, and Asp degrade to fumarate, Val, Met, and Ile break down to succinyl-CoA, and Asp and, of course, Asn degrade to OAA. Isoleucine is an essential nutrient because it is unsynthesized in the body. This amino acid is both a glucogenic and ketogenic amino acid. In microorganisms and plants, it is synthesized via several steps beginning with pyruvate and alpha-ketobutyrate. The enzymes involved in this biosynthesis include acetolactate synthase, acetohydroxy acid isomeroreductase, dihydroxy acid dehydratase, and valine aminotransferase.[21]


In clinical practice, plasma or urine amino acids undergo testing to evaluate patients with possible inborn metabolism problems. They can also assess many diseases, such as liver diseases, endocrine disorders, muscular diseases, neurological disorders, neoplastic diseases, renal failure, burns, and nutritional disturbances. Both high-performance liquid chromatography (HPLC) and gas chromatography (GC) have been used to quantitatively identify the plasma or urine amino acids in clinical settings.[22][23] Currently, capillary electrophoresis (CE), liquid chromatography with tandem mass spectrometry (LC-MS-MS), nuclear magnetic resonance (NMR) methods, and a chip-type miniaturization technology are also useful to detect amino acids in the laboratory.[24][25][26][27]

Clinical Significance

Amino acid disorders are identifiable at any age; most of them become evident during infancy or early childhood. Many inborn amino metabolism diseases occur in infancy or childhood. These disorders may include cystinuria, histidinemia, phenylketonuria (PKU), methyl-malonyl CoA mutase deficiency (MCM deficiency), albinism, and tyrosinemia. Other amino acid disorders may be encountered later in life, including homocystinuria, alkaptonuria, maple syrup urine disease (MSUD), and cystathioninuria. These disorders lead to clinical symptoms or signs of the specific amino acid disorder, which results in the deficiency or accumulation of one or more amino acids in the body's biological fluids, such as plasma or urine. [3]

The deficiency of Phe hydroxylase causes PKU. Currently, there are more than 400 mutations have been identified in the gene related to the cause of PKU.[28] This disease is usually heterozygous. Besides, the deficiency of enzymes such as dihydropteridine reductase (DHPR) or tetrahydrobiopterin (BH4) synthesis enzymes also leads to hyperphenylalaninemia.[29][30] The BH4 or generated product replacement therapy treats this enzyme deficiency-related PKU. In the case of the classic PKU, the Phe, phenyl lactate, phenylpyruvate, and phenylacetate are increased in the plasma, urine as well as other tissue samples. The phenyl pyruvic acid excreted in urine produces a "mousy" odor. Central nervous system symptoms, such as mental retardation, seizures, failure to walk or speak, tremors, and hyperactivity, also show in these patients. Another characteristic of classic PKU is hypopigmentation, which is due to the deficiency in the formation of melanin, which leads to pigmentation deficiency. Usually, the patients show light skin, fair hair, and blue eyes. Temporally, low Phe content synthetic nutrient supplemented with Tyr is the treatment of the classic PKU.

Albinism is a congenital disorder that is the defect of Tyr metabolism leading to a deficiency in melanin production. The characteristics of albinism are hypopigmentation by the total or partial absence of pigment in the hair, skin, and eyes. There is no cure for albinism because it is a genetic disorder.[31] At the moment, getting proper eye care, such as using sunglasses to prevent the ultraviolet (UV) rays damage from the sun and monitoring for signs of abnormalities of the skin, is the treatment of albinism.

Alkaptonuria is a rare disease with homogentisic acid oxidase defect, an enzyme in the Tyr degradation pathway. The urine specimen of the alkaptonuria patient shows some darkening on the surface after standing for fifteen minutes, which is due to homogentisate acid oxidation. And after two hours of standing, the patient's urine is entirely black. The characteristics of alkaptonuria include the accumulation of homogentisic aciduria, large joint arthritis, and the intervertebral disks of vertebrae deposit with dense black pigments.[32] A low protein diet with small in Phe and Tyr is the treatment of alkaptonuria, which helps reduce the homogentisic acid levels.

Tyrosinemia type 1 results from a deficiency in fumarylacetoacetate hydrolase, leading to the accumulation of fumarylacetoacetate and its metabolites (especially succinylacetone) in urine, which makes cabbage-like odor. The patients show renal tubular acidosis and liver failure.[33] The treatment is Phe and Tyr restriction dietary.

MCM deficiency is a disease due to the defect of methyl malonyl CoA mutase, which catalyzes isomerization between methyl malonyl-CoA and succinyl-CoA in the pathway.[34] It shows high levels of methyl malonyl CoA in the blood samples from the patients. Symptoms of MCM deficiency include vomiting, dehydration, fatigue, hypotonia, fever, breathing difficulty, and infections. Also, metabolic acidosis and developmental delay occur as long-term complications. The treatment of MCM deficiency includes a special diet with low proteins (low in Ile, Met, Thr, and Val amino acids) and certain fats but high in calories.

Maple syrup urine disease (MSUD) is a rare autosomal recessive disease with a partial or complete defect of branched-chain alpha-keto acid dehydrogenase. The enzyme can decarboxylate Leu, Ile, and Val. This deficiency leads to the accumulation of branched-chain alpha-keto acid substrates. These three amino acids cause functional abnormalities in the brain. The urine with a classic maple syrup odor is a hallmark characteristic of MSUD. MSUD patients show symptoms such as vomiting, feeding difficulties, dehydration, and severe metabolic acidosis.[35] 

In the clinic, a synthetic formula containing a limited amount of Leu, Ile, and Val is the suggested therapy for MSUD infants. MSUD (OMIM #248600) demonstrates a disturbance of the regular activity of the branched-chain α-ketoacid dehydrogenase (BCKAD) complex, the second step in the catabolic trail for the branched-chain amino acids (BCAAs) that includes leucine, isoleucine, and valine. MSUD can occur early in life, but late-onset MSUD is also common and include neurologic symptoms. These symptoms may include inappropriate, extreme, or erratic behavior and moods, hallucinations, oscillating hypertonia/hypotonia, ataxia, seizures, opisthotonos, and coma.

Cystathioninuria is a rare autosomal recessive metabolic disorder due to a deficiency in cystathionase. It links with the lower activity of the enzyme cystathionase. There are two types of primary cystathioninuria based on the inherited mutation of the CTH gene: vitamin B6 responsive and vitamin B6 unresponsive cystathioninuria.[36][37] It is characterized by the accumulation of cystathionine and its metabolites in plasma and urine, but no clinical symptoms are present. The treatment of cystathioninuria varies according to the category in different cystathioninuria patients. Increased consumption of vitamin B6 is considered the best treatment for the active form of vitamin B6.[38]

Homocystinuria is an inherited disorder due to the defect of the metabolism of Met amino acid. The most common cause is the enzyme cystathionine beta-synthetase deficiency, which results in the elevation of Met and homocysteine and low levels of Cys in plasma and urine.[39] The characteristics of homocystinuria include displacement of the lens of the eye, skeletal abnormalities, osteoporosis, premature arterial disease, and mental delay.[40][41] The treatment of homocystinuria involves the restriction of Met intake and supplementation with folate, vitamin B6, and B12.[42]

Histidinemia is a rare autosomal recessive inborn metabolic error due to the defect of the enzyme histidase.[43] It characteristically demonstrates high levels of His, histamine, and imidazole in blood, urine as well as cerebrospinal fluid. A low in His intake diet is suggested for treating histidinemia, though the restricted diet is unnecessary for most cases.[44]



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