Overview of Amino Acids Metabolism

Definition of Amino Acids

Amino acids are the most basic substances that make up the proteins of living organisms related to life activities, and they are one of the indispensable nutrients in living organisms. Amino acids can synthesize proteins (including enzymes) or certain important nitrogenous compounds (such as nucleotides, catecholamine hormones, certain neurotransmitters, etc.), or they can be converted into sugars or fats. Some amino acids are neurotransmitters in their own right, and some can be involved in certain metabolic activities.

Amino Acid Structure

General formula of the structure of amino acids:

Different side chain groups have different physicochemical properties.

Protein amino acids: In protein biosynthesis, they are carried by specialized tRNA and are directly involved in protein molecules. 22 types of protein amino acids. They have the same structural formula and differ in the side chain group (R group). All organisms contain 20 common amino acids. 2 uncommon protein amino acids are selenocysteine (21st) and pyrrole lysine (22nd). Selenocysteine is found only in selenocyte-containing proteins, while pyrrole lysine is found only in some prokaryotic organisms as a component of certain enzymes related to methanogenesis.

Non-protein amino acids: Cannot be directly incorporated into protein molecules or are post-translational modification products of protein amino acids, e.g., citrulline, ornithine, and hydroxyproline.

Definition of Amino Acid Metabolism

Amino acid metabolism encompasses the biochemical pathways responsible for the synthesis and breakdown of amino acids in living organisms. It involves a series of enzymatic reactions that regulate the production and utilization of these organic compounds. The primary goal of amino acid metabolism is to ensure a constant supply of amino acids for protein synthesis, while also fulfilling other metabolic demands such as energy production and the synthesis of various biomolecules.

Schematic representation of amino acid metabolism in different cell types (Sormendi et al, 2018)

Amino acid metabolism consists of two primary processes: biosynthesis and degradation.

Biosynthesis of Amino Acids

Biosynthesis of amino acids refers to the biochemical processes through which living organisms produce these essential building blocks of proteins. Amino acids are organic compounds characterized by having both an amino group (-NH2) and a carboxyl group (-COOH), bonded to a central carbon atom. There are 20 standard amino acids used by cells to build proteins, each with its own unique side chain. These amino acids are classified into two categories: essential amino acids, which cannot be synthesized by the organism and must be obtained from the diet, and non-essential amino acids, which the organism can synthesize from common metabolic intermediates.

Biosynthesis Pathways

The biosynthesis of amino acids involves various metabolic pathways occurring within cells. These pathways are highly regulated and interconnected with other metabolic processes.

Glycolysis and the Citric Acid Cycle (TCA cycle): Several amino acids are derived from intermediates of glycolysis and the TCA cycle. For example, α-ketoglutarate, oxaloacetate, and pyruvate serve as precursors for the synthesis of glutamate, aspartate, and alanine, respectively.

Transamination: This process involves the transfer of an amino group from one amino acid to a keto acid, forming a new amino acid and a new keto acid. Transaminases or aminotransferases catalyze these reactions.

Amino Acid Biosynthesis Pathways: Each amino acid has its specific biosynthetic pathway.

• Glutamate: Glutamate is a central amino acid in amino acid metabolism. It serves as a precursor for the biosynthesis of several other amino acids. Glutamate can be synthesized from α-ketoglutarate, an intermediate of the citric acid cycle, through the action of the enzyme glutamate dehydrogenase.
• Aspartate: Aspartate is another important precursor for amino acid biosynthesis. It can be synthesized from oxaloacetate, another intermediate of the citric acid cycle, via transamination reactions catalyzed by aspartate aminotransferase.
• Serine and Glycine: Serine can be synthesized from 3-phosphoglycerate, an intermediate of glycolysis, through a series of enzymatic reactions involving the conversion of 3-phosphoglycerate to 3-phosphohydroxypyruvate, and then to phosphoserine, which is subsequently hydrolyzed to serine. Glycine can be synthesized from serine via the removal of a methyl group by serine hydroxymethyltransferase.
• Histidine: Histidine biosynthesis involves a complex pathway that starts with the conversion of phosphoribosyl pyrophosphate (PRPP) to 5-phosphoribosylamine. This intermediate undergoes several enzymatic transformations to eventually form histidine.
• Arginine: Arginine can be synthesized from glutamate and aspartate via the urea cycle intermediates ornithine and citrulline. This pathway involves several enzymatic steps and occurs primarily in the liver.
• Leucine, Isoleucine, and Valine: These branched-chain amino acids (BCAAs) share a common biosynthetic pathway that starts with the condensation of pyruvate and acetyl-CoA to form α-ketoisovalerate. Further enzymatic steps lead to the production of the respective amino acids.
• Phenylalanine and Tyrosine: Phenylalanine can be hydroxylated to form tyrosine by the enzyme phenylalanine hydroxylase. Tyrosine biosynthesis also involves the conversion of chorismate, an intermediate of the shikimate pathway.
• Lysine Biosynthesis: Lysine biosynthesis occurs via the diaminopimelate (DAP) pathway or the α-aminoadipate pathway, depending on the organism.

Regulation

The biosynthesis of amino acids is tightly regulated to maintain proper balance and meet the metabolic demands of the cell. Regulation occurs at multiple levels, including transcriptional control of enzyme genes, allosteric regulation of enzyme activity, and feedback inhibition by end products of amino acid biosynthesis pathways.

Integration with Other Metabolic Pathways:

Amino acid biosynthesis pathways are interconnected with other metabolic pathways, such as carbohydrate metabolism, lipid metabolism, and nucleotide metabolism.

These connections allow for the coordination of cellular metabolism to ensure efficient utilization of resources and energy.

Degradation of Amino Acids

The degradation of amino acids is a crucial process that occurs in living organisms to maintain amino acid homeostasis, generate energy, and eliminate nitrogenous waste. This intricate process involves the sequential removal of amino groups, leading to the formation of carbon skeletons that can be further metabolized or excreted from the body.

Transamination and Deamination:

The initial steps of amino acid degradation involve the removal of amino groups through transamination or deamination reactions. Transamination transfers the amino group from an amino acid to an α-keto acid, generating a new amino acid and a different α-keto acid. This process is catalyzed by aminotransferase enzymes, which are specific to particular amino acids.

Alternatively, deamination removes the amino group directly from the amino acid, producing ammonia (NH₃) or ammonium ion (NH₄⁺) as a byproduct. Deamination reactions are catalyzed by deaminase enzymes and occur primarily in the liver. The resulting carbon skeletons are then further metabolized through various pathways, depending on the specific amino acid.

Fate of Carbon Skeletons:

The carbon skeletons derived from amino acid degradation can enter several metabolic pathways based on their structure and cellular requirements:

• Gluconeogenesis: Some amino acid carbon skeletons can be converted into intermediates of gluconeogenesis, the synthesis of glucose from non-carbohydrate precursors. This process is especially important during fasting or prolonged exercise when glucose levels need to be maintained.
• Ketogenesis: Certain amino acids, particularly ketogenic amino acids like leucine and lysine, can be converted into acetyl-CoA or acetoacetyl-CoA, precursors for the synthesis of ketone bodies. Ketogenesis occurs predominantly in the liver and provides an alternative fuel source for tissues, particularly the brain, during periods of prolonged fasting or low carbohydrate intake.
• Energy Production: Amino acid carbon skeletons can also enter the citric acid cycle as intermediates, where they undergo oxidation to produce ATP through oxidative phosphorylation. This process contributes to the overall energy balance of the organism and is essential for cellular functions.

Urea Cycle and Ammonia Detoxification:

One of the key challenges in amino acid degradation is the removal of toxic ammonia generated during transamination and deamination reactions. In the liver, ammonia is incorporated into urea through a series of reactions known as the urea cycle. Urea is a water-soluble compound that can be safely excreted from the body via the kidneys, preventing the accumulation of ammonia in the bloodstream.

The urea cycle consists of several enzymatic steps that sequentially incorporate ammonia into urea, which is then transported to the kidneys for excretion in the urine. The regulation of the urea cycle is tightly controlled to match the production of ammonia with the body's ability to eliminate it, ensuring nitrogen balance and preventing toxicity.

Regulation of Amino Acid Degradation:

The degradation of amino acids is regulated at multiple levels to maintain amino acid homeostasis and adapt to changing metabolic demands. Enzyme activity in degradation pathways is influenced by factors such as substrate availability, hormonal signals, and cellular energy status. Feedback inhibition by end products of degradation pathways helps to prevent excessive catabolism and maintain metabolic balance.

What is the Role of Amino Acids in Metabolism?

Amino acids serve as more than just the building blocks of proteins; they also play crucial roles in various metabolic pathways.

Protein Synthesis: Amino acids are essential for the synthesis of proteins, which are vital for the structure, function, and regulation of cells and tissues.

Energy Production: Amino acids can be catabolized to generate energy through pathways such as the citric acid cycle and oxidative phosphorylation.

Precursor Molecules: Certain amino acids serve as precursors for the synthesis of important molecules such as neurotransmitters, hormones, nucleotides, and other amino acids.

Regulation of Metabolic Pathways: Amino acids and their derivatives often act as allosteric regulators or coenzymes, modulating the activity of enzymes involved in various metabolic pathways.

What is a Disorder of Amino Acid Metabolism?

A disorder of amino acid metabolism refers to a group of genetic conditions characterized by the body's inability to properly process or metabolize certain amino acids. Amino acids are the fundamental building blocks of proteins and play essential roles in various physiological processes, including protein synthesis, neurotransmitter production, and energy metabolism. When there is a defect or deficiency in the enzymes responsible for metabolizing amino acids, it can lead to the accumulation of specific amino acids or their byproducts in the body, resulting in a range of health problems.

These disorders are typically inherited in an autosomal recessive manner, meaning that an individual must inherit two copies of the defective gene (one from each parent) to develop the disorder. However, some disorders of amino acid metabolism can also be caused by spontaneous genetic mutations.

There are numerous disorders of amino acid metabolism, each characterized by the accumulation of a specific amino acid or group of amino acids. Some of the most common disorders include:

• Phenylketonuria (PKU): PKU is caused by a deficiency of the enzyme phenylalanine hydroxylase, which is responsible for converting the amino acid phenylalanine into tyrosine. Without this enzyme, phenylalanine builds up in the blood and can lead to intellectual disability, developmental delays, seizures, and behavioral problems if left untreated.
• Maple syrup urine disease (MSUD): MSUD is characterized by a deficiency of the enzyme complex that breaks down the branched-chain amino acids (BCAAs) leucine, isoleucine, and valine. The accumulation of these amino acids and their toxic byproducts can result in neurological damage, feeding difficulties, ketoacidosis, and a distinctive odor of maple syrup in the urine.
• Tyrosinemia: Tyrosinemia encompasses a group of disorders caused by deficiencies in enzymes involved in the breakdown of the amino acid tyrosine. Depending on the specific enzyme affected, tyrosinemia can lead to liver and kidney damage, neurological symptoms, and eye problems.
• Homocystinuria: Homocystinuria is caused by deficiencies in enzymes involved in the metabolism of the amino acid methionine. Elevated levels of homocysteine, a byproduct of methionine metabolism, can lead to vascular problems, such as blood clots and premature atherosclerosis, as well as skeletal abnormalities, intellectual disability, and eye problems.
• Amino acid transport disorders: These disorders involve defects in the transport proteins responsible for moving amino acids across cell membranes. As a result, specific amino acids may not be properly absorbed or excreted, leading to their accumulation in the blood or urine. Examples include cystinuria, lysinuric protein intolerance, and Hartnup disease.

Treatment for disorders of amino acid metabolism typically involves dietary interventions, such as restricting the intake of the affected amino acids while ensuring an adequate intake of other nutrients. In some cases, supplementation with specific vitamins, cofactors, or amino acid formulations may be necessary to help normalize metabolic processes. Early diagnosis through newborn screening programs and prompt initiation of treatment are crucial for preventing or minimizing the long-term complications associated with these disorders. Additionally, ongoing monitoring and management by a multidisciplinary team of healthcare professionals, including geneticists, dietitians, and specialists in metabolic disorders, are essential for optimizing outcomes and improving the quality of life for affected individuals.

Amino Acid Analysis Methods

Amino acids are widely distributed in biological fluids and are involved in many biological processes such as the synthesis as proteins, fatty acids and ketone bodies. Changes in amino acid levels in living organisms have been found to be closely associated with several diseases in fluids, such as type 2 diabetes, kidney disease, liver disease and cancer. Therefore, the development of analytical methods for the determination of amino acids and the determination of their concentration in biological samples helps to study the physiological role of amino acids in relation to the prediction, diagnosis and mechanism of diseases.

The chromatography-mass spectrometry technique uses chromatography as the separation system and mass spectrometry as the detection system. The sample is separated in the mobile phase and chromatographic fraction. After ionization, the ion fragments are separated by mass number by the mass analyzer of the mass spectrometer. The mass spectra are obtained after passing through the detector. Ultra-Performance Liquid Chromatography-Tandem Mass Spectrometry (UPLC-MS/MS) technology combines the high separation power of chromatography with the structural identification advantages of mass spectrometry to achieve baseline separation of isomers, thus giving the possibility of amino acid detection with greater specificity, higher precision and wider detection range.

Creative Proteomics amino acid mass spectrometry services can be used to detect and analyze a wide range of amino acid levels in blood, urine, other biological fluids, and tissues.

Reference

1. Sormendi, S., & Wielockx, B. (2018). Hypoxia pathway proteins as central mediators of metabolism in the tumor cells and their microenvironment. Frontiers in immunology, 9, 40.