Amino acids

Amino acids are organic compounds that consist of a carbon atom attached to a carboxyl group, a hydrogen atom, an amino group, and a variable R group (side chain). In humans (and other eukaryotes), there are 21 different proteinogenic amino acids, 20 of which are encoded for protein synthesis by the genetic code, as well as selenocysteine, which is integrated via a special translation mechanism. They can be divided into essential amino acids (cannot be synthesized by the body) and nonessential amino acids (can be synthesized by the body). Amino acid derivatives include glycine, glutamate, histidine, arginine, tryptophan, and phenylalanine. Amino acid catabolism can occur via different metabolic routes, each with a specific purpose, including the production of metabolic fuels (e.g., pyruvate, acetyl-CoA), reuse in the synthesis of new proteins, and the creation of amino acid derivatives. Deficiencies in these metabolic routes can lead to a variety of conditions, which are covered in more detail in “Disorders of amino acid metabolism,” “Hyperphenylalaninemia,” and “Hyperammonemia.”

Structure

• Amino acid (AA) consists of a carbon atom attached to a/an:
  • Carboxyl group (-COOH)
  • Hydrogen atom
  • Amino group (-NH₂)
  • Variable R group (side chain): determines unique properties
• Only L-form amino acids are incorporated into proteins during translation.
• There are 21 standard proteinogenic amino acids in humans
  • 20 are encoded for protein synthesis by the genetic code
  • Selenocysteine is incorporated via a mechanism known as translational recoding
  • All proteinogenic amino acids are α-aminocarboxylic acids; they differ only in their side chains
  • All proteinogenic amino acids (with the exception of glycine) have a chirality center at the α-carbon atom

Glycine (Gly) is unique as the only achiral proteinogenic amino acid. Its R-group is a single hydrogen atom, so the alpha-carbon is not a chiral center (it is bound to two identical hydrogens).

Properties

Essential or nonessential

For essential AAs, think PVT (Private) TIM HALL: Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine, Leucine, Lysine

To remember glucogenic AAs, think: Arges Met His Valentine and gave her sweets.

For his movie roles, Brad PITT may eat a lot (glucogenic) or diet (ketogenic): Phenylalanine, Isoleucine, Threonine, Tryptophan

For ketogenic AAs, visualize 2 L-shaped keys: Leucine and Lysine.

Proline's unique side chain bonds back to its own alpha-amino group, forming a rigid pyrrolidine ring. This structural rigidity introduces a sharp kink into the polypeptide backbone, disrupting the regular structure of alpha-helices (making it a "helix-breaker").

Cysteine contains a thiol (SH) group. Two cysteines can oxidize to form a disulfide bridge (the resulting molecule is called cystine), which is critical for stabilizing the tertiary and quaternary structure of proteins.

Tryptophan is a precursor for the neurotransmitter serotonin and the hormone melatonin.

The hydroxyl (-OH) side chains of serine (S), threonine (T), and tyrosine (Y) are the key targets for kinase-mediated phosphorylation, a fundamental step in cell signaling.

Hydrophobic or hydrophilic

Acid-base properties

• Overview
  • The net charge and thus polarity of AAs can change according to the surrounding pH and availability of H⁺ available for protonation. When charged, AAs become polar/hydrophilic.
  • Acid dissociation constant (pKa)
    • Indicates the strength of a weak acid or base
    • Defined as the pH at which the ionized and unionized forms exist in equal concentrations
  • All AAs have at least two ionizable groups, each with its own acid dissociation constant (pKa).
  • These pKa values are determined experimentally and visualized on a titration curve, which plots pH versus the amount of strong base or acid added (see "Amino acid titration").
    • pKa of the α-carboxyl group = 2
    • pKa of the α-amino group = 9–10
  • Acidic/basic AAs have another pKa for their ionizable side chain group, which varies.
• Acidic amino acids: Side groups are negatively charged at body pH (both have a pKa of ∼ 4). ;
  • Asp: pKa of 3.9
  • Glu: pKa of 4.3
• Basic amino acids
  • Weakly basic: Side group has no charge at body pH (∼ 7.4).
    • His: pKa of 6
  • Side groups are positively charged at body pH. They could be found in histones binding negatively charged DNA.
    • Lys: pKa of 10.5
    • Arg: pKa of 12.5
• Isoelectric point (pI)
  • Specific pH at which an amino acid or another molecule has a net charge of zero
  • At this pH, the molecule exists as a zwitterion, with an equal number of positive and negative charges.
  • Calculation: derived from the average of the pKa values
  • Formula: pI = (pK_a1 + pK_a2)/2
  • Calculation examples
    • For alanine: pK_a1 (COOH) = 2.3 and pK_a2 (NH2) = 9.9
      • pI (alanine) = (pK_a1 + pK_a2)/2 = (2.3 + 9.9)/2 = 6.1
    • For lysine: pK_a1 (COOH) = 2.2 and pK_a2 (NH2) = 9.0 and pK_a3 (NH2) = 10.4
      • pI(lysine) = (pK_a2 + pK_a3)/2 = (9.0 + 10.4)/2 = 9.7

His (histidine) lies (lysine) are (arginine) base (basic amino acids).

Amino acid titration

• Definition: a method to determine the pKa values of an amino acid's ionizable groups
• Principle
  • The amino acid is first dissolved in a strong acid (low pH) to ensure all groups are fully protonated (e.g., COOH, NH³⁺+).
  • A strong base (e.g., NaOH) is then slowly added, and the pH is plotted versus the amount of base added.
  • The resulting curve shows multiple buffer regions and equivalence points, one for each ionizable proton.
• Half-equivalence points (buffer regions)
  • Flat zones on the curve where the pH changes very little
  • At the exact midpoint of any buffer region, pH = pKa for the functional group being titrated
  • At this point, the concentrations of the protonated (e.g., HA) and deprotonated (e.g., A‑) forms of that group are equal.
• Equivalence points (inflection points)
  • The steep, vertical zones on the curve, where the pH changes rapidly
  • Indicate that a functional group has been fully deprotonated
  • The isoelectric point (pI), the pH where the amino acid has a net charge of zero, occurs at an equivalence point
• Interpretation
  • Two pK_a values: The curve has two buffer regions. This indicates a neutral (non-ionizable) side chain (e.g., alanine, glycine, valine). The pK_a's correspond to the alpha-carboxyl (∼ 2-2.5) and alpha-amino (∼ 9-10) groups.
  • Three pK_a values: The curve has three buffer regions. This indicates an ionizable side chain (e.g., aspartate, lysine, histidine). The third pK_a (pK_aR) corresponds to the side chain and allows for the amino acid's identification.
    • Acidic (Asp, Glu): pK_aR ∼ 4
    • Basic (Lys, Arg): pK_aR ∼ 10.5-12.5
    • Histidine: pK_aR ∼ 6.0
    • Cysteine: pK_aR ∼ 8.4
    • Tyrosine: pK_aR ∼ 10.5

Depending on the pH of the surrounding medium, amino acids are protonated, partially protonated, or deprotonated. If pH > pKa, the group will be deprotonated (loses a proton). If pH < pKa, the group will be protonated (keeps its proton).

Histidine's pKa near physiological pH makes it an excellent buffer.

• Glycine
  • (+ Succinyl CoA + pyridoxine) → Porphyrin → Heme
  • (+ Aspartate + glutamine) → Purines
• Glutamate
  • (+ Pyridoxine) → GABA
  • (+ Glycine + cysteine) → Glutathione
• Histidine: (+ pyridoxine) → Histamine + CO² (decarboxylation)
• Arginine
  • (+ NADPH + THB) → Nitric oxide
  • Urea
  • Creatinine is synthesized from arginine + glycine
• Tryptophan
  • (+ Pyridoxine + riboflavin) → Niacin (= vitamin B₃) → NAD⁺/NADP⁺
  • (+ THB + pyridoxine) → Serotonin → Melatonin
• Phenylalanine
  • (+ THB) → Tyrosine (+ THB) → L-Dopa (+ pyridoxine) → Dopamine (+ vitamin C) → Norepinephrine (+ S-Adenosylmethionine) → Epinephrine
    • Tyrosine → Thyroxine (T₄) → T₃
    • L-Dopa → Melanin

Overview

• Metabolic routes: During protein catabolism, amino acids may undergo different metabolic routes for different purposes, including:
  • AA catabolism, leading to the creation of
    • Metabolic fuels (e.g., forming pyruvate, acetyl-CoA)
    • Urea for excretion of excess nitrogen
  • Reuse in the synthesis of new proteins (See “Translation and protein synthesis.”)
  • Creation of amino acid derivatives (See above.)
  • See “Protein degradation.”
• Sites of metabolism
  • Essential AAs: primarily the liver
  • Nonessential AAs: throughout the body
• Processes of AA metabolism
  • Biochemical reactions of AA
    • Splitting of the amino group (via transamination or deamination)
    • Splitting of the carboxyl group (via decarboxylation)
    • Pyridoxal phosphate (PLP) is an important cofactor, a derivative of vitamin B₆, used in transamination, decarboxylation, and deamination of serine.
  • Catabolism of the carbon skeleton of amino acids: can be reused as part of carbohydrate or lipid metabolism, or the citric acid cycle
  • The urea cycle: Excess nitrogen is converted into urea via the urea cycle and excreted in urine.

Transamination

• Description: transfer of an amino group from an AA to an α-ketoacid for breakdown, or to an α-ketoacid to form a nonessential AA
• Enzymes
  • Transaminases, particularly
    • Alanine aminotransferase (ALT)
    • Aspartate aminotransferase (AST)
  • Important cofactor: pyridoxal phosphate (PLP), a derivative of vitamin B₆, for transamination and decarboxylation reactions
• Location: Transaminases are found in most cells of the body, but they have greater concentrations in the liver and heart.
• Most common examples
  • ALT: alanine + α-ketoglutarate ⇄ pyruvate + glutamate
  • AST: aspartate + α-ketoglutarate ⇄ oxalacetate + glutamate
  • All AAs (except threonine and lysine) undergo transamination at some point in their catabolism.

Glutamate is involved in most transamination reactions and a very important part of AA metabolism.

Deamination

• Description: reaction in which an amino group from an AA is released as ammonium
• Examples
  • Glutamate dehydrogenase: glutamate + NAD(P)⁺ + H₂O ⇄ α-ketoglutarate + NH₄⁺ + NAD(P)H + H⁺
  • Serine dehydratase: serine + PLP ⇄ NH₄⁺ + pyruvate
  • Glutaminase: glutamine + H₂O → glutamate + ammonium (irreversible)
  • Asparaginase: asparagine + H₂O → aspartate + ammonium (irreversible)

Glutamate dehydrogenase can use either NAD+ or NADP+ as a cofactor.

Decarboxylation

• Description: release of the α-carboxyl group of an AA via splitting of CO₂
• Example: : synthesis of biogenic amines via aromatic L-amino acid decarboxylase (also known as DOPA decarboxylase), which also uses PLP

Routes of AA carbon skeleton metabolism

Glucogenic amino acids

• Are metabolized to pyruvate and to metabolites of the citric acid cycle, then either:
  • Oxidized to CO₂ in the CAC for production of energy OR
  • Utilized as a substrate for gluconeogenesis
• Byproducts
  • Pyruvate
    • Product of glycine, alanine, serine, and cysteine
    • Also, threonine → glycine and serine → pyruvate
  • Succinyl-CoA
    • Methionine and valine: metabolized to succinyl-CoA via propionyl-CoA and methylmalonyl-CoA
    • Methionine cycle: Methionine → S-adenosylmethionine (SAM) → S-adenosylhomocysteine → Homocysteine → Methionine
      • S-adenosylmethionine (SAM): plays an important role as a cofactor for methylation reactions (It donates its methyl group for anabolic pathways.)
      • S-adenosyl methionine synthase: an enzyme that catalyzes the conversion of methionine and ATP to S-adenosylmethionine; deficiency of this enzyme causes hypermethioninemia
      • Homocysteine: Demethylation of SAM results in homocysteine, which can be metabolized to cystathionine and then cysteine.
  • α-Ketoglutarate
    • Glutamine, arginine, histidine, proline → glutamate → α-ketoglutarate
  • Fumarate
  • Oxaloacetate
    • Transamination of aspartate → oxaloacetate
    • Deamination of asparagine → aspartate → oxaloacetate

Ketogenic amino acids

Lysine and leucine are metabolized to acetyl-CoA, then either:

• The acetyl group is oxidized to CO₂ in the citric acid cycle for production of energy OR
• Used to synthesize ketone bodies OR
• Used to synthesize fatty acids or cholesterol

Mixed gluconeogenic/ketogenic amino acids

• Tyrosine and phenylalanine: metabolized to fumarate and acetyl-CoA
  • Tyrosine: transamination through tyrosine transaminase, that is then metabolized through multiple steps to fumarate and acetyl-CoA
  • Phenylalanine: first metabolized to tyrosine via phenylalanine hydroxylase (requires O₂ and the reducing agent tetrahydrobiopterin), then further metabolized as described above
• Tryptophan: metabolized to alanine and acetyl-CoA, thereby also creating nicotinamide
• Isoleucine
  • Transamination to propionyl-CoA and acetyl-CoA
  • Propionyl-CoA is further metabolized to methylmalonyl-CoA to succinyl-CoA
• Threonine ^[1]
  • Glucogenic routes
    • → Ketobutyrate → propionyl-CoA (via dehydratase)
    • → Amino acetone → pyruvate (via dehydrogenase)
  • Ketogenic routes
    • → Glycine + acetaldehyde → acetyl-CoA (via aldolase)
    • + CoA → glycine + acetyl-CoA (via dehydrogenase coupled with a lyase)

Lysine and leucine are the only pure ketogenic AAs.

• Description
  • A cycle of reactions that produce urea; ((NH₂)₂CO) from ammonia (NH₃), bicarbonate (HCO₃⁻), and the amino group of aspartate
  • Requires 3 ATP for energy
  • Measured as blood urea nitrogen (BUN) for clinical use
• Function: renal excretion of nitrogen in form of urea
• Location: primarily occurs in the cytosol and mitochondria of liver cells and also in kidney cells
• Origin of ammonia
  • Ammonia develops as a product of various metabolic pathways throughout the body.
  • Because of its toxicity, ammonia must be bound to glutamine or alanine for transportation.
    • Glutamine cycle (most common): transport of ammonia as an amine group attached to glutamine to the liver
      • Glutamine synthetase attaches free ammonia to glutamate to form glutamine
      • Ammonia is then split from glutamate via oxidative deamination in hepatocytes
    • Alanine cycle
      • Transport of ammonia as an amine group on alanine from skeletal muscles to the liver
      • Created by ALT from pyruvate in muscle and transformed back to pyruvate in the liver via ALT

Urea cycle steps (Ornithine, Carbamoyl phosphate, Citrulline, Aspartate, Argininosuccinate, Fumarate, Arginine, and Urea): “Outrageously Cynical Criticism Antagonizes All my Friends At University”

The rate-limiting step of the urea cycle involves CPS1.

Location of the CPS1 enzyme is “M1tochondria.”

NH₂ groups for urea production are derived from carbamoyl phosphate and aspartate, whereas the carbon group comes from bicarbonate.

The mitochondrial carbamoyl phosphate synthetase 1 of the urea cycle should not be confused with the cytosolic carbamoyl phosphate synthetase 2, which is an important enzyme for pyrimidine biosynthesis.

Do not confuse urea with uric acid from purine metabolism.

• Synthesis of nonessential AAs occurs mainly in the liver.
• The carbon skeleton is taken from either the citric acid cycle or from carbohydrate catabolism.

• See “Disorders of amino acid metabolism” for details of the following conditions
  • Alkaptonuria
  • Homocystinuria
  • Phenylketonuria (PKU), hyperphenylalaninemia
  • Cystinosis
  • Cystinuria
  • Hartnup disease
  • Maple syrup urine disease
  • Histidinemia
  • Organic acidemias
  • Cystinosis
• Albinism

Hyperammonemia

• Normal intracranial ammonia physiology
  • Glutamate and ammonia exist in a chemical equilibrium with glutamine, mediated by the enzyme glutamine synthetase.
  • Glutamate serves as a substrate for glutamate decarboxylase to form GABA.
  • This mechanism controls GABA concentration and, thus, GABAergic tone.
• Pathophysiology
  • Elevated serum ammonia levels disrupt the balance between glutamine, glutamate, α-ketoglutarate, and GABA through the actions of glutamate dehydrogenase and glutamine synthetase, resulting in increased glutamine and increased glutamate levels → increased GABA synthesis and GABAergic tone → typical features of hyperammonemic encephalopathy: ^[2]
    • Excess glutamine → osmotic damage to astrocytes → cellular swelling and dysfunction → cerebral edema
    • Imbalance of the neurotransmitters → Inhibition of excitatory neurotransmission and activation of inhibitory neurotransmission
  • Low α-ketoglutarate → inhibition of TCA cycle
• Etiology
  • Acquired: most common in adults
    • Liver failure: naturally occurring nitrogenous wastes in the blood accumulate to toxic levels secondary to impaired urea cycle function in damaged hepatocytes and/or shunting of blood from the portal vein to collateral circulations→ hepatic encephalopathy
    • Kidney failure: inability to excrete excess ammonia as urea
    • Severe dehydration
    • Small intestinal bacterial overgrowth: urease-producing organisms in the gut produce excess ammonia
    • Medications (e.g., valproic acid toxicity → carnitine deficiency)
    • Reye syndrome
  • Hereditary: most often in children but heterozygotes can present as older children or adults
    • Urea cycle disorders, especially ornithine transcarbamylase deficiency, carbamoyl phosphate synthetase 1 deficiency, N-acetylglutamate synthase deficiency
    • Organic acidemias: most commonly methylmalonic acidemia
    • Other rare causes including congenital lactic acidosis conditions, dibasic amino aciduria conditions, inborn errors of mitochondrial fatty acid oxidation
• Clinical features
  • Pediatric patients
    • Poor feeding, lethargy
    • Hypotonia
    • Seizures
    • Respiratory distress
  • Adults
    • Vomiting
    • Flapping tremor (asterixis)
    • Blurred vision, slurred speech
    • Cerebral edema (caused by osmotic shifts due to change in glutamine levels), seizures, somnolence, and coma
• Management
  • Depends on the underlying cause and should be conducted ASAP to prevent central nervous system morbidity and possible mortality
  • Reduction of protein intake
  • Medications that lower serum ammonia level
    • Lactulose: lowers gastrointestinal pH levels and thereby fixes NH₄⁺ and promotes its excretion
    • Antibiotics i.e., rifaximin or neomycin: diminish bacterial population in the gut that produces excess ammonia
    • Phenylbutyrate, phenylacetate, or benzoate: form water soluble products with glycine or glutamine that can be excreted through kidneys