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Basics of Amino Acids

Amino acids Acids Chemical compounds which yield hydrogen ions or protons when dissolved in water, whose hydrogen can be replaced by metals or basic radicals, or which react with bases to form salts and water (neutralization). An extension of the term includes substances dissolved in media other than water. Acid-Base Balance (AAs) are composed of a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain (R group). There are hundreds of AAs found in nature, but only 20 are the building blocks of proteins Proteins Linear polypeptides that are synthesized on ribosomes and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of amino acids determines the shape the polypeptide will take, during protein folding, and the function of the protein. Energy Homeostasis in humans (proteinogenic). Nine of these 20 are “essential,” as they cannot be synthesized. Amino acids Acids Chemical compounds which yield hydrogen ions or protons when dissolved in water, whose hydrogen can be replaced by metals or basic radicals, or which react with bases to form salts and water (neutralization). An extension of the term includes substances dissolved in media other than water. Acid-Base Balance differ from one another only in the chemical nature of the R group. They are most commonly classified according to their interaction with water as hydrophobic, hydrophilic Hydrophilic Aminoglycosides, or ionic.

Last updated: 23 Apr, 2021

Editorial responsibility: Stanley Oiseth, Lindsay Jones, Evelin Maza

Structural Features

Basic structure

Each amino acid ( AA AA Amyloidosis) is composed of one alpha, or central, carbon bonded to:

  • One alpha amine group
  • One alpha carboxyl group
  • One hydrogen atom
  • One R group, which varies between AAs and gives them their unique properties
The basic structure of amino acids diagram

The basic structure of amino acids Acids Chemical compounds which yield hydrogen ions or protons when dissolved in water, whose hydrogen can be replaced by metals or basic radicals, or which react with bases to form salts and water (neutralization). An extension of the term includes substances dissolved in media other than water. Acid-Base Balance

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Stereochemistry

  • Isomers: molecules with identical formulas but different structures
  • Stereochemistry: property of molecules with the same formula and sequence of atoms but different 3-dimensional orientations in space
  • Chirality: property of molecules that are non-superimposable on their mirror images
    • AAs have D and L isomers.
    • Almost all proteinogenic AAs are found in the L configuration.
    • The chiral center of every AA AA Amyloidosis is the alpha carbon, except for glycine Glycine A non-essential amino acid. It is found primarily in gelatin and silk fibroin and used therapeutically as a nutrient. It is also a fast inhibitory neurotransmitter. Synthesis of Nonessential Amino Acids (because its R group is a hydrogen atom).
Isomer structure

Isomeric forms of amino acids Acids Chemical compounds which yield hydrogen ions or protons when dissolved in water, whose hydrogen can be replaced by metals or basic radicals, or which react with bases to form salts and water (neutralization). An extension of the term includes substances dissolved in media other than water. Acid-Base Balance

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R groups or side chains

R groups determine the differences in structure, function, and biological interactions of AAs.

R groups can be classified in 2 ways:

  1. Hydrophobic or hydrophilic Hydrophilic Aminoglycosides:
    • Non-polar or hydrophobic R groups: side chains do not interact with water; the protein folds so that these AAs are toward the core of the molecule. Grouped according to structure:
      • Aromatic R groups (a cyclic compound called a benzene ring)
      • Aliphatic R groups (branched or straight open-chain compound)
    • Polar or hydrophilic Hydrophilic Aminoglycosides R groups: Side chains interact with water; found on the surface of the molecule. Grouped according to ionic charge:
      • Uncharged R groups (neutral at physiological pH pH The quantitative measurement of the acidity or basicity of a solution. Acid-Base Balance)
      • Positively charged R groups (basic amine groups)
      • Negatively charged R groups (acidic carboxyl groups) 
  2. Hydrophobic, hydrophilic Hydrophilic Aminoglycosides, and ionic:
    • Hydrophobic: non-polar AAs containing aromatic or aliphatic R groups
    • Hydrophilic Hydrophilic Aminoglycosides: polar AAs with neutral charge containing hydroxyl, sulfhydryl, or carboxamide R groups
    • Ionic: AAs that acquire a positive (amines) or negative (carboxylates) charge by ionizing at physiological pH pH The quantitative measurement of the acidity or basicity of a solution. Acid-Base Balance
Non polar and polar r groups

Categories of R groups or side chains of amino acids Acids Chemical compounds which yield hydrogen ions or protons when dissolved in water, whose hydrogen can be replaced by metals or basic radicals, or which react with bases to form salts and water (neutralization). An extension of the term includes substances dissolved in media other than water. Acid-Base Balance

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Classifications

Essential and non essential amino acids

*Required only during periods of growth or positive nitrogen Nitrogen An element with the atomic symbol n, atomic number 7, and atomic weight [14. 00643; 14. 00728]. Nitrogen exists as a diatomic gas and makes up about 78% of the earth’s atmosphere by volume. It is a constituent of proteins and nucleic acids and found in all living cells. Urea Cycle balance.
**Synthesized from essential AAs.
*** Cysteine Cysteine A thiol-containing non-essential amino acid that is oxidized to form cystine. Synthesis of Nonessential Amino Acids analogue with selenium Selenium An element with the atomic symbol se, atomic number 34, and atomic weight 78. 97. It is an essential micronutrient for mammals and other animals but is toxic in large amounts. Selenium protects intracellular structures against oxidative damage. It is an essential component of glutathione peroxidase. Trace Elements instead of the usual sulfur. Not directly encoded in the genetic code

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R-group categories
Non-polar or hydrophobic Polar or hydrophilic Hydrophilic Aminoglycosides
Aromatic Positively charged or basic
  • Arginine Arginine An essential amino acid that is physiologically active in the l-form. Urea Cycle
  • Histidine
  • Lysine
Aliphatic
  • Alanine Alanine A non-essential amino acid that occurs in high levels in its free state in plasma. It is produced from pyruvate by transamination. It is involved in sugar and acid metabolism, increases immunity, and provides energy for muscle tissue, brain, and the central nervous system. Synthesis of Nonessential Amino Acids
  • Glycine Glycine A non-essential amino acid. It is found primarily in gelatin and silk fibroin and used therapeutically as a nutrient. It is also a fast inhibitory neurotransmitter. Synthesis of Nonessential Amino Acids
  • Isoleucine
  • Leucine
  • Methionine**
  • Proline Proline A non-essential amino acid that is synthesized from glutamic acid. It is an essential component of collagen and is important for proper functioning of joints and tendons. Synthesis of Nonessential Amino Acids
  • Valine
Uncharged
  • Asparagine Asparagine A non-essential amino acid that is involved in the metabolic control of cell functions in nerve and brain tissue. It is biosynthesized from aspartic acid and ammonia by asparagine synthetase. Synthesis of Nonessential Amino Acids
  • Cysteine Cysteine A thiol-containing non-essential amino acid that is oxidized to form cystine. Synthesis of Nonessential Amino Acids
  • Glutamine Glutamine A non-essential amino acid present abundantly throughout the body and is involved in many metabolic processes. It is synthesized from glutamic acid and ammonia. It is the principal carrier of nitrogen in the body and is an important energy source for many cells. Synthesis of Nonessential Amino Acids
  • Methionine**
  • Serine Serine A non-essential amino acid occurring in natural form as the l-isomer. It is synthesized from glycine or threonine. It is involved in the biosynthesis of purines; pyrimidines; and other amino acids. Synthesis of Nonessential Amino Acids
  • Threonine
  • Tyrosine Tyrosine A non-essential amino acid. In animals it is synthesized from phenylalanine. It is also the precursor of epinephrine; thyroid hormones; and melanin. Synthesis of Nonessential Amino Acids*
Negatively charged or acidic
  • Aspartate Aspartate One of the non-essential amino acids commonly occurring in the l-form. It is found in animals and plants, especially in sugar cane and sugar beets. It may be a neurotransmitter. Synthesis of Nonessential Amino Acids
  • Glutamate Glutamate Derivatives of glutamic acid. Included under this heading are a broad variety of acid forms, salts, esters, and amides that contain the 2-aminopentanedioic acid structure. Synthesis of Nonessential Amino Acids
*Can be considered non-polar or polar because the -OH group can form a hydrogen bond.
**Can be considered non-polar or polar because it contains a sulfur.

Chemical Properties of Amino Acids

  • Ionization: formation of ions and the acquiring of a negative or positive charge by the gain or loss of electrons. For AAs, this depends on the level of pH pH The quantitative measurement of the acidity or basicity of a solution. Acid-Base Balance
  • pKa: pH pH The quantitative measurement of the acidity or basicity of a solution. Acid-Base Balance at which half of the ionizable molecules have a proton and half do not
  • AAs are amphoteric molecules: possess basic and acidic properties
    • Carboxyl and amino groups have the same strength of acidity and basicity
  • At neutral pH pH The quantitative measurement of the acidity or basicity of a solution. Acid-Base Balance, the carboxyl group of an AA AA Amyloidosis is missing a proton, while the amino group has a proton (zwitterion form or dipolar ion).
  • Zwitterion: a molecule with one positively charged functional group (amine) and one negatively charged group (carboxyl), and a net charge of zero
    • Have high melting temperatures and good water solubility
    • pI: pH pH The quantitative measurement of the acidity or basicity of a solution. Acid-Base Balance at which the AA AA Amyloidosis is in its zwitterion form 
Zwitterion form

Zwitterion form

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  • If the pH pH The quantitative measurement of the acidity or basicity of a solution. Acid-Base Balance value < pI, the nitrogen Nitrogen An element with the atomic symbol n, atomic number 7, and atomic weight [14. 00643; 14. 00728]. Nitrogen exists as a diatomic gas and makes up about 78% of the earth’s atmosphere by volume. It is a constituent of proteins and nucleic acids and found in all living cells. Urea Cycle atom of the amine group gains a proton and AA AA Amyloidosiscation
  • If the pH pH The quantitative measurement of the acidity or basicity of a solution. Acid-Base Balance value > pI, the carboxyl group loses a proton and AA AA Amyloidosisanion
  • The presence of other carboxylic acids Acids Chemical compounds which yield hydrogen ions or protons when dissolved in water, whose hydrogen can be replaced by metals or basic radicals, or which react with bases to form salts and water (neutralization). An extension of the term includes substances dissolved in media other than water. Acid-Base Balance, amine, and hydroxyl groups in the side chains also contributes to the degree of ionization in varying pH pH The quantitative measurement of the acidity or basicity of a solution. Acid-Base Balance values.
Ionization

Example of ionization using aspartic acid. At the top are the 4 different forms that can exist with ionization. Notice how as equivalents of hydroxyl (OH), plotted on the x-axis, are added, the pH pH The quantitative measurement of the acidity or basicity of a solution. Acid-Base Balance (y-axis) increases. As pH pH The quantitative measurement of the acidity or basicity of a solution. Acid-Base Balance increases, the pK points are reached and progressively more hydrogen ions (protons) are released from the aspartic acid, lowering its charge.

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Catabolic Products of AAs

Catabolism of amino acids flow

The 3 categories of catabolic products of amino acids Acids Chemical compounds which yield hydrogen ions or protons when dissolved in water, whose hydrogen can be replaced by metals or basic radicals, or which react with bases to form salts and water (neutralization). An extension of the term includes substances dissolved in media other than water. Acid-Base Balance: glucogenic (green), ketogenic (red), and both glucogenic and ketogenic (blue). The glucose-pyruvate pathway on the left represents glycolysis Glycolysis Glycolysis is a central metabolic pathway responsible for the breakdown of glucose and plays a vital role in generating free energy for the cell and metabolites for further oxidative degradation. Glucose primarily becomes available in the blood as a result of glycogen breakdown or from its synthesis from noncarbohydrate precursors (gluconeogenesis) and is imported into cells by specific transport proteins. Glycolysis and gluconeogenesis Gluconeogenesis Gluconeogenesis is the process of making glucose from noncarbohydrate precursors. This metabolic pathway is more than just a reversal of glycolysis. Gluconeogenesis provides the body with glucose not obtained from food, such as during a fasting period. The production of glucose is critical for organs and cells that cannot use fat for fuel. Gluconeogenesis. The cyclic pathway on the right represents the citric acid cycle Cycle The type of signal that ends the inspiratory phase delivered by the ventilator Invasive Mechanical Ventilation. All amino acids Acids Chemical compounds which yield hydrogen ions or protons when dissolved in water, whose hydrogen can be replaced by metals or basic radicals, or which react with bases to form salts and water (neutralization). An extension of the term includes substances dissolved in media other than water. Acid-Base Balance are broken down into 1 of 6 intermediates (green boxes): pyruvate Pyruvate Derivatives of pyruvic acid, including its salts and esters. Glycolysis, acetyl-CoA Acetyl-CoA Acetyl CoA participates in the biosynthesis of fatty acids and sterols, in the oxidation of fatty acids and in the metabolism of many amino acids. It also acts as a biological acetylating agent. Citric Acid Cycle, oxaloacetate Oxaloacetate Derivatives of oxaloacetic acid. Included under this heading are a broad variety of acid forms, salts, esters, and amides that include a 2-keto-1, 4-carboxy aliphatic structure. Citric Acid Cycle, alpha-ketoglutarate, succinyl-CoA Succinyl-CoA Citric Acid Cycle, and fumarate Fumarate Citric Acid Cycle.

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The catabolism of AAs involves anaplerotic reactions (chemical reactions that form intermediates of metabolic pathways).

Amino acids Acids Chemical compounds which yield hydrogen ions or protons when dissolved in water, whose hydrogen can be replaced by metals or basic radicals, or which react with bases to form salts and water (neutralization). An extension of the term includes substances dissolved in media other than water. Acid-Base Balance can be classified by the catabolic products and into which metabolic pathways they will serve as intermediates:

  • Glucogenic AAs (green in figure above) → gluconeogenesis Gluconeogenesis Gluconeogenesis is the process of making glucose from noncarbohydrate precursors. This metabolic pathway is more than just a reversal of glycolysis. Gluconeogenesis provides the body with glucose not obtained from food, such as during a fasting period. The production of glucose is critical for organs and cells that cannot use fat for fuel. Gluconeogenesis intermediates
  • Ketogenic AAs (red in figure above) → ketogenesis Ketogenesis Ketone Body Metabolism intermediates
  • Glucogenic and ketogenic AAs (blue in figure above) → both pathways

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