Basics of Amino Acids

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

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).

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

Classifications

In addition to the 20 standard AAs, 2 rare proteinogenic 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 also recognized:

• Selenocysteine (Sec):
  • Similar to cysteine Cysteine A thiol-containing non-essential amino acid that is oxidized to form cystine. Synthesis of Nonessential Amino Acids but contains 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 (Se) instead of sulfur
  • Incorporated into specific human selenoproteins through a unique mechanism
• Pyrrolysine (Pyl):
  • Similar to lysine with an additional pyrroline ring
  • Found in some archaea and bacteria Bacteria Bacteria are prokaryotic single-celled microorganisms that are metabolically active and divide by binary fission. Some of these organisms play a significant role in the pathogenesis of diseases. Bacteriology, but not in humans

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 

• 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 Amyloidosis → cation
• 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 Amyloidosis → anion
• 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.

Catabolic Products of AAs

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