Basics of Amino Acids

Amino acids (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 in humans (proteinogenic). Nine of these 20 are “essential,” as they cannot be synthesized. Amino acids 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, or ionic.

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Structural Features

Basic structure

Each amino acid (AA) is composed of 1 alpha, or central, carbon bonded to:

  • 1 alpha amine group
  • 1 alpha carboxyl group
  • 1 hydrogen atom
  • 1 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

Image by Lecturio.

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 is the alpha carbon, except for glycine (because its R group is a hydrogen atom).
Isomer structure

Isomeric forms of amino acids

Image by Lecturio.

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:
    • 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 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)
      • Positively charged R groups (basic amine groups)
      • Negatively charged R groups (acidic carboxyl groups) 
  2. Hydrophobic, hydrophilic, and ionic:
    • Hydrophobic: non-polar AAs containing aromatic or aliphatic R groups
    • Hydrophilic: 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
Non polar and polar R groups

Categories of R groups or side chains of amino acids

Image by Lecturio.

Classifications

Essential and Non essential Amino Acids

*Required only during periods of growth or positive nitrogen balance.
**Synthesized from essential AAs.
***Cysteine analogue with selenium instead of the usual sulfur. Not directly encoded in the genetic code

Image by Lecturio.
R-group categories
Non-polar or hydrophobicPolar or hydrophilic
Aromatic
  • Phenylalanine
  • Tryptophan
  • Tyrosine*
Positively charged or basic
  • Arginine
  • Histidine
  • Lysine
Aliphatic
  • Alanine
  • Glycine
  • Isoleucine
  • Leucine
  • Methionine**
  • Proline
  • Valine
Uncharged
  • Asparagine
  • Cysteine
  • Glutamine
  • Methionine**
  • Serine
  • Threonine
  • Tyrosine*
Negatively charged or acidic
  • Aspartate
  • Glutamate
*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. 
  • pKa: pH 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, the carboxyl group of an AA is missing a proton, while the amino group has a proton (zwitterion form or dipolar ion).
  • Zwitterion: a molecule with 1 positively charged functional group (amine) and 1 negatively charged group (carboxyl), and a net charge of zero
    • Have high melting temperatures and good water solubility
    • pI: pH at which the AA is in its zwitterion form 
Zwitterion form

Zwitterion form

Image by Lecturio.
  • If the pH value < pI, the nitrogen atom of the amine group gains a proton and AA → cation
  • If the pH value > pI, the carboxyl group loses a proton and AA → anion
  • The presence of other carboxylic acids, amine, and hydroxyl groups in the side chains also contributes to the degree of ionization in varying pH 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 (y-axis) increases. As pH increases, the pK points are reached and progressively more hydrogen ions (protons) are released from the aspartic acid, lowering its charge.

Image by Lecturio.

Catabolic Products of AAs

Catabolism of Amino Acids Flow

The 3 categories of catabolic products of amino acids: glucogenic (green), ketogenic (red), and both glucogenic and ketogenic (blue). The glucose-pyruvate pathway on the left represents glycolysis and gluconeogenesis. The cyclic pathway on the right represents the citric acid cycle. All amino acids are broken down into 1 of 6 intermediates (green boxes): pyruvate, acetyl-CoA, oxaloacetate, alpha-ketoglutarate, succinyl-CoA, and fumarate.

Image by Lecturio.

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

Amino acids can be classified by the catabolic products and into which metabolic pathways they will serve as intermediates:

  • Glucogenic AAs (green in figure above) → gluconeogenesis intermediates
  • Ketogenic AAs (red in figure above) → ketogenesis intermediates
  • Glucogenic and ketogenic AAs (blue in figure above) → both pathways

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