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.

Last update:

Editorial responsibility: Stanley Oiseth, Lindsay Jones, Evelin Maza

Table of Contents

Share this concept:

Share on facebook
Share on twitter
Share on linkedin
Share on reddit
Share on email
Share on whatsapp

Structural Features

Basic structure

Each amino acid (AA) 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

Image by Lecturio.


  • 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.


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 hydrophobic Polar or hydrophilic
  • Phenylalanine
  • Tryptophan
  • Tyrosine*
Positively charged or basic
  • Arginine
  • Histidine
  • Lysine
  • Alanine
  • Glycine
  • Isoleucine
  • Leucine
  • Methionine**
  • Proline
  • Valine
  • 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 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 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.

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 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 Citric acid cycle The citric acid cycle, also known as the tricarboxylic acid (TCA) cycle or the Krebs cycle, is a cyclic set of reactions that occurs in the mitochondrial matrix. The TCA cycle is the continuation of any metabolic pathway that produces pyruvate, which is converted into its main substrate, acetyl-CoA. 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 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 intermediates
  • Glucogenic and ketogenic AAs (blue in figure above) → both pathways

USMLE™ is a joint program of the Federation of State Medical Boards (FSMB®) and National Board of Medical Examiners (NBME®). MCAT is a registered trademark of the Association of American Medical Colleges (AAMC). NCLEX®, NCLEX-RN®, and NCLEX-PN® are registered trademarks of the National Council of State Boards of Nursing, Inc (NCSBN®). None of the trademark holders are endorsed by nor affiliated with Lecturio.

Study on the Go

Lecturio Medical complements your studies with evidence-based learning strategies, video lectures, quiz questions, and more – all combined in one easy-to-use resource.

Learn even more with Lecturio:

Complement your med school studies with Lecturio’s all-in-one study companion, delivered with evidence-based learning strategies.

User Reviews




Esta página está disponible en Español.

🍪 Lecturio is using cookies to improve your user experience. By continuing use of our service you agree upon our Data Privacy Statement.