What Are Amino Acids?

Written by Johnathon Anderson, Ph.D., a research scientist specializing in regenerative medicine and serving as an Associate Professor at the University of California Davis School of Medicine 

What Are Amino Acids?

Amino acids are organic compounds that serve as the fundamental building blocks of proteins, enzymes, and a myriad of other biomolecules essential for life. Their structural diversity and functional versatility underlie countless biological processes, from catalysis and signaling to structural integrity and energy metabolism.

What is the Chemical Structure of Amino Acids?

The chemical structure of an amino acid is represented as:

H2N−C(H)(R)−COOH\text{H}_2\text{N}-\text{C}(\text{H})(\text{R})-\text{COOH}H2​N−C(H)(R)−COOH

Where:

• Central carbon (α-carbon): A chiral center (except in glycine) that is bonded to four groups.

• Amino group (-NH₂): Basic in nature, can accept protons.

• Carboxyl group (-COOH): Acidic in nature, can donate protons.

• Side chain (R-group): Unique to each amino acid, determining its chemical and physical properties.

What is Amino Acid Chirality?

Except for glycine, all amino acids exhibit chirality, existing in D- and L-forms. Only the L-form is utilized in proteins, a result of evolutionary preference.

How Are Amino Acids Classified?

Amino acids are classified based on the properties of their R-groups, influencing solubility, polarity, and reactivity. These include:

1. Nonpolar (Hydrophobic) Amino Acids

Examples: Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline

• These amino acids have nonpolar side chains, favoring environments away from water.

2. Polar (Uncharged) Amino Acids

Examples: Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine

• Their side chains contain groups like hydroxyl (-OH), amide (-CONH₂), or thiol (-SH), which interact with water.

3. Positively Charged (Basic) Amino Acids

Examples: Lysine, Arginine, Histidine

• These have side chains that can accept protons, contributing to positive charges at physiological pH.

4. Negatively Charged (Acidic) Amino Acids

Examples: Aspartic acid, Glutamic acid

• Their side chains contain carboxylic acid groups that donate protons, imparting a negative charge.

Essential vs. Non-Essential Amino Acids

Essential Amino Acids

These cannot be synthesized by the human body and must be obtained through diet:

• Examples: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine.

Non-Essential Amino Acids

These can be synthesized endogenously:

• Examples: Alanine, Asparagine, Aspartic acid, Glutamic acid, Serine.

Conditionally Essential Amino Acids

Under certain physiological or pathological conditions, some non-essential amino acids become essential:

• Examples: Arginine, Cysteine, Glutamine, Tyrosine.

What Are Biological Functions of Amino Acids?

1. Protein Building

Amino acids polymerize to form peptides and proteins, which are crucial for structural integrity, enzymatic activity, and transport.

2. Enzyme Catalysis

Amino acid residues in active sites facilitate catalytic processes, such as proton transfer and substrate stabilization.

3. Signaling Molecules

Certain amino acids (e.g., glutamate and glycine) act as neurotransmitters in the nervous system.

4. Precursors to Biomolecules

• Tryptophan → Serotonin

• Tyrosine → Dopamine, Epinephrine

• Histidine → Histamine

5. Metabolic Roles

Amino acids participate in gluconeogenesis, urea cycle, and nucleotide synthesis.

What is the Chemical Reactivity of Amino Acids?

Zwitterion Formation

At physiological pH (~7.4), amino acids exist as zwitterions, with both positive and negative charges:

• Amino group: NH3+\text{NH}_3^+NH3+​

• Carboxyl group: COO−\text{COO}^-COO−

Isoelectric Point (pI)

The pH at which an amino acid carries no net charge. This value depends on the ionizable groups in the molecule.

Peptide Bond Formation

Amino acids are linked by peptide bonds, formed via a condensation reaction between the carboxyl group of one amino acid and the amino group of another. The reaction releases water:

R1-COOH+R2-NH2→R1-CONH-R2+H2O\text{R1-COOH} + \text{R2-NH}_2 \rightarrow \text{R1-CONH-R2} + \text{H}_2\text{O}R1-COOH+R2-NH2​→R1-CONH-R2+H2​O

What Are the Applications of Amino Acids?

1. Clinical and Therapeutic

• Used in parenteral nutrition for critically ill patients.

• Supplements like branched-chain amino acids (BCAAs) support muscle recovery.

2. Industrial and Pharmaceutical

• Precursors for drugs (e.g., L-DOPA for Parkinson’s disease).

• Flavor enhancers in food (e.g., monosodium glutamate).

3. Research

• Isotopically labeled amino acids enable protein structure elucidation via NMR spectroscopy.

 Amino Acid Chart and Categories

Amino acids are categorized based on the properties of their side chains (R-groups), which influence their behavior in proteins. Below is an overview:

What are the Essential Amino Acids?

Humans require 20 amino acids for protein synthesis, of which nine are essential and must be obtained from the diet:

• Histidine: Involved in histamine production, essential for immune response.

• Isoleucine: Supports hemoglobin production and muscle metabolism.

• Leucine: Stimulates muscle protein synthesis.

• Lysine: Critical for collagen formation and calcium absorption.

• Methionine: Precursor for S-adenosylmethionine, essential in methylation reactions.

• Phenylalanine: Precursor for neurotransmitters like dopamine and norepinephrine.

• Threonine: Integral to immune function and glycine synthesis.

• Tryptophan: Converts to serotonin and melatonin, impacting mood and sleep.

• Valine: Provides energy during muscle exertion.

What is the Structure of Amino Acids?

The general structure of an amino acid consists of:

1. A central carbon atom (α-carbon).

2. An amino group (-NH₂): Confers basicity.

3. A carboxyl group (-COOH): Contributes acidity.

4. A hydrogen atom.

5. An R-group (side chain): Defines the unique properties.

Example: Alanine

• Structure: CH₃-CH(NH₂)-COOH

• R-group: Methyl (-CH₃)

Chirality

All amino acids except glycine are chiral, with two stereoisomers (D- and L-forms). In biological systems, only the L-isomers are incorporated into proteins.

Amino Acid Coding Systems

One-Letter Code

The one-letter code is a simplified representation of amino acids, essential in genetic and protein sequence annotation. Example:

• Alanine: A

• Valine: V

Use in Bioinformatics: Sequences like MVHLTPEEKSAV (hemoglobin β-chain) represent proteins compactly.

Three-Letter Code

The three-letter code provides a balance of brevity and clarity:

• Alanine: Ala

• Valine: Val

Use in Biochemistry: Common in structural analyses and enzyme studies.

Practical Conversion

The one- and three-letter systems are interoperable:

• Example Sequence: Ala-Val-Leu ↔ AVL