Amino Acid Structures

Amino acids are the building blocks of proteins, each with a unique structure defined by their side chains. Understanding their general structure, chirality, and properties is essential for grasping how they function in biological systems and contribute to protein synthesis.

1. General structure of amino acids

   • Amino acids consist of a central carbon (alpha carbon) bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a variable side chain (R group).
   • The side chain determines the unique properties and classification of each amino acid.
   • There are 20 standard amino acids that are the building blocks of proteins.

2. Alpha carbon and chirality

   • The alpha carbon is the central carbon atom in an amino acid structure.
   • Most amino acids (except glycine) are chiral, meaning they exist in two enantiomeric forms (L and D).
   • Chirality is important in biological systems, as enzymes and receptors are often specific to one enantiomer.

3. Zwitterion form

   • At physiological pH (around 7.4), amino acids exist predominantly as zwitterions, where the amino group is protonated (+NH3) and the carboxyl group is deprotonated (-COO-).
   • This dual charge allows amino acids to be soluble in water and participate in biochemical reactions.
   • The zwitterionic form is crucial for the formation of proteins and their interactions.

4. Peptide bond formation

   • Peptide bonds are formed through a dehydration synthesis reaction between the carboxyl group of one amino acid and the amino group of another.
   • This bond links amino acids together to form polypeptides and proteins.
   • Peptide bonds are planar and exhibit partial double-bond character, restricting rotation and influencing protein structure.

5. Side chain properties (polar, nonpolar, charged)

   • Side chains can be classified as polar (hydrophilic), nonpolar (hydrophobic), or charged (acidic or basic).
   • Polar side chains can form hydrogen bonds and are often found on the surface of proteins, interacting with the aqueous environment.
   • Nonpolar side chains tend to cluster in the interior of proteins, stabilizing the structure through hydrophobic interactions.

6. Essential vs. non-essential amino acids

   • Essential amino acids cannot be synthesized by the body and must be obtained through diet (e.g., leucine, lysine).
   • Non-essential amino acids can be synthesized by the body and are not required in the diet (e.g., alanine, aspartate).
   • Understanding the distinction is important for nutrition and protein synthesis.

7. Acidic and basic amino acids

   • Acidic amino acids (e.g., aspartic acid, glutamic acid) have side chains that contain carboxyl groups, giving them a negative charge at physiological pH.
   • Basic amino acids (e.g., lysine, arginine) have side chains that contain amino groups, resulting in a positive charge at physiological pH.
   • The charge of these amino acids plays a critical role in protein structure and function.

8. Aromatic amino acids

   • Aromatic amino acids (e.g., phenylalanine, tyrosine, tryptophan) contain an aromatic ring in their side chains.
   • These amino acids are important for protein structure and can absorb UV light, which is useful in protein quantification.
   • They often participate in stacking interactions and contribute to the stability of protein structures.

9. Sulfur-containing amino acids

   • Sulfur-containing amino acids (e.g., cysteine, methionine) play key roles in protein structure and function.
   • Cysteine can form disulfide bonds, which stabilize protein tertiary and quaternary structures.
   • Methionine is often the initiating amino acid in protein synthesis.

10. Amino acid abbreviations (three-letter and one-letter codes)

    • Each amino acid has a standardized three-letter abbreviation (e.g., Ala for alanine) and a one-letter code (e.g., A for alanine).
    • These abbreviations are widely used in scientific literature and protein sequences for brevity and clarity.
    • Familiarity with these codes is essential for understanding protein structure and function in biological chemistry.