Peptides and Amino Acids

By Peptide Information     April 21, 2025

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Amino acids are organic compounds containing an α-amino group (α-NH₂) and an α-carboxyl group (α-COOH), with the general formula RCH(NH₂)COOH. The α-carbon atom is linked to a specific side-chain group (R group), forming the fundamental structural units of biological macromolecules. There are 20 natural amino acids involved in protein synthesis in nature, which achieve functional differentiation through differences in the chemical properties of their side chains (polarity, charge, hydrophobicity). Peptides are linear polymers formed by two or more amino acids connected via amide bonds (-CO-NH-) through dehydration condensation, representing oligomeric or polymeric products of amino acids. Classified by the number of amino acid residues, they are divided into oligopeptides (2–10 residues) and polypeptides (more than 10 residues), with molecular weights typically ranging from 0.2 to 10 kDa. They serve as intermediate functional units in the transition from amino acid monomers to protein macromolecules.

Relationship and Core Differences Between Peptides and Amino Acids  

Amino acids are the structural precursors and building blocks of peptides, which are functional oligomers formed by covalent linkage of amino acids through amide bonds. The two exhibit significant differences in molecular dimension, structural hierarchy, and functional attributes:

Molecular Composition: 

Amino acids are independent monomeric molecules (molecular weight 75–204 Da), possessing free amino and carboxyl groups along with side chains. Peptides are aggregates of multiple amino acids, in which the free states of amino and carboxyl groups are eliminated via amide bonds to form a continuous peptide bond backbone (-NH-CO-).

Structural Complexity: 

Amino acids have only primary structure (chemical composition), while peptides possess linear sequences (primary structure) and potential conformational plasticity. Short peptides exist as flexible chains, and long peptides can form local secondary structures (such as short α-helix fragments or β-turns), though they lack stable three-dimensional structures.

Functional Hierarchy: 

Amino acids primarily act as raw materials for biosynthesis and metabolic intermediates. Peptides, however, can directly exert biological functions, with their activities dependent on specific amino acid sequences and dynamic conformations.

Amino Acids: The Molecular Foundation of Peptides  

Natural amino acids composing peptides are classified into five categories based on the chemical properties of their side chains:

Nonpolar Aliphatic Amino Acids: Highly hydrophobic side chains mediate intrachain hydrophobic interactions, influencing peptide folding tendencies.

Polar Uncharged Amino Acids: Side chains contain polar groups such as hydroxyl groups, participating in hydrogen bond formation and post-translational modifications (e.g., phosphorylation).

Aromatic Amino Acids: Side chains with conjugated ring structures endow peptides with ultraviolet absorption properties (near 280 nm) and molecular recognition capabilities.

Acidic Amino Acids (aspartic acid, glutamic acid) and Basic Amino Acids (lysine, arginine): Side chains contain dissociable groups, determining the charge distribution, isoelectric point, and water solubility of peptides.

Amino acids are incorporated into the ribosome through the ribosomal translation process, using mRNA codons as templates and carried by aminoacyl-tRNA. They are sequentially linked via peptide bond formation, with their sequence information strictly determined by genetic encoding, serving as the molecular basis for peptide functional specificity.

Structural Features and Functional Expansion of Peptides  

The basic structure of peptides includes an N-terminal amino group, a C-terminal carboxyl group, and a repeating amide bond backbone. Their molecular properties change with an increase in the number of amino acid residues:

Oligopeptides (2–10 residues): Predominantly exist as flexible linear conformations. For example, the dipeptide carnosine (β-alanyl-L-histidine) participates in antioxidant activities in muscle tissue, and the pentapeptide enkephalin acts as an endogenous opioid substance regulating pain sensation.

Polypeptides (more than 10 residues): Can form local ordered structures. For instance, thyrotropin-releasing hormone (a tripeptide, pGlu-His-Pro-NH₂) enhances stability through cyclization modification, and antimicrobial peptides exert bactericidal effects by inserting amphiphilic α-helices into bacterial cell membranes.

The functional advantages of peptides stem from their "moderate molecular size"—retaining the chemical reactivity of amino acid side chainswhile achieving target binding signal transduction, and metabolic regulationthrough multiresidue cooperative interactions.

Divergent Pathways of Biosynthesis and Chemical Synthesis  

The biosynthesis of amino acids is strictly regulated by cellular metabolic pathways; for example, glutamate is generated via the amination of α-ketoglutarate, an intermediate of the tricarboxylic acid cycle. Peptide biosynthesis relies on ribosomal or nonribosomal synthesis mechanisms:

-Ribosomal Synthesis: mRNA carries genetic information into the ribosome, where tRNA matches codons and carries amino acids. Peptide chains are formed through the steps of aminoacyl-tRNA binding, peptide bond formation, and translocation, suitable for synthesizing natural peptides and protein precursors.

Nonribosomal Synthesis: Common in microbial secondary metabolites, amino acids are assembled directly by multi-enzyme complexes, allowing the incorporation of non-natural amino acids.

Chemical synthesis methods achieve stepwise amino acid coupling through protective group strategies, suitable for the precise preparation of short peptides (＜50 residues). These methods offer advantages such as controllable sequences and high purity, widely applied in the development of polypeptide drugs.

Synergistic Mechanisms of Side Chains and Peptide Functions  

The cooperative interactions of amino acid side chains in peptide chains are crucial for functional realization:

Charge Complementation: Acidic and basic amino acid residues stabilize local peptide conformations via ionic bonds.

Hydrophobic Aggregation: Nonpolar amino acid side chains form hydrophobic cores in aqueous solutions, driving peptide chains to fold into specific conformations.

Covalent Modifications: Serine and threonine in peptide chains can be phosphorylated, and asparagine can be glycosylated. These modifications significantly alter peptide hydrophobicity, charge states, and biological activities.

The diversity of side chains enables peptides to target specific biomolecules through sequence design, making them ideal tools in drug development for mimicking natural ligands or blocking protein-protein interactions.

Terminological Definition and Scientific Expression Norms  

In academic contexts, the distinction between "amino acids" and "peptides" follows these principles:

Monomers vs. Polymers: Independent α-amino carboxylic acid molecules are termed "amino acids," regardless of their free or bound states.

Amide Bond Linkage: Products formed by two or more amino acids linked via amide bonds are termed "peptides," emphasizing their oligomeric nature.

Functional Association: When discussing the form of amino acids in peptide chains, the term "amino acid residue" is used to distinguish from the chemical properties of free amino acids.

Accurate terminology use helps clearly define molecular hierarchies and avoids confusion between "amino acids" and "peptides" in terms of polymerization degree and functional attributes.