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Peptide Glossary

Peptide Glossary

Amino Acid
Amino acids are biologically important organic compounds containing amine (-NH2) and carboxyl (-COOH) functional groups, along with a side-chain (R group) specific to each amino acid. The R-group (side chain) is what makes each amino acid unique. Side chains contain mainly hydrogen, carbon, and oxygen atoms. Some amino acids have sulfur or nitrogen atoms in their R-groups. Amino acids can be classified according to the core structural functional groups' locations as alpha-(α-), beta- (β-), gamma- (γ-) or delta- (δ -) amino acids; other categories relate to polarity, pH level, and side-chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur.

Peptides are biologically occurring short chains of amino acid monomers linked by peptide (amide) bonds. The covalent chemical bonds are formed when the carboxyl group of one amino acid reacts with the amine group of another. Traditionally, peptides are defined as molecules that consist of between 2 and 50 amino acids, whereas proteins are made up of 50 or more amino acids.

Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three-dimensional structure that determines its activity.

Peptide Synthesis
Peptide synthesis is characterized as the formation of a peptide bond between two amino acids. Peptides are synthesized by coupling the carboxyl group of one amino acid to the amino group of another amino acid molecule. Due to the possibility of unintended reactions, protecting groups are usually necessary. Chemical peptide synthesis most commonly starts at the carboxyl end of the peptide, and proceeds toward the amino-terminus. This is the opposite direction of protein biosynthesis.

Liquid-phase Peptide Synthesis
Liquid-phase peptide synthesis is a classical approach to peptide synthesis. This method is slow and labor-intensive, though, because the product has to be manually removed from the reaction solution after each step. Additionally, this approach requires another chemical group to protect the C-terminus of the first amino acid. A benefit of liquid-phase synthesis, though, is that because the product is purified after each step, side reactions are easily detected. It has been replaced in most labs by solid-phase synthesis (see below). 

Solid-phase Peptide Synthesis
Solid-phase peptide synthesis (SPPS) is the most common method of peptide synthesis today. Instead of C-terminal protection with a chemical group, the C-terminus of the first amino acid is coupled to an activated solid support, such as polystyrene or polyacrylamide. This type of approach has a two-fold function: the resin acts as the C-terminal protecting group and provides a rapid method to separate the growing peptide product from the different reaction mixtures during synthesis.

Cyclic Peptides
Cyclic peptides are polypeptide chains in which the amino termini and carboxyl termini; amino termini and side chain; carboxyl termini and side chain; or side chain and side chain are linked with a covalent bond that generates the ring.

Peptide Bond
Peptide bond is a covalent chemical bond formed between two consecutive amino acid monomers when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O).

Peptide Mapping
Peptide mapping is a commonly used strategy in protein identification by breaking them up with enzymes and looking at the resulting pattern of their amino acid sequences.

Peptide Mimetics
Peptide mimetics and peptidomimetics have been used interchangeably for the description of compounds discovered through a variety of research strategies, including compounds identified by random screening approaches. A peptide mimetic can be a molecule such as a peptide, a modified peptide or any other molecule that biologically mimics active ligands of hormones, cytokines, enzyme substrates, viruses or other bio-molecules. This peptide mimetic may antagonize, stimulate, or otherwise modulate the physiological activity of the natural ligands.

Peptide Fingerprint
A chromatographic pattern produced by partial hydrolysis of a protein and 2-D mapping of the resulting peptide fragments.

Peptide Library
A peptide library is a tool for protein-related study. A peptide library contains a great number of peptides that have a systematic combination of amino acids. Usually, peptide library is synthesized on solid phase, mostly on resin, which can be made as flat surface or beads. The peptide library provides a powerful tool for drug design, protein–protein interactions, and other biochemical as well as pharmaceutical applications.

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