Amino Acid Sequence
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What is an Amino Acid Sequence?
An amino acid sequence, also called the primary structure of a peptide or protein, is the specific linear order in which amino acid residues are connected by peptide bonds in a polypeptide chain. This sequence is conventionally written from the N-terminus (amino end) to the C-terminus (carboxyl end) and is typically represented using either the one-letter or three-letter amino acid codes. For example, the tripeptide glutathione is written as Glu-Cys-Gly (three-letter) or ECG (one-letter). The amino acid sequence is the most fundamental piece of information about a peptide, as it dictates the molecule's physical properties, three-dimensional folding, and biological function.
How Sequence Determines Function
The specific arrangement of amino acids in a peptide's sequence determines virtually all of its properties. The sequence dictates the molecular weight, net charge at physiological pH, hydrophobicity, solubility, and susceptibility to enzymatic degradation. For longer peptides and proteins, the primary sequence also governs how the chain folds into secondary structures (alpha helices, beta sheets) and tertiary structures (the overall 3D shape), which in turn determine biological activity. Even a single amino acid substitution can dramatically alter a peptide's binding affinity, stability, or function.
Sequence Notation Conventions
Three-Letter Code
Uses abbreviations like Ala, Gly, Leu, Phe for each amino acid. Preferred for short peptides and when clarity is paramount (e.g., H-Ala-Gly-Cys-Lys-OH).
One-Letter Code
Uses single letters like A, G, L, F for each amino acid. Preferred for longer sequences due to compactness (e.g., AGCKL). Common in database entries and bioinformatics.
Sequence Verification in Quality Control
Confirming the correct amino acid sequence is a critical step in peptide quality control. Mass spectrometry is the primary method used to verify that the synthesized peptide matches the intended sequence. Tandem mass spectrometry (MS/MS) can fragment the peptide at peptide bonds, producing a series of fragment ions that allow the sequence to be read and confirmed. The amino acid sequence is always reported on the Certificate of Analysis and should be verified by the researcher before incorporating the peptide into any experimental protocol.