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Reference
What Are Peptides?
A peptide is a short chain of amino acids joined end to end by peptide bonds. That is the whole definition, and everything else on this page follows from it: what the units are, how the bond between them forms, and why the boundary between a peptide, a polypeptide and a protein is a matter of convention rather than chemistry.
The short version
- Amino acids are the units. Twenty standard amino acids are encoded in the genetic code, each sharing the same backbone and differing only in a side chain.
- The peptide bond is an amide bond. It forms when the carboxyl group of one amino acid reacts with the amino group of the next, releasing a molecule of water.
- Peptide, polypeptide, protein. The same kind of chain at three lengths. The boundaries between them are conventional, not chemical, which is why sources disagree on where they sit.
- Sequence is identity. Change the order of the residues and it is a different molecule, which is why mass spectrometry on a batch Certificate of Analysis is checking the sequence and not only the weight.
Reference
From amino acid to polypeptide chain
The chemistry in order: the units, the bond that joins them, and what the resulting chain is called at each length.
Amino acids, the building blocks of proteins
Every standard amino acid is built the same way. A central carbon carries four things: an amino group, a carboxyl group, a hydrogen atom, and a side chain that differs in each one. The side chain is the only part that varies, and it is what makes one amino acid behave differently from another. Some are charged, some repel water, some are small enough to let a chain bend sharply. Twenty of them are encoded in the genetic code, and they are the building blocks of proteins in the literal sense that proteins contain nothing else.
The peptide bond
Two amino acids join when the carboxyl group of the first reacts with the amino group of the second. A molecule of water is lost in the process, which is why the reaction is called a condensation. What remains is a peptide bond, and a peptide bond is a particular case of an amide bond: the same linkage chemists meet elsewhere, here joining two amino acids. Because the electrons in it are shared across the linkage rather than sitting still, the bond is flat and does not rotate freely, and that rigidity is much of why chains fold into predictable shapes rather than flopping about at random.
Residues, and which end is which
Once an amino acid is part of a chain it has lost the water that went into forming the bond, so it is no longer strictly an amino acid. The convention is to call it a residue, and to count chain lengths in residues. A chain has direction: one end carries a free amino group and is called the N-terminus, the other carries a free carboxyl group and is the C-terminus. Sequences are written and numbered from N to C by convention, which is why BPC-157 is written GEPPPGKPADDAGLV and not the reverse.
Peptide, polypeptide or protein
These are the same kind of molecule at increasing lengths, and the dividing lines are conventions rather than facts about chemistry. Two residues make a dipeptide, three a tripeptide. Short chains of roughly two to twenty are often called oligopeptides. Beyond that the term polypeptide takes over, and a polypeptide chain that folds into a stable working shape is generally called a protein, with around fifty residues cited most often as the informal threshold. Sources disagree on the exact numbers, and nothing physical changes at the boundary. It is a naming habit, not a transition.
Why the sequence is the molecule
A peptide is defined by which residues it contains and the order they sit in. Reorder them and the result is a different compound with different properties, even though the formula and the mass are unchanged. This is the practical reason a Certificate of Analysis reports mass spectrometry alongside a purity figure: the mass confirms the chain is the one it claims to be, and HPLC reports how much of what is in the vial is that chain rather than something else.
Common questions
What is a peptide?
A short chain of amino acids joined by peptide bonds. The chemistry is identical to that of a protein, and the difference between the two names is length rather than kind.
What is a peptide bond?
The linkage joining two amino acids in a chain. It forms when the carboxyl group of one reacts with the amino group of the next and a molecule of water is released. Chemically it is an amide bond, and its resistance to rotation is why peptide chains adopt predictable shapes.
What are peptide bonds made of?
The bond is between the carbon of one carboxyl group and the nitrogen of the next amino group. Nothing is added to make it. The bond forms from atoms already present, and water is what leaves.
What is a polypeptide?
A longer chain of amino acids, past the point where the word peptide is usually used. There is no agreed residue count at which one becomes the other, and different sources place it differently.
What is a polypeptide chain?
The chain itself: a sequence of residues linked from N-terminus to C-terminus. A protein may consist of one polypeptide chain or of several folded together.
What are amino acids?
Small molecules built around a central carbon carrying an amino group, a carboxyl group, a hydrogen and a variable side chain. The side chain is the only difference between them.
How many amino acids are there?
Twenty are encoded in the standard genetic code and are listed in the table above. Others exist in nature and in synthetic chemistry, and research peptides often contain modified or non-standard residues deliberately, which is one reason a molecular weight can differ from what the standard twenty would predict.
Are peptides natural?
Both. Peptides occur throughout biology, and they are also made synthetically. A synthesised peptide with the same sequence as a natural one is the same molecule. Origin does not change the chemistry, though it very much changes what documentation exists for a given batch.
Are peptides steroids?
No, and the two are unrelated. Steroids are built on a four-ring carbon skeleton and are not chains of anything. Peptides are amino acids joined by peptide bonds. They differ in structure, in how they are made and in how they behave, and the only thing they share is being discussed in the same conversations.
Related
- How lyophilised peptides behave, and what changes once they are in solution
- What a Certificate of Analysis reports, and how mass spectrometry confirms a sequence
- Work out concentration from vial strength and solvent volume
- What to establish about a supplier before ordering
- The full catalogue, with specifications and published prices