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The term chain, in biochemistry, usually denotes either a polypeptide chain or a polynucleotide chain. A polypeptide chain is a sequence of amino acids covalently linked by peptide bonds. The chain structures of proteins are most easily visualized with backbone representations. A short polypeptide consisting of 50 or fewer amino acids is termed a peptide. A polynucleotide chain is a sequence of nucleotides covalently linked by ribose (or deoxyribose)-phosphodiester bonds, e.g. either DNA or RNA.

Polypeptide (protein) chains are linear, with rare exceptions where a side-chain forms an isopeptide bond. Polypeptide chains may be covalently linked together, most commonly by disulfide bonds, or less commonly by other types of protein crosslinks.

Each protein chain has two ends, an amino terminus (positively charged) and a carboxy terminus (negatively charged). The first residue in a protein chain becomes the amino terminus, with new amino acids being added at the carboxy terminus. The sequence of amino acids is specified by messenger RNA, which is a copy of the sequence of codons in the template strand of the DNA gene. The first residue in a nucleic acid chain becomes the 5' (phosphate) terminus, with new nucleotides being added at the 3' (hydroxy) terminus.

Protein molecules may consist of one or more polypeptide chains. Those with more than one chain may be termed homo-oligomers or hetero-oligomers, homo-multimers or hetero-multimers. The functional form of the molecule, termed the biological unit, often contains a different number of chains than does the crystallographic asymmetric unit. Examples are given in the article on biological units.

In a protein molecule consisting of multiple chains, the chains are usually held together by non-covalent bonds, but sometimes by covalent bonds, usually disulfide bonds. See quaternary structure.

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