Melanophores contain eumelanin, a type of melanin, that appears black or dark-brown because of its light absorbing qualities. It is packaged in vesicles called melanosomes and distributed throughout the cell.

Eumelanin is generated from tyrosine in a series of catalysed chemical reactions. It is a complex chemical containing units of dihydroxyindole and dihydroxyindole-2-carboxylic acid with some pyrrole rings. The key enzyme in melanin synthesis is tyrosinase. When this protein is defective, no melanin can be generated resulting in certain types of albinism. In some amphibian species there are other pigments packaged alongside eumelanin.

For example, a novel deep (wine) red-colour pigment was identified in the melanophores of phyllomedusine frogs. This was subsequently identified as pterorhodin, a pteridine dimer that accumulates around eumelanin core, and it is also present in a variety of tree frog species from Australia and Papua New Guinea. While it is likely that other lesser-studied species have complex melanophore pigments, it is nevertheless true that the majority of melanophores studied to date do contain eumelanin exclusively.

Humans have only one class of pigment cell, the mammalian equivalent of melanophores, to generate skin, hair, and eye colour. For this reason, and because the large number and contrasting colour of the cells usually make them very easy to visualise, melanophores are by far the most widely studied chromatophore.

However, there are differences between the biology of melanophores and that of melanocytes. In addition to eumelanin, melanocytes can generate a yellow/red pigment called phaeomelanin.

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