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I read in Tortora and Derrickson Anatomy and Physiology that :

Another type, called brown adipose tissue obtains its darker color from a very rich blood supply , along with numerous pigmented mitochondria that participate in aerobic cellular respiration.

From Wikipedia :

...brown adipocytes contain numerous smaller droplets and a much higher number of (iron-containing) mitochondria, which make it brown.

The conclusion seems to be that there should be some iron containing pigment in the mitochondria of BAT which (along with a rich blood supply) gives brown colour to the BAT.

What is the brown pigment present in the mitochondria of BAT ? Is it the uncoupler protein - thermogenin ?

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You quote it yourself: The adipocytes contain higher numbers of mitchondria (which contain iron) and this makes the cells look brown. See red blood cells for example. The high iron content makes the color in both cases. – Chris May 6 '14 at 13:03
@Chris But what is the iron doing in mitochondria? Cofactor to some enzyme present in excessive amounts ? – biogirl May 6 '14 at 13:06
There are different functions: Mitochondria store iron, then it is part of enzymes in the form of iron-sulphur complexes and is also important in the heme synthesis. See this paper if you want to got into the details. – Chris May 6 '14 at 13:11
up vote 2 down vote accepted

Brown fat is so-called because it contains a large number of mitochondria, certainly greater than its white fat counterpart. The reason for the excess in mitochondria is to participate in thermogenesis (incidentally, brown fat is also called thermogenic adipose tissue). Nearly all mammals have brown fat (excluding pigs), especially those that hibernate. Brown fat require larger numbers of mitochondria in order for the fat to be used in beta oxidation (which is carried out directly by mitochondria), and subsequently produces heat via the electron transport chain. This also requires greater access to oxygen from the blood, and as a result, greater capillary density also darkens the appearance of the gross tissue. Mitochondria themselves are dark because of the iron content; vitamins B2, B6 and B12; as well as the pigmented flavins (FADx).

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I just wanted to add that newborns have more brown fat than adults because this allows them to generate more heat. It is very important for newborns to generate more heat because their volume/surface ratio is smaller than that of adults, and so, their energy exchange would be unbalanced, if not for this brown fat that supplies the "offset". – antortjim Apr 6 '15 at 20:09

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