What does homogenized milk have that skim milk lacks?

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Mixtures are combinations of two or more pure substances that do not chemically interact.  There are two types of mixtures: homogeneous mixtures and heterogeneous mixtures. 

In a homogeneous mixture, the particles (atoms, molecules, etc..) are completely and thoroughly mixed and will not naturally separate.  In a heterogeneous mixture the particles will separate and coalesce into the original components.

Milk is a complex mixture of many types of compounds.  Two of them are water and fat.  Normally, water and fat will form heterogeneous mixtures.  You can mix them together by agitation, but eventually they will separate back into water and fat.  In "homogenized" milk the fat has been broken into such small particles that the normal Brownian motion of the water molecules in the milk provides enough agitation to keep the fat from coalescing and separating from the water.

So, "homogenized" milk has fat molecules mixed in the water whereas, skim milk has had the fat removed so it is no longer part of the mixture.

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