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Short answer- the chondrocytes are embedded in the matrix because matrix is what these cells produce, and there's no where else for it to go! So, basically, you've got it backwards, chondrocytes can be as smooshy and forgiving as a skin cell, so they don't need protection; they're there to provide protection in the form of cartilage to other organs or surfaces.

Longer answer- Cartilage is composed of cells (chondrocytes) that live in little spaces (lacuna, lacunae for plural). These cells are the ones that create the matrix, which is further composed of collagen fibers, ground substance (proteoglycans mostly) and elastic fibers. The proportions of the above result in different characteristics of the material- more elastic fibers and fewer collagen fibers result in bendy cartilage, like you find in your nose and ears. Lots of collagen and proteoglycans results in harder tissue, as you would find in your windpipe (trachea) and between joints of your bones. Interestingly, cartilage is one of the few "avascular" tissues (no blood vessels) in the body- it survives by absorbing oxygen and excreting waste by diffusion through the matrix. This is one of the reasons it's so slow to heal, so take care of those sprained ankles!

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