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The double bonds in naturally occurring fatty acids present in our body are in cis configuration while the enzymes for beta oxidation can act on trans double bond. Then what will be the significance of cis double bond in naturally occurring fatty acids? Why the naturally occurring fatty acids don't have double bond in trans configuration?

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Trans double bonds in fatty acids may disrupt cellular membranes because of their shape. Normally the fatty acid tails on phospholipids are kind of lined up, allowing them to form a double layer. You can imagine them being more or less rectanglular, and 2 layers of these rectangles form the membrane, with fatty acid tails pointing in. Since cis double bonds don't disrupt the shape, they fit in ok. Trans double bonds kink the tail, and make the membrane less ordered. This is pure speculation, so I'm leaving it as comment. –  user137 Aug 1 at 5:33
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@user137.. you are correct.. But it is not about kinking.. trans-fatty acids make the membrane rigid because they pack closely. –  WYSIWYG Aug 1 at 6:12

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The diversity of fatty acids produced by an organism is limited by the diversity of enzymes which synthesize them. Unsaturated fatty acids contain carbon-carbon double bonds which do not isomerize. The capacity for humans to produce cis fatty acids is probably selected for because of their lower melting point which prevents arterial clogging. Cold blooded animals utilize cholesterol to increase membrane fluidity when their body temperature is low.

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