Polyunsaturated fatty acids (PUFA) like stearidonic acid (SDA; 18: 4 n-3) eicosapentaenoic acid (EPA; 20: 5 n-3), and docosahexaenoic acid (DHA; 22: 6 n-3) and its chain fragment models were studied at B3LYP/631G(d) levels of theory. Significant conformations for the cis and trans isomers were selected to obtained the thermodynamic functions (Delta H, Delta S, Delta G) for the cis-trans isomerization and for folding using the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d) level of theory. The structural analysis shows that there are significant differences in thermodynamic function of the trans- and cis-PUFAs. The trans-cis isomerization energy values reinforce the consistency and the relative accuracy of theoretical model calculations. The observed flexibility of naturally cis PUFAs could be explained by a very special "smooth basin" PES of the motif of sp(2)-sp(3)-sp(2) hybrid states as reported previously (J. Phys. Chem. A 2005, 109, 520-533). We assumed that intrinsic thermodynamic functions may describe this flexible folding process. The folding enthalpy as well as the folding entropy suggests that there is a new role of the cis-PUFAs in membranes: these cis isomers may have a strong influence on membrane stability and permeability. The average length of the cis helix and beta PUFA was approximated. The difference between the lengths of these two structures is approximately 10 angstrom.