Heparin is a heteropolysaccharide (a polysaccharide formed by different kinds of monosaccharides).
In fact, Heparin is a family of molecules that are usually composed by the repetition of a sulfated amino sugar and an acid sugar. The most abundant pair of monosaccharides whose repetition forms heparin is this one
The physiological function of heparin is subject of discussion: it is related to the inflammation process and not to coagulation in physiological conditions.
Heparin inhibits the coagulation process by inhibiting, indirectly, the action of Thrombin.
Normally, during the coagulation process, Thrombin (factor II), a proteolytic enzyme, (as many coagulation factors), catalyzes the conversion of fibrinogen to fibrin, activates factors V, VIII and XI and also promotes platelet activation.
Antithrombin is an antiprotease protein with an important role in the regulation of normal coagulation. It inhibits mainly the proteases of the intrinsic pathway of coagulation, but also affects other factors or the extrinsic and the complement pathways.
Heparin increases the inhibitory action of antithrombin in thousands of times. Heparin can act through two mechanisms:
1.- An allosteric mechanism, in which Heparin provokes conformational changes in antithrombin that increases its ability to inhibit some of the coagulation factors,
2.- By forming ternary complexes Heparin-antithrombin-Thrombin.
Since it is necessary that the heparin molecule be big enough to bind properly to antithrombin and thrombin for forming the ternary complex (Heparin molecule should have more than 18 monosaccharides for allowing the simultaneous binding), small molecules of Heparin have no effect on Thrombin but maintain anticoagulant activity affecting other factors, mainly factor X. Because of this fact and that natural Heparin molecules are very heterogeneous, Low Molecular Weight Heparins (LMWHs), that show better pharmacokinetics properties, have been developed in order to achieve a better medical regulation of the anticoagulant therapy.
The medical uses and indications of Heparins and LMWH are discussed in detail in this article of the American Heart Association.
AHA Scientific Statement