Molecular machines are the most important physical attribute of living systems, they are hierarchically organized structures. We substantiate the concept according to which the chiral duality of carbon compounds is the physical symmetry basis of structure formation in molecular biology, and the homochirality of amino acids, ribose and deoxyribose is a resource of free energy and a tool for stratification of intramolecular and supramolecular structural levels. The causes and peculiarities of the chirality sign alternation for the intramolecular structural levels of L-D-L-D for proteins and D-L-D-L for DNA are discussed. Folding in macromolecules is considered as an autowave process of self-organization in active media with varying dimension. It is noted that in the intermolecular interactions in these biomacromolecules there is a domination of the sign of chirality of the intramolecular structure of the higher level that directly participates in interactions. The introduction of a common symmetry factor - chirality - into consideration of the spatial organization of macromolecules allows to consider the physical nature of hierarchies as well as the space of transformations and interactions of substances in metabolism and biosynthesis as a periodic system of chiral structures. We propose and substantiate that the alternating chiral hierarchy of the conjugate levels of macromolecular structures in proteins and nucleic acids has a general biological significance: it causes their discreteness, serves as a folding tool, the structural basis of the "allocated mechanical" degrees of freedom in the designs of macromolecular machines, and also one of the mechanisms of the block/saltatory progress of the evolutionary process.