Tertiary structure and function of transfer-RNA

Abstract

Summary. In analogy to the globular protein structures the predominant stabilization factor of which is surface energy a compact model with the smallest possible surface of the tertiary structure of t-RNA is suggested. The principle of folding is --according to the clover leaf model --the superposition of the three leaves. The three loops form a ring (loop-stack). The stem can be placed on this molecular body bringing the CCA end into the vicinity of the loop-stack, where the CCA end can be bound. The structures of the RNA chain are subordinated to this globular structural principle. Under the influence of the GT~CG sequence the CCA end is able to undergo structural changes, thus allowing to explain the role of t-RNA in the aminoacylation process and the structural differences between t-RNA, aminoacyl-t-RNA, and peptidyl-t-RNA. Furthermore it is possible to comment on the existence of the characteristic and modified bases, the role of magnesium ions and the chemical reactions of these compounds. IntroduetionWater is necessary for the stabilization of tertiary structures of biological macromolecules. The properties of water are decisive for the arrangement of hydrophobic groups in the interior and of hydrophilic groups on the surface of the molecule. The tendency to reduce the surface as much as possible exists because free energy, the thermodynamic criterion for reaction equilibrium of the stabihty of a tertiary structure, depends on the size of the surface and the interfacial tension [84].That is the reason for the formation of micelles and why most proteins prefer globular structures in aqueous solutions. Decisive for the stability of the tertiary structure of such chain molecules like proteins and nucleic acids is the sequence, because it determines the order of the hydrophobic and hydrophilie forces and the possibilities of hydrogen bond formation. Hydrophilic groups which can be bound together in the interior of the structure by hydrogen bridges will not participate in the formation of the surface, because these bonds are energetically more favoured than hydrogen bridges of these groups with the surrounding water. Additional binding through coordinative or ionic bonds with the help of cations can be of great influence on the resulting structure.In the case of nucleic acids two groups have to be distinguished, DNA and RNA. These two classes do not only seem to differ in their stabilization principle [6i] but show also other evident differences.Generally DNA is built by two very long complementary chains. For such long complementary chains the double helix seems to be the best suited structure.