Amino bent hydrogen bonds

The sequence of amino acids dictates certain geometric constraints for the polypeptide. These constraints include maximum lengths between covalent bonds, limiting angles in which bonds can be bent, and van der Waals radii, which limit how tightly structures can be packed. These factors, mixed with forces that help preferentially stabilize structures, such as hydrogen bonds, ionic attractions/ repulsions, hydrophobic interactions, and others, ultimately determine the shape that a peptide has over a short distance. The structure resulting from all these interactions is called the secondary structure of the protein. 

In Zubay s model, the polynucleotide sequence is bent in the middle. Under conditions in which all except five bases are paired to form hydrogen bonds of the same type as those found in Watson and Crick s model for DNA, the base pair sequence is twisted to form a regular helix. At the acceptor end of the molecule, the pCpA sequence is free and can therefore accept the amino acid, and the first cytosine of the pCpCpA sequence forms hydrogen bonds with a complementary guanine. The loop of the helix is formed by three free bases and plays an important role in connecting the tRNA molecule with messenger RNA. Zubay s model was soon superceded by new and more sophisticated models that were proposed when the base sequence of transfer RNA became known. 

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