Helix pairing, tertiary protein structure

Just as main-chain NH 0=C hydrogen bonds are important for the stabilization of the a-helix and / -pleated sheet secondary structures of the proteins, the Watson-Crick hydrogen bonds between the bases, which are the side-chains of the nucleic acids, are fundamental to the stabilization of the double helix secondary structure. In the tertiary structure of tRNA and of the much larger ribosomal RNA s, both Watson-Crick and non-Watson-Crick base pairs and base triplets play a role. These are also found in the two-, three-, and four-stranded helices of synthetic polynucleotides (Sect. 20.5, see Part II, Chap. 16). 

Similarly to proteins, both DNA and RNA have a secondary and a tertiary structure. The secondary structure of DNA shows two chains running in opposite directions, coiled in a left-handed (double) helix about the same axis. All the bases are inside the helix, and the sugar phosphate backbone is on the outside (see e.g. [1]). The chains are held together by hydrogen bonds between the bases with adenine always paired with thymine and guanine paired with cytosine. The base pairing in DNA is shown below ... 

The double helix of DNA [25] and the more complex tertiary structures of RNA [26] are linked together by hydrogen bridges between pairs of nudeobases (approx. 0.5-1.8 kcal mol per Watson-Crick base pair) [27] and by hydrophobic "stacking forces . Fluorinated carbocyclic analogs of these nudeobases have been used to study and elucidate the factors underlying base pairing, replication, and the interaction of the bases with proteins such as DNA polymerases [28]. 

An important thing for physics is that a DNA double helix s shape does not really depend very much on the sequence of monomers. (This is because the pairs are mutually complementary and are hidden inside the double helix.) In this sense, DNA is like a piece of paper or a computer memory — a media suitable for recording any message. It is for precisely this reason that the DNA texts can be altered. Otherwise, the result of evolution would be not the best suited organisms, but merely DNA molecules with lower energy. In contrast, the tertiary structures of proteins strongly depend on their primary structures this allows different proteins to carry out so many different functions, and does not allow proteins to serve as inheritable information storage. 

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