Figure 1–6 The conformation of an RNA molecule. (A) nucleotide pairing between different regions of the same RnA polymer chain causes the molecule to adopt a distinctive shape. (B) The three-dimensional structure of an actual RnA molecule produced by hepatitis delta virus; this RnA can catalyze RnA strand cleavage. The blue ribbon represents the sugar-phosphate backbone and the bars represent base pairs (see movie 6.1).  (B, based on A.R. Ferré-d’Amaré, k. Zhou, and J.A. doudna, Nature 395:567–574, 1998. With permission from macmillan  Publishers ltd.)
Figure 1–7 How a protein molecule acts as a catalyst for a chemical reaction. (A) In a protein molecule, the polymer chain folds up into a specific shape defined by its amino acid sequence. A groove in the surface of this particular folded molecule, the enzyme lysozyme, forms a catalytic site.
(B) A polysaccharide molecule (red)—a polymer chain of sugar monomers—binds to the catalytic site of lysozyme and is broken apart, as a result of a covalent bond-breaking reaction catalyzed by the amino acids lining the groove (see movie 3.9). (PdB code: 1lyd.)
The monomers of protein, the amino acids, are quite different from those of DNA and RNA, and there are 20 types instead of 4. Each amino acid is built around the same core structure through which it can be linked in a standard way to any other amino acid in the set; attached to this core is a side group that gives each amino acid a distinctive chemical character. Each of the protein molecules is a polypeptide, created by joining its amino acids in a particular sequence. Through billions of years of evolution, this sequence has been selected to give the protein a useful function. Thus, by folding into a precise three-dimensional form with reactive sites on its surface (Figure 1–7A), these amino-acid polymers can bind with high specificity to other molecules and can act as enzymes to catalyze reactions that make or break covalent bonds. In this way they direct the vast majority of chemical processes in the cell (Figure 1–7B).
Proteins have many other functions as well—maintaining structures, generating movements, sensing signals, and so on—each protein molecule performing a specific function according to its own genetically specified sequence of amino acids. Proteins, above all, are the main molecules that put the cell’s genetic information into action.
Thus, polynucleotides specify the amino acid sequences of proteins. Proteins, in turn, catalyze many chemical reactions, including those by which new DNA molecules are synthesized. From the most fundamental point of view, a living cell is a self-replicating collection of catalysts that takes in food, processes this food to derive both the building blocks and energy needed to make more catalysts, and discards the materials left over as waste (Figure 1–8A). A feedback loop that connects proteins and polynucleotides forms the basis for this autocatalytic, self-reproducing behavior of living organisms (Figure 1–8B).
All cells Translate RnA into Protein in the same Way