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3.5 TERTIARY STRUCTURE The term ‘‘tertiary structure’’ refers to the arrangement of secondary structure elements and amino acid side chain interactions that define the three-dimensional structure of the folded protein. Imagine that a newly synthesized protein exists in nature as a fully extended polypeptide chain— it is said then to be unfolded (Figure 3.13A) [Actually there is debate over how fully extended the polypeptide chain really is in the unfolded state of a protein; some data suggest that even in the unfolded state, proteins retain a certain amount of structure. However, this is not an important point for our present discussion.] Now suppose that this protein is placed under the set of conditions that will lead to the formation of elements of secondary structure at appropriate locations along the polypeptide chain (Figure 3.13B). Next, the individual elements of second ary structure arrange themselves in three-dimensional space, so that specific contacts are made between amino acid side chains and between backbone groups (Figure 3.13C). The resulting folded structure of the protein is referred to as its tertiary structure.
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