Blue helical structures

RGURE 8-27 Base-paired helical structures in an RNA. Shown here is the possible secondary structure of the M1 RNA component of the enzyme RNase P of coli, with many hairpins RNase R which also contains a protein component (not shown), functions in the processing of transfer RNAs (see Rg. 26-23). The two brackets indicate additional complementary sequences that may be paired in the three-dimensional structure. The blue dots indicate non-Watson-Crick G=U base pairs (boxed inset). Note that G=U base pairs are allowed only when presynthesized strands of RNA fold up or anneal with each other. There are no RNA polymerases (the enzymes that synthesize RNAs on a DNA template) that insert a U opposite a template G, or vice versa, during RNA synthesis... 

In both starch and glycogen the glucose emits of the main chains are linked with a-1,4 linkages. An extended conformation is not possible and the chains tend to undergo helical coiling. One of the first helical structures of a biopolymer to be discovered (in 1943)76 77 was the left-handed helix of amylose wound around molecules of pentaiodide (I5 ) in the well-known blue starch-iodine complex78 (Fig. 4-8). Tire helix contains six residues per turn, with a pitch of 0.8 nm and a diameter of nearly 14 nm. Amylose forms complexes of similar structure with many other small molecules.79... 

Starch is composed of macromolecular components, a-amylose and (i-aim -lose. The former reacts irreversibly with iodine to form a red adduct. (i-Aim losc. on the other hand, reacts with iodine forming a deep blue complex. Because this reaction is reversible, [3-amyl0sc is an excellent choice for the indicator. The undesired alpha fraction should be removed from the starch. The soluble starch that is commercially available, principally consists of (3-amylose. (3-Amylose is a polymer of thousands of glucose molecules. It has a helical structure into which iodine is incorporated as I5. ... 

Figure 4.18. Graphic display of macromolecular interaction with Cn3D. The display window of Cn3D illustrates the 3D structure of Zn finger peptide fragments (secondary structure features) bound to the duplex oligonucleotides (brown backbone). Zinc atoms are depicted as spheres. The alignment window shows the amino acid sequence depicting the secondary structures (blue helices and arrows for a-helical and /J-strand structures, respectively) and interacting (thin brown arrows) residues. The structure file, 1A1K.val, is derived from lAAY.pdb.

The helical structure of amylose also serves as the basis for an interesting and useful reaction. The inside of the helix is just the right size and polarity to accept an iodine (I2) molecule. When iodine is lodged within this helix, a deep blue starch-iodine complex results (Figure 23-19). This is the basis of the starch-iodide test for oxidizers. The material to be tested is added to an aqueous solution of amylose and potassium iodide. If the material is an oxidizer, some of the iodide (I-) is oxidized to iodine (I2), which forms the blue complex with amylose. 

Since several synthetic polymers also develop a blue color upon reaction with iodine, it is likely that they have a helical structure similar to that of amylose. Therefore it is probable that the aforementioned complexes of synthetic polymers with starch can exist in the form of a double helix. 

Figure 1.2. The Double Helix. The double-helical structure of DNA proposed by Watson and Crick. The sugar-phosphate backbones of the two chains are shown in red and blue and the bases are shown in green, purple, orange, and yellow.

It has been known for almost 200 years that starch gives a deep blue color when a solution of potassium iodide and iodine is added [47]. More than a century later it was suggested that the complex consisted of a helical polysaccharide, with triiodide in the center of the helix [48]. Using flow dichroism, it was demonstrated that the triiodide was stacked in a linear structure, as required for the helical model [49]. Another study of the optical properties of crystals of the amylose-triiodide complex showed it to be consistent with a helical structure [50] and X-ray diffraction showed the triiodide complex gave the dimensions of a unit-cell of a helix with six glucose residues per turn [51]. This confirmed a helical structure for the amyiose complex with triiodide that predated the helical models proposed by Pauling for polypeptides [52] and the double helical model for DNA by Watson and Crick [53] by 10 years. 

ORD and EPR measurements indicated that the ligand field of the single cupric ion is distorted from the regular square-planar configuration [(109) and refs, cited therein similar considerations had been applied to the Cu(II) sites in the copper protein ceruloplasmin (96)]. This could also explain the very intense blue color observed. ORD data in the ultraviolet region indicated little or no helical structure in this plant protein (109). CD spectra of stellacyanin in the range 300 to 1100 nm were reported (98). 

FIGURE 16.5 Structure of triose phosphate isomerase. This enzyme consists of a central core of eight parallel j8 strands (orange) surrounded by eight a helices (blue). This structural motif, called an afi barrel, is also found in the glycolytic enzymes aldolase, enolase, and pyruvate kinase. Histidine 95 and glutamate 165, essential components of the active site of triose phosphate isomerase, are located in the barrel. A loop (red) closes off the active site on substrate binding. 

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