Helix shaped chain

Figure 10. Schematic of a portion of a helix-shaped chain of type—(A —B)n— having m/t ratio of 18/5. The chain structure is described by only 2 g.c., i.e.,

In the present work, we extend the method to compensate for the hydrogen bonds present in carbohydrates. The hydroxylated character of carbohydrate polymers influences between-chain interactions through networks of hydrogen bonds that occur during crystallization. Frequently, several possible attractive interactions exist that lead to different packing arrangements, and several allomorphic crystalline forms have been observed for polysaccharides such as cellulose, chitin, mannan and amylose. The situation is even more complex when water or other guest molecules are present in the crystalline domains. Another complication is that polysaccharide polymorphism includes different helix shapes as well. 

Chiral recognition in complexes, linked by hydrogen bonds, has been studied experimentally and theoretically. In some cases, chiral systems can aggregate and form long chains or helix shape structures. The subsequent chemical processes along the chains can invert the chirality of the molecules producing what we have called racemization waves [37]. The control and rationalization of these processes are of the utmost importance in the development of novel molecules designed as switches. 

A study of the chiral discrimination in diaziridine clusters has been carried out using DFT computational methods [38]. The most stable neutral structure corresponds to that with the monomers in alternated chirality. The proton transfer within the neutral diaziridine chain proceeds with high TS barriers. The protonation of the fist diaziridine of the chain tends to produce a spontaneous proton transfer from the first monomer to the second (Fig. 3.18). The studied processes of proton transfer in the charged system show small barriers. The proton transfer in the neutral or protonated systems produces an inversion of the chirality of the monomers as the process evolves along the chain producing chirality waves. Finally, the calculated ORP of the clusters is very dependent on the cluster size, cyclic or helix shape, and on the number of monomers that form the cluster. 

Amylose - the glucose units are joined together in a line. The resulting polymer chain can be linear, or can twist around on itself, eventually forming a helix shape. The chains can pack together to form compact semi-crystalline granules of up to 100 pm in size, as shown for both the linear and helical form on the right... 

We have so far described the structure of DNA as an extended double helix The crys tallographic evidence that gave rise to this picture was obtained on a sample of DNA removed from the cell that contained it Within a cell—its native state—DNA almost always adopts some shape other than an extended chain We can understand why by doing a little arithmetic Each helix of B DNA makes a complete turn every 3 4 X 10 m and there are about 10 base parrs per turn A typical human DNA contains 10 base parrs Therefore... 

The above discussion points out the difficulty associated with using the linear dimensions of a molecule as a measure of its size It is not the molecule alone that determines its dimensions, but also the shape in which it exists. Linear arrangements of the sort described above exist in polymer crystals, at least for some distance, although not over the full length of the chain. We shall take up the structure of polymer crystals in Chap. 4. In the solution and bulk states, many polymers exist in the coiled form we have also described. Still other structures are important, notably the helix, which we shall discuss in Sec. 1.11. The overall shape assumed by a polymer molecule is greatly affected... 

Proteins have four levels of structure. Primary structure describes a protein s amino acid sequence secondary structure describes how segments of the protein chain orient into regular patterns—either a-helix or /3-pleated sheet tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape and quaternary structure describes how individual protein molecules aggregate into larger structures. 

The secondary structure of a protein is the shape adopted by the polypeptide chain—in particular, how it coils or forms sheets. The order of the amino acids in the chain controls the secondary structure, because their intermolecular forces hold the chains together. The most common secondary structure in animal proteins is the a helix, a helical conformation of a polypeptide chain held in place by hydrogen bonds between residues (Fig. 19.19). One alternative secondary structure is the P sheet, which is characteristic of the protein that we know as silk. In silk, protein... 

FIGURE 19.19 A representation of part of an a helix, one of the secondary structures adopted by polypeptide chains. The cylinder encloses the "backbone" of the polypeptide chain, and the side groups project outward from it. The thin lines represent the hydrogen bonds that maintain the helical shape. 

A helical peptide backbone. The side chains are omitted to emphasize the shape of the helix. Notice the... 

Each protein has a unique three-dimensional shape called its tertiary structure. The tertiary structure is the result of the bends and folds that a polypeptide chain adopts to achieve the most stable structure for the protein. As an analogy, consider the cord in Figure 13-39 that connects a computer to its keyboard. The cord can be pulled out so that it is long and straight this corresponds to its primary structure. The cord has a helical region in its center this is its secondary structure. In addition, the helix may be twisted and folded on top of itself This three-dimensional character of the cord is its tertiary structure. 

It has been suggested that the Sup35p filament may be a bundle of four cylindrical //-sheets or nanotubes (Kishimoto et al., 2004). The nanotube is a hypothetical structure (Perutz et al, 2002) whose winding of the polypeptide chain is topologically similar to that of a //-helix but it is round in cross section and water filled whereas //-helices have cross sections with triangular or other shapes and water is largely excluded from their interiors (Kajava and Steven, 2006). The model of Kishimoto et al. envisaged six coils... 

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