Tracing the chain

The first case study shows how a knowledge of steel microstructures can help us trace the chain of events that led to a damaging engineering failure. 

Anything that breaks the chain by converting the active chain-carrying species into an ordinary uncreactive molecule inhibits the reaction, and since the chains are often long an inhibitor may be effective in very small traces. The chain-starting catalysts may also be effective in very small amounts provided that no inhibitor is also present. The fact that a reaction is a chain reaction sensitive to small amounts of catalysts and inhibitors does not necesssarily mean that it is a radical chain, but the nature of the substances effective as catalysts or inhibitors will usually differentiate a radical chain from an ionic one. An example of an ionic chain reaction is the polymerization of an olefin-Lewis acid system when water is added as a co-catalyst. Water is so very effective that it is suspected that the polymerization observed in some cases with the driest obtainable reaction mixtures is due to the presence of minute and unavoidable amounts of water. 

For structures not determined by molecular replacement, the chemical sequence of the protein must be fit into the experimental electron density map (Figure 2.7). This is called model building or chain tracing. As one would expect, the success or failure of chain tracing is dependent upon the quality of the electron density map. Thus, map quality evaluation is very important before one attempts to trace the chain. Good (traceable) electron maps should display most of the following features. 

Initially the polypeptide backbone of the protein ((-NH-CHR-CO)n) is sought in the map, and this procedure is called tracing the chain. The model used... 

Al-Tabari very o n quotes his sources verbatim and traces the chain of transmission (isndd) to an original source. The chains of transmitters are, for the sake of brevity, rendered fay only a dash (—) between the individual links in the chain. Thus, "According to Ibn... 

Our purpose in this introduction is not to trace the history of polymer chemistry beyond the sketchy version above, instead, the objective is to introduce the concept of polymer chains which is the cornerstone of all polymer chemistry. In the next few sections we shall introduce some of the categories of chains, some of the reactions that produce them, and some aspects of isomerism which multiply their possibilities. A common feature of all of the synthetic polymerization reactions is the random nature of the polymerization steps. Likewise, the twists and turns the molecule can undergo along the backbone of the chain produce shapes which are only describable as averages. As a consequence of these considerations, another important part of this chapter is an introduction to some of the statistical concepts which also play a central role in polymer chemistry. 

The various mechanical properties of polyamides may be traced in many instances to the possibility of intermolecular hydrogen bonding between the polymer molecules and to the relatively stiff chains these substances possess. The latter, in turn, may be understood by considering still another equilibrium, this one among resonance structures along the chain backbone ... 

The number of branches in HDPE resins is low, at most 5 to 10 branches per 1000 carbon atoms in the chain. Even ethylene homopolymers produced with some transition-metal based catalysts are slightly branched they contain 0.5—3 branches per 1000 carbon atoms. Most of these branches are short, methyl, ethyl, and -butyl (6—8), and their presence is often related to traces of a-olefins in ethylene. The branching degree is one of the important stmctural features of HDPE. Along with molecular weight, it influences most physical and mechanical properties of HDPE resins. 

A, B, and C, surrounded by a helices. The polypeptide chain is colored in sections from the N-terminus to facilitate following the chain tracing in the order green, blue, yellow, red and pink. The red region corresponds to the active site loop in the serpins which in ovalbumin is protruding like a handle out of the main body of the structure. (Adapted from R.W. Carrell et al.. Structure 2 257-270, 1994.)... 

Progress in deducing more structural details of these fibers has instead been achieved using NMR, electron microscopy and electron diffraction. These studies reveal that the fibers contain small microcrystals of ordered regions of the polypeptide chains interspersed in a matrix of less ordered or disordered regions of the chains (Eigure 14.9). The microcrystals comprise about 30% of the protein in the fibers, are arranged in p sheets, are 70 to 100 nanometers in size, and contain trace amounts of calcium ions. It is not yet established if the p sheets are planar or twisted as proposed for the amyloid fibril discussed in the previous section. 

From a map at low resolution (5 A or higher) one can obtain the shape of the molecule and sometimes identify a-helical regions as rods of electron density. At medium resolution (around 3 A) it is usually possible to trace the path of the polypeptide chain and to fit a known amino acid sequence into the map. At this resolution it should be possible to distinguish the density of an alanine side chain from that of a leucine, whereas at 4 A resolution there is little side chain detail. Gross features of functionally important aspects of a structure usually can be deduced at 3 A resolution, including the identification of active-site residues. At 2 A resolution details are sufficiently well resolved in the map to decide between a leucine and an isoleucine side chain, and at 1 A resolution one sees atoms as discrete balls of density. However, the structures of only a few small proteins have been determined to such high resolution. 

The final variable to be mentioned here is the presence of impurities. These may be metallic fragments residual from Ziegler-type processes or they can be trace materials incorporated into the polymer chain. Such impurities as catalyst fragments and carbonyl groups incorporated into the chain can have a serious adverse influence on the power factor of the polymer, whilst in other instances impurities can have an effect on aging behaviour. 

Traceability is achieved by coding items and their records such that you can trace an item back to the records at any time in its life. The chain can be easily lost if an item goes outside your control. If, for example, you provide an item on loan to a development organization and it is returned some time later, without a certified record of what was done to it, you have no confidence that the item is in fact the same one, unless it has some distinguishing features the inspection history is now invalidated because the operations conducted on the item were not certified. Traceability is only helpful when the chain remains unbroken. It can also be costly to maintain. The system of traceability that you maintain should be carefully thought out so that it is economic. There is little point in maintaining an elaborate traceability system for the once in a lifetime event when you need it, unless your very survival, or society s survival, depends upon it. 

The inspection authority for a document is the person who approved it. There may be other personnel in the chain such as the issuing authority or the publishing authority, but the person who verified the content is normally the approval authority. With documents that carry signatures you have less protection from prying users and so here is a good reason for excluding the name of the author or approver from the finished document if it is to be used externally. Separate document development records can be used to trace authors and approvers to specific documents. 

However, other molecules exist which form free radicals of such high stability that they effectively stop the chain process. These molecules are called retarders or inhibitors the difference is one of degree, retarders merely slowing down the polymerisation reaction while inhibitors stop it completely. In practice vinyl monomers such as styrene and methyl methacrylate are stored with a trace of inhibitor in them to prevent any uncontrolled polymerisation before use. Prior to polymerisation these liquids must be freed from this inhibitor, often by aqueous extraction and/or distillation. 

Once an electron density map has become available, atoms may be fitted into the map by means of computer graphics to give an initial structural model of the protein. The quality of the electron density map and structural model may be improved through iterative structural refinement but will ultimately be limited by the resolution of the diffraction data. At low resolution, electron density maps have very few detailed features (Fig. 6), and tracing the protein chain can be rather difficult without some knowledge of the protein structure. At better than 3.0 A resolution, amino acid side chains can be recognized with the help of protein sequence information, while at better than 2.5 A resolution solvent molecules can be observed and added to the structural model with some confidence. As the resolution improves to better than 2.0 A resolution, fitting of individual atoms may be possible, and most of the... 

Figure 3 illustrates the correspondence of the calculated backbone trace with that of the backbone atoms. Figure 4 illustrates the sequence ofthe protein and the occurrence of the two breaks in the chain. 

This symposium concerns models for predicting the fate of chemicals in the environment. Strictly speaking, the topic of this paper does not fall into the usual definition of fate models. However, every fate model has at least one source term. Although the source term for one fate model may be the output of another fate model (as when air transport models provide the deposition rates that are the inputs to an aquatic fate model), the chain always has to be traced to the original sources, whether they are natural or associated with human activities. 

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