Macromolecules structural hierarchy

Each class of molecules has a similar structural hierarchy subunits of fixed structure are connected by bonds of limited flexibility to form macromolecules with three-dimensional structures determined by noncovalent interactions. These macromolecules then interact to form the supramolecular structures and organelles that allow a cell to carry out its many metabolic functions. Together, the molecules described in Part I are the stuff of life. We begin with water. 

In the next paragraphs, we briefly review the various levels of structural hierarchy first for single-component homopolymers as the simplest class of macromolecules. 

Fig. 3.5 Structural hierarchy in liquid-crystalline fibers. The mechanical performance of highly oriented polymers can approach the ultimate theoretical properties at high degrees of elongation. Anisotropic, rod-like macromolecules, like aromatic copolyesters composed of 2,6-naphthyl and 1,4 phenyl units, often form oriented structures, which can exhibit liquid crystallinity. Extensive structural studies of fibers of these oriented copolyesters showed a hierarchical structure like the one depicted in this Figure. In aramids (Kevlar or Twaron) similar structures may exist. Adopted with permission from [17]...

Certain properties, common to all types of macromolecule, can be derived from such analyses. All seem to have a certain individuality and many have the ability to specifically recognize and interact with other substances. They are all, to a greater or lesser extent, flexible molecules, capable of adapting their shape in response to their particular microenvironment within the cell. They ail have a pronounced intolerance to extreme conditions, a fragility that makes them fall apart if treated harshly. Finally they all may be described in terms of a structural hierarchy of primary, secondary and tertiary structures that we need to look at in a little more detail. 

Along with the traditional manner of the description of the chemical structure of linear copolymers by means of the hierarchy of probabilities P Uk of sequences of units Uk(k = 1,2,...), there is one more mode of the description of this structure. It is based on the consideration of the hierarchy of chemical correlation functions (so-called chemical correlators) (Kuchanov, 1978, 2000). The simplest among them, Yaj3(fc), has the meaning of probability to find two randomly chosen monomer units of types a and j3 divided along a macromolecule by any sequence Uk consisting of k units. This two-point correlator is of the utmost importance because its generating function enters into the expression for spinodal (Kuchanov,... 

A hierarchy of approximations now exists for calculating interactions between a charged particle and a charged, planar interface in electrolyte solutions. At moderate surface potentials less than approximately 2(kT/e the linear Poisson-Boltzmann equation provides a good approximation in many circumstances, provided the solution is a 1 1 electrolyte at low to moderate ionic strength. The relative simplicity of the linear equation makes it particularly useful for examining problems that are complicated in other ways, such as interactions involving many particles, interactions with deformable interfaces, and interactions where the detailed structure and properties of the particle (or macromolecule) play an important role. 

Crystalline and amorphous silicons, which are currently investigated in the field of solid-state physics, are still considered as unrelated to polysilanes and related macromolecules, which are studied in the field of organosilicon chemistry. A new idea proposed in this chapter is that these materials are related and can be understood in terms of the dimensional hierarchy of silicon-backbone materials. The electronic structures of one-dimensional polymers (polysilanes) are discussed. The effects of side groups and conformations were calculated theoretically and are discussed in the light of such experimental data as UV absorption, photoluminescence, and UV photospectroscopy (UPS) measurements. Finally, future directions in the development of silicon-based polymers are indicated on the basis of some novel efforts to extend silicon-based polymers to high-dimensional polymers, one-dimensional superlattices, and metallic polymers with alternating double bonds. 

Now, as to the structure of the new edition. Essentially, it follows the old in that Chapter 1 introduces the basic chemical terms to those who are unfamiliar with them, and Chapters 2 and 3 deal respectively with the properties of the small and giant molecules of which the cell is composed. In the earlier edition, the structure of the. cell itself was not discussed until much later this time, and because of the importance we attach to showing some subcelluiar organelles as composed of higher order hierarchies of macromolecules, the account of the cell forms Chapter 4. This concludes the section on biochemistry as analysis, and we turn in Chapters 5 and 6 to work, enzymes and metabolism. The core of biochemical energetics and metabolism is in Chapters 7 and 8, and it is these... 

The knowledge based structural prediction (Blundell et al, 1987) depends on analogies between a biomacromolecule of known sequence and other biomacromolecules of the same class with known 3D structure at all levels in the hierarchy of biomacromolecular organization. In the numerically based statistical methods, the structural rules and parameters (conformational propensities) for each residue are extracted by statistical analyses of the structural database and used to predict the structure along the sequence of the macromolecule. Examples of the statistical methods that are commonly applied to predict secondary structure and folding preference of proteins will be illustrated. 

Figure 32 Brush-like hierarchy of proteoglycan aggregate in cartilage (a) TEM micrograph of the aggregate (b) protein backbone with glucosami-noglycan side chains and (c) chemical structure of the disaccharide repeating unit of the side chains. Reprinted from Seog, J. Dean, D. Plaas, A. H. K. etal. Macromolecules 2002, 35 (14), 5601-5615, with permission from ACS. °...

Fig. 1). As was shown above, atoms, common molecules, macromolecules, microbodies, cells, tissues. .. an oiganism, population etc. are meant under hierarchical structures. This, in essence, means that the evolution of lower-hierarchy stmctuies proceeds much quicker than that of the organism itself, whose biomass serves the environment for its atoms, molecules, cells, etc. Just in this connection, for every biosystem it is possible to isolate its habitation medium, i.e., a peculiar thermostat with certain parameters. Such quasi-closed subsystems possessing their own thermostats, uniting, form athermod5mamic system of a higher hierarchical level. 

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