Biochemical dimension

In the same line, Mansny showed that CCI4 is a sonrce of dichlorocarbene ligand, which also shows how CCI4 conld be metabolized by cytochrome P450 and revealed for the first time the biochemical dimension of metallo-carbenes - ... 

Interpretable high-resolution structural infomiation (e.g. preservation of dimensions, or correlation of the stmctiiral detail with a physiologically or biochemically controlled state) is therefore obtained exclusively from samples in which life has been stopped very quickly and with a sufficiently high time resolution for the cellular dynamics [19]. Modem concepts for specimen preparation therefore try to avoid traditional, chemical... 

Synge, RLM, Experiments on Electrical Migration of Peptides and Proteins Inside Porous Membranes Influences of Adsorption, Diffusion, and Pore Dimensions, Biochemical Journal 65, 266,1957. 

Y. Belosludtsev, B. Iverson, S. Lemeshko, R. Eggers, R. Wiese, S. Lee, T. Powdrill, and M. Hogan, DNA microarrays based on noncovalent oligonucleotide attachment and hybridization in two dimensions. Anal. Biochem. 292, 250—256 (2001). 

Wardle DA, Giller KE (1996) The quest for a contemporary ecological dimension to soil biology - discussion. Soil Biol Biochem 28 1549-1554... 

Most of the naturally occurring chelating agents are substituted hydroxamates which are produced by a variety of protista so that iron(III) subsequently becomes available for biochemical processes. Neilands (73) has suggested that the hydroxamates facilitate the transport of iron across cell membranes. The distribution of hydroxamates in the biosphere appears limited. However, if there was a wider distribution of hydroxamates in the environment then the management of actinide wastes could become a problem of horrifying dimensions if these chelators facilitated the transport of actinides across cell membranes. 

Flow dynamics predict that flow through a pipe is nonuniform with regard to velocity across the diameter of a pipe, for instance. The flow at pipe walls is assumed to be zero. In our idealized biochemical reactor, this concept is represented by a boundary layer in contact with the biofilm. It does not have, of course, a discrete dimension. Rather, it is represented as an area in the structure that has reduced flow and therefore different kinetics than what we would assume exist in a bulk liquid. The boundary layer is affected by turbulence and temperature and this is unavoidable to a degree. Diffusion within the boundary layers is controlled by the chemical potential difference based on concennation. Thus the rate of transfer of pollutant to the organisms is controlled by at least two physical chemical principles, and these principles differentiate an attached growth bioreactor from a suspended growth bioreactor. 

Gyclodextrin cavities form the early models of host molecules involved in supramolecular assemblies. There are many other molecules known as cryptands which can be designed to offer a cavity of fairly precise dimensions to accommodate various ions or metal complexes. It may be possible to locate not just one, but two, guest molecules inside a cryptand cavity, and this may lead to new electron transfer reactions in restricted environments another step towards synthetic photoinduced biochemical reactions. 

While searching for the meaning of these equalities, James Watson noted that hydrogen-bonded base pairs with the same overall dimensions could be formed between A and T and between G and C (fig. 25.4). The A-T base-paired structure has two hydrogen bonds, whereas the G-C base pair has three. The hydrogen-bonded pairs are formed between bases of opposing strands and can only arise if the directional senses of the two interacting chains are opposite or antiparallel (fig. 25.5). With this notion in mind Francis Crick took a closer look at the x-ray diffraction pattern produced by DNA and was able to interpret the diffraction pattern in terms of a helix (see Methods of Biochemical... 

Trichohyalin contains extensive repeat sequence blocks, which are predicted to form an elongated, flexible single-stranded o-helical rod (Lee et al, 1993). These predictions are consistent with biochemical and electron microscopical analysis showing an extended shape with overall dimensions of 85 nm. Similar to profilaggrin, the N-terminus comprises an S-100 protein-like calcium-binding domain. 

Conventionally, the first attribute known about an enzyme used to be its function, usually in a crude extract. This property was screened for in microbial cultures or in tissue samples. The crude extract was then purified to homogeneity and the protein subjected to biochemical studies to learn of its pH and T profiles, its pi and subunit composition, catalytically important residues, and other properties. Proteolytic digestion of the protein with subsequent Edman degradation led to the primary sequence, but no information on the secondary structures such as a-heli-ces and [5-sheets or the folding in three dimensions of the polypeptide chain. The primary sequence could have been used to deduct the gene sequence but, with the degeneration of the code, several possibilities for certain amino acids occur, which makes prediction of the gene sequence a risk. 

Miniaturized systems for performing chemical/biochemical reactions and analysis require cavities, channels, pumps, valves, storage containers, couplers, electrodes, windows and bridges [53]. The typical dimensions of these components are in the range of a few micrometers to several millimeters in length or width, and between 100 nm and 100 pm in depth and height. An extensive set of techniques for fabricating these microstructures is discussed in Sect. 3. 

Figure 1.1. Representative organizations of biochemical components. Three component areas of biochemistry—structural, dynamic, and information biochemistry—are represented as organizations in space (dimensions of biomolecules and assemblies), time (rates of typical biochemical processes), and number (number of nucleotides in bioinformatic...

Paul Weisz suggested in a lucid note published in 1973 that cells, and indeed even entire organisms, have evolved in a way that maintains unity effectiveness factor [24]. That is, the size of the catalytic assembly is increased in nature as the overall rate at which that assembly operates decreases, and the relationship between characteristic dimension and activity can be well approximated by the observable modulus criterion for reaction limitation. It is possible that Weisz s arguments may fail under process conditions, and internal gradients within a compartment or cell may be important. However, at present it appears that the most important transport limitations and activities in cells are those that operate across cellular membranes. Therefore, to understand and to manipulate key transport activities in cells, it is essential that biochemical engineers understand these membrane transport processes and the factors influencing their operation. A brief outline of some of the important systems and their implications in cell function and biotechnology follows. 

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