Information encoding

A structure descriptor is a mathematical representation of a molecule resulting from a procedure transforming the structural information encoded within a symbolic representation of a molecule. This mathematical representation has to be invariant to the molecule s size and number of atoms, to allow model building with statistical methods and artificial neural networks. 

A structure descriptor is a mathematical representation of a molecule resulting from a procedure transforming the structural information encoded within a symbolic representation of a molecule. 

Nucleus The nucleus is separated from the cytosol by a double membrane, the nuclear envelope. The DNA is complexed with basic proteins (histones) to form chromatin fibers, the material from which chromosomes are made. A distinct RNA-rich region, the nucleolus, is the site of ribosome assembly. The nucleus is the repository of genetic information encoded in DNA and organized into chromosomes. During mitosis, the chromosomes are replicated and transmitted to the daughter cells. The genetic information of DNA is transcribed into RNA in the nucleus and passes into the cytosol where it is translated into protein by ribosomes. 

FIGURE 11.1 The fundamental process of information transfer in cells. Information encoded in the nucleotide sequence of DNA is transcribed through synthesis of an RNA molecule whose sequence is dictated by the DNA sequence. As the sequence of this RNA is read (as groups of three consecutive nucleotides) by the protein synthesis machinery, it is translated into the sequence of amino acids in a protein. This information tmiisfer system is encapsulated in the dogma DNA RNA protein. 

Transcription (Section 28.4) The process by which the genetic information encoded in DNA is read and used to synthesize RNA in the nucleus of the cell. A smal I portion of double-stranded DNA uncoils, and complementary ribonucleotides line up in the correct sequence for RNA synthesis. 

Further degradation of the information encoded in the electron beam takes place in the recording step since the signal is proportional to the square modulus of the image wave-function, i.e. neglecting small second order terms ... 

It can be readily anticipated that the new instrumentation, having extended the point resolution of the microscope up to its information limit [117], will provide even better high resolution images of nanoclusters, and also that it will not supersede, but emphasize, the role of EH, as the relevant structural information encoded in the phase (which is still completely lost in the recording process) can be retrieved corrected by all coherent aberrations. 

The atomic-level structural information encoded into the E-state generates a chemical space that can be efficient in QSAR modeling and in the virtual screening... 

The moving invariant manifolds determine the reactivity or nonreactivity of an individual trajectory under the influence of a specific noise sequence. They thus provide the most detailed microscopic information on the reaction dynamics that one can possibly possess. In practice, though, one is more often interested in macroscopic quantities that are obtained by averaging over the noise. To illustrate that such quantities can easily be derived from the microscopic information encoded in the TS trajectory, we calculate the probability for a trajectory starting at a point (q, v) in the space-fixed phase space to end up on the product side of the... 

RNA RNA (ribonucleic acid) is an information encoded strand of nucleotides, similar to DNA, but with a slightly different chemical structure. In RNA, the letter U (uracil) is substituted for T in the genetic code. RNA delivers DNA s genetic message to the cytoplasm of a cell where proteins are made. 

This approach yields spectral densities. Although it does not require assumptions about the correlation function and therefore is not subjected to the limitations intrinsic to the model-free approach, obtaining information about protein dynamics by this method is no more straightforward, because it involves a similar problem of the physical (protein-relevant) interpretation of the information encoded in the form of SD, and is complicated by the lack of separation of overall and local motions. To characterize protein dynamics in terms of more palpable parameters, the spectral densities will then have to be analyzed in terms of model-free parameters or specific motional models derived e.g. from molecular dynamics simulations. The SD method can be extremely helpful in situations when no assumption about correlation function of the overall motion can be made (e.g. protein interaction and association, anisotropic overall motion, etc. see e.g. Ref. [39] or, for the determination of the 15N CSA tensor from relaxation data, Ref. [27]). 

Caspar and Klug (1962) made an important distinction between two fundamental types of assembly processes. True self-assembly was conceptualized as a series of reactions relying on the propensity of subunits to condense and form assembled structures strictly as a result of the information encoded in the architecture of the components. On the other hand, template-directed assembly may be considered as a process depending on the presence of a separate template that imparts structural constraints on the pathway for constructing the final assembled structure. True self-assembly is observed, for example, in the formation of many oligomeric proteins. Indeed, Friedman and Beychok (1979) have re-... 

The significance of Sanger s work is immense. It proved for the first time that the structure of a protein is unique that is, aU molecules of bovine insulin, for example, possess the same sequence of amino acids along the polypeptide chains. This sequence has no obvious order, but it is unique. This singular finding requires that there is a genetic code information encoded in a molecule which specifies the sequence of amino acids in the insulin molecule and, for that matter, in all protein molecules. 

Transcription is the term used to describe the synthesis of RNA from a DNA template. Translation is the process by which information in RNA is used to synthesise a polypeptide chain. In a little more detail, the genetic information encoded in DNAis first transcribed into acomplementary copy of RNA (a primary RNA transcript) which is then processed to form messenger RNA (mRNA). This leaves the nucleus and is translated into a polypeptide in the cytosol. This then folds into a three-dimensional structure and may be further biochemically modified (post-transla-tional modification) to produce a protein (Figure 20.18). 

Raman spectroscopy is a powerful tool for probing orientation, stress, and strain. Galiotis et al. have written a review on the determination of stress and strain in composites and fibers using Raman spectroscopy [179]. Young et al. discuss the complexities of correct interpretation of molecular orientation information encoded in Raman spectra of polymers [180]. Caution and a suitable number of control studies are necessary to prevent faulty conclusions. 

Translation of the information encoded in DNA, expressed as a particular nucleotide sequence, into a protein, expressed as an amino acid sequence, depends on the genetic code. In this code, sequences of three nucleotides (termed a codon) represent one of the 20 amino acids that compose the protein molecule. Because there are 64 codons which can be constructed for the four different bases, and only 20 different amino acids that are coded for, several amino acids may be coded for by more than one codon. There are also three codons, called stop codons, that terminate the transfer of information. Furthermore, although all cells contain the same complement of genes, certain cells (for example, the neurons) have specialized genes that encode specific proteins for the synthesis of specific transmitters. The expression of such genes is under the control of regulatory proteins called transcription factors which control the transcription of mRNAs from the genes they control. 

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