Unique encoding

There are two related aspects to creating a unique representation of a chemical structure. One is to provide a unique encoding for a chosen representation, which primarily involves determining an order in which the atoms should be listed, while the other is to determine which of a number of possible variations in the way that equivalent structures can be represented (positions of double bonds, charges, mobile hydrogens, etc.) should be chosen. The former process... 

Example 14-5. The symmetric group acts on the Boolean algebra by permuting the groimd set. Every [Pg.248]

A potentially general method of identifying a probe is, first, to purify a protein of interest by chromatography (qv) or electrophoresis. Then a partial amino acid sequence of the protein is deterrnined chemically (see Amino acids). The amino acid sequence is used to predict likely short DNA sequences which direct the synthesis of the protein sequence. Because the genetic code uses redundant codons to direct the synthesis of some amino acids, the predicted probe is unlikely to be unique. The least redundant sequence of 25—30 nucleotides is synthesized chemically as a mixture. The mixed probe is used to screen the Hbrary and the identified clones further screened, either with another probe reverse-translated from the known amino acid sequence or by directly sequencing the clones. Whereas not all recombinant clones encode the protein of interest, reiterative screening allows identification of the correct DNA recombinant. 

Each such segment of encoded information defines a gene, and expression of the gene leads to synthesis of the specific protein encoded by it, endowing the cell with the functions unique to that particular protein. Proteins are the agents of biological function they are also the expressions of genetic information. 

The unique characteristic of each protein is the distinctive sequence of amino acid residues in its polypeptide chain(s). Indeed, it is the amino acid sequence of proteins that is encoded by the nucleotide sequence of DNA. This amino acid sequence, then, is a form of genetic information. By convention, the amino acid sequence is read from the N-terminal end of the polypeptide chain through to the C-terminal end. As an example, every molecule of ribonucle-... 

Notice that in this example, the speed of the packet is inversely proportional to the packet s spatial size. While there is certainly nothing unique about this particular representation, it is interesting to speculate, along with Minsky, whether it may be true that, just as the simultaneous information about position and momentum is fundamentally constrained by Heisenberg s uncertainty relation in the physical universe, so too, in a discrete CA universe, there might be a fundamental constraint between the volume of a given packet and the amount of information that can be encoded within it. 

About 78 human genes encoding a variety of K+ channels and auxiliary subunits have been identified (Fig. 1 Table 1). While the K+ channels are diverse, they share with a unique conducting pore highly selective for K+ ions. TheK+ channels ar e tetramers composed of four a subunits that form the conducting pore. On the basis of primary amino acid sequence of a subunit, K+ channels can be classified into three major families (Fig. 2). 

Mitochondria are unique organelles in man and higher animals in that they contain their own genome. Mitochondrial DNA (mtDNA) in humans is a small (16.5 kb), circular genome that encodes only 13 proteins, 22 transfer RNA (tRNA), and 2 ribosomal RNA (rRNA) molecules. mtDNA is inherited only from the mother and is present in multiple copies within one mitochondrion. 

Mitochondria are unique organelles in that they contain their own DNA (mtDNA), which, in addition to ribosomal RN A (rRNA) and transfer RN A (tRNA)-coding sequences, also encodes 13 polypeptides which are components of complexes I, III, IV, and V (Anderson et al., 1981). This fact has important implications for both the genetics and the etiology of the respiratory chain disorders. Since mtDNA is maternally-inherited, a defect of a respiratory complex due to a mtDNA deletion would be expected to show a pattern of maternal transmission. However the situation is complicated by the fact that the majority of the polypeptide subunits of complexes I, III, IV, and V, and all subunits of complex II, are encoded by nuclear DNA. A defect in a nuclear-coded subunit of one of the respiratory complexes would be expected to show classic Mendelian inheritance. A further complication exists in that it is now established that some respiratory chain disorders result from defects of communication between nuclear and mitochondrial genomes (Zeviani et al., 1989). Since many mitochondrial proteins are synthesized in the cytosol and require a sophisticated system of posttranslational processing for transport and assembly, it is apparent that a diversity of genetic errors is to be expected. 

This complex consists of four subunits, all of which are encoded on nuclear DNA, synthesized on cytosolic ribosomes, and transported into mitochondria. The succinate dehydrogenase (SDH) component of the complex oxidizes succinate to fumarate with transfer of electrons via its prosthetic group, FAD, to ubiquinone. It is unique in that it participates both in the respiratory chain and in the tricarboxylic acid (TC A) cycle. Defects of complex II are rare and only about 10 cases have been reported to date. Clinical syndromes include myopathy, but the major presenting features are often encephalopathy, with seizures and psychomotor retardation. Succinate oxidation is severely impaired (Figure 11). 

The MoFe proteins are all a2 2 tetramers of 220-240 kDa, the a and (3 subunits being encoded by the nifD and K genes, respectively. The proteins can be described as dimers of a(3 dimers. They contain two unique metallosulfur clusters the MoFeTSg homocitrate, FeMo-cofactors (FeMoco), and the FesSy, P clusters. Neither of these two types of cluster has been observed elsewhere in biology, nor have they been synthesized chemically. Each molecule of fully active MoFe protein contains two of each type of cluster 2-7). 

Figure 37-14. Alternative promoter use in the liver and pancreatic B cell glucokinase genes. Differential regulation of the glucokinase GK) gene is accomplished by the use of tissue-specific promoters. The B cell GK gene promoter and exon 1B are located about 30 kbp upstream from the liver promoter and exon 1L. Each promoter has a unique structure and is regulated differently. Exons 2-10 are identical in the two genes, and the GK proteins encoded by the liver and B cell mRNAs have identical kinetic properties.

Recently, Teymour and coworkers developed an interesting computational technique called the digital encoding for copolymerization compositional modeling [20,21], Their method uses symbolic binary arithmetic to represent the architecture of a copolymer chain. Here, each binary number describes the exact monomer sequence on a specific polymer chain, and its decimal equivalent is a unique identifier for this chain. Teymour et al. claim that the... 

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