Sequences metabolic

Organism Genome sequenced Metabolic network characteristics Reference... 

RNA sequencing] metabolic disease diabetes (1 insulin production insulin resistance)... 

An intricate system of interrelated control mechanisms regulate biochemical reaction sequences. Metabolic pathways are controlled not only by specific activity and inherent kinetic properties of enzymes in the pathway but also by the intracellular concentration of certain essential substrates, activators or inhibitors. PP-ri-bose-P is an essential substrate of purine, pyrimidine and pyridine biosynthesis. The intracellular concentration of PP-ribose-P represents a balance between its synthesis by PP-ribose-P synthetase and its utilization which is catalyzed by several different phosphori-bosyltransferase (PRT) enzymes as well as non-specific phosphatases. Alterations in the rate of synthesis or degradation of PP-ribose-P, whether drug induced or secondary to an inborn error, could potentially change the intracellular concentration of this compound. 

Template recognition is the process of finding the most similar sequence. The researcher must choose how to compute similarity. It is possible to run a fast, approximate search of many sequences or a slow, accurate search of a few sequences. Sequences that should be analyzed more carefully are the same protein from a different species, proteins with a similar function or from the same metabolic pathway, or a library of commonly observed substructures if available. 

Microorganisms exhibit nutritional preferences. The enzymes for common substrates such as glucose are usually constitutive, as are the enzymes for common or essential metabohc pathways. Furthermore, the synthesis of enzymes for attack on less common substrates such as lactose is repressed by the presence of appreciable amounts of common substrates or metabolites. This is logical for cells to consei ve their resources for enzyme synthesis as long as their usual substrates are readily available. If presented with mixed substrates, those that are in the main metabolic pathways are consumed first, while the other substrates are consumed later after the common substrates are depleted. This results in diauxic behavior. A diauxic growth cui ve exhibits an intermediate growth plateau while the enzymes needed for the uncommon substrates are synthesized (see Fig. 24-2). There may also be preferences for the less common substrates such that a mixture shows a sequence of each being exhausted before the start of metabolism of the next. 

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

Many other multisubstrate examples abound in metabolism. In effect, these situations are managed by realizing that the interaction of the enzyme with its many substrates can be treated as a series of uni- or bisubstrate steps in a multi-step reaction pathway. Thus, the complex mechanism of a multisubstrate reaction is resolved into a sequence of steps, each of which obeys the single- and double-displacement patterns just discussed. 

Allosteric regulation acts to modulate enzymes situated at key steps in metabolic pathways. Consider as an illustration the following pathway, where A is the precursor for formation of an end product, F, in a sequence of five enzyme-catalyzed reactions ... 

Metabolic Regulation Favors Different Pathways for Oppositely Directed Metabolic Sequences... 

FIGURE 18.7 Parallel pathways of catabolism and anabolism must differ in at least one metabolic step in order that they can be regulated independently. Shown here are two possible arrangements of opposing catabolic and anabolic sequences between A and P. 

An important tool for elucidating the steps in the pathway was the use of metabolie inhibitors. Adding an enzyme inhibitor to a cell-free extract caused an accumulation of intermediates in the pathway prior to the point of inhibition (Figure 18.12). Each inhibitor was specific for a particular site in the sequence of metabolic events. As the arsenal of inhibitors was expanded, the individual steps in metabolism were revealed. 

FIGURE 18.12 The use of inhibitors to reveal the sequence of reactions in a metabolic pathway, (a) Control Under normal conditions, the steady-state concentrations of a series of intermediates will be determined by the relative activities of the enzymes in the pathway, (b) Plus inhibitor In the presence of an inhibitor (in this case, an inhibitor of enzyme 4), intermediates upstream of the metabolic block (B, C, and D) accumulate, revealing themselves as intermediates in the pathway. The concentration of intermediates lying downstream (E and F) will fall. 

Another widely used approach to the elucidation of metabolic sequences is to feed cells a substrate or metabolic intermediate labeled with a particular isotopic form of an element that can be traced. Two sorts of isotopes are useful in this regard radioactive isotopes, such as and stable heavy isotopes, such as or (Table 18.3). Because the chemical behavior of isotopically labeled compounds is rarely distinguishable from that of their unlabeled counterparts, isotopes provide reliable tags for observing metabolic changes. The metabolic fate of a radioactively labeled substance can be traced by determining the presence and position of the radioactive atoms in intermediates derived from the labeled compound (Figure 18.13). 

All overview of the glycolytic pathway is presented in Figure 19.1. Most of the details of this pathway (the first metabolic pathway to be elucidated) were worked out in the first half of the 20th century by the German biochemists Otto Warburg, G. Embden, and O. Meyerhof. In fact, the sequence of reactions in Figure 19.1 is often referred to as the Embden-Meyerhof pathway. 

Most of the enzymes mediating the reactions of the Calvin cycle also participate in either glycolysis (Chapter 19) or the pentose phosphate pathway (Chapter 23). The aim of the Calvin scheme is to account for hexose formation from 3-phosphoglycerate. In the course of this metabolic sequence, the NADPH and ATP produced in the light reactions are consumed, as indicated earlier in Equation (22.3). 

Cells require a constant supply of N/ X)PH for reductive reactions vital to biosynthetic purposes. Much of this requirement is met by a glucose-based metabolic sequence variously called the pentose phosphate pathway, the hexose monophosphate shunt, or the phosphogluconate pathway. In addition to providing N/VDPH for biosynthetic processes, this pathway produces ribos 5-phosphate, which is essential for nucleic acid synthesis. Several metabolites of the pentose phosphate pathway can also be shuttled into glycolysis. 

Fatty acids with odd numbers of carbon atoms are rare in mammals, but fairly common in plants and marine organisms. Humans and animals whose diets include these food sources metabolize odd-carbon fatty acids via the /3-oxida-tion pathway. The final product of /3-oxidation in this case is the 3-carbon pro-pionyl-CoA instead of acetyl-CoA. Three specialized enzymes then carry out the reactions that convert propionyl-CoA to succinyl-CoA, a TCA cycle intermediate. (Because propionyl-CoA is a degradation product of methionine, valine, and isoleucine, this sequence of reactions is also important in amino acid catabolism, as we shall see in Chapter 26.) The pathway involves an initial carboxylation at the a-carbon of propionyl-CoA to produce D-methylmalonyl-CoA (Figure 24.19). The reaction is catalyzed by a biotin-dependent enzyme, propionyl-CoA carboxylase. The mechanism involves ATP-driven carboxylation of biotin at Nj, followed by nucleophilic attack by the a-carbanion of propi-onyl-CoA in a stereo-specific manner. 

Pefloxacin (33) is the N-methyl analogue of norfloxacin (58) and is at least partly converted to it by metabolic enzymes in vivo. It has been launched in France for the treatment of a number of infections including those caused by sensitive strains of Pseudomonas aeruginosa. It can be synthesized starting with the Gould-Jacobs reaction of 3-chloro-4-fluoroaniline (28) and diethyl ethoxymethylenemalonate in an addition-elimination sequence leading to 29 which undergoes... 

Metabolism of S-Adenosylhomocysteine (Section 11.6) involves the following sequence. Propose a mechanism for the second step. 

Figure 9.2 Generalised metabolic sequences of sterol side chain degradation by micro-organisms.

Temozolomide undergoes spontaneous hydrolysis and decarboxylation at physiological pH value and thereafter a methyldiazonium ion is released. This ion forms DNA adducts within guanine rich DNA sequences. Temozolomide has high bioavailability and is metabolized in the liver. 

Biological raw data are stored in public databanks (such as Genbank or EMBL for primary DNA sequences). The data can be submitted and accessed via the World Wide Web. Protein sequence databanks like trEMBL provide the most likely translation of all coding sequences in the EMBL databank. Sequence data are prominent, but also other data are stored, e.g.yeast two-hybrid screens, expression arrays, systematic gene-knock-out experiments, and metabolic pathways. 

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