Biochemical examples

Except for the biochemical example just cited the stractures of all of the alcohols m Section 5 9 (including those m Problem 5 13) were such that each one could give only a single alkene by p elimination What about ehmmahon m alcohols such as 2 methyl 2 butanol m which dehydration can occur in two different directions to give alkenes that are conshtutional iso mers Here a double bond can be generated between C 1 and C 2 or between C 2 and C 3 Both processes occur but not nearly to the same extent Under the usual reachon con dihons 2 methyl 2 butene is the major product and 2 methyl 1 butene the minor one... 

Biochemical examples of these two modes of reactivity are Nucleophilic acyl substitution... 

The second function, and the one pertinent to this section, is the decarboxylation of oxalosuccinic acid to 2-oxoglutaric acid. This is simply a biochemical example of the ready decarboxylation of a P-ketoacid, involving an intramolecular hydrogen-bonded system. This reaction could occur chemically without an enzyme, but it is known that isocitric acid, the product of the dehydrogenation, is still bound to the enzyme isocitrate dehydrogenase when decarboxylation occurs. 

I. Inorganic sulfur compounds containing another (usually more electropositive) element. When the other element is an alkali or alkaline earth, the sulfide is ionic in character. Metal sulfides often have unusual stoichiometries. Examples of sulfides include H2S, Na2S, FeS, and HgS. 2. Organic sulfides are also referred to as thioethers and have the general structure R—S—R. Biochemical examples of sulfides include methionine, cystathionine, and djenkolic acid. If the two R groups are identical, the substance can be referred to as a symmetrical sulfide (biological examples of which are lanthionine and homo-lanthionine). 

The racemization of an amino acid provides a biochemical example that can be related directly to Eq. 6-9. A solution of an L-amino acid will be efficiently changed into the racemic mixture of 50% d and 50% l by the action of an enzyme (a racemase) with no uptake or evolution of heat. Thus, AH = 0 and the only change is an entropy change. Let us designate 2 for the pure isomer as 2. Since there are just two choices of configuration for each of the N molecules in 1 mole of the racemate we see that for the racemate... 

We have seen instances in the various biochemical examples that we have cited of a close coupling between an exergonic and an endergonic process. The need for such couplings to account for the observed appearances of the products of endergonic processes (for example, the synthesis of complex biological molecules from simple ones) was recognized for some time before the details... 

In microbial fermentation processes, biomass acts as the catalyst for substrate conversion and at the same time it is produced by the process itself. This is a biochemical example of... 

We have already dealt with some general aspects of biochemical self-assembly in Section 2.10 including the remarkable formation of viral capsids. There are some biochemical examples, however, that translate readily into supramolecular chemical concepts and have been pivotal in defining the field. One such system is the tobacco mosaic virus, a virus that is very harmful to a variety of crops including tobacco, tomato, pepper, cucumbers and species such as ornamental flowers. This system consists of a helical virus particle measuring some 300 X 18 nm (Figure 10.6). A central strand of RNA is sheathed by 2130 identical protein subunits, each of which contains 158 amino acids. What is remarkable about... 

The shift from bio-based specialties to commodities is already visible in the marketplace with biopolymers made from corn. The first example is NatureWorks from Cargill, which is made from corn sugar-derived lactic acid. As in the biochemicals examples described above, the environmental benefits are eye-opening NatureWorks already requires 25 to 55 percent less fossil resources, and it is planned to replace fossil resources completely in the next four to six years (Euro-paBio and McKinsey Company, 2003). Other high-potential biomaterials are a polymer based on 1,3-propanediol from DuPont and Genencor (Sorona ) and... 

In one of many examples of the Darwinian echo chamber, in Tower of Babel Robert Pennock approvingly quotes Orr s reasonsing about hypothetical part A and part (B), but is equally reticent about spelling out how such reasoning applies to real mousetraps or biochemical examples. 

One recent trend has been away from using a photochromic dye itself merely as an individual component of a solution, polymer film or bulk polymer matrix. Instead, the photochromic is chemically linked to a polymer, which may be a natural polymer such as a cellulose derivative, an enzyme, a protein, or synthetic polymers from acrylates, urethanes, and vinyl compounds. The properties of the polymer can then be modified by external irradiation, and conversely, the properties of the photochromic are modified by the polymer. A recent biochemical example is the photocontrolled binding of monosaccharides to concanavalin A (Con A) modified with spiropyran units.208... 

Such complexes are sometimes called supramolecules. The choice of which molecule is the host and which is the guest is somewhat arbitrary, but the larger molecule is usually deemed the host. Enzyme-substrate complexes are a prime biochemical example of such interactions. Cram, Pedersen, and Lehn shared the 1987 Nobel Prize in chemistry for their pioneering work in the area of molecular recognition and supramolecular chemistry. The recent chemical literature is replete with examples in which NMR has been used to study such complexa-tion.6... 

Chemical Biophysics Quantitative Analysis of Cellular Systems by Daniel Beard and Hong Qian Alls a significant niche. The text is a concise yet clear exposition of the fundamentals of chemical thermodynamics and kinetics, aimed specifically at practitioners of the new science of systems biology. It is marvelously illustrated with biochemical examples that will aid those who aim to analyze and model the workings of biological cells. 

Two common six-membered rearrangements of 1,5-dienes have Y as either oxygen (Claisen rearrangement) or carbon (Cope rearrangement). Both are reversible and favor the more stable product. The preceding example problem demonstrated that they were thermally allowed An+2 suprafacial retention processes. As in the Cope example problem above, the transition state for the reaction commonly resembles the chair conformation of cyclohexane. Figure 12.29 shows a biochemical example of the Claisen rearrangement. 

Figure 12.29 The concerted thermal rearrangement of chorismate to prephenate is a biochemical example of a Claisen rearrangement that is part of the bacterial biosynthesis of the amino acids phenylalanine and tyrosine.

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