Elongation Processes

Amorphous polymers assume their unperturbed dimensions in the solid state (see Section 5.6.2). Even the dimensions of partially crystalline polymers 

The maximum attainable chain end-to-end distance on stretching is that when the whole molecule lies in a trans conformation. This maximum achievable length is given by Equation (4-8). Consequently, the maximum elongation ratio max is 

the amorphous regions crystallize. Annealed polymers, however, are more highly crystalline. In this case, the crystallites must be partially dissolved before the molecular axes can be oriented. 

Freezing in of orientations is made use of with what are called heat-shrink films Heat-shrink films are stretched or drawn biaxially, and these films are used to solidly encapsulate mold components. The wrapped goods are then warmed, whereby the film expands slightly below the glass transition temperature (for amorphous polymers) or the melting temperature (for crystalline polymers). At the transition temperature, however, the molecular segments become mobile the molecules tend to assume their unperturbed dimensions and the film shrinks in upon itself. 

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Figure 38-8. Diagrammatic representation of the peptide elongation process of protein synthesis. The small circles labeled n - 1, n, n -I-1, etc, represent the amino acid residues of the newly formed protein molecule. EFIA and EF2 represent elongation factors 1 and 2, respectively. The peptidyl-tRNA and aminoacyl-tRNA sites on the ribosome are represented by P site and A site, respectively.

The poly(C)-directed oligoguanylate synthesis from guanosine 5 -phosphoric 2-methylimidazolide has been studied kinetically.11571 An intermediate elongation process on polycytidylate acting as template is illustrated schematically below. 

The stepwise polymerisation of activated amino acids leads to the formation of activated dimers, which very often cyclise to diketopiperazines and are thus removed from the chain elongation process (Orgel, 1989). 

P. putida grown with hexanoic acid contained approximately 75, 11, and 10 mol% of 3HHx,3HO, and 3HD units and also small amounts of four unsaturated repeating units. The mechanism for the formation of 3HO unit was investigated by 13C NMR study, which showed that the most of 3HO units found in this PHA were formed by the reaction of hexanoic acid with acetyl-CoA [53]. These results confirmed that P. putida produces 3HA units by fatty acid synthesis pathway, through a -oxidation and chain elongation process. 

Methylthiobutyl glucosinolate derives from L-methionine by a complex elongation process leading to dihomomethionine. Four of the five carbons of methionine are retained, one being lost in a decarboxylation. The two necessary additional carbons each derive from a methyl group of acetyl-S-CoA by a complex, multi-step condensation mechanism (Equation 11) ... 

As noted earlier, microtubule elongation has been characterized largely with respect to the involvement of guanine nucleotides and the modes of drug inhibition of microtubule formation. There have also been a number of important studies on the influence of microtubule-associated proteins and solution variables on the kinetics and thermodynamics of microtubule self-assembly. Of these, the characterization of the so-called mitotic spindle poisons has been particularly complex because of the variety of agents and the diversity of systems studied. For this reason, we shall concentrate on the other factors affecting the elongation process. 

Experiments with chloroplasts showed an apparent inhibition of fatty acid synthesis by PAN (at 72 ppm for 10 min). The result is difficult to interpret the inhibition could be attributed to inactivation of one of the enzymes of the multistep system or to oxidation of the reductant (reduced NADP, or NADPH) required in the chain elongation process. 

Then the peptidyl-tRNA at the A site is translocated to the P site by the ribosome moving along the mRNA a codon at a time, exposing the A site for a new aminoacyl-tRNA appropriate for the particular codon, and a repeat of the elongation process occurs. The cycles of elongation and translocation continue until a termination codon is reached, and the peptide or protein is then hydrolysed and released... 

Another characteristic of such a mechanism is autocatalysis, as the number of cat-alytically active species increases with each condensation step (assuming that the catalytic activity is maintained in the elongation process). 

Figure 3.6. Polyketlde chains use an iterative process akin to the fatty acid chain elongation process. However, an extra layer of chemical diversity can be generated by feeding different starter units into the system consequently, the polyketlde biosynthetic system has been compared to a Lego system where a few modules can be joined together in many different ways.

In principle, bifunctional aldehydes should be able to engage in twofold enzymatic aldol additions to both of their acceptor carbonyls in a fashion to be classified as a tandem reaction, that is, without the need for isolation of intermediates. Depending on the specificity of the enzyme used and on the functionalization in the starting material, the isomeric constitution as well as the absolute and relative stereochemistry should be deliberately addressable. Therefore, we engaged in a program to evaluate the scope and the Hmitations of such two-directional chain elongation processes for the construction of extended poly functional molecules [36]. 

An example for how protein phosphorylation can influence the transcription process is the transition from the initiation to the elongation process for RNA polymerase II (see 1.4.2.4). 

Additional information <44> (<44> transgenic plants bearing gene for enzyme antisense RNA, inhibition of cell elongation process [35]) [35]... 

Usually the products of Cj-elongation are intermediates, rather than the target amino sugars. The elongation can be repeated iteratively [20]. Cyanohydrin formation belongs to the most typical C,-elongation processes. Addition of trimethylsilyl cyanide to a-amino aldehydes of type 1 in the presence of Lewis acid yielded a mixture of diastereoisomers 2 and 3 [21] (Scheme 3). 

Polycarboxylic acid synthases. Several enzymes, including citrate synthase, the key enzyme which catalyzes the first step of the citric acid cycle, promote condensations of acetyl-CoA with ketones (Eq. 13-38). An a-oxo acid is most often the second substrate, and a thioester intermediate (Eq. 13-38) undergoes hydrolysis to release coenzyme A.199 Because the substrate acetyl-CoA is a thioester, the reaction is often described as a Claisen condensation. The same enzyme that catalyzes the condensation of acetyl-CoA with a ketone also catalyzes the second step, the hydrolysis of the CoA thioester. These polycarboxylic acid synthases are important in biosynthesis. They carry out the initial steps in a general chain elongation process (Fig. 17-18). While one function of the thioester group in acetyl-CoA is to activate the methyl hydrogens toward the aldol condensation, the subsequent hydrolysis of the thioester linkage provides for overall irreversibility and "drives" the synthetic reaction. 

At the bottom of Fig. 17-18 several stages of the a-oxo acid elongation process are arranged in tandem. We see that glyoxylate (a product of the acetyl-CoA-glyoxylate cycle) can be built up systematically to... 

It is of interest to compare two chain elongation processes by which two-carbon units are combined. 

Oxoacid chain elongation process. Used three times... 

Termination of transcription involves stopping the elongation process at a region on the DNA template that signals termination and release of the RNA product and the RNA polymerase. Most terminators are similar in that they code for a double-stranded RNA stem-and-loop structure just preceding the 3 end of the transcript (fig. 28.11). Such structures cause RNA polymerase to pause, terminate, and detach. Two types of terminators have been distinguished. The first is sufficient without any accessory factors it contains about six uridine residues following the stem and loop (see fig. 28.11). The second type of terminator lacks the polyU stretch and requires a protein factor called rho to facilitate release. 

Overview of reactions in protein synthesis. (aab aa2, aa3 = amino acids l, 2, 3.) Protein synthesis requires transfer RNAs for each amino acid, ribosomes, messenger RNA, and a number of dissociable protein factors in addition to ATP, GTP, and divalent cations. First the transfer RNAs become charged with amino acids, then the initiation complex is formed. Peptide synthesis does not start until the second aminoacyl tRNA becomes bound to the ribosome. Elongation reactions involve peptide bond formation, dissociation of the discharged tRNA, and translocation. The elongation process is repeated many times until the termination codon is reached. Termination is marked by the dissociation of the messenger RNA... 

Herpes viruses are almost exclusively treated with nucleoside analogues that inhibit viral DNA polymerase. Just as with HIV NRTIs, the nucleoside analogues used against herpes viruses lack a functional 3 -OH and terminate the chain elongation process of nucleotide polymerases. The nucleoside analogues in Figure A.49 all have a role in treating... 

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