Elongation phase

Consider the case where the protein consists of o /3 dimers exclusively at the very beginning of an assembly experiment. Suppose further that spontaneous nucleation is sufficiently infrequent as the polymerization reaction reaches 5-10% of its maximal amplitude achieved over the remaining course of elongation. In this case, a reduction of the protomer concentration from about 20 to 18 JU.M would reduce the apparent extent of nucleation by a factor of about 10-20, such that the polymer number concentration remains fixed throughout the ensuing elongation phase. If nucleation were viewed as a one-step cooperative event, then the rate of nucleation would be proportional to the ith power of the protomer concentration if /protomers cooperatively form the polymerization nucleus ... 

Johnson and Borisy first showed that the lag phase in the plot of turbidity (i.e., polymer weight concentration) versus time accounted for only 5—10% of the entire amplitude obtained upon completion of the polymerization process. By fitting the elongation phase to a single exponential process, these investigators arrived at the correct conclusion that microtubule number concentration becomes relatively stable within the first minutes... 

Fig. 1.32. Phosphorylation of the C-terminal domain of RNA polymerase II and the beginning of transcription. The transition from the initiation complex to actual begin of transcription is regulated via phosphorylation of the C-terminal domain (CTD) of RNA polymerase II. In the above model it is assumed that initially a complex is formed between TFIID and a holoenzyme of RNA polymerase consisting of RNA polymerase II and associated factors (mediators, SRB proteins) and the basal transcription factors. Phosphorylation of the C-terminal domain effects the dissociation of the RNA polymerase from the initation complex and the transition to the elongation phase. A protein kinase, which is part of TFIIH, is responsible for the phosphorylation. The nature of the signal that induces phosphorylation of RNA polymerase II remains unknown. SRB suppressor of RNA polymerase B. After Koleske and Young (1995).

Inhibition of the transition from the initiation phase to the elongation phase. 

Elongation The elongation phase of replication includes two distinct but related operations leading strand synthesis and lagging strand synthesis. Several enzymes at the replication fork are important to the synthesis of both strands. Parent DNA is first unwound by DNA helicases, and the resulting topological stress is relieved by topo-isomerases. Each separated strand is then stabilized by... 

Unlike DNA polymerase, RNA polymerase does not require a primer to initiate synthesis. Initiation occurs when RNA polymerase binds at specific DNA sequences called promoters (described below). The 5 -triphos-phate group of the first residue in a nascent (newly formed) RNA molecule is not cleaved to release PPj, but instead remains intact throughout the transcription process. During the elongation phase of transcription, the growing end of the new RNA strand base-pairs temporarily with the DNA template to form a short hybrid... 

CTD. This causes a conformational change in the overall complex, initiating transcription. Phosphorylation of the CTD is also important during the subsequent elongation phase, and it affects the interactions between the transcription complex and other enzymes involved in processing the transcript (as described below). 

During synthesis of the initial 60 to 70 nucleotides of RNA, first TFIIE and then TFIIH is released, and Pol II enters the elongation phase of transcription. 

Compare systhesis of the leading and lagging strands in the elongation phase of DNA replication. Explain why DNA polymerases may have difficulty in replicating the 3 -end of the lagging strand of linear DNA. How has this problem been solved in many bacterial and viral systems In eukaryotic cells ... 

The extent of methylation of a gene is correlated with its ability to transcribe. Given that DNA methylation usually reduces transcription, two important, closely related questions remain unanswered How is methylation regulated in vivo How does methylation interfere with transcription Since methylation is known not to interfere with the elongation phase of RNA synthesis, it seems likely that methylation blocks initiation. The binding of polymerase and other regulatory proteins at the initiation locus is sensitive to modification of these nucleotides. The precise inhibition mechanisms, however, await further elucidation. 

Elongation factors. Protein factors uniquely required during the elongation phase of protein synthesis. Elongation factor G (EF-G) brings about the movement of the peptidyl-tRNA from the A site to the P site of the ribosome. 

At high SAN contents of 40 wt%, cell nucleation initially starts in the SAN phase and rapid cell growth appears. The elongated phase structure and the generally elevated phase size of SAN promote rapid cell coalescence, leading to an in-... 

Growth observed but not divided into nucleation and elongation phases... 

Eukaryotic cells contain at least four different DNA-dependent RNA polymerases. Their localization, cellular transcripts, and susceptibility to the cyclic octapeptide a-amanitin (derived from poisonous mushrooms) are shown in Table 11.3. a-Amanitin blocks the elongation phase of RNA synthesis. Although the structures of these enzymes are much more complex than that of the prokaryotic RNA polymerase, the basic mechanism is very similar to that of the prokaryotic enzyme. 

Inhibition of protein synthesis in eukaryotic cells by the Cephalotaxus alkaloids harringtonine, homoharringtonine, and isoharringtonine has been studied.16 In model systems, these alkaloids were found not to inhibit any of the initiation steps but to block certain parts of the elongation phase of translation. 

As already discussed, the replication of a replicon can be divided into three stages initiation, elongation and termination. During the elongation phase, DNA chain growth takes place at... 

The elongation phase of DNA replication in bacteria has been seen to involve many enzymes and proteins, and some are associated with discrete functional complexes, such as the DNA polymerase III holoenzyme. Initiation of replication also uses several proteins, and mutations in their genes have been very helpful in identifying these proteins. 

The elongation phase of polypeptide synthesis and its termination are described in Example 17.8. The A site is shown to be filled by AA2-tRNA where the codon xxx is located. 

During the elongation phase of fiber development, the cell is delimited by a primary cell wall and covered by a waxy layer or cuticle (Figure 2.1). 

Moir, R., Spann, T., Herrmann, H. and Goldman, R. (2000) Dismption of nuclear lamin organization blocks the elongation phase of DNA replication. J. Cell Biol. 149, 1179—1192. 

The self-assembly of tubulin to form microtubules was described initially in a classic polymerization model of nucleated helical polymerization by Maruyama and Oosawa (4). Assembly involves two phases a nucleation phase followed by an elongation phase. With purified systems in vitro, nucleation can... 

The elongation phase of fatty acid synthesis starts with the formation of acetyl ACP and malonyl ACP. Acetyl transacylase and malonyl transacylase catalyze these reactions. 

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