Elongation and Termination

Pol II does not elongate efficiently when alone in vitro. Under those circumstances, it can synthesize only 100-300 nucleotides per minute, whereas the in vivo rates are between 1500 and 2000 nucleotides per minute. The difference is due to elongation factors. One is TFIIF, which, in addition to its role in the formation of the preinitiation complex, also has a separate stimulatory effect on elongation. A second elongation factor, which was named TFIIS, was more recently discovered. 

Elongation is controlled in several ways. There are sequences called pause sites, where the RNA polymerase hesitates. This is very similar to the transcription attenuation we saw with prokaryotes. Elongation can also be aborted, leading 

TFIID (which contains the TATA-box binding protein, TBP) binds to the TATA box. TFIIA and TFIIB then bind, followed by recruitment of RNA polymerase II and TFIIF. TFIIH and TFIIE then bind to form the preinitiation complex (PIC). Kinases phosphorylate the C-terminal domain of Pol II, leading to the open complex in which the DNA strands are separated. RNA is produced during elongation as Pol II and TFIIF leave the promoter and the other general transcription factors behind. Pol II dissociates during the termination phase, and the CTD is dephosphorylated. Pol II/TFIIF is then recycled to bind to another promoter. 

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DNA synthesis during S phase of the cell cycle resulting in a doubling of the genomic DNA. Replication can be subdivided into three distinct phases initiation, elongation, and termination. 

The processes of DNA and RNA synthesis are similar in that they involve (1) the general steps of initiation, elongation, and termination with y to 3 polarity (2) large, multicomponent initiation complexes and (3) adherence to Watson-Crick base-pairing rules. These processes differ in several important ways, including the... 

Transcription exhibits three phases initiation, elongation, and termination. All are dependent upon distinct DNA czV-elements and can be modulated by distinct tranS jzim protein factors. 

The biosynthesis of polyketides (including chain initiation, elongation, and termination processes) is catalyzed by large multi-enzyme complexes called polyketide synthases (PKSs). The polyketides are synthesized from starter units such as acetyl-CoA, propionyl-CoA, and other acyl-CoA units. Extender units such as malonyl-CoA and methylmalonyl-CoA are repetitively added via a decarboxylative process to a growing carbon chain. Ultimately, the polyketide chain is released from the PKS by cleavage of the thioester, usually accompanied by chain cyclization [49]. 

Figure 12.2 Schematic representation of the CHS and STS reactions. The reaction pathway highlights the initiation, elongation, and termination phases of the polyketide extension reaction.

Translation involves three stages initiation, elongation and termination. A brief summary of these processes is provided below. However, the first step in polypeptide synthesis, from intracellular amino acids, is the formation of aminoacyl-tRNA. This reaction is particularly important so that the biochemistry is discussed in some detail. In addition, it is also important in the regulation of the rate of translation (see below). 

Figure 20.24 The physiological pathway of polypeptide synthesis. The flux-generating step is that catalysed by the aminoacyl-tRNA synthetases, indicated by the broad arrow. The assumption implicit in this interpretation is that the physiological pathway starts with the intracellular amino acids and ends with the peptide that is formed in the elongation and termination processes. For the majority of enzymes, the concentration of intracellular amino acids is higher than the K, for the synthetase (Chapter 3).

In eukaryotic cells, the number of initiation factors is larger and initiation is therefore more complex than in prokaryotes. The cap at the 5 end of mRNA and the polyA tail (see p. 246) play important parts in initiation. However, the elongation and termination processes are similar in all organisms. The individual steps of bacterial translation can be inhibited by antibiotics (see p. 254). 

The translation of the mRNA into proteins is the final step in the biological flow of information (see Fig. 6.1). Similar to other macromolecular polymerizations, protein synthesis can be divided into initiation, chain elongation, and termination. Critical players in this process are the aminoacyl transfer RNAs (tRNAs). These molecules form the interface between the mRNA and the growing polypeptide. Activation of tRNA involves the addition of an amino acid to its acceptor stem, a reaction catalyzed by an aminoacyl-tRNA synthetase. Each aminoacyl-tRNA synthetase is highly specific for one amino acid and its corresponding tRNA molecule. The anticodon loop of each aminoacyl-tRNA interacts... 

As in procaryotes, the elementary steps of initiation, elongation and termination can be distinguished in eucaryotic transcription. Aside from the specific RNA polymerases, transcription in eucaryotes requires the action of numerous other proteins which are collectively known as transcription factors. Transcription factors are required at the level of initiation, elongation, and termination and are accordingly known as initiation factors, elongation factors and termination factors of transcription. 

Replication of DNA occurs with very high fidelity and at a designated time in the cell cycle. Replication is semiconservative, each strand acting as template for a new daughter strand. It is carried out in three identifiable phases initiation, elongation, and termination. The reaction starts at the origin and usually proceeds bidirectionally. 

Our discussion of RNA synthesis begins with a comparison between transcription and DNA replication (Chapter 25). Transcription resembles replication in its fundamental chemical mechanism, its polarity (direction of synthesis), and its use of a template. And like replication, transcription has initiation, elongation, and termination phases—though in the literature on transcription, initiation is further divided into discrete phases of DNA binding and initiation of RNA synthesis. Transcription differs from replication in that it does not require a primer and, generally, involves only limited segments of a DNA molecule. Additionally, within transcribed segments only one DNA strand serves as a template. 

Transcription is catalyzed by DNA-dependent RNA polymerases, which use ribonucleoside 5 -triphosphates to synthesize RNA complementary to the template strand of duplex DNA. Transcription occurs in several phases binding of RNA polymerase to a DNA site called a promoter, initiation of transcript synthesis, elongation, and termination. 

An understanding of protein synthesis, the most complex biosynthetic process, has been one of the greatest challenges in biochemistry. Eukaryotic protein synthesis involves more than 70 different ribosomal proteins 20 or more enzymes to activate the amino acid precursors a dozen or more auxiliary enzymes and other protein factors for the initiation, elongation, and termination of polypeptides perhaps 100 additional enzymes for the final processing of different proteins and 40 or more kinds of transfer and ribosomal RNAs. Overall, almost 300 different macromolecules cooperate to synthesize polypeptides. Many of these macromolecules are organized into the complex three-dimensional structure of the ribosome. 

The process of transcription of a typical gene of E. coli can be divided into three phases initiation, elongation, and termination. [Note Within the DNA molecule, regions of both strands can serve as templates for specific RNA molecules. However, only one of the two DNA strands serves as a template within a specific stretch of double helix.]... 

A large number of components are required for the synthesis of a polypeptide chain. These include all the amino acids that are found in the finished product, the mRNA to be translated, tRNAs, functional ribosomes, energy sources, and enzymes, as well as protein factors needed for initiation, elongation, and termination of the polypeptide chain. 

Initiation, elongation, and termination (or release) factors are required for peptide synthesis. Some of these protein factors perform a catalytic function, whereas others appear to stabilize the synthetic machinery. 

The pathway of protein synthesis translates the three-letter alphabet of nucleotide sequences on mRNA into the twenty-letter alphabet of amino acids that constitute proteins. The mRNA is translated from its 5 -end to its 3 -end, producing a protein synthesized from its amino-terminal end to its carboxyl-terminal end. Prokaryotic mRNAs often have several coding regions, that is, they are polycistronic (see p. 420). Each coding region has its own initiation codon and produces a separate species of polypeptide. In contrast, each eukaryotic mRNA codes for only one polypeptide chain, that is, it is monocistronic. The process of translation is divided into three separate steps initiation, elongation, and termination. The polypeptide chains produced may be modified by posttranslational modification. Eukaryotic protein synthesis resembles that of prokaryotes in most details. [Note Individual differences are mentioned in the text.]... 

Requirements include all the amino acids that eventually appear in the finished protein, at least one specific type of tRNA for each amino acid, one aminoacyl-tRNA synthetase for each amino acid, the mRNA coding for the protein to be synthesized, fully competent ribosomes, protein factors needed for initiation, elongation, and termination of protein synthesis, and ATP and GTP as energy sources. 

RNA interacts with specific G proteins known as initiation, elongation, and termination factors. 

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