Promoter polymerase

Furthermore, no, np, nop, and hm stand for the free promoters, polymerase, polymerase-promoter closed complex, and RNA molecule counts. 

The newly introduced variables are R, which represents a repressor molecule Dr, that stands for the promoter-repressor complex Drr, which corresponds to the promoter-polymerase-repressor complex hr, hdr, hopr, representing the corresponding molecular counts and and k, the association and dissociation rate constants for the binding and unbinding of the repressor to its corresponding site on the promoter. 

The lysis-lysogeny decision depends upon which of the two promoters in the operator region is able to bind polymerase, and that, in turn, depends upon the binding of the Cro and repressor proteins to three binding sites—ORl, OR2, and OR3—in OR. These binding sites are situated in the middle of the operator in such a way that ORl and OR2 overlap the promoter... 

Cro, by contrast, acts purely as a repressor. When it is bound to its high-affinity site at OR3, it prevents repressor synthesis by obstructing the access of polymerase to the left-hand promoter. In the absence of repressor, RNA polymerase can bind to the Cro promoter, and Cro can be synthesized along with the early phage genes to its right. 

The DNA part of each control module can be divided into three main regions, the core or basal promoter elements, the promoter proximal elements and the distal enhancer elements (Figure 9.1). The best characterized core promoter element is the TATA box, a DNA sequence that is rich in A-T base pairs and located 25 base pairs upstream of the transcription start site. The TATA box is recognized by one of the basal transcription factors, the TATA box-binding protein, TBP, which is part of a multisubunit complex called TFIID. This complex in combination with RNA polymerase 11 and other basal transcription factors such as TFIIA and TFIIB form a preinitiation complex for transcription. 

Figure 9.2 Schematic model for transcriptional activation. The TATA box-binding protein, which bends the DNA upon binding to the TATA box, binds to RNA polymerase and a number of associated proteins to form the preinitiation complex. This complex interacts with different specific transcription factors that bind to promoter proximal elements and enhancer elements.

The general transcription factor TFllD is believed to be the key link between specific transcription factors and the general preinitiation complex. However, the purification and molecular characterization of TFllD from higher eucaryotes have been hampered by its instability and heterogeneity. All preparations of TFllD contain the TATA box-binding protein in combination with a variety of different proteins called TBP-associated factors, TAFs. When the preinitiation complex has been assembled, strand separation of the DNA duplex occurs at the transcription start site, and RNA polymerase II is released from the promoter to initiate transcription. However, TFIID can remain bound to the core promoter and support rapid reinitiation of transcription by recruiting another molecule of RNA polymerase. 

A vector for in vitro expression of DNA inserts as RNA transcripts can be constructed by putting a highly efficient promoter adjacent to a versatile cloning site. Figure 13.15 depicts such an expression vector. Linearized recombinant vector DNA is transcribed in vitro using SPG RNA polymerase. Large amounts of RNA product can be obtained in this manner if radioactive ribonucleotides are used as substrates, labeled RNA molecules useful as probes are made. 

FIGURE 13.15 Expression vectors carrying the promoter recognized by the RNA polymerase of bacteriophage SPG are useful for making RNA transcripts in vitro. SPG RNA polymerase works efficiently in vitro and recognizes its specific promoter with high specificity. 

These vectors typically have a polylinker adjacent to the SPG promoter. Successive rounds of transcription initiated by SPG RNA polymerase at its promoter lead to the production of multiple RNA copies of any DNA inserted at the polylinker. Before transcription is initiated, the circular expression vector is linearized by a single cleavage at or near the end of the insert so that transcription terminates at a fixed point. 

The conversion of the information in DNA into proteins begins in the nucleus of cells with the synthesis of mRNA by transcription of DNA. In bacteria, the process begins when RNA polymerase recognizes and binds to a promoter... 

The gene promoter is a nucleotide sequence in DNA near the start of a gene, consisting of regulatory elements to which transcription factors and RNA polymerase bind. This leads to activation of the gene promoter and transcription of the corresponding gene. 

General or basic transcription factors are required for every gene to allow the proper recruitment of RNA polymerases to ensure transcriptional activity. They bind to core promoters in the vicinity of transcriptional start sites in a sequential manner. 

Consensus sequence in the promoter region of many eukaryotic genes that bind a general transcription factor and hence specifies the position where transcription is initiated by the RNA polymerase. 

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