Site eucaryotic

Figure 9.1 The transcriptional elements of a eucaryotic structural gene extend over a large region of DNA. The regulatory sequences can be divided into three main regions (1) the basal promoter elements such as the TATA box, (2) the promoter proximal elements close to the initiation site, and (3) distal enhancer elements far from the initiation site.

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. 

The two homologous repeats, each of 88 amino acids, at both ends of the TBP DNA-binding domain form two stmcturally very similar motifs. The two motifs each comprise an antiparallel p sheet of five strands and two helices (Figure 9.4). These two motifs are joined together by a short loop to make a 10-stranded p sheet which forms a saddle-shaped molecule. The loops that connect p strands 2 and 3 of each motif can be visualized as the stirmps of this molecular saddle. The underside of the saddle forms a concave surface built up by the central eight strands of the p sheet (see Figure 9.4a). Side chains from this side of the P sheet, as well as residues from the stirrups, form the DNA-binding site. No a helices are involved in the interaction area, in contrast to the situation in most other eucaryotic transcription factors (see below). 

Cis-acting DNA elements can he near the start site of transcription or be quite distanced from it. Fmthermore, there are examples among eucaryotes in which the cis element is foimd within the transcribed region. If the cis element is located far from the site of action and its effect is also orientation-independent, then it is termed an enhancer. Fmthermore, one frequently observes in eucaryotes so called composite control regions which contain various cis elements. In this case, several transcription factors act cooperatively in the initiation of transcription. Examples for such cooperative effects are observed among the genes controlled by nuclear receptors. 

Procaryotes and eucaryotes differ decisively in the structure of the transcription start site and the complexity of the transcription appartus. For a better understanding we want to briefly summarize procaryotic transcription and then contrast it to eucaryotic transcription (review Eick and Heumarm, 1994). 

Fig. 1.30. Structure of a typical eucaryotic transcription start site. Enhancer elements and UAS elements (UAS upstream activating sequences) are binding sites for positive and negative regulatory DNA-binding proteins. The TATA box is the binding site for the TATA box binding protein (TBP) and serves to position the RNA polymerase holoenzyme on the promoter. For promoters that do not possess a TATA box, this function is fulfilled by an initiator region.

In higher eucaryotes the 3 -end of matme mRNA is not produced as a result of termination of transcription. Rather, the 3 -end of the primary transcript is cut at a specific site and a poly-A sequence is appended. Polyadenylation precedes the splicing of the primary transcript. 

A main control of DNA replication occurs at the level of initiation of replication. The replication of a DNA sequence starts at specific sequence sections of the DNA, known as replication origins. In yeast, the initiation sites of DNA replication have been very well defined and characterized at the sequence level. In higher eucaryotes, in contrast, initiation has a broad initiation zone and it has not been possible to identify a defined initiation sequence. The size of the genome in eucaryotes necessitates the use of many replication origins, which can be activated in a defined time sequence and position-specific order. 

The terminal oligosaccharide structures (glycans) in glycoconjugates which are associated with the eucaryotic cell represent specific contact and recognition sites for other cells, microorganisms, viruses, proteins, hormones and toxins. 

Aebi, M., Hornig, H., and Weissman, C. 1987. 5 Cleavage site in eucaryotic pre-mRNA splicing is determined by the overall 5 splice region, not by the conserved 5" GU. Cell 50, 237-246. 

Directly beneath the ceU wall is a membrane called the cytoplasmic membrane that surrounds the cytoplasm. In the eucaryotes, an organelle caUed mitochondrion, and, in the photosynthetic eucaryotes, an organeUe caUed chloroplast are the sites for the electron-tranport and the respiratory enzyme systems. The bacteria do not have the mitochondrion nor the chloroplast, but the functions of these organelles are embedded within the sites in the cytoplasmic membrane. The cytoplasm is the Uving material which the cell is composed of, minus the nucleus. 

Chloroplast—The site for the electron-tranport and the respiratory enzyme systems in photosynthetic eucaryotes. 

In eucaryotic cells, glycolysis, gluconeogenesis and fatty acid synthesis takes place in the cytosol, while the Krebs cycle is isolated within mitochondria glycogen is made in glycogen granules, lipid is synthesized in the endoplasmic reticulum and lysosomes carry on a variety of hydrolytic activities. As in procaryotic cells, ribosomes in the cytosol are the site of protein synthesis. 

Table 1. Sites of Methylation on Procaryotic and Eucaryotic Proteins...

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