Repeated sequences characterization

Several collagen types do not form fibrils in tissues (Table 48—2). They are characterized by interruptions of the triple hehx with stretches of protein lacking Gly-X-Y repeat sequences. These non-Gly-X-Y sequences result in areas of globular structure interspersed in the triple hehcal structure. 

As a second messenger, DAG is rapidly metabolized under normal conditions, and the predominant route is via phosphorylation to PA, a reaction catalyzed by DAG kinase, for which multiple forms of 64-140 kDa have been identified and characterized. All possess a C-terminal catalytic domain and two or three cysteine-rich repeat sequences. The a, 3 and y forms possess E-F hands and are thus likely to be regulated by changes in the concentration of cytosolic Ca2+. Expression of the mRNA for the a, P, y, C, and 0 forms of DAG kinase appears to be highest in the brain. Once DAG is phosphorylated to PA, this in turn can be converted into PI via CDP-DAG (Fig. 20-2B). 

Helical heptad repeat sequences have been reported to be well behaved although they are difficult to characterize by NMR spectroscopy due to spectral overlap. The motifs that have been shown to have native-like properties, and are not highly repetitive, have cores composed of aromatic amino acid side chains of, for example, phenylalanine and tryptophan. In four-helix bundle motifs [1, 2], the /1/la-motif BBAl [5] and the /1-sheet protein Betanova [9], the formation of the folded structure appears to be strongly dependent on such residues although the energetics have not been calculated by substitution studies. As a tentative rule, therefore, the probability of success in the design of a new protein is probably much higher if residues are included that can form aromatic clusters in the core (Fig. 5). 

Telomeres (Greek telos, end ) are sequences at the ends of eukaryotic chromosomes that help stabilize the chromosome. The best-characterized telomeres are those of the simpler eukaryotes. Yeast telomeres end with about 100 bp of imprecisely repeated sequences of the form... 

Studies of overall genome composition based on reassociation kinetics (Simpson et ai, 1982 Cox et ai, 1990 Marx et a/., 2000) and analysis of fully sequenced bacterial artificial chromosome (BAC) clones from the 5. mansoni genome project show that platyhelminth genomes contain abundant highly and moderately repetitive sequence (Fig. 2.1). Much of the repetitive DNA comprises two classes of integrated mobile elements class I elements, which include long terminal repeat (LTR) retrotransposons and retroviruses, non-LTR retro-transposons and short interspersed nuclear elements (SINES) and transpose via an RNA intermediate, and class II elements (trans-posons), which transpose as DNA (Brindley et ai, 2003). Additionally, small dispersed or tandemly repeated sequences are common. A wide variety of these sequences have been isolated and characterized from a variety of taxa (Table 2.4). 

All of the mammalian transposable elements that have been characterized to date seem to be the result of transpositions that proceeded through an RNA intermediate. This process is known as retrotransposition or retroposition. Three classes of these retrotransposable elements are known in mammals (1) SINEs, or short interspersed repeated sequences such as the human Alu family and rodent Bl (2) LINEs, or long interspersed repeated sequences such as LI in a variety of mammalian species and (3) retrovirus-like elements, such as THE 1 in humans and mys and IAP in rodents. Retrovirus-like elements have long terminal repeats (LTRs) that often surround two open reading frames (ORFs) like those of retroviruses, but they lack the ability to leave one cell and enter another. LINEs also have two ORFs, but have no LTRs. SINEs have no LTRs and no ORFs. Transposition of all of these elements must involve reverse transcription of the RNA intermediate in some cases the required reverse transcriptase is apparently encoded by the element itself. 

Sequencing has shown that the repeated sequences are insertion sequences similar to those widely distributed in the bactena and in eucarya. The first of these characterized was ISHl, an insertion in the bacteriorhodopsin gene of Halobacterium halobium S9. The... 

More than 10% of all proteins contain sets of two or more domains that are similar to one another. The afore-described sequence search methods can often detect internally repeated sequences that have been characterized in other proteins. Where repeated units do not correspond to previously identified domains, their presence can be detected by attempting to align a given sequence with itself. 

Third, strict isochores cannot exist in any natural DNA (i) because coding sequences are made up of codons, in which the compositions of the three positions are correlated with each other (D Onofrio and Bernardi, 1992) (ii) because non-coding sequences are com-positionally correlated with the coding sequences that they embed (Bernardi et al., 1985b Clay et al., 1996 see Chapter 3 below) and (iii) because interspersed repeats are characterized by their own specific sequences. More detailed discussions of this problem were presented by Clay and Bernardi (2001a,b), Clay et al. (2001) and Clay (2001). 

When many monosaccharides are linked together, the result is a polysaccharide. Polysaccharides that occur in organisms are usually composed of a very few types of monosaccharide components. A polymer that consists of only one type of monosaccharide is a homopolysaccharide a polymer that consists of more than one type of monosaccharide is a heteropolysaccharide. Glucose is the most common monomer. When there is more than one type of monomer, frequently only two types of molecules occur in a repeating sequence. A complete characterization of a polysaccharide includes specification of which monomers are present and, if necessary, the sequence of monomers. It also requires that the type... 

All wheat prolamins are characterized by the presence of repeated sequences. These are rich in proline and glutamine and appear to be based on similar motifs in the S-rich and S-poor groups. However, whereas these repeats are present only in the N-terminal parts of the S-rich prolamins, they account for almost the whole protein in the S-poor group. The repetitive sequences present in the HMW subunits are located in the center of the proteins, and are based on several motifs which are not related to those present in the S-rich and S-poor prolamins (Figure 13.8) [21, 22]. 

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