Protein sequences control

If a monoclonal antibody was generated by immunization with a full-length native protein rather than a peptide, then the immunized mouse will generate antibodies that recognize both linear and conformationally dependent epitopes. Only a small subset of these monoclonal antibodies will likely be useful for clinical use on formalin-fixed, paraffin-embedded tissue (FFPE) samples. Those that are useful tend to have epitopes that are linear the epitopes are not dependent on the protein s three-dimensional conformation (see Chapter 16). Therefore, for antibodies generated in response to immunization with full-length proteins, the peptides that serve as positive controls will be linear stretches of amino acids derived from the native protein sequence, as listed in protein databases. 

An extensive variety of neuromuscular diseases have been uncovered as congenital conditions involving not only the nAChR and AChE but also proteins that control their expression and synaptic localization. These are discussed in Ch. 43. Study of the underlying genotype or sequence differences has also proved helpful in unraveling the involvement of various amino acid residue determinants in function [41]. 

The X-ray structures of other aconitases have appeared in the literature. Recently, the crystal structure of human iron regulatory protein, IRPl, in its aconitase form, has been published. Iron regulatory proteins (IRPs) control the translation of proteins involved in iron uptake, storage, and utilization by binding to specific noncoding sequences of the corresponding mRNAs known... 

The principle means by which the activity of sequence-specific DNA-binding proteins is controlled have aheady been presented in section 1.2. The importance of these mechanisms for regulation in eucaryotes will be discussed below. Altogether, the demands on eucaryotic organisms with regard to the regulation of transcription activity are much more complex than for procaryotes. This tenet holds for the structure of the transcription apparatus as well as for the mechanism of transcription regulation. 

DNA contains numerous other protein binding sites which are not palindromes but whose sequences represent additional encoded information. The RNA transcripts likewise contain sequences that direct the catalytic machinery involved in splicing, that bind to ribosomal proteins, that control rates of transcription, and that cause termination of transcription. 

Carboxyl groups of certain glutamate side chains in proteins that control bacterial chemotaxis are methylated reversibly to form methyl esters.130 This carboxylmethylation occurs as part of a reaction sequence by which the bacteria sense compounds that can serve as food or that indicate the presence of food... 

Fig. 1. CAT activities in seeds of transgenic tobacco plants containing hs promoter-CAT constructs. A, Schematic structure of chimaeric genes introduced into tobacco. Details of the construction are described by Schoffl et al. (1989,1991). HSE sequences with the consensus C-GAA-TTC-G are symbolised by boxes the synthetic HSE2 is represented by two overlapping soybean HSEs. The CaMV promoter is a truncated silent version of the 35S promoter, providing only the TATA box and the transcription start site. B, CAT assays were performed as described by Schoffl et al. (1989), using 50 pg protein from seed extracts and 10 jig from leaf extracts. Dry seeds (ds) without imbibition and 20 h imbibed seeds (is), derived from the same plant, were used. Heat treatment (hs) was carried out for 2h at 40 °C prior to protein extraction. Control extracts (c) were prepared from leaves incubated at 25 °C. cm, WC-chloramphenicol acm, acetylated form of cm.

Plasmids for bacterial expression of proteins with N- or C-terminal Cys-tag have been described previously (1). They were made by inserting the coding sequence for Cys-tag (Lys-Glu-Ser-Cys-Ala-Lys-Lys-Phe-Gln-Arg-Gln-His-Met-Asp-Ser) and a Ser-Gly linker in the appropriate sites in the commercially available pET29 plasmid for bacterial expression of proteins under control of T7 promoter (Novagen, WI). So far, expression of Cys-tagged proteins in insect, yeast, or mammalian hosts has not been tested. 

A complete sequence of DNA bases, or chromosome, encodes instructions including those required by a complex supramolecular protein assembly, the ribosome, to form the extensive proteins that control much of biological structure and... 

Besides having a much lower molar mass than DNA, RNA generally forms only single-strand helices. RNA is often found associated with proteins inside cells. The most prevalent bases in RNA are the same as those in DNA, except that uracil is present instead of thymine. Three common types of RNA are ribosomal (rRNA), transfer (tRNA), and messenger RNA (mRNA). They are all involved in protein synthesis, controlling the sequence of amino acids that make up the primary structure. Thus the base sequence in RNA is related to the amino acid sequence in the protein that is made from it. 

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