Amino acids overview

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

In bacteria, each step in fatty-acid sjmthesis is catalyzed by separate enzymes. In vertebrates, however, fatty-acid synthesis is catalyzed by a large, multienzyme complex called a synthase that contains two identical subunits of 2505 amino acids each and catalyzes all steps in the pathway. An overview of fatty-acid biosynthesis is shown in Figure 29.5. 

There are numerous transmitter substances. They include the amino acids glutamate, GABA and glycine acetylcholine the monoamines dopamine, noradrenaline and serotonin the neuropeptides ATP and NO. Many neurones use not a single transmitter but two or even more, a phenomenon called cotransmission. Chemical synaptic transmission hence is diversified. The basic steps, however, are similar across all neurones, irrespective of their transmitter, with the exception of NO transmitter production and vesicular storage transmitter release postsynaptic receptor activation and transmitter inactivation. Figure 1 shows an overview. Nitrergic transmission, i.e. transmission by NO, differs from transmission by other transmitters and is not covered in this essay. 

Figure 15-4. Overview of amino acid metaboiism showing the major pathways and end products.

Figure 15-7. Intracellular location and overview of major metabolic pathways in a liver parenchymal cell. (AA —metabolism of one or more essential amino acids AA <->, metabolism of one or more nonessential amino acids.)...

Fig. 1. Schematic overview of Aspergillus niger pectin lyase genes pel A to pelF aa, amino acid m.p. mature protein.

Polybasic carboxylic hydroxy and amino acid aided synthetic routes directed towards obtaining mixed inorganic materials, especially for battery and fuel cell applications, are overviewed. It has been shown that, in spite of enormous number of papers on the subject, significant efforts should be undertaken in order to understand the basic principles of these routes. Possible influence of the structure of reactants employed in the process (acids, poly hydroxy alcohols, metal salts) is put forward, and some directions of future work in the field are outlined. 

J. Robins, M. Jones, E. Matisoo Smith, Amino Acid Racemization Dating in New Zealand An Overview, Auckland University (2001). 

Table 10.1 Overview of some polypeptide growth factors. Many can be grouped into families on the basis of amino acid sequence homology, or the cell types affected. Most growth factors are produced by more than one cell type and display endocrine, paracrine or autocrine effects on target cells by interacting with specific cell surface receptors...

Figure 12.9 Overview of the production of Refludan (recombinant hirudin). The exact details of many steps remain confidential for obvious commercial reasons. A number of QC checks are carried out on the final product to confirm the product s structure. These include amino acid composition, HPLC analysis and peptide mapping...

An overview of some of the processes involved in synaptic transmission is shown in Figure 10-1. Many of the processes are discussed below or in other chapters of this book. Many different types of substance are neurotransmitters. Classical neurotransmitters, such as ACh (see Ch. 11) and norepinephrine (NE see Ch. 12), are low-molecular-weight substances that have no other function but to serve as neurotransmitters. The predominant excitatory neurotransmitter in the brain, glutamate, and the inhibitory neurotransmitter in the spinal cord, glycine, are common and essential amino acids (see Chs 15 and 16). 

It is clear that in this brief overview of molecular biology, we have not covered a number of important areas that have an important impact on the study of metalloproteins. These include molecular cloning and recombinant DNA technology, which allow proteins to be over-expressed and individual amino acids to be mutated to any other of the 19 protein amino acids genome and proteome analysis that enables the sequences of all the genes of the entire organisms to be determined, and the quantification, localization, interactions and, where possible, activities and identification of all of the proteins in an organism,... 

Electrophoresis as a method of study of molecular differences has its limitations. It can demonstrate variation of the primary structure only if it changes migration in the electric field, which is the case only for a fraction (about one third) of the conceivable variants the others are electrophoretically silent. On the other hand, different amino acid replacements may cause the same electrophoretic variant and thus be indistinguishable. Furthermore, the whole method was applicable only to selected types of proteins and could not yield a genetically satisfactory overview. 

From these six intermediates, only three end-products are produced carbon dioxide, glucose or fat, and the first two are quantitatively the most important. A simple overview of these processes is given in Figure 8.7. (The details of the reactions that convert the individual amino acids to one of the intermediates are given in Appendix 8.3.)... 

Figure 21.24 An overview of amino acid metabolism, particularly amino acid metabolism, in a patient suffering from cancer. The tumour acts as a sink for glucose, amino acids and glutamine. As tumour grows in size, the sink is exaggerated and cachexia develops. This diagram can be considered with that in Figure 21.22 in order to include fatty acids in tumour metabolism. Note the thicker line to indicate magnitude of release of glutamine by muscle.

A large number of metabolic pathways are available for amino acid degradation, and an overview of these is presented here. Further details are given on pp. 414 and 415. 

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