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BIO2093_DMS4_sequence_similarity
BIO2093_DMS4_sequence_similarity

... • A protein family is a group of evolutionarilyrelated proteins. • Members of a protein family have similar threedimensional structures, functions and sequence similarity. • Families can include proteins with the same function in different organisms (orthologues). • Can also include members of multi ...
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Homology among (βα) 8 Barrels: Implications for the Evolution of

... barrel-like enzymes, and used this to infer homology. The signi®cance of these ®ndings, and how likely they were to have arisen by chance, is dif®cult to assess. The SCOP protein structure database (Murzin et al., 1995) currently distinguishes 23 superfamilies of TIM barrel, where the members of a s ...
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... been treated in numerous journal papers, books, and pamphlets published by national and international organizations. The three recent reviews (Lin and Tanaka 2006; Hahn-H€agerdahl et al. 2006; Lynd et al. 2008) give short, but well-balanced accounts of the prospects of ethanol production, technologi ...
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Amino acid synthesis

Amino acid synthesis is the set of biochemical processes (metabolic pathways) by which the various amino acids are produced from other compounds. The substrates for these processes are various compounds in the organism's diet or growth media. Not all organisms are able to synthesise all amino acids. Humans are excellent example of this, since humans can only synthesise 11 of the 20 standard amino acids (aka non-essential amino acid), and in time of accelerated growth, arginine, can be considered an essential amino acid.A fundamental problem for biological systems is to obtain nitrogen in an easily usable form. This problem is solved by certain microorganisms capable of reducing the inert N≡N molecule (nitrogen gas) to two molecules of ammonia in one of the most remarkable reactions in biochemistry. Ammonia is the source of nitrogen for all the amino acids. The carbon backbones come from the glycolytic pathway, the pentose phosphate pathway, or the citric acid cycle.In amino acid production, one encounters an important problem in biosynthesis, namely stereochemical control. Because all amino acids except glycine are chiral, biosynthetic pathways must generate the correct isomer with high fidelity. In each of the 19 pathways for the generation of chiral amino acids, the stereochemistry at the α-carbon atom is established by a transamination reaction that involves pyridoxal phosphate. Almost all the transaminases that catalyze these reactions descend from a common ancestor, illustrating once again that effective solutions to biochemical problems are retained throughout evolution.Biosynthetic pathways are often highly regulated such that building-blocks are synthesized only when supplies are low. Very often, a high concentration of the final product of a pathway inhibits the activity of enzymes that function early in the pathway. Often present are allosteric enzymes capable of sensing and responding to concentrations of regulatory species. These enzymes are similar in functional properties to aspartate transcarbamoylase and its regulators. Feedback and allosteric mechanisms ensure that all twenty amino acids are maintained in sufficient amounts for protein synthesis and other processes.
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