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Chapter

Cover Introduction to Bioinformatics

Metabolic pathways  

This chapter explores metabolic pathways, which are the road maps defining the possible transformations of metabolites. They form a network, representable as a graph, usually with the metabolites as nodes, and reactions connecting them as edges. The enzyme that catalyses each reaction labels the edge. The chapter then looks at the defining principles of the Enzyme Commission and the Gene Ontology ConsortiumTM classifications of the functions of biological molecules. It considers the importance of accurate annotation of enzyme function in databases, before outlining the databases of metabolic networks. The chapter also discusses the physicochemical basis of enzymatic catalysis, and the quantities needed to characterize their kinetics. Finally, it examines how the algorithms for comparison of nucleic acid and amino acid sequences can be generalized to compare and align metabolic pathways.

Chapter

Cover Introduction to Genomics

Metabolomics  

This chapter expounds on metabolomics, which is focused on metabolites, that is, molecules undergoing a transformation in a biological system. The chapter notes that the metabolic networks of any organism correspond to graphs with metabolites as nodes and linking reactions as edges. It highlights the defining principles of the Enzyme Commission and the Gene Ontology Consortium classifications of the functions of biological molecules. It mentions the significance of accurate enzyme function annotations in databases of metabolic networks. The chapter also considers the ways in which metabolic pathways differ between species. It points out the physicochemical basis of enzymatic catalysis and the quantities needed to characterize enzyme kinetics—information needed to consider modelling flows through metabolic networks. It also talks about the difficulties in modelling the metabolic networks' traffic patterns.

Chapter

Cover Protein Science

Protein Function  

This chapter evaluates the wide variety of ways that proteins support the structures and life processes of viruses, cells, and organisms. It begins by looking at structural proteins, enzymes and enzyme kinetics, and antibodies. The chapter then considers transmembrane transport proteins—including channels, gates, and pumps—and receptors, all embedded in the general phospholipid bilayer membrane structure. Finally, it studies the role of transmembrane proton gradients in the electron transport chain and adenosine triphosphate (ATP) synthesis. Two catalogues of protein function are available. The first is the Enzyme Commission classification, which covers only catalytic functions. It has been extended by the Gene Ontology classification, devised in 2000 in connection with the task of annotating the Drosophila melanogaster genome.