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Chapter

Cover Molecular Biology

The chemical basis of life  

This chapter discusses how enzymes catalyse chemical reactions and how enzyme activity is regulated in the cell. The behaviour of molecules in living cells is governed by the laws of chemistry and physics. The thermodynamic and kinetic principles underlying chemical reactions in the cell can be used to describe biological processes and predict how cells will respond to different conditions. The chapter then shows how to apply these principles to understand and predict binding interactions and enzyme catalysis. Enzymes catalyse reactions by lowering the activation energy barrier through a variety of strategies. These include binding preferentially to the transition state of the chemical reaction and binding simultaneously to two substrates, orienting them favourably for reaction. Many enzymatic reactions obey Michaelis–Menten kinetics.

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.