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Chapter

Cover Biochemistry and Molecular Biology

Mechanisms of metabolic control and their applications to metabolic integration  

This chapter highlights metabolic pathways that must be regulated to avoid futile substrate cycling. It determines how enzyme activities may be controlled by changing the amount of enzyme or by changing the rate of catalysis of enzymes. Control points in metabolic pathways usually occur at irreversible steps in which the forward and backward reactions can be separately controlled. The chapter cites allosteric control, which is a powerful concept essential for cells to exist. Allosteric enzymes are multisub-unit proteins which contain allosteric sites to which molecules attach and affect the activity. The chapter notes the effect of substrate concentration on reaction rates which is sigmoidal rather than hyperbolic.

Chapter

Cover Thrive in Biochemistry and Molecular Biology

Integration of mammalian metabolism  

This chapter explores the integration of mammalian metabolism. All metabolic pathways are coordinated to meet the needs of the whole body as they vary with changes in exercise and nutrition. The chapter then looks at the key organs, metabolites, and hormones in metabolic integration. It also considers the key aspects of fuel utilization. Finally, the chapter highlights the principles of hormone signalling in metabolism. There are two main classes of receptors: G-protein-coupled receptors (GPCR) and receptor tyrosine kinases (RTKs). Receptor activation stimulates production of second messengers — diffusible molecules inside the cell which transmit the signal to intracellular components. Often a cascade of protein kinases amplifies the effect of a few activated receptor molecules by phosphorylating downstream target proteins.

Chapter

Cover Chemical Aspects of Biosynthesis

Ecological chemistry  

This chapter reviews the use of secondary metabolites as mediators of interactions between organisms and the identification of inter- and intra-species interactions known as ecological chemistry. It assesses speculation on the origins of the main secondary metabolic pathways wherein secondary metabolites that are produced by plants and insects arose in response to the continually changing interactions that occur between species. It also discusses how plants and insects have been co-evolving for millions of years. This resulted in plants developing biosynthetic pathways that produce toxic or distasteful compounds. The chapter mentions how insects have devised means of overcoming the defences of plants, even using their deterrent chemicals for their own purposes. It notes subtle changes in the levels of particular enzymes. These alter the structure or quantity of a secondary metabolite and lead to an improvement in the survival prospects of the producer species.

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 Thrive in Biochemistry and Molecular Biology

Mammalian metabolic pathways  

This chapter addresses the mammalian metabolic pathways. It begins by explaining catabolism and anabolism. Catabolism is the breakdown of organic molecules to release energy in a usable form of ATP. ATP acts as an energy 'currency' in the cell and it is not stored in the cell. Meanwhile, anabolism is the biosynthesis of complex molecules using energy, usually in form of ATP. The chapter then looks at glucose breakdown and synthesis; the tricarboxylic acid (TCA) cycle; and oxidative phosphorylation. It also considers the breakdown and synthesis of glycogen, lipid, ketone body, and amino acid. Finally, the chapter examines the pentose phosphate pathway, as well as lactate and ethanol metabolism.

Chapter

Cover Biochemistry

Metabolism: Transforming Energy and Biomolecules  

This chapter evaluates the process of metabolism. Although there are many different sets of reactions, or metabolic pathways, involved here, only a small number are fundamental to all cells. The chapter focuses on two metabolic pathways that are particularly well understood by biochemists because of their importance for life: aerobic respiration and photosynthesis. To appreciate cellular metabolism, it is important to understand how energy is transferred between different molecules and converted to different forms. Moving and transforming energy is fundamental to how cells function, and the biochemists that study this topic describe it as bioenergetics. One of the key theoretical concepts that is particularly useful for understanding this biochemical topic is 'free energy'. This concept helps identify whether biochemical reactions are favourable or not. The chapter looks at adenosine triphosphate (ATP), as well as endosymbiosis.

Book

Cover Introduction to Bioinformatics

Arthur M. Lesk

Introduction to Bioinformatics starts off by introducing the topic. It then looks at genetics and genomes. It moves on to consider the panorama of life. The text also considers alignments and phylogenetic trees. There is a chapter on structural bioinformatics and drug discovery. The text also examines scientific publications and archives, particularly media, content, access, and presentation. Artificial intelligence is considered as well, in addition to machine learning. There is an introduction to systems biology that follows towards the end. The book's final chapters look at metabolic pathways and control of organization.

Chapter

Cover Molecular Biology of Cancer

Reprogrammed metabolism and diet  

This chapter highlights the role of diet in cancer prevention and causation. It explores our understanding that some food constituents exert their cancer-relevant effects by their ability to regulate gene expression: a paradigm of how environmental factors work together with genes, rather than the concept of environment versus genes. The chapter also describes the new therapeutic approaches that exploit our knowledge of reprogrammed metabolism and the molecular mechanisms of food constituents. The chapter then shifts to demonstrate the preventative factors of diet and causative factors of diet. It also investigates the link between nutrients, cancer, and hormone action. Next, the chapter addresses the drug strategies that target metabolic pathways. It also considers “enhanced” foods and dietary supplements for chemoprevention.

Chapter

Cover An Introduction to Medicinal Chemistry

Anticancer agents  

This chapter introduces cancer cells which have defects in the normal regulatory controls governing cell growth and division. These arise from mutations resulting in the activation of oncogenes and the inactivation of tumour suppression genes. The chapter describes defects in signalling pathways that are commonly found in cancer cells, stimulating cell growth and division that are a result of the overproduction of a crucial protein in the pathway or the production of an abnormal protein. It also shows how the production of regulatory proteins that suppress cell growth and division is suppressed in many cancers. The chapter talks about cancer cells which can have intrinsic or acquired resistance to anticancer drugs. It explains how resistance may be due to poor uptake of the drug, increased production of the target protein, mutations that prevent the drug binding to its target, alternative metabolic pathways, or efflux systems that expel drugs from the cell.