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Book

Cover Carbohydrate Chemistry

Benjamin G. Davis and Antony J. Fairbanks

Carbohydrate Chemistry argues that carbohydrates are a vital part not only of metabolism, but are implicated as key coding molecules in a host of subtle biological events. The exploration of the role and the manipulation of this wonderful class of molecules is an exciting and ever-changing field. This text aims to remove some of the mystery that often surrounds carbohydrate chemistry, by highlighting and summarizing some of the central principles and ideas and by illustrating them with both classical and state-of-the-art examples.

Chapter

Cover Pharmaceutical Chemistry

Stereochemistry and Drug Action  

Rosaleen J. Anderson, Adam Todd, Mark Ashton, and Lauren Molyneux

This chapter mentions the forms of common analgesic ibuprofen, which have mostly identical physical properties but have three-dimensional shapes that are different. The three-dimensional shape of biological molecules and drugs is profoundly important for their action. The chapter introduces the concepts of isomerism, structure, and shape, particularly with reference to the activity of drugs and relates strongly to hybridization and bonding. The chapter defines the term ‘isomerism’, which is used to describe the ways in which molecules can have identical compositions in terms of carbon, hydrogen, and nitrogen. However, differences in their patterns of bonding or conformation may lead to dramatically different three-dimensional shapes. There are many drugs used in medicine which exhibit isomerism and it is essential to have a good understanding of this.

Chapter

Cover Biophysical Techniques

Infrared and Raman spectroscopy  

Introduction Molecules are said to undergo vibrational motion when their bonds stretch or bend. The energy of most molecular vibrations corresponds to the infrared (IR) region of the electromagnetic spectrum. Vibrations may be detected directly by measuring an IR spectrum or indirectly by...

Chapter

Cover Biochemistry

Lipids and Membranes  

This chapter describes lipids as naturally occurring water-insoluble substances that perform a stunning array of functions in living organisms. It presents some lipids that are vital energy reserves and others that are the primary structural components of biological membranes. Other lipid molecules act as hormones, antioxidants, pigments, or vital growth factors and vitamins. The chapter describes the structures and properties of the major lipid classes found in living organisms as well as the structural and functional properties of biomembranes. It also looks at the structure and function of each major type of lipid and investigates lipoproteins, complexes of protein and lipid that transport lipids in animals. It finishes with an overview of membrane structure and function.

Chapter

Cover Genetics

Transcription: Reading and Expressing Genes  

This chapter discusses the DNA sequence that comprises a gene which is expressed by the transcription of the gene into an RNA molecule. It details the regulation of transcription and describes cells with the same DNA sequence that have different appearances and functions because they transcribe different genes. It also considers transcript initiation as the key step through which gene expression can be controlled, noting that the transcription processes that are regulated by the cell are also those that have been subject to the most evolutionary variation. The chapter deals with gene expression, which is the process of transcribing a subset of the genes in a genome into RNA to mediate a biological function that differs across time and space. It looks at the processes of gene expression that provide the framework to highlight the many opportunities for control and evolutionary change.

Chapter

Cover Plant Systematics

Methods and Principles of Biological Systematics  

This chapter provides a background on biological systematics which focuses on the discovery of phylogeny and how phylogenies can be used to understand the processes underlying diversification. The chapter outlines how to determine the history of a group and discusses how this history can be used to uncover patterns of diversification and to construct a form of classification. Phylogeny can be understood as the history of DNA molecules: DNA replicates in a semi-conservative fashion to produce two daughter molecules that replicate again to produce their own two daughter molecules — a process that goes back to the beginning of life on Earth. This DNA replication process is diagrammed in phylogenetic trees to show ancestor-descendant relationships and trace the history of life. This chapter introduces these trees and analyzes the shape or topology of the trees that is determined by the connections between the branches that can be rotated around the nodes.

Chapter

Cover Molecular Biology

Biological molecules  

This chapter reviews how molecules are built up by linking atoms together with covalent bonds and explores the way in which molecules interact with one another non-covalently in the aqueous environment of the cell. There are four major classes of biological molecules that play essential roles in all organisms: nucleotides, amino acids, carbohydrates, and lipids. Each of them can be found in cells both as individual small molecules or covalently linked to form larger molecules known as polymers or macromolecules. Nucleic acids are polymers of nucleotides that are responsible for carrying genetic information. Proteins, on the other hand, are polymers of amino acids that function as workhorses, carrying out most of the chemical reactions in the cell and giving cells their structure and shape. Many biological molecules can be covalently modified in ways that alter their chemical properties and allow their function to be regulated.

Chapter

Cover The Physicochemical Basis of Pharmaceuticals

Drug Partitioning and Transport Across Biological Barriers  

This chapter addresses drug partitioning and transport across biological barriers. In order to exert a therapeutic response, drug molecules must interact with target receptors. Drug transport across biological barriers is influenced by the partitioning of the drug molecule between aqueous and lipid phases. Factors that influence the type of journey the drug molecules experience include the following: the ability of drug molecules to partition into biological fluids and tissues, the site of the target receptor, the route of administration, and the delivery system used to deliver the drug. The chapter then introduces drug–target receptor interactions, highlighting factors influencing the partitioning of drug molecules and describing the biological barriers drug molecules encounter during delivery. It explores the main transport mechanisms by which drug molecules are transported across these biological barriers.

Chapter

Cover Biochemistry and Molecular Biology

Principles of energy release from food  

This chapter explores biological oxidation, which involves the removal and transfer of electrons to another acceptor molecule. It discusses biochemical systems which commonly involve the enzymatic removal of two hydrogen atoms from a metabolite molecule. In the cell a variety of electron/hydrogen carriers exist in the transfer of electrons to oxygen. The chapter considers nicotinamide adenine dinucleotide (NAD+) as an important carrier and a dinucleotide that contains the vitamin nicotinamide, which can accept two electrons and a hydrogen atom, to form NADH. Flavin adenine dinucleotide (FAD) is of similar structure but the accepting group is the vitamin riboflavin.

Chapter

Cover Biophysical Techniques

Biological molecules  

The aim of this tutorial is to remind readers about some of the molecules of life, their nomenclature and some of their properties. Nucleic acids are made from linear chains of nucleotides (Figure T1A). Phosphate groups bridge the 3’and 5’positions of...

Book

Cover Computational Chemistry

H. Grant Guy and Richards W. Graham

Computational Chemistry starts by arguing that the uses of computers in chemistry are many and varied. This ranges from the modelling of solid state systems to the design of complex molecules which can be used as drugs. This text introduces the many methods currently used by practising computational chemists and shows the value of computers in modern chemical research. The text describes the various computational techniques available and explains how they can be applied to single molecules, to assemblies of molecules, and to molecules undergoing reaction. An introductory chapter outlines the hardware and software available, and looks at some applications and developments. Subsequent chapters cover quantum mechanics, molecular mechanics, statistical mechanics, the modelling of biomolecules, and drug design. Whilst emphasizing the use of computers to model biological systems, the chapters explain how the methods can be applied to a whole range of chemical problems.

Chapter

Cover Inorganic Chemistry in Biology

The s-block  

This chapter cites elements of groups one and two that have one s- and two s-outer electrons, which can be lost in giving the predominant +1 and +2 oxidation states. It discusses ionic bonds that predominate compounds in the elements and radii of the ions of biological relevance. It also reviews the aquated ion that includes inner shell coordination and outer shell attraction of solvent molecules. The chapter describes s-cations as generally poor complexers that require strong binding and chelating or macrocyclic ligands or proteins to form stable entities. It analyses group one and group two in terms of providing the background electrolytes for living systems.

Book

Cover Animal Physiology

Richard W. Hill, Daniel J. Cavanaugh, and Margaret Anderson

Animal Physiology is composed of six parts. Part I looks at the fundamentals of physiology including animal, environment, molecules, cells, genomics, proteomics, physiological development, and transport of solids and water. Part II covers food, energy, and temperature. It looks at topics such as nutrition, feeding, digestion, energy metabolism, aerobic and anaerobic forms of metabolism, thermal relations, and food. The next part looks at integrating systems: neurons, synapses, sensory processes, nervous system organization, biological clocks, endocrine and neuroendocrine physiology, reproduction, and integrating systems in action. The next part covers movement and muscle. Part V is about oxygen, carbon dioxide, and internal transport. The final part of the book looks into water, salts, and excretion.

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.