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Chapter

Cover Chemical Aspects of Biosynthesis

The shikimic acid pathway: biosynthesis of phenols, lignans, flavonoids, etc.  

This chapter emphasizes the pivotal importance of shikimic acid in metabolism as it is the progenitor of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. The chapter reviews the discovery of the importance of the shikimic acid which arose from the studies of mutants of the bacterium Escherichia coli. It also mentions certain mutant strains which were obtained following the exposure of the parent bacterium to ionizing radiation that grow in the presence of amino acids, para-aminobenzoic acid, and para-hydroxybenzoic acid. The chapter analyszes the bacteria possessing modified genes which could not code for the production of the enzymes needed to convert glucose into key acids. It explores the biosynthetic pathway to shikimic acid, which begins with the reaction of phosphoenol pyruvate with the four-carbon sugar erythrose-4-phosphate.

Chapter

Cover Functional Groups

Carboxylic acids and derivatives  

This chapter discusses trends in general reactions, carboxylic acids, acyl chlorides and acid anhydrides, esters, and amides. It reviews the chemistry of carboxylic acids and their derivatives. This is mostly concerned with the attack of nucleophiles. It explains that acids generally do not react in this way because they have an acidic H, but after protonation they are prone to nucleophilic attack. The chapter also demonstrates a general reaction that consists of addition and elimination and refers to a stereoelectronic factor that favours the approach of the nucleophile at 90° to the carbonyl group. The chapter describes methanoic acid as unique in being a reducing agent and the strongest acid. Other acids are resistant to oxidation. It mentions the Schmidt reaction as something that is restricted to acids in which the R group is stable to strong mineral acid.

Chapter

Cover Pharmaceutical Chemistry

Proteins and Enzymes  

Alex White and Helen Burrell

This chapter talks about proteins. These make up a highly important class of macromolecules in biochemistry and are considered to be biopolymers constructed from amino acid monomers. Compared with nucleic acids, proteins have varied and complex three-dimensional structures, due in part to the greater variety of monomers used to construct them. The chapter describes the unique three-dimensional structure of protein which is directly related to the function it performs. The chapter covers the detail of the structures, citing a myriad of functions in cells and organelles, such as antibodies, collagen, membrane-bound receptors, and enzymes. Enzymes and receptors are of particular importance to pharmacy as many drugs interact with them to bring about their therapeutic activity.

Chapter

Cover Foundations of Inorganic Chemistry

Hydrogen  

This chapter evaluates hydrogen, which is by far the most abundant element in the universe and all the other chemical elements are made from it. Without hydrogen there would be no water to drink, and DNA molecules would not form the double-helix structure that allows our genetic code to be copied and passed on to future generations. Hydrogen can form a positive ion like the metals of Group 1 but, since it is one electron short of a noble gas configuration, it can also form a negative ion and a single covalent bond, like the halogens of Group 17. Hydrogen forms compounds with many other elements but the properties of these hydrides vary considerably. The chapter then considers the self-ionization behaviour of water, which may be regarded as an acid—base reaction. It also looks at sulphuric acid and nitric acid.

Chapter

Cover Organic Chemistry

Acids and Bases  

This chapter begins by outlining definitions of acids and bases based on Johannes N. Brønsted and Gilbert N. Lewis. Substances that taste sour have long been known as acids. Bases, on the other hand, are compounds which counteract or neutralize acids. The chapter then reviews the dissociation of a Brønsted acid in aqueous solution. It also presents the two important properties of buffer solutions. First, they allow us to prepare an aqueous solution of a desired pH using a weak acid and its conjugate base (a salt of the acid). The second important property of a buffer solution is that its pH will remain approximately constant if relatively small amounts of a further acid or base are added. Next, the chapter focuses on the factors which affect acid and base strengths. It also analyzes the basicity of organic compounds and the solvent effects on acid-base reactions.

Chapter

Cover Chemistry3

Acids and bases  

This chapter describes two broader definitions of acids and bases and introduces the Brønsted–Lowry theory, in which an acid is defined as a proton donor and a base is defined as a proton acceptor. It also reviews the Lewis theory, in which an acid is defined as an electron pair acceptor and a base is defined as an electron pair donor. This is considered a wide definition as all Brønsted–Lowry acids are Lewis acids, but not all Lewis acids are Brønsted–Lowry acids. The chapter identifies the conjugate acid and conjugate base for an acid–base reaction. It details how to calculate the pH of a solution of a strong or weak acid and a strong or weak base and determine the position of an acid–base equilibrium using Ka and Kb.

Chapter

Cover Foundations of Chemical Biology

Introduction to aminoacids and proteins  

This chapter introduces proteins as biological polymers that play important roles in the chemical processes of life and represent 15% of the total cell mass. It explains the chemistry of amino acids and how their properties change when they are polymerized in a protein, which are important in the analysis of the molecular basis of the is properties of proteins. It also describes proteins as linear polymers that are derived from α-amino acid monomers, noting that α-amino acids are carboxylic acid with an amino group, a hydrogen atom, and a further substituent attached to the α-carbon. The chapter looks at the distinguishing feature of proteins as they are composed of a variety of monomer units linked together in a defined sequence. It analyses the variety of possible proteins that underpins the diverse roles for which they are suited.

Chapter

Cover Making the Transition to University Chemistry

Acid–base Equilibrium  

This chapter explains the acid-base equilibrium. This involves the transfer of protons in line with the Brønsted–Lowry theory. A strong acid or strong base is fully ionized in an aqueous solution, while weak acids or bases are only partially ionized in an aqueous solution. Acid-base titrations measure the unknown concentration of one solution by reaction with another standard solution with a familiar concentration. The chapter also notes how indicators are typically water-soluble weak organic acids with varying colours at different pH values. It explores the alternative theory of acid-base reactions proposed by Gilbert Lewis: a Lewis acid is an electron-pair acceptor, while a Lewis base is an electron-pair donor.

Chapter

Cover Organic Chemistry

Nucleophilic Substitution Reactions of Carboxylic Acid Derivatives  

Tadashi Okusecyama and Howard Maskill

This chapter concentrates on the interconversions of carboxylic acid derivatives, which generally take place by nucleophilic substitution via addition-elimination mechanisms. It first describes carboxylic acids which contain a carboxy functional group (a carbonyl with a hydroxy group attached) bonded to an alkyl residue. Carboxylic acid derivatives, on the other hand, are obtained by replacing the hydroxy with another group bonded through O, N, S, or halogen. This class of compounds includes esters (Y = OR'), anhydrides (Y = OCOR'), amides (Y = NR' 2), and acyl halides (Y = halogen). The chapter argues that all carboxylic acid derivatives can be converted back to carboxylic acids by hydrolysis. Next, the chapter considers relative reactivities of carboxylic acid derivatives and the acid-base catalysis.

Chapter

Cover Chemical Aspects of Biosynthesis

Fatty acids and derivatives  

This chapter deals with glycerides. These provide an energy store as they can be broken down to acetate and used for biosynthesis or fed into the citric acid cycle for the construction of other small building blocks. The chapter discusses the oleic acid that is produced by many species of Compositae. This has an anti-microbial function, while the arachidonic acid is produced by the broad bean in response to stress and has an antifungal function. The chapter also describes arachidonic acid as the biosynthetic precursor of a large family of metabolites known as eicosanoids. The chapter mentions the biosynthesis of fatty acids. These are under the control of enzymes called fatty acid synthases. It analyszes bacterial synthases that compromise aggregates of six or seven discrete enzymes.

Chapter

Cover Foundations of Organic Chemistry

Acids and bases  

This chapter examines acids and bases. The Brønsted–Lowry theory states that acids are proton donors, and bases are proton acceptors. Acid/base reactions are largely equilibria and are therefore under thermodynamic control. Many organic acids, such as ethanoic acid, are weak acids. The equilibrium constants are small, much less than 1, and remarkably little of the acid donates its proton to water in aqueous solution. Moreover, many organic acids and bases are largely insoluble in water. The chapter then considers the reactivity of bases as leaving groups and nucleophiles, before comparing acid strengths and base strengths. It also looks at amino acids, which are the building blocks of proteins; they are compounds which have major structural and catalytic roles in all living organisms.

Chapter

Cover Aquatic Environmental Chemistry

The acidity of water  

This chapter examines the acidity of natural water, which depends on the nature of material dissolved in it and its interaction with other materials such as the rocks, the organisms living in it, and added pollutants. Rivers and lakes in granite areas, for example, are unable to neutralize any added acidity and are therefore highly susceptible to the effects of acid rain. Significant increases in the acidity of these water bodies produces an environment which is not well suited to life for a number of reasons. Firstly, most organisms are not well adapted to acidic conditions or changes in acidity. In addition, acidification leads to the dissolution of a number of toxic elements which can poison flora and fauna. In limestone areas, however, the water can neutralize moderate quantities of added acid. The chapter then considers the chemical nature of water, before studying polyprotic acids and the solubility of gases.

Chapter

Cover Core Carbonyl Chemistry

Reactions of nucleophiles with other carboxylic acid derivatives  

This chapter focuses on reactions of nucleophiles with other carboxylic acid derivatives. The esters which were considered in the previous chapter lie roughly in the middle of a reactivity series in which the ease of nucleophilic attack at the carbonyl carbon decreases from left to right. Thiol esters are between ordinary esters and carboxylic acid anhydrides in reactivity. The carboxylic acids themselves are the least reactive because they are converted to carboxylate complexes on which nucleophilic attack is very difficult. The chapter then looks at amides. Ammonia and amines simply form salts with carboxylic acids, and these are stable except at high temperatures. Acyl chlorides react very easily with ammonia and amines.

Chapter

Cover Pharmaceutical Chemistry

Nucleic Acids  

Alex White and Andrew Evans

This chapter discusses the varied roles of molecules and the classes of cells that form the basis of all life. It presents information on the basic structure and functions of cells and considers the molecules involved in their structure and function. The chapter outlines the chemistry of nucleic acids, which are larger than most molecules and are often referred to as macromolecules. It then reviews the principles of chemistry that can be applied to the study of these molecules to help understand their functions in the cells of a human body. In addition, the involvement of nucleic acids in the genetic code is explored. The chapter covers how it is stored, used, protected, repaired, and passed from generation to generation.

Chapter

Cover Human Virology

General properties of viruses  

This chapter describes viruses as small organisms that retain infectivity after passage through filters small enough to hold back bacteria. Bacteria are measured in terms of the micrometre (μm), which is 10-6 of a metre. For viruses, the nanometre (nm) is used as the unit, which is a thousand times smaller. The chapter points out that viruses are totally dependent on living cells, either eukaryotic or prokaryotic, for their replication and existence, and possess and carry enzymes of their own. Viruses cannot reproduce and amplify and translate into proteins the information in their genomes without the assistance of the cellular architecture and protein translation machinery, namely ribosomes. The chapter discusses viruses that possess only one species of nucleic acid, either DNA or RNA, and have a component for attaching or ‘docking’ to cells so that they can commandeer the cells as virus production factories.

Chapter

Cover Biochemistry

Nitrogen Metabolism I: Synthesis  

This chapter talks about nitrogen, which is found in a vast array of biomolecules, such as amino acids and the nitrogenous bases which are used in the synthesis of proteins and the nucleic acids. Other essential nitrogen-containing biomolecules include the porphyrins, certain membrane lipids, and a diverse group of metabolically important biomolecules that are synthesized in smaller amounts. The chapter traces nitrogen from nitrogen fixation, the process that converts inert N2 to biologically useful ammonia through the synthesis of the major nitrogen-containing biomolecules. It describes the nitrogen cycle as the biogeochemical cycle in which nitrogen atoms flow through the biosphere. Several biochemical processes convert nitrogen from one form to another.

Chapter

Cover Periodicity and the s- and p-Block Elements

Acids and bases  

This chapter focuses on acids and bases. The broadest definition of acids and bases is the Lewis definition. In this scheme, a Lewis acid is an electron-pair acceptor while a Lewis base is an electron-pair donor. Meanwhile, the Brønsted–Lowry concept is probably the second most commonly employed description of acids and bases, although in aqueous solution it is by far the most widely used. In this scheme, an acid is defined as a proton donor and a base as a proton acceptor. It is important to note that the concept of Lewis acidity and basicity incorporates the Brønsted–Lowry approach as a special case. The chapter then looks at element oxides and hydroxides, as well as the Lewis acidity of the heavier p-block elements. It also considers hard and soft acids and bases.

Chapter

Cover Biochemistry

Lipids and Proteins: The Building Blocks of a Cell  

This chapter discusses lipids and proteins, which are two of the key components of cellular life in every environment. Lipids are essential components of cell membranes. They can be used to store energy, they are able to provide a waterproof coating to animals, and they are the basic building blocks of essential molecules that include hormones, vitamins, and pigments. They are classified in different ways and they include fatty acids, phospholipids, and triglycerides. Proteins are essential to all cells since almost all tasks that cells perform at some point involve proteins. The versatility of proteins is due to the great variety of shapes that they can adopt. Overall structures are dictated by their primary structure and the sequence of amino acids, but these take on different secondary structural conformations, patterns, and shapes. These come together to form three-dimensional conformations, or tertiary structures, that are unique to each protein.

Chapter

Cover Amino Acid and Peptide Synthesis

α-Amino acid synthesis  

This chapter examines proteinogenic α-amino acids that are produced industrially by fermentation methods and chemical synthesis on a vast scale. It highlights the principal application of α-amino acids as food additives and cheap starting materials for laboratory work. It also considers the synthesis of α-amino acids as an active field wherein there is demand for specifically labelled, unnatural, and unusual amino acids. The chapter explores the general methods of synthesis of α-amino acids, including the displacement reactions on α-halo acids, Strecker synthesis, approaches through hydantoins, and via oxazolones. It describes reactions that lead to racemic products and reviews the traditional general approach to the resolution of racemates, which is to derivatize an optically active reagent.

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.