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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 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 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.

Book

Cover Amino Acid and Peptide Synthesis
Amino Acid and Peptide Synthesis introduces the study of amino acids and peptides, which is becoming increasingly important to chemists as a result of the growing overlap of mainstream organic chemistry with bioorganic chemistry and biochemistry. This introductory text begins with a brief survey of the role and diversity of amino acids, peptides, and proteins in nature, and goes on to describe and explain the principal methods of chemical synthesis.

Chapter

Cover Foundations of Chemical Biology

Epilogue: where to from here?  

This chapter reviews some of the intrinsic chemical properties of important types of biological molecules, particularly amino acids, sugar phosphate derivatives, and related macromolecules. It explains that a small number of fundamental chemical properties can be used to understand many of the biological functions of molecules. The chapter also discusses the chemical potential of the functional groups found in biological molecules, highlighting the way in which amphiphilic molecules can adopt ordered, functionalized structures in an aqueous environment. The chapter analyses the availability of ordered structures with diverse chemical functional groups which provide the foundations for the molecular basis of life. It refers to macromolecules that adopt extended structures that are used by biology as fibres and for information storage.

Chapter

Cover Amino Acid and Peptide Synthesis

α-Carboxy protection  

This chapter describes the amino groups of amino acids and peptides as more nucleophilic than their carbonyl groups when it comes to acylation. It explains how amino acids and peptides with unprotected carboxy groups can be used for peptide bond formation if separately preactivated carboxy components are employed. It also cites esterification as the usual means of carboxy protections, wherein the parent carbolic acid can be regenerated from the esters by acyl-oxygen or alkyl-oxygen fission. The chapter considers the fundamental alkyl-oxygen cleavage chemistry as qualitatively the same as that for alkoxycarboxyl groups, which are esters of a special kind. It notes that there is no significant distinction between methyl and ethyl esters.

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 Amino Acid and Peptide Synthesis

Introduction  

This chapter provides a background on proteins, which are natural polymers that are assembled under nucleic acid control from a menu comprising L-α-amino acids of general structure and the ‘imino’ acid L-proline. Amide or peptide bonds link the building blocks and give backbones and side-chains containing a variety of simple functionalities to macromolecules. The chapter also describes structures elaborated by inter- or intra-chain covalent connection, non-covalent association, coordination of metal ions, attachment of auxiliary components, or chemical modification that includes acetylation, hydroxylation, methylation, and carboxylation. The chapter explains that peptides are molecules constructed in the same way as proteins, but on a smaller scale. It emphasizes that the classification ‘peptide’ is suitable for molecules with fewer amino acid residues.

Chapter

Cover Amino Acid and Peptide Synthesis

Strategy and tactics  

This chapter explains how a coherent plan can be drawn up in order to illustrate the appropriate methods for the synthesis of peptides in many stages. It focuses on peptide bond formation, wherein tripeptides can be assembled from amino acids by two stepwise elongation strategies: [1 + (2 + 3)] and [(1 + 2) + 3]. It also mentions the convergent strategy in tetrapeptides, which condenses amino acids and dipeptide fragments when they are joined together. The chapter refers to attraction in the scope of a fragment condensation strategy that shows the production of a set of related analogues with variable sequences in one region. It clarifies why fragment condensation is better performed at some positions than others, pointing out that it is a constrained strategy that has complicated protective group tactics.