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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 Biochemistry and Molecular Biology

Nitrogen metabolism: amino acid metabolism  

This chapter refers to amino acids which are supplied in the diet from protein hydrolysis in the gut. This includes proteins in the body that are constantly degraded and resynthesized. The chapter clarifies how the body can synthesize about ten of the amino acids. The rest must be obtained from the diet, but all 20 are needed for protein synthesis. Amino acids are also used to synthesize a wide variety of other molecules. The chapter discusses amino acids in excess of immediate requirements and shows that these are deaminated as the amino nitrogen is mainly converted into urea in mammals and excreted. The carbon-hydrogen skeletons are oxidized to release energy or converted into fat or glycogen according to the metabolic controls operating at the time and the particular amino acid.

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 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 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.

Chapter

Cover Essentials of Human Nutrition

Protein  

Colleen S. Deane, Daniel J. Wilkinson, and Philip J. Atherton

This chapter is concerned with proteins, the fundamental structures of life. They exist as functional elements within every cell and undergo extensive metabolic interaction. This widespread metabolic interaction is intimately linked to the metabolism of energy and other nutrients. At the most basic level, proteins are made from a combination of 20 different amino acids, which determines the structure and function. Dietary protein and exercise are the two key stimuli that promote positive protein turnover, which can be accurately and reliably measured using stable isotope methods. The potency of the anabolic response to dietary protein is dependent upon the protein quality, which can be measured via the Digestible Indispensable Amino Acid Score, Protein Digestibility Corrected Amino Acid Score, and/or using stable isotope tracers. In situations of protein deficiency, significant body mass can be lost, drastically impairing health and quality of life, requiring dietary protein therapy to help overcome/manage these conditions.

Chapter

Cover Biochemistry and Molecular Biology

Food digestion, absorption, and distribution to the tissues  

This chapter looks at digestion, wherein the polysaccharides and proteins of food are hydrolysed into their monomer subunits or simple sugars and amino acids in order to be absorbed by the intestinal epithelial cells in the bloodstream. The chapter looks at triacylglycerols or fats (TAGs) which are hydrolysed into fatty acids and monoacylglycerol, the process which is aided by bile salts that emulsify the fats to give a large surface area for the enzyme lipase to attack. The storage of fat is primarily in the adipocytes or fat cells of adipose tissue, where it occurs in large amounts as TAG. The chapter describes insulin, which is released in response to high glucose levels and stimulates fat and glycogen storage. Glucagon, released from the pancreas when blood glucose is low, stimulates release of glucose from the liver and of fatty acids from fat cells.

Chapter

Cover Biochemistry and Molecular Biology

Protein synthesis and controlled protein breakdown  

This chapter defines protein synthesis as the joining together of amino acids in the correct sequence to form a polypeptide chain. This involves three phases: initiation, chain elongation, and termination. The chapter analyzes messenger RNA (mRNA) and shows that it encodes the amino acid sequence of the protein in the form of triplets of bases known as codons. Of the 64 codons, AUG is the initiator or start codon, encoding methionine, and three codons are stop codons and the genetic code is degenerate as most amino acids are encoded by more than one codon. The chapter outlines the sequence of codons in an mRNA molecule. This is translated by cytosolic ribosomes. Ribosomes have a large and a small subunit, each containing RNA and many proteins.

Chapter

Cover Biochemistry and Molecular Biology

The structure of proteins  

This chapter focuses on proteins, which are made up of one or more polypeptide chains constructed from 20 species of amino acids. The length and sequence of each polypeptide is specified by its gene. The chapter describes 20 different amino acids which are of differing sizes and degrees of hydrophobicity, hydrophilicity, and electrical charge. These present the possibility of a vast variety of different proteins. The primary structure is the linear amino acid sequence, while the secondary structure involves folding of the polypeptide backbone. The chapter explains that the main secondary structure motifs are the α helix and the β-pleated sheet, which are stabilized by hydrogen bonding. The tertiary structure involves the further folding of the secondary structure motifs into the three-dimensional form of the protein.

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 Thrive in Human Physiology

The endocrine system  

This chapter reviews how the endocrine system, together with the nervous system, controls the multitude of physiological processes in the body and ensures that homeostasis is achieved. It discusses the formation of hormones from derivatives of amino acids, peptides and proteins, and lipids. It also analyszes the chemical nature of the process by which anan individual hormone determinesing where its receptor is located. The chapter clarifies how the overall plasma levels are maintained at the appropriate level proportion by negative feedback mechanisms, although hormone secretion may display circadian rhythms. It mentions the pituitary gland. This is described as the master endocrine gland by virtue of the number of physiological processes it controls.

Chapter

Cover An Introduction to Medicinal Chemistry

Enzymes: structure and function  

This chapter discusses the structure and function of enzymes, which are proteins that act as the body's catalysts by binding substrates and participating in the reaction mechanism. It examines the active site of an enzyme. This is usually a hollow or cleft in the protein. Here, important amino acids are present and these either bind substrates or participate in the reaction mechanism. The chapter also explains substrate binding, showing how this involves an induced fit where the shape of the active site alters to maximize binding interactions. The chapter reviews the Michaelis constant, which is equal to the substrate concentration at which the rate of the enzyme-catalysed reaction is half of its maximum value. The chapter finally mentions the Lineweaver–Burk plot and illustrates that this provides more accurate values for the maximum rate and K M.

Chapter

Cover Biochemistry

Amino Acids, Peptides, and Proteins  

This chapter discusses proteins as molecular tools. These perform an astonishing variety of functions. In addition to serving as structural materials in all living organisms, proteins are involved in diverse functions as catalysis, metabolic regulation, transport, and defence. Proteins are composed of one or more polypeptides, unbranched polymers of 20 different amino acids. The chapter looks at the genomes of organisms which specify the amino acid sequences of thousands or tens of thousands of proteins. It describes proteins as a diverse group of macromolecules that are directly related to the combinatorial possibilities of the 20 amino acid monomers. Amino acids can be theoretically linked to form protein molecules in any imaginable size or sequence.

Chapter

Cover Biochemistry and Molecular Biology

General principles of nutrition  

This chapter shows that nutrition is the science of food and the substances contained in it. The chapter notes that the main components of diet are macronutrients, which provide the bulk of the diet, and micronutrients, which include essential vitamins and minerals. The chapter explains that protein is needed to supply essential amino acids and fat is needed to supply essential fatty acids and provide sufficient energy in the diet. Most diets provide 10-15% of the energy in the form of protein and the remainder is made up of carbohydrate and fat. The chapter talks about the consumption of saturated fat, which is one of the risk factors for cardiovascular disease and some cancers, whereas consumption of polyunsaturated fat is considered healthy. A high consumption of sucrose can lead to dental caries.

Chapter

Cover Genetics

The Central Dogma of Molecular Biology  

This chapter explains that the Central Dogma of molecular biology is that DNA provides the template to make RNA, which provides the template to make a polypeptide that contributes to phenotypes. It illustrates the structure of DNA and the Central Dogma, highlighting features of the DNA molecule that have an impact on its function. It points out modifications to the traditional view of the Central Dogma and introduces the basic structure of a gene. The chapter describes information content that flows from DNA to RNA to polypeptide, which is inherent in the structures of the molecules and encodes the amino acid sequence of the polypeptide. It also shows that, according to genome analysis, a surprising number of RNA molecules do not serve as templates for making polypeptides but are functional themselves.

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 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.