bluuebunny/crossref_metadata_2025 huggingface dataset:
Collision theory
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter explores collision theory, which is the simplest quantitative account of reaction rates and can only be used for the discussion of reactions between simple species in the gas phase. It shows how basic collision theory considers the impact of one molecule on another, taking into account how the resulting excitation energy accumulates in the bond where it is needed. It also discusses the bimolecular gas-phase reaction that takes place when reactants collide, provided their relative kinetic energy exceeds a threshold value and certain steric requirements are fulfilled. The chapter draws on the kinetic theory of gases, especially the expression for the mean speed of molecules and extends the account of the Lindemann–Hinshelwood mechanism of gas-phase reactions. It draws on the Maxwell–Boltzmann distribution of molecular speeds.
Genomics
Authors: Chappell Lia , Lindsay Sarah J , Jones Phil , Parkhill Julian , Roberts Jonathan , Holroyd Nancy , Szpak Michal , Gale Francesca
Published: September 2023

Genomics starts with a look at rare diseases from a genomics perspective. It then moves on to consider cancer genomics. There follows a chapter about genomes and ethics. Pathogen genomics is also examined in detail. There is also a chapter on parasite genomics. Human evolution is considered next. Finally, reading and writing genomes is looked into.
Biochemistry
Authors: Bowater Richard , Bowater Laura , Husband Tom
Published: September 2023

Biochemistry introduces this topic with an examination of carbohydrates, asking why we need them in our lives. It then looks at the building blocks of a cell, namely, lipids and proteins. Nucleotides and nucleic acids are the next topic to be covered. The text moves on to consider metabolism. It asks what it means and how energy is transformed. Other questions asked include: how is a metabolic balance maintained? How can we solve the problems of the future with natural products? Finally, the text looks at bioenergy and the environment.
How to Succeed in Organic Chemistry
Authors: Elliott Mark C.
Published: September 2023

How to Succeed in Organic Chemistry first lays out the foundations for the topic and looks at the basics. It talks about isomers, chemical names, how to name organic compounds, double bond equivalents, bond polarization, and electronegativity. The second section is about building on the foundations. It looks at breaking bonds, enthalpy, carbocations, carbanions, and reactivity. The third section looks at shape. The section that follows looks at types of selectivity. Section 5 is about rotating bonds and looks at cyclohexanes. The sixth section is about elimination. The seventh section is all about building skills.
Cell Signalling
Authors: Hancock John T.
Published: September 2023

Cell Signalling starts with a brief history and general principles of cell signalling. It then turns to an examination of signals and their perception. It also discusses modifications to proteins that control cell signalling. Next, it looks at intracellular signals. The text also covers cell development before explaining cell signalling disorders, cancers, and apoptosis. Towards the end, the text moves on to stress responses and the changing cell environment. Finally, the book looks to the future, including challenges and perspectives in cell signalling, such as how its manipulation may enable new medical treatments or increase efficiency in agriculture.
The Heart of the Matter
Authors: Fullick William , Fullick James
Published: September 2023

This chapter looks at the significance of having a healthy cardiovascular system. It acknowledges how terrifying it would be to have something wrong with a person's heart or circulation system. Thus, surgery offers numerous different options for successful treatments for cardiovascular diseases in parts of the world where healthcare is accessible and affordable. Diseases of the cardiovascular system may affect the blood vessels themselves, or affect the valves, electrical system or muscle of the heart. The chapter then looks into several cardiovascular system issues, such as arrhythmias, aneurysms, ailing pumps, and congenital heart problems before considering the procedure of heart transplantation.
A Breath of Fresh Air
Authors: Fullick William , Fullick James
Published: September 2023

This chapter explores the anatomy and physiology of the respiratory system. It examines the mechanics of ventilation while also elaborating on the division of the respiratory system into upper and lower respiratory tracts. Both the upper and lower respiratory tract are very vulnerable to smoking-related damage, as they directly receive inhaled smoke from cigarettes and other tobacco products. The chapter cites how cancers, the best-known and most feared diseases which affect the gas exchange system, can occur at any level of the respiratory tract. It then explains how surgery aims to improve quality of life through tonsillectomies or can be life-saving, when it comes to a lung transplant.
An Introduction to Medicinal Chemistry
Authors: Patrick Graham L.
Published: September 2023

An Introduction to Medicinal Chemistry delves into all aspects of this multidisciplinary field. Firstly, the text introduces and presents an overview. Chapters then look at drug targets, their structure, and their function. They examine proteins, enzymes, receptors, and nucleic acids. The next group of chapters is about pharmacodynamics and pharmacokinetics. Then the text turns to look at drug discovery, design, and development. It presents case studies. After this, the chapters look at tools and included is an examination of computers used in medicinal chemistry. Finally, the text presents a number of topics in medicinal chemistry such as antibacterial agents, antiviral agents, anticancer agents, opioid analgesics, and antiulcer agents.
Drugs and drug targets: an overview
Authors: Patrick Graham L.
Published: September 2023

This chapter considers drugs as compounds that interact with a biological system to produce a biological response, noting how drugs are unsafe and vary in the side effects they might have. The chapter discusses the therapeutic index, which is a measure of a drug's beneficial effect at a low dose versus its harmful effects at a higher dose. It also looks at the principle of selective toxicity. This implies that useful drugs show toxicity against foreign or abnormal cells. The chapter reviews the classification of drugs by their pharmacological effect, their chemical structure, their effect on a target system, and their effect on a target structure. It highlights structures produced during the development of a new drug that are not considered for the clinic.
Receptors and signal transduction
Authors: Patrick Graham L.
Published: September 2023

This chapter considers what happens once a receptor has been activated, noting that the interaction of a receptor with its chemical messenger is the first step in a complex chain of events involving several secondary messengers which lead to a change in cell chemistry. The chapter explains the methodology behind signal transduction pathways which follow the activation of G-protein-coupled receptors (GPCRs). It notes that 30% of all drugs on the market interact with these kinds of receptor. It also talks about transduction pathways for kinase receptors and shows that these offer new targets for novel drugs, particularly in the area of anticancer therapy. The chapter describes the signalling cascade initiated by receptor–ligand binding which results in substantial signal amplification, which does not require the original chemical messenger to enter the cell. It examines kinases and illustrates that these are involved in the desensitization of receptors.
Nucleic acids: structure and function
Authors: Patrick Graham L.
Published: September 2023

This chapter talks about the structure and function of nucleic acids, citing examples of important drugs that act directly on nucleic acids. It describes two types of nucleic acid: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). It also examines the primary structure of DNA which consists of a sugar–phosphate backbone with nucleic acid bases attached to each sugar moiety. The chapter highlights how the DNA double helix is coiled up into a tertiary structure, analyzing the coiling and uncoiling of the double helix that require topoisomerase enzymes. It looks at the genetic code that consists of nucleic acid bases, which are read in sets of three during the synthesis of a protein.
Statins
Authors: Patrick Graham L.
Published: September 2023

This chapter considers statins as an important group of cholesterol-lowering drugs which act as enzyme inhibitors. It talks about the market for cholesterol-lowering drugs, which is the largest in the pharmaceutical sector and is dominated by statins. It also highlights statin medications, atorvastatin and simvastatin, which recorded revenues of US$7 billion and US$5.3 billion, respectively, in 2002. The chapter looks at how these cholesterol-lowering drugs were discovered and how they interact with their target at the molecular level. It highlights the role of cholesterol in coronary heart disease and how the inhibition of an enzyme can lower cholesterol levels.
Combinatorial and parallel synthesis
Authors: Patrick Graham L.
Published: September 2023

This chapter covers combinatorial and parallel synthesis, which are methods that involve rapidly preparing large numbers of compounds in an automated or semi-automated fashion. It highlights techniques developed to meet the urgent need for new lead compounds for the ever-increasing number of novel targets discovered by genomic and proteomic projects. The chapter also considers parallel synthesis as an effective method of producing large numbers of analogues for drug discovery, studies into structure-activity relationships (SARs), and drug optimization. The chapter reviews solid-phase synthetic methods that have proved valuable for producing compounds for lead discovery, structure-activity relationships, and drug optimization. It demonstrates how different linkers are used depending on the functional group present on the starting material and the functional group desired on the product.
Antiviral agents
Authors: Patrick Graham L.
Published: September 2023

This chapter provides a background on viruses that pose a serious health threat and require new antiviral agents. It looks into vaccination, which is effective against many viruses but is less effective against viruses that readily mutate. It also analyzes the research on antiviral drugs which increased during the 1980s as a result of the AIDS epidemic and the need to find drugs to combat HIV. The chapter reviews antiviral research which has been aided by advances in viral genomics and genetic engineering, as well as by the use of X-ray crystallography and molecular modelling. It highlights nucleoside analogues, which are prodrugs that are activated by phosphorylation to a triphosphate structure.
Antibodies and other biologics
Authors: Patrick Graham L.
Published: September 2023

This chapter considers the antigen as a foreign protein which is identified by the body's immune system, while antibodies are host proteins that identify and bind to antigens and promote the immune response. It discusses B-Cells and T-cells, which are lymphocytes which are integral to the immune response. It also details the complement system that is made up of bloodborne proteins. These are attracted by an antibody–antigen complex and create protein complexes that attract phagocytes and create pores in the target cell membrane. The chapter examines chimeric antibodies which are part human and part mouse in character and are less likely to promote the HAMA response. It describes antibodies that have been clinically approved for the treatment of various tumours and other antibodies that have proved useful in the treatment of a wide range of disorders.
Factor Xa inhibitors
Authors: Patrick Graham L.
Published: September 2023

This chapter describes factor Xa as a key enzyme involved in thrombosis and clot formation. It considers factor Xa inhibitors as potential anticoagulants for the treatment of deep-vein thrombosis and pulmonary embolism. It also highlights the first factor Xa inhibitors to reach the market and covers the design process that led to the discovery of apixaban, rivaroxaban, and edoxaban. The chapter looks back at the initial design of Factor Xa inhibitors, which include a central scaffold containing two substituents capable of interacting with the S1 and S4 subsites. It reviews the progress in designing clinically effective agents that became possible when it was discovered that potent inhibitors could be obtained by using hydrophobic binding groups for the S1 and S4 subsites.
The Marine Environment and Biodiversity
Authors: Kent Michael
Published: September 2023

The Marine Environment and Biodiversity introduces the key features of the marine environment and explores definitions of marine biodiversity at different levels of biological organization: genetic, species, ecosystem, and functional. It also discusses how changes in ocean features due to human activities are having a negative impact on marine biological diversity. Topics covered include the ocean in motion and seawater matters. The text also asks: what is marine biodiversity? It shows how we can measure marine biodiversity and considers what marine biodiversity can do for us. Finally, the text poses the question: what are we doing to marine biodiversity?
Numbers, variables, and units
Authors: Steiner Erich
Published: September 2023

This chapter introduces different concepts that are used in chemistry. It acknowledges that chemistry, like other physical sciences, comprises experiment and theory—both involving the manipulation of numbers and of the symbols that are used to represent numbers and physical quantities. The chapter describes the terms function, constant, and variable. It also discusses natural numbers, integers, rational and irrational numbers, algebraic numbers, and transcendental numbers. Furthermore, it reviews factorization or the decomposition of a number into a product of other numbers, explaining the fundamental theorem of arithmetic. The chapter then tackles the decimal representation of numbers, explaining the Archimedean and Euler numbers. The discussion also reviews complex numbers and the International System of Units, the recommended system for chemistry.
Second-order differential equations. Some special functions
Authors: Sainsbury Malcolm
Published: September 2023

This chapter explains special functions or second-order homogeneous linear equations with non-constant coefficients. They have particular solutions that play an important role in the mathematics of the physical sciences. The chapter tackles the standard methods used to solve these equations. It begins with a description of the power-series method before introducing the Frobenius method—explaining the Frobenius method and indicial equation. The chapter also shows how the power-series method is used to obtain the physically significant particular solutions of the Legendre equation. These solutions are called Legendre polynomials and they occur whenever a physical problem in three dimensions is formulated in terms of spherical polar coordinates. The chapter ends with an explanation of other special functions: the Hermite, Laguerre, and Bessel functions.
Integration
Authors: Steiner Erich
Published: September 2023

This chapter explains the concept of integration as the inverse operation to differentiation. It starts off by introducing the concepts of indefinite integrals, integrand, variable of integration, and integration constant, among others. It also explains differential and integral operators before discussing the definite integral. The chapter describes the limits of integration as well as the range of integration. Furthermore, it tackles integral calculus and its use in the determination of geometric properties, in particular, the area of a plane figure and the length of a curve in a plane. Then the discussion progresses to the static properties of matter, and the dynamics of velocity and distance, force and work, as well as work and energy.
Sequences and series
Authors: Steiner Erich
Published: September 2023

This chapter discusses the concept of a series, which is a set of terms to be summed, and which make up a sequence. The discussion underscores that series occurs in all branches of the physical sciences and that the representation of functions as series is an essential tool for the solution of many physical problems. The chapter describes both arithmetic and geometric progressions, as well as the limits of sequences. It also tackles finite and infinite series and the tests of convergence. The chapter then explains the MacLaurin and Taylor series before finally giving an overview of operations with the power-series.
Complex numbers
Authors: Steiner Erich
Published: September 2023

This chapter focuses on complex numbers, which occur in several branches of mathematics that are important in the physical sciences. Complex numbers are often involved in the solutions of the differential equations of motion in both classical and quantum mechanics. The chapter tackles the algebra of complex numbers, noting that these can also be added, subtracted, multiplied, and divided in much the same way as ordinary real numbers. It also shows graphical representations and introduces concepts such as the complex plane, real axis, imaginary axis, and modulus. It describes de Moivre's formula before progressing to a discussion on complex functions and Euler's formula. Lastly, it tackles periodicity and the evaluation of integrals.
Functions of several variables
Authors: Steiner Erich
Published: September 2023

This chapter looks at functions of several variables which occur widely in the physical sciences, such as the thermodynamic functions of state and all physical properties of a system whose values depend on position. The chapter explains the graphical representation of functions of two or more variables. It discusses partial differentiation, alternative notations, and stationary points. It also describes the concept of optimization—finding the extremum values of a function—and the method of Lagrange multipliers. The chapter then tackles the total differential and total derivative before introducing the concepts of the Laplacian operator and harmonic function. It likewise explains exact differentials, line integrals, and double integrals.
First-order differential equations
Authors: Steiner Erich
Published: September 2023

This chapter focuses on first-order differential equations, which describe some simple rate processes in physics and chemistry, biology, engineering, economics, and the social sciences. First-order differential equations contain a first derivative only. The chapter starts by explaining what it means to solve a differential equation. Then it describes separable differential equations and looks at their application in chemical kinetics. The chapter also discusses first-order linear equations—differentiating between homogeneous and inhomogeneous equations. It ends with an explanation of an important application of linear differential equations: the modeling of electric circuits where Kirchhoff's voltage law, Ohm's law, as well as the concepts of resistance, inductance, and capacitance, are involved.
Matrices and linear transformations
Authors: Steiner Erich
Published: September 2023

This chapter discusses matrix algebra, the branch of mathematics concerned with the theory of systems of linear equations. Matrix algebra is used for the manipulation of systems of equations, and for the construction of numerical methods of solution of the problems that give rise to such systems in the physical sciences, in engineering, and in statistics. The chapter presents the elements of matrix algebra, beginning with special matrices: the square matrix, column matrix, row matrix, and transpose matrix. It also demonstrates matrix equality, addition, and multiplication by a scalar. Then it discusses the inverse matrix, linear transformations, as well as orthogonal matrices and orthogonal transformations. Lastly, it explains symmetry operations with a brief introduction to symmetry groups.
Analytical methods
Authors: Price Nicholas C. , Nairn Jacqueline
Published: September 2023

This chapter explores the analytical methods used to study proteins, including protein concentration, electrophoresis, enzyme assays, and binding assays. It is important to know the amount of protein at different stages in a purification procedure so that the specific activity of the protein being purified can be calculated. Electrophoresis techniques enable the separation of proteins according to their size, net charge or a combination of size and net charge. Meanwhile, an enzyme assay is a test of the amount of catalytic activity present in a sample of enzyme. Finally, the methods for measuring binding can be divided into two principal categories: those in which the protein-ligand complex is physically separated from either free protein or free ligand; and those in which some property is used to distinguish between the complex and the free interacting partners.
The sprinter
Authors: Maughan Ronald J. , Gleeson Michael
Published: September 2023

This chapter examines anaerobic metabolism. The sprinter has to sustain a very high-power output over a relatively short period of time. As the intramuscular supply of adenosine triphosphate (ATP) is sufficient to last only about two seconds, there is a pressing need to resynthesize ATP extremely quickly, and this is achieved by the breakdown of intramuscular stores of phosphocreatine and the rapid activation of glycolysis. Both of these processes occur without the utilization of oxygen; that is, they are anaerobic means of regenerating ATP. However, sprinting is not entirely anaerobic. There is a contribution of carbohydrate oxidation to ATP resynthesis during sprinting that increases as the duration and distance of the sprint increases. The chapter then describes the concept of the cellular energy charge and explains why there is a loss of adenine nucleotides during very high-intensity exercise.
Adaptations to training
Authors: Maughan Ronald J. , Gleeson Michael
Published: September 2023

This chapter reflects on the principles of training to improve performance in sport. The level of success that an individual can achieve is limited by their genetic potential, and this sets an upper ceiling to performance. To reach that potential, however, requires a sustained period of intensive training, at least for most athletes. Despite the tendency for athletes to attempt to copy the details of the training programmes of their sporting heroes, this is seldom successful. This is in part because of a lack of the physiological, biochemical, and psychological characteristics that are prerequisites for success, but also in part because there is a great variation between individuals in their trainability. Indeed, the type of training—and the frequency, intensity, and duration of training sessions—will vary greatly between sports, and will also be different for different individuals. The chapter then considers the danger of developing an overtraining syndrome.
Core Maths for the Biosciences
Authors: Reed Martin B
Published: September 2023

Core Maths for the Biosciences consists of two parts. Part 1 looks atconsiders arithmetic, algebra, and functions. Here, chapters cover precision and accuracy, data tables, graphs, molarity and dilutions, variables, functions, equations, and linear functions. They also look at quadratic and polynomial functions, fitting curves, periodic functions, and exponential and logarithmic functions. Part 2 looks atfocusses on calculus and differential equations. It Chapters examines instantaneous rate-of-change, the rules of differentiation, applications of differentiation, techniques of integration, and the definite integral.
Data tables, graphs, interpolation
Authors: Reed Martin B
Published: September 2023

This chapter talks about finding patterns as the essence of mathematics, which can be done if the data involves measurement of two or more physical variables. It illustrates how to plot graphs of data-points on paper and in MS Excel, and it demonstrates the basic patterns to look for, such as direct and inverse proportion, and linear relations. It also elaborates how to construct a data table and a data plot, which begins by tabulating the data and then plotting the data values as points on a graph. The chapter highlights a typical experiment, wherein the experimenter allows the independent variable to increase or decrease and measures the value of the dependent variable. It clarifies how data-point plots show the relationship between the variables through a graph.
Techniques of integration
Authors: Reed Martin B
Published: September 2023

This chapter describes integral calculus, wherein integration is the inverse process to differentiation and is referred to as anti-differentiation. It defines the integral of a function f(x) as the most general function as it produces f(x)' when differentiated. It also highlights the physical meaning and geometrical significance of derivatives, which can be defined and used to work out the derivatives of functions from first principles. The chapter analyses integration as an inverse problem that finds a function that produces f(x) when differentiated. It refers to the use of the absolute value of x inside the logarithm function in order to find logarithms of positive numbers.
Introduction to the scientific literature
Authors: Aysha Divan
Published: September 2023

This chapter starts off with an overview of different types of scientific publications and introduces the concepts of credibility and accountability in scientific publishing. It emphasizes that scientific material is communicated through a number of different channels including scientific journals, textbooks, theses, conference proceedings, and the Internet. The chapter notes that these materials can be classified as primary or secondary sources of literature and as peer-reviewed or non-peer-reviewed literature, and it provides a definition of each category It also details the peer-review process. Finally, the chapter elaborates on the journal hierarchy. It examines the publication process for a journal article, from selecting a journal and consulting the instructions for authors to actual publication.
Reviewing scientific literature
Authors: Aysha Divan
Published: September 2023

This chapter seeks to provide a framework for reviewing the scientific literature and, in particular, original research papers with a critical eye. It notes that the guidelines presented in the text refer to reviewing a research paper after it has been published, but they can be equally applied to the review of material prior to its publication. The chapter also presents a brief overview of the aims underpinning the review of scientific literature. Then, it looks at post-publication review, which takes place in a variety of ways, including discussions at journal clubs, correspondence with the editors, and citations in other research papers. Lastly, the chapter determines the knowledge and skills necessary for conducting a successful review and displays an annotated example of a written review of a published research paper.
Writing a research paper
Authors: Aysha Divan
Published: September 2023

This chapter focuses on the process of writing up research findings in the form of a research paper for publication. Research papers, as the chapter defines them, are published in peer-reviewed academic journals and are an essential part of scientific communication as they report new information, which advances important conceptual or practical understanding of a particular problem or theory. These articles are detailed descriptions of the nature of the problem studied, the methodology used, the results achieved, and the conclusions reached. The chapter also examines the conventional components of the research article (title, authors, abstract, introduction, methods, results, discussion, references, acknowledgments, and supplementary information). It then describes a strategy for writing the research paper and analyses the aim and typical content of each component of the paper. Finally, the chapter includes annotated examples of work to illustrate the content and structure of the various components.
Writing a Master’s dissertation or a PhD thesis
Authors: Aysha Divan
Published: September 2023

This chapter explicates the process of writing up research findings in the form of a dissertation or a thesis. It argues that both dissertation and thesis consist of a critical review of the background literature, a statement of the research objectives, the materials and methods used to test the research questions, the results obtained, and a critical discussion of the results. The chapter outlines the basic requirements of a Master's dissertation and a PhD thesis. It details the components of the dissertation and the thesis and reviews the expected content for each component. Lastly, the chapter examines the strategy for writing the dissertation or thesis and it offers guidance on preparing for the oral examination associated with them.
Pharmaceutical Solutions
Authors: Moynihan Humphrey A. , Crean Abina M.
Published: September 2023

This chapter discusses the main concepts relating to the dissolution and solubility of pharmaceutical compounds. Solubility and solutions are of key importance pharmaceutically as drug molecules need to be in solution in the biological fluids surrounding the site of action to achieve a therapeutic effect. Common expressions of solubility for pharmaceutical uses include mole fractions, molarity, molality, percentages, parts per million, and equivalents. Two types of solvent medium exist in the body: water-based and lipid-based. During the dissolution process, solute molecules leave their previous, usually solid, state, and become solvated within suitable cavities in the solvent medium. The solubility of compounds in particular compounds is influenced by various factors including molecular weight, hydrogen-bonding capacity, and the presence of hydrophilic or hydrophobic groups. Meanwhile, acidic or basic pharmaceuticals can be completely converted into salts by choice of suitable counterions. While in aqueous solution, drug compounds may be susceptible to hydrolytic degradation.
Pharmaceutical Equilibria
Authors: Moynihan Humphrey A. , Crean Abina M.
Published: September 2023

This chapter examines pharmaceutical equilibria. Medicines are systems of several components and phases existing at equilibrium. Equilibrium processes are controlled by the energetics, or thermodynamics, of the system. Energetics and equilibrium processes control the movement of the drug molecule between phases during its transport to the target receptor. Systems then undergo change so as to minimize enthalpy and/or maximize entropy. The thermodynamic property that takes into account both the enthalpy and entropy of the system is the free energy. Many important pharmaceutical systems have many phases in which components are transferring between phases. The chapter then looks at the phase rule. During transport of a drug from the point of delivery to the target receptor, the drug molecule has to undergo a number of phase transitions. This involves mass-transfer processes, including diffusion, dissolution, partitioning, and gas absorption.
Leaving groups
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter explains leaving groups. It discusses the energy profile in line with leaving groups by using a diagram to emphasize its points. The chapter notes bond strength and stability as factors which are important for a good leaving group. Leaving group ability is a good guide to working out which reactions will go and which will not. The chapter highlights how some reactions do not occur despite their predicted mechanisms. It shares how relative energies of the species are vital in predicting whether reactions will go readily or not. The chapter also shows how to reverse reactions that do not take place by using ketone reacting to acyl chlorides as an example. It cites neutral nitrogen as the best leaving group.
Residue-specific considerations
Authors: Jones John
Published: September 2023

This chapter highlights a peptide bond formation with the α-amino group of lysine that requires prior blockade of the ε-amino group. It explains that the required differentiation can be achieved by using the fact that the side-chain amino group is the more basic and nucleophilic because there is an electron-withdrawing group next to the α-amino group. It also considers cyclic, branched, and conjugated structures, which involve cyclization, that is, is the attachment of other peptides and the conjugation of carbohydrate or other moieties through specific side-chains. The construction of these assemblies involving cyclization requires the availability of protective group combinations with additional dimensions of orthogonality. The chapter illustrates special methods for protecting lysine side-chains.
Acidity, basicity, and pKa
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter assesses acidity, basicity, and pK
a. An acid is a species having a tendency to lose a proton, while a base is a species having a tendency to accept a proton. The measure of acidity or basicity is called pK
a; the value of pK
a tells us how acidic (or not) a given hydrogen atom in a compound is. Knowing about pK
a is useful because many reactions proceed through protonation or deprotonation of one of the reactants, and it is obviously useful to know what strength acid or base is needed. The chapter then considers nitrogen compounds as acids and bases, and looks at carbon acids, the development of the drug cimetidine, and Lewis acids and bases.
Nucleophilic substitution at saturated carbon
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter discusses nucleophilic substitution at saturated carbon. In the first step, the nucleophile attacks the C=O π bond. It is immediately obvious that the first step is no longer possible at a saturated carbon atom. The electrons cannot be added to a π bond as the CH2 group is fully saturated. In fact there is no way for the nucleophile to add before the leaving group departs because this would give an impossible five-valent carbon atom. Instead, two new and different mechanisms become possible. Either the leaving group goes first, and the nucleophile comes in later, or the two events happen at the same time. The first of these possibilities is called the SN1 mechanism. The second mechanism, which shows how the neutral carbon atom can accept electrons provided it loses some at the same time, is called the SN2 mechanism.
Review of spectroscopic methods
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter presents a review of spectroscopic methods. It begins by looks at spectroscopy and carbonyl chemistry. Carbonyl compounds can be divided into two main groups: aldehydes and ketones, and acids and their derivatives. Which spectroscopic methods most reliably distinguish these two groups? Which help separate aldehydes from ketones? Which allows us to distinguish the various acid derivatives? The most consistently reliable method for doing this is 13C nuclear magnetic resonance (NMR). It does not matter much whether the compounds are cyclic or unsaturated or have aromatic substituents, they all give carbonyl 13C shifts in about the same regions. The chapter then looks at NMR spectra of alkynes and small rings.
Electrophilic aromatic substitution
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter assesses electrophilic aromatic substitution. Formation of the enol tautomer is catalysed by acid or by base, and because the ketone and enol are in equilibrium, enolization in the presence of D2O can lead to replacement of the protons in the α positions of ketones by deuterium atoms. Because the enolization and deuteration process can be repeated, eventually all of the α-protons are replaced by deuterium. The way this ketone is deuterated provides evidence that its enol form exists, even though the keto/enol equilibrium greatly favours the ketone form at equilibrium. The chapter discusses similar reactions of a compound that exists entirely in its enol form. That very stable enol is phenol and its stability is a consequence of the aromaticity of its benzene ring. The chapter then looks at alkyl benzenes, halogens, and the Friedel–Crafts chemistry.
Rotational motion and the hydrogen atom
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter considers the quantum mechanics of translation and vibration. Both types of motion can be solved in certain cases, and both are important not only in their own right but also because they form a basis for the description of more complicated types of motion. It mentions translational motion, which has the advantage of introducing in a simple way many of the striking features of quantum mechanics. The chapter describes certain features of wavefunctions that are common to all the problems. The combination of features of wavefunctions with the solution of the Schrödinger equation results in one of the most characteristic features of quantum mechanics, the quantization of energy.
The magnetic properties of molecules
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

This chapter explores the properties of molecules exposed to an electric field, noting that the source of the field may be external or, when considering intermolecular forces, another molecule. It points out how the field may be either constant in time or oscillatory. Knowledge of the influence of an electric field enables the discussion of a variety of related molecular properties. The chapter covers the relative permittivity of a bulk sample, the refractive index, optical activity, and intermolecular properties, drawing on the material on perturbation theory. It explores the consequences of a simple perturbation and establishes an expression for the polarizability, a measure of the ability of the molecule to respond to an electric field and acquire an electric dipole moment.
Carbohydrate recognition in cell adhesion and signalling
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

This chapter describes carbohydrate recognition in cell adhesion and signalling. Some lectins that serve as receptors for specific glycans recognize foreign cell surfaces and mediate or modulate immune responses to pathogens while others bind to endogenous carbohydrates and mediate adhesion or signalling events at the cell surface. Indeed, cell adhesion and signalling are mediated by structurally diverse lectins that recognize diverse glycans. One common feature of these systems is that they often involve transient interactions between cells that are moving relative to each other. Mice lacking individual lectins of the types discussed in the chapter are viable, but suffer from developmental or immunological abnormalities. The phenotypes of these mice demonstrate the importance of lectin recognition events in the precise orchestration of cell–cell interactions in mammals.
Glycobiology and development
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

This chapter highlights the relationship between glycobiology and development. Much of our knowledge of the biological functions of glycosylation derives from observing the phenotypes that result from mutations in genes encoding glycosyltransferases and glycan-binding receptors. The genetic and biochemical results described in the chapter provide compelling evidence that many types of glycosylation play important roles in establishing the basic body plan of vertebrates and invertebrates, in the development of organs, and in the maturation of the nervous and immune systems. In several cases, specific glycan structures needed for these processes have been identified, but in most cases we lack a clear understanding of how these glycans exert their effects. A major goal for the future will be to define how these glycans work, either through binding to specific receptors or by modulating the behaviour of molecules at the surfaces of interacting cells.
Capillarity and the mechanics of surfaces
Authors: Barnes Geoffrey , Gentle Ian
Published: September 2023

This chapter explains surface tension as a phenomena observed in systems containing an interface in which one of the phases is a liquid. It refers to the rise of liquid in a narrow tube as an example of surface tension, which is characterized by the drops of liquid tending to be spherical and the water spreading evenly on some surfaces. It also reviews the origin of surface tension from a molecular point of view, which considers the forces acting on a molecule at the surface of a liquid compared to those acting on one in the bulk. The chapter analyses the methods for measuring the surface tensions of solids that are at best approximate and often involve questionable assumptions. It highlights an example wherein the measured increase in vapour pressure for small spherical particles of solid can be used with the Kelvin equation.
Insoluble monolayers and Langmuir-Blodgett films
Authors: Barnes Geoffrey , Gentle Ian
Published: September 2023

This chapter reviews the adsorption at the gas-liquid interface of amphiphiles whose hydrophilic-lipophilic balance made them soluble in water. It discusses adsorbed films substances that have significant dynamic and equilibrium relationships with one of the bulk phases, noting that much information about the adsorbed films can be obtained from these relationships and from measurements on the bulk phase. It also examines amphiphiles with a stronger lipophilic or hydrophobic moiety that are less soluble in water and in the extreme are practically insoluble. The chapter cites water-insoluble amphiphiles that have special properties and are able to form insoluble films at the air-water interface. It analyses substances that may form monolayers that consist of molecules that are amphiphilic.
Spectroscopy
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter discusses mass spectrometry, infrared (IR) spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy. The basic function of a mass spectrometer is to measure the mass of a molecule or, more correctly, an ion. A mass spectrometer can only separate and detect charged ions; neutral molecules cannot be detected. Both positive and negative ions can be detected, depending on the technique used. In IR spectroscopy, IR radiation is shone through a sample and certain frequencies (energies) are absorbed as molecules move to higher vibrational energy levels. Meanwhile, NMR looks at the environments of nuclei within molecules and is able to detect which nuclei are close to one another on the bonding network.
Main-group chemistry
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter focuses on the chemistry of what are usually called the ‘main group’ elements, which are those in the s- and p-blocks. Although the main group elements are very diverse, ranging from the most typical metals through semi-metals to the most typical non-metals, the reason that they are often considered together is that these elements show a gradual variation in their chemical properties which can largely be understood using a small number of key concepts. The elements from Groups 12–18 show variable oxidation states. For a given element, the highest oxidation state of (group number minus 10) is often only shown by the fluoride or oxide of that element. Metal halides may be hydrolysed, depending on the acidity of the aquo ions; hydrolysis of non-metal halides gives acidic solutions. Meanwhile, metal oxides tend to be basic or amphoteric while non-metal oxides tend to be acidic.
Chemical thermodynamics
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter describes chemical thermodynamics. The First Law of Thermodynamics is concerned with the conservation of energy. Like all physical laws, the First Law cannot be proved, but its validity is established by the fact that the predictions it makes are in accord with experiments and observations. The work done when a gas expands against an external force is particularly important for two reasons: firstly, it helps in understanding the important concept of a reversible process; secondly, it is crucial in understanding why enthalpy is a useful state function. The chapter then looks at how the molar Gibbs energy of a gas in a mixture depends on its partial pressure. The temperature dependence of the equilibrium constant is given by the van't Hoff isochore.
Introduction: parasites, pathogens, and immunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter begins by considering parasitism. It seeks to understand questions such as: Why are there parasites? What do they want? Is it better to be a parasite or not? Why do some parasites cause disease while others are harmless? The chapter then looks at studies on infectious organisms (microbiology) and the means by which the host can try to control them (immunology). It uses the term 'pathogen' for microorganisms that get into larger animals and do harm. The chapter introduces the five classes of pathogen which cause infectious disease: the
viruses, bacteria, fungi, protozoa,
and
helminths
(worms), together with those strange bits of infectious protein, the
prions
. Finally, the chapter analyzes immunity in its broadest sense, including the devices by which hosts try to keep parasites out as well as those they use against the ones that get in.
Prions
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter unfolds the identification of a novel form of pathogen: the prion. It emphasizes that the name, coined by Stanley Prusiner in 1982, represents the existence of a protein that is infectious. A few authorities are still unconvinced, but the evidence for prions as pathogens is now fairly overwhelming. The chapter then demonstrates some of the key steps in the development of the prion theory. Next, the chapter elaborates on the striking feature of the pathology of prion diseases: the apparent lack of immune responses to the damaged brain tissue. It then reviews the discovery that lichen-derived enzymes can apparently degrade prion proteins.
Defence, immunity, the immune system
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter outlines the development of a whole new understanding of the causes and effects of infectious disease and how to treat such diseases. It elucidates the two new disciplinesmicrobiology and immunologytogether with the gradual identification of a body wide repertoire of organs, cells, and molecules devoted to controlling infection: the immune system. The chapter also discusses the problem of defence against a pathogen, then demonstrates the three levels of defence: external defences, the innate immune system, and the adaptive immune system. The chapter then highlights that an immune system requires three sets of components to work properly: recognition molecules, disposal mechanisms, and a communication system. Finally, the chapter presents the distinction of the two parts of the immune system: the innate and the adaptive immune systems.