bluuebunny/crossref_metadata_2025 huggingface dataset:
Pharmacogenetics and Personalized Medicine
Authors: Jennings Barbara , Thalange Nandu , Willis Gavin
Published: September 2023

This chapter presents pharmacogenetics and personalized medicine. It defines pharmacodynamics as being concerned with the effects of drugs on target cells and tissues, while pharmacokinetics is the study of the movement of drugs on target cells and tissues. The chapter discusses the adverse impact and ethical principle of a doctor's oath of doing no harm. It highlights the actionable mutations in the development of cancer and companion diagnostics. The chapter also explores pharmacogenomics. It cites the benefits and issues of treatment stratification and personalized medicine. Lastly, it notes that data about the biomarkers can be collected from tests of individual loci and gene panels, or whole genome analysis.
Protein Science
Authors: Lesk Arthur
Published: September 2023

Protein Science introduces the essential topics in protein science by describing the basic chemical structure of proteins, the factors that stabilize protein structures, protein function, and protein evolution. It begins by placing proteins in their general context in life. They are synthesized as amino-acid sequences encoded in genomes, and fold spontaneously to three-dimensional structures. This is the point where life makes the tremendous leap from the one-dimensional world of genome and amino-acid sequences, to the three-dimensional world of protein structures—indeed, the world which we inhabit.
Setting The Stage
Authors: Lesk Arthur
Published: September 2023

This chapter surveys the properties of proteins. The fundamental features of individual proteins relate to the following: the way that the sequences of amino acids assembled into polypeptide chains, the three-dimensional structures into which they fold, and the functions they perform. Proteins are created through going through the stages of Francis Crick's Central Dogma which involve the regions of the genome. They are then transcribed to RNA and translated by ribosomes to the amino-acid sequences of proteins. Next, they fold spontaneously to native structures. This is the point where life makes the leap from the one-dimensional world of DNA, RNA, and amino-acid sequences, to three-dimensions. The chapter then identifies the variety of functions that proteins provide, including structural components of cells and tissues, and the catalytic activities of enzymes. Regulation of protein expression and activity—to a large extent, by proteins—is essential in organizing the activities of cells. Finally, the chapter looks at the two main mechanisms of protein evolution, which include mutations at individual sites that allow local exploration of sequence space, and the ‘mixing and matching’ of different domains. Conversely, mutations that lead to protein dysfunction are the cause of many diseases.
Power Analysis: An Introduction for the Life Sciences
Authors: Colegrave Nick , Ruxton Graeme D.
Published: September 2023

Power Analysis starts by asking: what is statistical power and why is low power undesirable? It then moves on to considering ways in which we can improve the power of an experiment. It asks how we can quantify power by simulation. It also examines simple factorial designs and extensions to other designs. Next, it asks how we can deal with multiple hypotheses. Finally, it looks at how to apply the simulation approach presented in this book beyond null hypothesis testing.
What is statistical power?
Authors: Colegrave Nick , Ruxton Graeme D.
Published: September 2023

This chapter defines the terms 'population' and 'sample' in the context of a scientific study and identifies the null hypothesis associated with any scientific question. It determines what inferences can and cannot be drawn from a p-value and elaborates the concepts of Type I and Type II error in terms of null hypothesis testing. It also explains statistical power and analyses its link to Type II error. The chapter discusses the study of an appropriate representative sample of the population of interest and the use of statistics as an attempt to make generalizations about the population that the sample represents. It introdduces tools developed by statisticians that use information from samples to draw inferences about the populations that they represent.
Extensions to other designs
Authors: Colegrave Nick , Ruxton Graeme D.
Published: September 2023

This chapter covers how to simulate experimental studies where the predictor variable is continuous and there is a straight-line relationship between the response and the predictor. Moreover, it explores simulations that include other kinds of relationships, such as a quadratic one. It also demonstrates how to deal with response variables which are not continuous, as well as with variation that does not follow a normal distribution. The chapter looks at another common type of biological study in which both the response and the predictor variable are continuous. It talks about the possibility of having a different number of replicates at each level and explores situations where the relationship is either linear or non-linear.
Applying our simulation approach beyond null hypothesis testing: parameter estimation, bayesian, and model-selection contexts
Authors: Colegrave Nick , Ruxton Graeme D.
Published: September 2023

This chapter talks about the performance of a simulation analysis in the contexts of the precision of a parameter estimate, Bayesian statistics, and model selection. It describes null hypothesis testing as an absolute dominant form of statistical inquiry that remains important to a lot of researchers in many different areas of the life sciences. It also reviews toolkits of statistical approaches which are in common use alongside null hypothesis testing. The chapter reviews the simulation approach to power in the context of null hypothesis testing and other contexts that estimate the size of a parameter or select from a number of alternative models. It uses examples to explore simulation analysis in the context of precision of parameter estimation.
Atkins’ Physical Chemistry
Authors: Atkins Peter , Paula Julio de , Keeler James
Published: September 2023

Physical Chemistry provides a comprehensive overview of this topic. It starts off with looking into the properties of gases. It then covers the First, Second, and Third Laws. Next it looks into physical transformations of pure substances, simple mixtures, and chemical equilibrium. The text also considers quantum theory, atomic structure and spectra, molecular structure, molecular symmetry, and molecular spectroscopy. There follows a chapter about magnetic resonance. The text then looks at statistical thermodynamics. The last quarter of the book considers molecular interactions, solids, molecules in motion, chemical kinetic, and reaction dynamics. The last chapter covers processes at solid surfaces.
Real gases
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter evaluates real gases, which do not obey the perfect gas law. The extent of deviations from perfect behaviour is summarized by introducing the compression factor. Meanwhile, the virial equation is an empirical extension of the perfect gas equation that summarizes the behaviour of real gases over a range of conditions. The chapter then considers the critical constants before explaining the van der Waals equation. The van der Waals equation is a model equation of state for a real gas expressed in terms of two parameters, one, representing molecular attractions and the other, representing molecular repulsions. It captures the general features of the behaviour of real gases, including their critical behaviour.
The measurement of entropy
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter studies the measurement of the entropy of a substance, which is important to make the Second Law quantitative. This is achieved by measuring heat capacities. The chapter then looks at the calorimetric measurement of entropy. Entropies are determined calorimetrically by measuring the heat capacity of a substance from low temperatures up to the temperature of interest and taking into account any phase transitions in that range. The chapter also explains the Debye extrapolation, the Nernst heat theorem, and the Third Law of thermodynamics. Finally, it considers the standard reaction entropy, which is the difference between the molar entropies of the pure, separated products and the pure, separated reactants, all substances being in their standard states.
Atomic spectra
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter explains the general idea behind atomic spectroscopy. It details how lines in the spectrum (in either emission or absorption) occur when the electron distribution in an atom undergoes a transition wherein its energy changes by ΔE. The spectra of many-electron atoms are more complicated than that of hydrogenic atoms. Even though similar principles apply, Coulombic and magnetic interactions between the electrons give rise to a variety of energy differences, which are summarized by constructing term symbols. The chapter notes how total angular momentum in light atoms is obtained based on Russell–Saunders coupling, while jj-coupling is used for heavy atoms.
Decay of excited states
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter considers the decay of excited states. Radiative decay is a process in which a molecule discards its excitation energy as a photon. Moreover, the process can be determined to be ‘fluorescence’ or ‘phosphorescence’ depending on the nature of the excited state after the removal of exciting radiation. The chapter explains that non-radiative decay refers to the transfer of excess energy into the vibration, rotation, and translation of the surrounding molecules. It also considers the use and features of lasers, which primarily acts to discard the excess energy of an excited state by using radiation to induce stimulated emission.
The electric properties of molecules
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter discusses molecular interactions, which are responsible for the formation of condensed phases, and large molecular assemblies, which arise from the electric properties of molecules. It explores how the electronic structures of molecules account for these molecular interactions. It also points out that the nuclei of atoms exert control over the electrons in a molecule, which affects the distribution of the electrons and how it responds to external fields. The chapter examines why electric properties of molecules are responsible for many of the properties of bulk matter. It highlights the small imbalances of charge distributions in molecules and the ability of electron distributions to be distorted that allow molecules to interact with one another and respond to externally applied fields.
Macromolecules
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter focuses on macromolecules that give rise to special problems that include the investigation and description of their molar masses and shapes. It discusses how to describe the structural features of macromolecules in order to understand their physical and chemical properties. It also looks at the structure of a macromolecule that takes on different meanings at the different levels at which the arrangement of the chain or network of its building blocks is considered. The chapter describes macromolecules as large molecules that are assembled from smaller molecules biosynthetically in organisms, by chemists in the laboratory, or in an industrial reactor. It deals principally with synthetic macromolecules, such as polymers like nylon and polystyrene.
Diffusion
Authors: Atkins Peter , de Paula Julio , Keeler James
Published: September 2023

This chapter considers the diffusion of solutes and various physical properties as an important process in liquids. It introduces the concept of a general ‘thermodynamic force’. This can be regarded as being responsible for the motion of molecules and used to construct the important ‘diffusion equation’, which describes how solutes spread out in space with increasing time. The chapter explains how the diffusion of chemical species through space controls the rates of many chemical reactions in chemical reactors, living cells, and the atmosphere. The chapter draws on arguments relating to the calculation of flux and the notion of drift speed. It uses the concept of chemical potential to discuss the direction of spontaneous change and a statistical argument to explore the properties of a random coil.
Constitutional Isomers and Chemical Names
Authors: Elliott Mark C.
Published: September 2023

The Purpose of The Exercise

It’s really about getting more practice! Sometimes it’s that simple. The added layer here is that it isn’t always possible to draw a plausible structure for any given molecular formula. A good chemist will spot the impossible formulae...
Bonding and Antibonding Orbitals
Authors: Elliott Mark C.
Published: September 2023

Electrons reside in orbitals. In stable molecules, these tend to be bonding orbitals— there is a high probability of finding electron density between the nuclei involved in the bond.

Whenever we form a bonding orbital by overlap of electrons from two atoms, we always form...
Electronegativity in Context
Authors: Elliott Mark C.
Published: September 2023

The Purpose of The Exercise

We have looked at substitution reactions, so you are now in a position to consider whether you could attack a particular carbon in a structure and have ‘something’ leave. That ‘something’ needs to be able to cope with a negative...
A Closer Look at Bond Dissociation Energies
Authors: Elliott Mark C.
Published: September 2023

This is a new type of chapter. The purpose is to give you a bit more detail. The downside of this is that some of the ideas are quite complicated. I wanted to keep this material with the rest of the discussion of bond dissociation...
Energetics and Reaction Profiles
Authors: Elliott Mark C.
Published: September 2023

Introduction—Reaction Profiles

In Basics 11 we looked at the energy differences between starting materials and products. We might be tempted to think that if a reaction product is more stable than the starting material, the reaction would proceed. It’s a lot more complicated...
Methyl Groups Are Electron-Releasing
Authors: Elliott Mark C.
Published: September 2023

What’S The Problem?

So, here is the thinking.

A methyl group stabilizes a carbocation and destabilizes a carbanion. Therefore, methyl is electron-releasing.

Actually, it’s fine up to that point, as long as we are talking about carbocations and carbanions. It just doesn’t apply to stable...
Getting Used to Drawing Stereoisomers
Authors: Elliott Mark C.
Published: September 2023

The Same Structure Drawn In Different Ways

We are going to use amino acids as examples in the following discussion. The proteins and enzymes in your body are polymers of amino acids, and with only one exception, the amino acids are chiral. Only one enantiomer...
Selectivity in Organic Chemistry—Regioselectivity
Authors: Elliott Mark C.
Published: September 2023

Regioselectivity

A regioselective reaction produces more of one isomer than another. We haven’t looked at the hydration (addition of water) of alkenes, but this doesn’t matter. Each isomer is produced by the same reaction but at a different end of the...
Substitution Reactions of Cyclohexanes
Authors: Elliott Mark C.
Published: September 2023

This is another ‘Applications’ chapter, so you need to do the work, rather than just reading through and convincing yourself that you understand everything. We are applying what we have discussed about substitution reactions to cyclohexane systems.
More Conformers of Cyclohexanes and Related Compounds
Authors: Elliott Mark C.
Published: September 2023

Now you are getting used to cyclohexane chairs, we need to look at the other possible conformers.

Watch Video Tutorial 5.5 for more guidance
Epoxide Opening Reactions
Authors: Elliott Mark C.
Published: September 2023

Introduction

An epoxide is a compound with a three-membered ring containing an oxygen atom. We encountered them in Basics 28 and Applications 2.

An epoxide is an ether in a ring.

All of the ring atoms in an epoxide are sp3 hybridized....
Competing SN2 Substitution and E2 Elimination
Authors: Elliott Mark C.
Published: September 2023

Answer 1

Here are the resonance forms, showing that the lone pair on the nitrogen in the seven-membered ring is conjugated with the C=N double bond. It isn’t available.
Complex Substitution Stereochemistry
Authors: Elliott Mark C.
Published: September 2023

Answer 1

Here they are.
Afterword
Authors: Elliott Mark C.
Published: September 2023

So, you’ve got to the end. Hopefully you have enjoyed reading this book. More importantly, I hope you have understood all of the explanations and learned quite a lot of organic chemistry.

Did you ‘just’ read this book?

If you did, then that’s okay. The...
Receptors: structure and function
Authors: Patrick Graham L.
Published: September 2023

This chapter examines the structure and function of receptors, which are membrane-bound proteins that contain an external binding site for hormones or neurotransmitters. It looks at neurotransmitters and hormones and shows how they do not undergo a reaction when they bind to receptors but instead they depart the binding site unchanged once they have passed on their message. The chapter also describes interactions that bind a chemical messenger to the binding site and shows that this must be strong enough to allow the chemical message to be received, but weak enough to allow the messenger to depart. The chapter examines receptors controlling ion channels. These are an integral part of the ion channel. Finally, the chapter looks at ligand-gated ion channel receptors. These consist of protein subunits with the receptor binding site being present on one or more of the subunits.
Drug design: optimizing target interactions
Authors: Patrick Graham L.
Published: September 2023

This chapter discusses interactions that involve dipole moments or induced dipole moments. These play a role in binding a lead compound to a binding site. The chapter demonstrates how reactive functional groups, such as alkyl halides, may lead to irreversible covalent bonds being formed between a lead compound and its target. It also examines the relevance of a functional group to binding, which can be determined by preparing analogues where the functional group is modified or removed. The chapter outlines functional groups, such as alcohols, amines, esters, amides, carboxylic acids, phenols, and ketones, and looks at how these can interact with binding sites by means of hydrogen bonding. It reviews alkyl substituents and carbon skeleton of the lead compound which can interact with hydrophobic regions of binding sites by means of van der Waals interactions.
The design of oxamniquine
Authors: Patrick Graham L.
Published: September 2023

This chapter explores the development of oxamniquine by Pfizer pharmaceuticals, which the chapter uses as an example of how traditional strategies can be used in the development of a drug where the molecular target is unknown. It describes oxamniquine as an important drug in developing countries. This drug is used in the treatment of schistosomiasis. After malaria, schistosomiasis is the most endemic parasitic disease in the world, affecting about 236 million people in 78 countries and causing up to 200,000 deaths each year. The chapter highlights the effectivity of oxamniquine as a single oral dose for treating infections of S. mansoni. Oxamniquine is known to inhibit nucleic acid synthesis in schistosomal cells.
Design of a thymidylate synthase inhibitor
Authors: Patrick Graham L.
Published: September 2023

This chapter looks at an early example of how the strategies of de novo drug design and structure-based drug design were used together to develop an active compound which went forward for clinical trials. It reviews the research involved i the design of inhibitors for the enzyme thymidylate synthase. It also explains how thymidylate synthase catalyses the methylation of deoxyuridylate monophosphate (dUMP) to deoxythymidylate monophosphate (dTMP) using 5, 10-methylenetetrahydrofolate as a coenzyme. The chapter describes inhibitors which are structurally related to the natural substrate and cofactor. It explores the use of the de novo drug to design a novel structure unrelated to natural substrates.
Antibacterial agents
Authors: Patrick Graham L.
Published: September 2023

This chapter looks at antibacterial agents, such as the sulphonamides, penicillins, and cephalosporins, which act by inhibiting enzymes and synthetic enzyme inhibitors. It explores the principle of chemotherapy. This involves the design of chemicals that show selective toxicity against bacterial cells, rather than mammalian cells. It also traces early antibacterial agents, such as salvarsan, prontosil, and the sulphonamides. It examines the discovery of penicillin and several classes of antibiotics that were isolated from fungal strains. The chapter discusses five main targets that antibacterial agents act on: cell metabolism, cell wall, plasma membrane, protein synthesis, and nucleic acid function. It mentions steric shields and looks at how these can be added to penicillins to protect them from bacterial β-lactamase enzymes.
Anti-ulcer agents
Authors: Patrick Graham L.
Published: September 2023

This chapter looks at peptic ulcers, which are localized erosions of the mucous membranes and occur in the stomach and duodenum. It analyzes hydrochloric acid (HCl) present in gastric juices which results in increased irritation, noting how drugs that inhibit the release of HCl act as anti-ulcer agents. It also talks about chemical messengers, namely histamine, acetylcholine, and gastrinc, that stimulate the release of HCl from stomach parietal cells by acting on their respective receptors. The chapter examines the use of H2-antagonists, which are anti-ulcer drugs that act on H2 receptors present on parietal cells. These reduce the amount of acid released. It describes the alignment of dipole moments between a drug and its binding site and shows how this plays a role in the binding and activity of H2-antagonists.
What Is Marine Biodiversity?
Authors: Kent Michael
Published: September 2023

This chapter covers what is meant when we talk about marine biodiversity. The term ‘biodiversity’ is a value-laden term because of its links to biological conservation. Marine biodiversity can be studied at any level of biological organization, from biomolecules to the biosphere. Whether or not viruses should be included as part of biodiversity depends on how life is defined. The chapter then differentiates between genetic diversity, species diversity, ecosystem diversity, and functional diversity. Genetic diversity includes the variation of genetic information in individuals, species, populations, and the biosphere. High genetic diversity is associated with high ecosystem resilience. Species diversity is the most common level of biological organization at which marine biodiversity is assessed. Meanwhile, marine ecosystem diversity is considered in relation to marine habitats and the importance of keystone species.
Presenting Scientific Data in R
Authors: Humphreys Rosalind K. , Ruxton Graeme D.
Published: September 2023

Presenting Scientific Data with R provides a guide to data presentation using R. It offers valuable and applicable advice on how to choose the most appropriate type of graph for different types of data, and guides readers from the basics of plotting clear figures to producing polished and effective visuals, illustrating the core concepts and features of excellent graphing. This text uses simple biology-based example data sets to take readers from the essential aspects of basic plots to more advanced graphing techniques and details. The text starts off with an introduction. It then considers pie charts and tables for qualitative data. Next it looks at bar charts. There follow chapters on presenting single-sample data (i.e. histograms and boxplots) and comparing multiple samples. There is also a chapter that covers scatterplots for quantitative data. Finally, the text finishes with a couple of chapters on day-to-day customizing everything using R and specialist customizing everything using R.
Introduction and getting started
Authors: Humphreys Rosalind K. , Ruxton Graeme D.
Published: September 2023

This chapter introduces the importance of good graphing. It starts by acknowledging that data is the heart of all science. Since gathering data could be a messy process, data visualization allows the organization of data into a clear summary that showcases the findings in an accessible and engaging way. However, the best type of figure to use in graphing depends on the type of data and the data to express. For example, choosing colours for the graph can allow people to clearly communicate extra information with clarity and visual appeal. The chapter explains that R is a hugely flexible graph-drawing package that can be used with RStudio's user-friendly interface to achieve professional-quality figures.
Customizing everything using R: more specialist
Authors: Humphreys Rosalind K. , Ruxton Graeme D.
Published: September 2023

This chapter outlines walk-throughs of R code using specific data examples. The aim of this is to provide generic and editable code for a range of plotting and design features. The chapter showcases the R code using examples of a bar chart and a scatterplot as a base to reference its respective customization. Design components (frames, images, background images, arrows, symbols, and shapes) can be added to figures with relatively little effort. Moreover, high-quality figures with inset plots can be achieved by modifying plot space parameters in an effort to avoid misleading readers when using a non-zero y-axis. The chapter also considers tricks used how to annotate images or geographic maps in the R plotting space.
The Biochemical Basis of Sports Performance
Authors: Maughan Ronald J. , Gleeson Michael
Published: September 2023

The Biochemical Basis of Sports Performance looks at this topic by type of sport. Firstly, however, it introduces with an assessment of the biochemical basis of exercise and sport. The first sport it tackles is weightlifting, for which muscle strength and function are vital. It looks at protein in enzymes and the nutritional effects on strength training and performance. Next, it turns to the sprinter, for whom anaerobic metabolism is important. Then, it looks at middle-distance events and talks the reader through the glycolytic pathway amongst other elements. After that comes the endurance athlete who needs to consider energy supply and aerobic power. The game player follows and here fatigue in sprint sports is looked into. The text then moves on to a more general discussion of what constitutes sporting talent. It ends with a look at adaptations to training: training for speed, strength, middle-distance, endurance, and training strategies.
The Physicochemical Basis of Pharmaceuticals
Authors: Moynihan Humphrey A. , Crean Abina M.
Published: September 2023

Physicochemical Basis of Pharmaceuticals explores the physical and chemical phenomena which affect the formulation and bio-availability of drug substances to give a treatment of the essential concepts affecting the absorption and distribution of drugs. The first chapter covers pharmaceuticals and medicines. The next chapter looks at pharmaceutical solutions. There follows a chapter on pharmaceutical equilibria. Then there is a chapter on the pharmaceutical solid base. The text also looks at two phase solid-liquid disperse systems and biological interfaces. The final chapter is about physiochemical aspects of pharmacokinetics and pharmacodynamics.
Amino Acid and Peptide Synthesis
Authors: Jones John
Published: September 2023

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.
Introduction
Authors: Jones John
Published: September 2023

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.
Strategy and tactics
Authors: Jones John
Published: September 2023

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.
Solid phase peptide synthesis
Authors: Jones John
Published: September 2023

This chapter discusses solid phase peptide synthesis, an idea which first appeared in a scientific publication by Merrifield in 1963. It explains why the term ‘solid phaseȉ is misleading, elaborating that the reactions do not take place in or on the surfaces of solid phases, but in gel systems produced by the penetration of solvent and solute molecules into the polymeric matrix. The chapter also reviews how solid phase methods dominate synthetic peptide research and have been extended to other fields, such as peptide sequence analysis and oligonucleotide synthesis. The chapter looks at Merrifield's description of a synthesis of bradykinin, which served as the prototype for the standard approach associated with his name. It explores Merrifield's approach, wherein polystyrene that is crosslinked by the incorporation of a small amount of divinylbenzene is chloromethylated. It also covers the Sheppard approach introduced in the 1970s
GFR a tour de force
Authors: Jones John
Published: September 2023

This chapter describes the green fluorescent protein (GFP) of the jellyfish Aequorea victoria, which is a single chain protein of 238 residues and used as a visible marker in molecular biology and biomedical work. The fluorophore is formed by a unique and incompletely understood backbone modification of the region Ser65-Tyr66-Gly67, which is spontaneous when conditions are right. It also discusses fragment condensation in solution with relatively stable side-chain permanent protection, which is in conjunction with Boc α-amino temporary protection. The chapter also gives an example of short protected fragments of about 10 residues each that were prepared by stepwise solid phase peptide synthesis. It highlights protected peptides anchored through an acid-stable, base-liable ester that can be assembled by a Merrifield approach.
1H NMR: Proton nuclear magnetic resonance
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter highlights proton (1H) nuclear magnetic resonance (NMR). Proton NMR differs from 13C NMR in a number of ways. 1H is the major isotope of hydrogen, while 13C is only a minor isotope. 1H NMR is quantitative: the area under the peak shows the number of hydrogen nuclei, while 13C NMR may give strong or weak peaks from the same number of 13C nuclei. Moreover, protons interact magnetically (couple) to reveal the connectivity of the structure, while 13C is too rare for coupling between 13C nuclei to be seen. Finally, 1H NMR shifts give a more reliable indication of the local chemistry than that given by 13C spectra. Nevertheless, proton NMR spectra are recorded in the same way as 13C NMR spectra: radio waves are used to study the energy level differences of nuclei in a magnetic field, but this time they are 1H and not 13C nuclei.
Organometallic chemistry
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter examines organometallic chemistry. It introduces the concepts of metal–ligand interaction, describes the most important reactions that can occur while ligands are bound to the metal, and demonstrates the power of organometallic chemistry in synthesis. The efficiency of transition metal-catalysed reactions means that they are routinely used in industrial synthesis. There is a simple guide to the stability of transition metal complexes: the 18-electron rule. If a complex satisfies the 18-electron rule it means that the metal at the centre of the complex has the noble gas configuration of 18-electrons in the valence shell, and the complex is likely to be stable. The chapter then considers that palladium is the most widely used metal in homogenous catalysis, before looking at the Heck reaction.
Glycobiology of plants, bacteria, and viruses
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

This chapter focuses on the glycobiology of plants, bacteria, and viruses. The use of oligosaccharides derived from cell walls as signalling molecules in plants and the adoption of mammalian cell surface glycans as receptors for bacteria and viruses illustrate how glycans have been adapted to serve new functions during evolution. It is interesting to note that many of the non-mammalian lectins described in the chapter bind to mammalian glycan structures similar or identical to structures recognized by mammalian lectins. In other cases, sugar-binding activity seems to have arisen independently in the context of novel protein folds. Nevertheless, the themes of shallow, weak monosaccharide-binding sites that are extended and combined to achieve higher affinity is repeated in each branch of organisms and the sugar–protein interactions rely on many of the same types of hydrogen bonding and hydrophobic interactions.
Chemical Structure and Reactivity
Authors: Keeler James , Wothers Peter
Published: September 2023

Chemical Structure and Reactivity is made up of two main parts. Part I covers the fundamentals and looks at molecules and molecular structures, electrons in atoms, symmetry, electrons in molecules, bonding in solids, thermodynamics, reactions, and organic chemistry. Part II delves deeper into the topics and examines spectroscopy, organic chemistry, transition metals, quantum mechanics and chemical thermodynamics, chemical kinetics, and electrochemistry.
Electrons in molecules: polyatomics
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter begins by showing how symmetry considerations make it possible to construct molecular orbital diagrams for simple triatomics. In these molecules, the MOs extend over all the atoms—that is, the bonding is delocalized. In fact, it is a general feature of the MO approach that atomic orbitals on many atoms contribute to each MO. Unfortunately, this means that as the number of atoms (and hence orbitals) increases, it rapidly becomes almost impossible to draw up useful qualitative MO diagrams. Hybrid atomic orbitals provide a convenient localized description of bonding in larger molecules. Due to the directional nature of the hybrid atomic orbitals, their overlap gives bonds which are localized between two atoms. This greatly simplifies the description of the bonding in larger molecules, as it can be broken down into a set of interactions between just two atoms at a time.
Trends in bonding
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter addresses how an understanding of the way in which orbital energies and sizes vary across the periodic table enables one to rationalize the nature of the bonding between elements. It begins by considering the electronic configuration of the elements, and the energies of the occupied orbitals. The variation in orbital energies across the periodic table can be understood in terms of the increase in nuclear charge, the extent to which different electrons screen one another from the nucleus, and the shell to which a particular orbital belongs. The concept of the effective nuclear charge experienced by an electron is a useful way of rationalizing trends in the sizes of orbitals, ionization energies, and electron affinities. The chapter then looks at the bonding between atoms of the same element, and how the nature of this bonding affects the structure and physical properties of the element.
Organic chemistry 3: reactions of π systems
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter evaluates reactions in which C=C double bonds are formed and the reactions which such molecules undergo, including elimination reactions. Given that C=C double bonds are electron rich, their most characteristic reactions are with electrophiles. The chapter looks at typical examples of these reactions and the factors that control which carbon is attacked in an unsymmetrical double bond. It then turns to the enols and enolates, which are formed from aldehydes and ketones under acidic and basic conditions. The chapter also considers aromatic systems, exemplified by benzene. The special stability of the π system in a benzene ring means that the molecule tends to react in such a way that the aromatic ring is preserved. As a result, the reactions of benzene are quite different to those of simple π systems, being mainly electrophilic substitution rather than addition.
Helminths (worms)
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter outlines the general structure and function of worms. It notes that the vast majority of worms are free living, and only three classes of them include pathogens of humans: roundworms, tapeworms, and flukes. The chapter first describes the three species of the blood fluke Schistosoma and their complex life cycles. Schistosomiasis (also known as bilharzia) probably originated in the Nile valley, and has been identified in Egyptian mummies. The chapter then shifts to demonstrate the life cycle of nematodes, focusing on the filarial nematodes, non-filarial nematodes with a tissue phase, and intestinal nematodes. Next, the chapter investigates the life cycle of cestodes, which usually require an intermediate host in which a cystic stage develops. It then looks at how helminths can be controlled by drug treatment.
Ectoparasites
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter highlights the importance of ectoparasites as vectors for many major diseases. It first defines ectoparasites as the arthropods that live on or in the skin, often feeding on blood. The chapter then shifts to describe the mites, which parasitize a wide range of animals and plants. It then investigates the ticks, which live on the skin surface and feed on blood. The chapter assesses their complex life cycle, and how they are vectors for a number of serious diseases. The chapter also describes lice and the three species of human lice. Lice are wingless insects, parasitic on a variety of animals. Next, the chapter examines bacterial and rickettsial diseases in animals such as fleas. It then considers other insect vectors.
Disease due to innate immunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter examines the ways in which innate immune mechanisms can lead to pathology. It describes a group of microbial molecules which can cause havoc in the immune system. The chapter then distinguishes three related terms: septicaemia, sepsis, and septic shock. Focusing on a discussion about endotoxin and cytokines, the chapter then explores the number of systems affected by lipopolysaccharide (LPS), an innocuous-looking molecule, and other cytokine-mediated diseases. There is evidence that several inflammatory bowel diseases, notably ulcerative colitis and Crohn's disease, may be due to excessive local cytokine secretion. Finally, the chapter investigates how the activation of complement may lead to tissue damage in extreme cases. It then considers the destructive power of phagocytes, particularly polymorphs.
Immunodeficiency I: primary defects of innate immunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter concentrates mainly on immunodeficiency affecting the innate immune system. It elucidates the genetics of primary immunodeficiency, noting that primary defects are genetic abnormalities, usually single recessive mutations. They may be inherited if the mutation is in a gene present in the germ-line; if not, they are somatic and will only affect one individual. The chapter also reviews how the same genetic difference might affect different pathogens in different ways. It then emphasizes the most common primary defects affecting the innate system: those involving complement and phagocytic cells, which give rise to quite characteristic patterns of infection. Finally, the chapter talks about the deficiency of the mannose-binding lectin, MBL, other deficiencies in innate recognition, and chronic granulomatous disease. It also considers the causes of secondary immunodeficiency.
Adaptive immunity: introduction
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter begins with the description of adaptive immunity. It notes that the term uses the word adaptive because of the way this type of immunity allows both species and individuals to tailor-make their own set of recognition molecules, adapted to the microbes they actually encounter. In immunological language, the system displays high specificity and memory. The chapter then explores the other properties which distinguish lymphocytes from other immunological cells. It brings out the essential differences between lymphocytes and phagocytic cells. The chapter also outlines the lymphoid system, the total mass of lymphocytes in the body, then explains the fundamental part of lymphocyte function. It then considers the antigen, antigen-recognition molecules, clonal selection, and memory. The chapter concludes by discussing the regulation of adaptive immunity.
Bacterial disease and immunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter recalls the key properties of bacteria and the all-important distinction between extracellular and intracellular habitat. It reviews the immunological and therapeutic features of the most important pathogenic bacteria. The chapter begins with a discussion on staphylococcal infection, streptococcal infection, and clostridial infection. It then examines a disease of farm animals and farmers, anthrax, and other bacterial skin infections. The chapter also explicates the most important mycobacterial infection and one of the world's major health problems: tuberculosis. It then looks at respiratory infections, whooping cough, and the causes of meningitis. Next, the chapter considers some venereal diseases such as gonorrhoea and syphilis. It also considers plague, tularemia, and brucellosis, then discusses three infections: chlamydial infection, rickettsial infection, and mycoplasma infection.
Helminth disease and immunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter analyzes the features of worm infections. Though differing in detail, the chapter highlights that worm infections have four features in common: well-developed evasion mechanisms leading to chronicity; a bias towards the TH2 type of adaptive response; a tendency to induce strong immunopathology; and varying degrees of immunosuppression. The chapter first discusses a disease called schistosomiasis and explicates the immunity against schistosomiasis. The chapter then examines pathological immunity against filarial nematodes and discusses the disease filariasis. Finally, the chapter looks at the case of hydatid disease, and considers other tapeworm infections. It also elaborates on the increase in IgE levels and eosinophil counts in worm infections.
Physical Chemistry: Quanta, Matter, and Change
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Physical Chemistry starts off by looking at the foundations of the subject and provides the reader with some mathematical background. It then looks at quantum mechanics, taking into consideration the quantum mechanics of motion, molecular structure, and molecular symmetry. It then considers Fourier transforms, molecular spectroscopy, magnetic resonance, statistical thermodynamics, probability theory, the first law of thermodynamics, and multivariate calculus. The final part of the book examines physical equilibria, chemical equilibria, molecular motion, chemical kinetics, reaction dynamics, and processes in fluid systems and solid states.
Energy
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Force 9

Momentum 9

Brief illustration 2.1: The moment of inertia 10

Newton’s second law of motion 10

Brief illustration 2.2: Newton’s second law of motion 11

Energy: a first look 11

Work 11

Brief illustration 2.3: The work...
Biophysical Techniques
Authors: Campbell Iain D.
Published: September 2023

Biophysical Techniques starts off by introducing the topics that come under the umbrella of biophysical techniques. It then considers molecular principles in the biophysical sphere. It looks at transport and heat. Then it considers scattering, refraction, and diffraction. The text also looks at electronic and vibrational spectroscopy. Next, it moves on to magnetic resonance. Microscopy and single molecule studies are also examined in detail. Finally, computational biology is presented as a topic to end with.
Thrive in Immunology
Authors: Cunningham Anne C.
Published: September 2023

Thrive in Immunology first provides a detailed introduction to immune responses and looks specifically at cells, mediators, and structures and it asks: how is the immune system activated? It then considers what the immune system destroys. Finally, at the end of the text, the last section consider the role of the immune system in health and disease.
The Physiology of Training for High Performance
Authors: MacDougall Duncan , Sale Digby
Published: September 2023

The Physiology of Training for High Performance consists of three parts. Part I, which is about the physiological bases for athletic training, starts off with an introduction to training for high performance. It moves on to look at the biochemical bases and cardiorespiratory bases for performance. It looks at muscle physiology and then finishes with the neuromuscular bases for performance. Part II covers training for different sports and activities. It looks at endurance sports, anaerobic events, team sports, as well asnd training for power, strength, and speed as well. The last part, which presents additional factors affecting performance, looks at peaking, tapering, and overtraining; stretching and flexibility, and, finally, some other considerations, including nutrition, testing, altitude, and para-athletics.