bluuebunny/crossref_metadata_2025 huggingface dataset:
Human Infectious Disease and Public Health
Authors: Fullick William
Published: September 2023

Human Infectious Disease and Public Health starts off by looking at the historical development of our understanding of human infectious diseases, which it describes as ‘the silent enemy’. It then moves on to consider a number of important pathogens such as bacteria, fungi, viruses, parasites, prions, and cultures. This overview of pathogens is followed by a chapter which looks at the different defence mechanisms with which the human immune system fights off disease. The next two chapters cover how developments in the medical field have helped with fighting infections, firstly in terms of medication and, secondly, in terms of vaccination. The final chapter looks at global outbreaks and asks what a post-antibiotic landscape would look like.
Fighting against infection: a chemical approach
Authors: Fullick William
Published: September 2023

This chapter highlights the advances in medicine and microbiology over the past century which have led to huge advances in the way we treat infectious diseases—and how we can prevent them from occurring in the first place. These include antibiotics, antivirals, antifungal medications, and antiparasitic medications. Antibiotics are either bacteriostatic (halting division and growth of bacteria without killing them) or bacteriocidal (acting to destroy bacteria directly). They have a number of different common mechanisms of action, with many antibiotics working against multiple different types of bacteria. Meanwhile, antiviral medications must work to inhibit all reproduction of the virus otherwise resistant mutants will quickly appear. Many viral infections cannot be treated with antiviral agents, as each drug must be very specific to the individual virus (or small group of viruses).
Global outbreaks, a post-antibiotic landscape, and the evolutionary arms race
Authors: Fullick William
Published: September 2023

This chapter reflects on the future of infectious diseases. Improving global transport links, as well as the demand for food from all over the world, makes it easier than ever before for diseases to spread over great distances. Worldwide organizations such as the World Health Organization (WHO) aim to coordinate the efforts of local, national, and international public health organizations to track, treat, and prevent infectious disease. However, these efforts can sometimes be hindered by cultural or political boundaries, and sometimes disease can even be inadvertently spread by local customs or superstitions. Infectious diseases have evolved alongside humanity, and are constantly involved in an 'evolutionary arms race'. They develop ways to subvert our defences, or even manipulate our behaviour for their own good. New antibiotics are both difficult and expensive to discover, and many infections are now developing resistance to multiple different antibiotics.
Internal energy, enthalpy, and thermochemistry
Authors: Price Gareth
Published: September 2023

This chapter examines the origin of heat or enthalpy changes in terms of fundamental considerations of how and where energy occurs in molecules and how it changes when substances undergo chemical or physical change. It talks about how enthalpy changes give information on reaction mechanisms and which chemical bonds are involved during reactions. It also introduces heat capacity, a property of substances that is used to quantify energy changes due to heat transfer. The chapter covers nuclear energy changes governed by Albert Einstein's equation, which involves the loss in mass when nuclei are transformed at the speed of light. It discusses isolated systems that occur where there can be no exchange of heat or matter with the surroundings and a closed system that contains a fixed amount of matter but allows exchange of heat.
Entropy and Gibbs energy
Authors: Price Gareth
Published: September 2023

This chapter describes chemical reactions that occur very readily and go effectively to completion, causing the reactants to completely transform into products. It refers to other reactions that occur readily but do not go to completion, as they form an equilibrium mixture of reactants and products. It also explains the reaction of hydrogen and oxygen described as spontaneous, which is a reaction that proceeds in only one direction and continue without any outside intervention. The chapter highlights the main usefulness of entropy in chemistry which comes in predicting the direction of chemical change and comes from a large number of empirical observations embodied in the second law of thermodynamics. It traces the development of quantitative models for the entropy of systems in the nineteenth century, which relied on the consideration of heat–work cycles and the efficiency of heat engines.
Equilibrium in chemical reactions
Authors: Price Gareth
Published: September 2023

This chapter applies the concept of Gibbs energy to describe the factors that govern chemical equilibrium. It determines how far a reaction will go before it comes to equilibrium and how to find the equilibrium yield and make predictions about the effect that changed the experimental conditions on equilibrium. It also discusses the Gibbs energy of the system which changes throughout a reaction, depending on the proportions of reactants and products. The chapter mentions an equilibrium reaction with straightforward stoichiometry, such as the reaction of dinitrogen tetroxide to form nitrogen dioxide. It points out how adding or removing one of the components of a reaction affects the activity of the other components in the equilibrium mixture, since it will change the mole fractions.
Photosynthetic Life Origin, Evolution, and Future
Authors: Murphy Denis , Cardona Tanai
Published: September 2023

Photosynthetic Life brings together the latest research to show how the process of photosynthesis has evolved over the last three to four billion years — from its beginnings in bacteria to the various refinements now present in modern land plants. Chapters explain how repeated endosymbiotic and gene gain/loss events have led to the evolution of the various algal groups and related non-photosynthetic groups, and how photosynthesis was modified as plants evolved and diversified into different ecological niches around the world. The role of photosynthesis in the alteration of the geology and biology of the earth, which enabled the colonisation of the land by plants and animals, is also explored. Finally, this title examines the limitations of photosynthesis and the emerging biotechnological improvements that could make this vital process even more attractive as a source of clean energy, food and other industrial products.
Eukaryotic photosynthesis
Authors: Murphy Denis , Cardona Tanai
Published: September 2023

This chapter argues that oxygenic photosynthesis is the most important form of photosynthesis on Earth, which accounts for an estimated 3000-fold greater amount of carbon fixation. It discusses the emerging evidence that oxygenic photosynthesis might have its origins close to the beginnings of cellular life at around or before 4 Ga. It also recognizes oxygenic photosynthesis as the only form that was acquired by eukaryotes following a unique endosymbiotic event between a eukaryotic heterotroph and a cyanobacterium. The chapter focuses on the mechanisms of oxygenic photosynthesis in eukaryotes, and cites algae and plants. It also presents a comparative analysis of the extant cyanobacterial mechanisms which had a momentous effect on biological evolution.
Evolution of the algae
Authors: Murphy Denis , Cardona Tanai
Published: September 2023

This chapter investigates how the original primary endosymbiotic event between a eukaryotic heterotroph and a cyanobacterium led to multiple lineages of photosynthetic organisms. This included all of the main eukaryotic groups. It highlights original primary endosymbiosis which led directly to a single daughter lineage, the Archaeplastida, wherein all extant primary red and green algae and land plants emerged. It also explains that early red and green algae were highly efficient photosynthetic eukaryotes and these exploited a wide range of marine habitats. The chapter looks at how oxygenic photosynthesis increased atmospheric oxygen levels at around 0.6 Ga, which enabled the evolution of complex multicellular plants and animals. This set the stage for the colonization of land. The chapter describes certain algal groups which later evolved into non-photosynthetic heterotrophs, including important parasitic species of plants and animals.
Future prospects for photosynthesis and plant evolution
Authors: Murphy Denis , Cardona Tanai
Published: September 2023

This chapter reviews contemporary land flora and notes that it is increasingly dominated by human activities, such as agriculture. It points out that agriculture drastically reduced the global area occupied by natural vegetation and replaced it with a small number of domesticated plants used to feed either people or their livestock. It also looks at important photosynthetic processes that are amenable to improvement via biotechnology. The chapter talks about light-harvesting and electron-transfer mechanisms in crops that might be improved by incorporating features of cyanobacterial systems. It points out huge challenges facing photosynthetic life on Earth, emphasizing how many plant and animal groups are facing extinction. The chapter states that it is vital that strategies are developed to minimize human impacts.
Identification tests
Authors: Perry John
Published: September 2023

This chapter examines biochemical reactions that allow for differentiation of clinically important bacteria, looking at the application of identification tests. Bacterial identification is traditionally based on a presumptive assignment to a genus or species based on morphological and cultural characteristics, followed by confirmation using biochemical tests. The chapter explains how bacterial hydrolases can be detected and provides examples of specific hydrolases produced by pathogens. It demonstrates how carbohydrate metabolism and amino acid metabolism by bacteria can be exploited in bacterial identification, before showing how susceptibility tests can assist microbial identification. The chapter then discusses the principles of MALDI-TOF and immunological tests for bacterial identification, along with their benefits to diagnosis of infection. It also considers the pitfalls and quality issues with biochemical identification tests.
Susceptibility testing and antibiotic assay
Authors: Andrews Jenny
Published: September 2023

This chapter evaluates antimicrobial susceptibility tests. Antibiotics have played a major role in the treatment of infectious disease since the discovery of penicillin in the 1920s. However, while numerous antibiotics are available, laboratory support is required to determine which is the correct antibiotic for the treatment of a particular infection. The primary purpose of an antimicrobial susceptibility test performed in the laboratory (in vitro) is to assist clinicians in the choice of appropriate agents they can use for antimicrobial therapy. The chapter begins by outlining the commonly used antibiotics. It then looks at current national and international guidelines and methods available, including broth methods, automated susceptibility testing, and antibiotic assays. The chapter also considers enzymatic methods of resistance, studying the types and importance of β-lactamases, as well as the detection of antimicrobial resistance by molecular methods.
Investigation of respiratory samples
Authors: Hill-King Louise
Published: September 2023

This chapter explores the investigation of respiratory samples. Respiratory infections are among the most common causes of morbidity, and most individuals will succumb to a respiratory infection at some point in their lives. Clinicians send respiratory samples, such as sputum, to the microbiology laboratory in order to identify the causative organisms and to obtain guidance for administering appropriate treatment. The chapter describes the laboratory investigations that are used for detection of pathogenic organisms in lower respiratory tract samples. It begins by providing an overview of the anatomy of the respiratory tract and outlining the organisms that constitute normal respiratory flora. The chapter then looks at the common respiratory pathogens and how they cause respiratory disease, before explaining the routine tests used for processing respiratory samples. It also discusses infections associated with cystic fibrosis and mycobacteria, and examines the health and safety issues associated with respiratory samples.
Investigation of gastrointestinal specimens
Authors: Ford Michael , Nye Kathy
Published: September 2023

This chapter studies the investigation of gastrointestinal (GI) specimens. One of the most common types of infection, even in the Western world, is a GI infection characterized by diarrhoea and/or vomiting. In the developing world, due to poor sanitation, GI disease is extremely common and associated with significant morbidity and mortality. The chapter then looks at how microbiologists detect and identify the major, known microbiological causes of GI disease before offering an insight into their epidemiology, pathogenicity, and clinical management. Despite GI samples being most unpleasant to process, most biomedical scientists would agree that enteric microbiology is one of the most interesting and challenging areas to work in. The chapter also considers food and water microbiology.
Clinical parasitology
Authors: Worthington Tony
Published: September 2023

This chapter focuses on clinical parasitology, which is an important sub-discipline of pure parasitology and may be defined as the study of human infections caused by ecto- and endoparasites. During the twenty-first century, parasites have come to contribute to an ever-increasing number of human blood, tissue, and gastrointestinal infections that are often associated with important risk factors. The chapter begins by differentiating between protozoa, nematodes, cestodes, and trematodes. It looks at the diagnosis of gastrointestinal parasitic infections acquired through the gastrointestinal tract, before describing the examination of faeces for ova, cysts, and parasites (OCP). The chapter then examines immunological and molecular techniques, and discusses the treatment of parasitic infections acquired through the gastrointestinal tract.
Laboratory investigations of viral infections
Authors: Harwood Jayne
Published: September 2023

This chapter examines laboratory investigations of viral infections, which are among the most common and important causes of human disease. Viruses are metabolically inert, making them totally dependent upon living cells for replication and their existence. This means that until they enter a host cell capable of supporting their replication, they exist as inactive particles. The chapter begins by describing the basic organization, size range, and structure of viruses. It then explains the specimens required and the procedures used in the routine virology laboratory for the diagnosis of viral infections. The chapter also looks at serology and antiviral chemotherapy before outlining common viral infections.
Procedures for sample collection, transport, and processing
Authors: Holliday Malcolm
Published: September 2023

This chapter describes the procedures for sample collection, transport, and processing. Great care must be taken to make sure that the quality of samples for microbiological investigations are as good as possible. Indeed, collecting the sample properly is the single most important stage of the whole process of microbiological examination. If the way the sample is collected is not correct, contaminating organisms may be introduced that will confuse the result, and it is always possible that a poorly taken sample may not have actually collected anything from the site of infection. The chapter then looks at the health and safety risks of collecting, transporting, and processing microbiology samples. It also outlines the legislation covering the collection and transport of microbiological samples, the basic microbiological sample processing methods, and the methods of inoculation of culture media.
Rarity and Extinction
Authors: Gilbert Francis , Gilbert Hilary
Published: September 2023

This chapter examines the consequences of changes in the size of a patch of suitable habitat. Reductions in island or habitat area lead to extinction of some of the populations because of the reduced resources and increased isolation. Meanwhile, habitat fragmentation leads to an extinction debt because it takes time for populations to die out. Creating corridors between isolated patches can help prevent some extinctions, but they cannot abolish them entirely. Setting aside nature reserves for conservation is obviously a good thing to do, but it will also not be enough as the reserves become isolated patches of natural habitat in a sea of man-made agricultural or urban landscapes. Ultimately, a landscape approach to conservation is needed for it to be successful.
Ecosystem Services and Human Wellbeing
Authors: Gilbert Francis , Gilbert Hilary
Published: September 2023

This chapter highlights the importance of conservation for human wellbeing. Nature provides us with ecosystem services vital to our health and wellbeing. However, these services have been taken for granted until now. There is a relationship between biodiversity and ecosystem service delivery; loss of biodiversity leads to losses in the ecosystem service, both in its level and its reliability. Traditionally, nature has been valued at zero, hence decision-makers rarely opt for nature conservation rather than using land for other purposes. It is vital that we value ecosystem services correctly and fully so that the real cost of their loss is realized. Often when the full costs and benefits are assessed, nature conservation turns out to be the most cost-effective and valuable option.
Making the most of tutorials and workshops
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

This chapter focuses on tutorials and workshops. These form key elements of teaching within most degree programmes and can be employed in a variety of formats. The chapter uses the term ‘tutorial’ to refer to small group teaching when there might be typically up to ten students with one lecturer. ‘Workshop’, on the other hand, refers to any sessions where there might be up to around thirty students with one lecturer. It also highlights the important feature that both workshops and tutorials share: they are student-centred and are about students participating in the session. The chapter describes small-group tutorials, which can be quite a daunting prospect as many students are unsure of their knowledge base and ability to discuss ideas. However, it clarifies that tutorials and workshops are highly useful in developing a range of important skills that will be of value to one’s studies and career development.
Choosing the right writing style
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

This chapter focuses on writing for scientific purposes, which is often very different from writing used for other forms of communication. It elaborates that scientific writing normally requires the use of a formal, impersonal style, noting the importance to use words accurately and avoid slang, informal phrases, and generalities. It also points out that the style for scientific writing is normally impersonal and avoids the use of personal pronouns such as ‘I’ and ‘we’ and the expression of subjective viewpoints. The chapter discusses the use of generalizations that often clouds the meaning of what is written or indicates a lack of confidence on the part of the writer. It explores the challenges of writing reflectively for scientists, as all their training has been to write in the dispassionate third person with objectivity.
Getting the most out of revision
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

This chapter shows how to revise well, implying that it is important to revise effectively in order to do well in exams. It stresses getting the revision part right as important to significantly increasing a student’s chances of doing well and alleviating some of the pressure and stress of exams. It also considers what revision actually is, which in general terms involves going over a subject previously covered again, usually in preparation for some kind of exam or test. The chapter explains that how a student goes over a subject again is critical to whether or not the revision is effective. It clarifies that effective revision makes knowledge easier to understand, remember, and apply.
Coordination chemistry
Authors: Aspinall Helen C.
Published: September 2023

This chapter begins by discussing coordination chemistry in aqueous solution, and then moves on to the more varied coordination chemistry that is seen in non-aqueous solution. It covers the complexes of f-elements, excluding those with Ln- or An-carbon bonds. The chapter also highlights the importance of chelating and macrocyclic ligands in f-element coordination chemistry, particularly in aqueous solution. Both lanthanoids and actinoids are generally considered as hard Lewis acids, and so their coordination chemistry is dominated by hard O and N donor ligands. Bonding is highly ionic in most cases, resulting in labile complexes that can have highly irregular coordination geometries dictated by ligand steric factors. Large ionic radii result in high coordination numbers, except where ligands are exceptionally sterically demanding.
Applications
Authors: Aspinall Helen C.
Published: September 2023

This chapter assesses the many potential applications of the f-elements and their compounds. By volume, the main applications of the rare earths are in metallurgy and alloys, and in permanent magnets. The unique optical and magnetic properties of the lanthanoids are key to many of the applications of these elements. For example, Eu and Tb are used as phosphors in fluorescent lighting, and the Nd:YAG laser is the most widely used IR laser. Complexes of Gd are used as contrast agents in MRI imaging. There is a constant challenge in rare earth technology to find uses for the more abundant elements (La and Ce) that are inevitably produced alongside elements such as Nd that are in high demand but available in lower abundance. Meanwhile, the use of U in nuclear reactors is the main application of the actinoids. However, there are also smaller-scale applications based on their radiochemical properties.
Extraction and purification of lanthanoids and actinoids
Authors: Aspinall Helen C.
Published: September 2023

This chapter addresses the extraction and purification of lanthanoids and actinoids. The rare earth elements are by no means rare, but the isolation of the individual elements was a major challenge. This is because of the similarity in their chemistry, which results in their occurrence as mixtures in all of their ores. Fractional crystallization was the only method available until the development of ion exchange chromatography. Industrial separation of the rare earths is now achieved by solvent extraction. Th and U occur separately in nature, making their isolation much more straightforward than that of the lanthanoids. The most important aspects of actinoid separation are isotopic enrichment of natural uranium to the 235U content required for nuclear reactors, and the processing of spent nuclear fuels.
Plant Diseases and Biosecurity
Authors: Beales Paul , Elphinstone John , Fox Adrian , Lane Charles , McCann Derek , Tim Lacey , Maguire Kerry , Turnbull Alice
Published: September 2023

Plant Diseases and Biosecurity begins by looking at the basic principles of plant disease. It then moves on to fungi and fungal-like organisms. Plant pathogens are considered in the next chapter. The text also looks at viruses and virus-like pathogens of plants. Plant biodiversity is described in detail. Another chapter looks at surveillance and considers traditional and emerging techniques used by plant health regulators. Disease management in crops is also examined. Finally, the book looks at biological controls and integrated crop management.
Fundamentals
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter describes the structure of an atom in terms of protons, neutrons, and electrons and explains the terms mass number and atomic number and how a simple mass spectrometer can be used to show the isotopic composition of an element. Chemical knowledge is constantly increasing as new compounds are constantly being synthesized and data on the behaviour of chemical systems are being collected and analysed in research laboratories around the world. The chapter highlights the states of matter and phase changes in terms of a kinetic–molecular model of matter. Working out the empirical formula of a compound from its elemental composition and understanding the relationship between empirical formula and molecular formula are also included. The chapter also shows how a simple mass spectrometer can be used to show the isotopic composition of an element.
Acids and bases
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter describes two broader definitions of acids and bases and introduces the Brønsted–Lowry theory, in which an acid is defined as a proton donor and a base is defined as a proton acceptor. It also reviews the Lewis theory, in which an acid is defined as an electron pair acceptor and a base is defined as an electron pair donor. This is considered a wide definition as all Brønsted–Lowry acids are Lewis acids, but not all Lewis acids are Brønsted–Lowry acids. The chapter identifies the conjugate acid and conjugate base for an acid–base reaction. It details how to calculate the pH of a solution of a strong or weak acid and a strong or weak base and determine the position of an acid–base equilibrium using Ka and Kb.
Halogenoalkanes
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter begins with an overview of the structure and reactivity of halogenoalkanes, followed by a discussion of the most important methods of preparing these compounds. Halogenoalkanes are particularly useful intermediate compounds in organic synthesis as they react with nucleophiles and as bases to form valuable products and bases in elimination reactions, which is an important way of making alkenes. The chapter explains why different carbon–halogen bonds in halogenoalkanes react differently from one another. It details how halogenoalkanes react in SN1, SN2, E1, E2 reactions, including factors that affect SN2 versus SN1 reactions and factors that affect E2 versus E1 reactions. The factors that influence substitution versus elimination reactions are also covered.
Hydrogen
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter considers hydrogen to have the simplest atoms of all the elements, which means that the hydrogen atom is the only one for which the Schrödinger equation can be solved exactly. Hydrogen is the most abundant element in the Universe, and the tenth most abundant element on Earth by mass, but it does not occur naturally on Earth in the elemental form. The chapter confirms why binary hydrides can be protic or hydridic and describes the character of a particular hydride. It illustrates how to predict whether the bonding in a binary hydride is covalent or ionic, and whether a covalent hydride is likely to contain bridging hydrogen atoms. Calculating the effects of replacing hydrogen by deuterium on infrared stretching frequencies is also covered.
p-Block chemistry
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter describes p-block elements as those with the valence electron configuration ns2 npx, where x is between 1 and 6. Some elements of the p-block have properties that are intermediate between those of metals and non-metals, and these elements are often called metalloids. The chapter explains trends in behaviour across the periods and down the groups of the p-block and confirms why the metal/non-metal divide runs diagonally through the p-block. It illustrates how to use enthalpy cycles together with bond enthalpies to determine the differences in stabilities of compounds going down a group. The structures and key reactions of the p-block oxides, hydroxides, oxoacids, and halides are also covered.
Physical Chemistry for the Life Sciences
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

Physical Chemistry for the Life Sciences explains how the principles of physical chemistry apply to the processes of life. Molecular assemblies, macromolecules, proteins, nucleic acids: they form a substantial part of all living organisms, from plants to humans. Indeed, they are critical for keeping them alive. But how do they operate? Chemical processes are at the core of life: understanding life means unveiling the physical principles on which it is built. The first few chapters look at biochemical thermodynamics, considering the first law and the second law. It also looks at phase equilibria, chemical equilibrium, and thermodynamics of ion and electron transport. The next set of chapters is about the kinetics of life processes. It looks at the rates of reactions, accounting for rate laws, and complex biochemical processes. The text then turns to biomolecular structure, and discusses microscopic systems and quantization, the chemical bond, and macromolecules and self-assembly. Finally, the text examines biomolecular spectroscopy, including optical techniques and photobiology and magnetic resonance.
Work and heat
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter is about energy transfer. Energy is the capacity to do work, including the work of building molecules. Heat is the transfer of energy due to a temperature difference. This chapter shows how chemical thermodynamics is formulated in terms of the work a system can do and how much heat is transferred to or from the surroundings. Both types of energy transfer play a role in biological processes such as building elaborate biomolecules, maintaining the internal temperature of an organism, and muscle contraction. Here, the chapter covers heat, work, and the measurement of both. It also discusses the terms ‘systems’ and ‘surroundings’ and how they apply to thermodynamics.
Internal energy and enthalpy
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter discusses internal energy and enthalpy. The ‘internal energy’ is a property that keeps track of energy transactions and is central to the formulation of the First Law of thermodynamics. The property known as the ‘enthalpy’ plays a special role when processes occur at constant pressure, as in many biological systems. As this chapter shows, the most fundamental way to monitor the energy involved in a biological process is in terms of the internal energy. The internal energy of an isolated system is constant; the heat released by a system at constant pressure is equal to the enthalpy change of the system. This is because the enthalpy is a state function; a change in enthalpy between two states of a system is independent of the path between them.
Calorimetry
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter focuses on calorimetry. Calorimetry is the study of the heat released or absorbed during physical and chemical processes. It is a major way of measuring changes in thermodynamic properties and is used to monitor energy resources and their use in organisms. Additionally, a calorimeter is a device for monitoring these transfers of energy. This chapter explores four common types of calorimeters used in investigations of nutrients, fuels, and biological processes, including the screening of compounds for protein binding activity in the course of drug development. These are the bomb calorimeters, the isobaric calorimeters, the differential scanning calorimeters, and the isothermal titration calorimeters.
Entropy in biology
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter concentrates on entropy in biology. All processes in biology are accompanied by an increase in entropy of the universe, i.e., those that include the biochemical processes of metabolism and the processes that result in the formation of structure. To assess whether a reaction can occur spontaneously, the chapter shows how we can evaluate the total change in entropy that occurs when pure, unmixed reactants change into pure, unmixed products. It also discusses a very important aspect of the role of entropy and its ability to drive the emergence of form — the hydrophobic effect in which hydrophobic groups, which are groups of atoms that have little or no ability to attract water molecules, tend to cluster together and away from the aqueous environment in which they are immersed. The chapter concludes with a case study which utilises hydrophobicities to predict protein structure.
The thermodynamic properties of water
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter discusses how hydrogen bonding influences many physical properties of water. Water has unusually high melting and boiling points, reflecting the extensive array of intermolecular hydrogen bonds that form in its solid and liquid phases. The origin of hydrogen bonding in water reflects in part the underlying polarity of the water molecule. That polarity has a major biological consequence because the resulting high relative permittivity (dielectric constant) of water makes liquid water an excellent solvent for the substances that participate in the chemical reactions that occur in cells. To explain this, the chapter first delves into the phases of water. Next, it discusses characteristic points in the thermodynamics of water. Surface tension is also addressed.
The thermodynamic background
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter shows that reactions tend to proceed in the direction of decreasing Gibbs energy and towards a composition summarised by an equilibrium constant. It emphasises the importance of the thermodynamic criteria for spontaneous change and equilibration, as is central to an understanding of the molecular processes that occur in cells. The chapter begins by stating that, at constant temperature and pressure, a reaction mixture tends to adjust its composition until its Gibbs energy is a minimum. From there, the chapter discusses the variation of reaction Gibbs energy with composition. Reactions at equilibrium are then explored. The chapter ends with a case study involving the binding of oxygen to myoglobin and haemoglobin.
The standard reaction Gibbs energy
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter focuses on standard reaction Gibbs energy. It explains how equilibrium constants and standard reaction Gibbs energies may be calculated from the standard Gibbs energies of formation of reactants and products. Additionally, the standard Gibbs energy of the formation of a compound is a measure of its thermodynamic stability. From there, the chapter relates the biochemical and thermodynamic standard states of solutes. Additionally, stability and instability are discussed. The chapter shows that standard Gibbs energies of formation of compounds are a measure of the ‘thermodynamic altitude’ of a compound above or below a ‘sea level’ of stability represented by the elements in their reference states.
Proton transfer equilibria
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter is concerned with the transfer of protons between molecules. This is an enormously important cellular process and plays a central role in maintaining the appropriate pH, a measure of hydrogen ion concentration, in the various compartments of cells. The chapter first discusses Brønsted–Lowry theory of acids and bases, which states that an acid is a proton donor, and that a base is a proton acceptor. Next the chapter turns to the protonation and deprotonation of molecules, which are key steps in many biochemical reactions. Hereafter, this chapter turns to polyprotic acids, which is a molecular compound that can donate more than one proton. The chapter concludes with a case study on the fractional composition of a solution of lysine.
Electron transfer reactions
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter focuses on electron transfer reactions. It shows how the transfer of electrons can be studied in the laboratory by setting up an electrochemical cell and monitoring the potential difference between electrodes. The link with thermodynamics is provided by the relation between this electrical potential difference and the reaction Gibbs energy. It follows that measurements of the potential difference can be used to determine thermodynamic properties, including the equilibrium constants of reactions. The procedures are simplified by expressing overall potential differences in terms of the contributions from each electrode and the processes occurring at the electrodes in terms of ‘half-reactions’.
Electron transport chains
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter considers electron transport chains. Two of the most fundamental metabolic processes, aerobic respiration and photosynthesis, which play such a critical role in maintaining life on Earth, require a succession of electron transfers. In both processes the electron transfers take place in membrane-localized electron transport chains that contain multiple electron carriers. These carriers are proteins and other types of molecules that can cycle between oxidized and reduced forms as electrons pass along the chain. Each couple (the oxidized and reduced forms of the carrier, Ox/Red) has a characteristic potential that corresponds to its reduction half-reaction, and the direction of spontaneous electron transport is typically in the direction of increasing potential. Here, the chapter considers electron transfer between redox centres, before examining the respiratory chain and photosynthesis.
Enzyme action
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter defines reaction rates and shows how to set up the expressions for the rate laws when enzymes are involved. Enzymes are biological catalysts that work by providing a pathway with a lower activation energy than the uncatalysed reaction. They are essential for life because the chemical reactions that have been selected by cells are inherently slow. Enzymes control these reactions in space and time. Here, the chapter introduces the Michaelis–Menten mechanism, which provides a chemical kinetics framework for describing simple enzymatic reactions. The chapter also establishes a way of assessing the efficiency of an enzyme in carrying out its role.
Diffusion in biological systems
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter concerns diffusion in biological systems. It explains that many of the molecules that make up a cell and its contents are free to move. The important feature of all these migrations is that they are not driven processes: they do not require inputs of energy to ensure that an ion or molecule moves in a particular direction. Instead the movement is spontaneous and occurs in response to the combined effects of concentration and membrane potential. When such a process occurs spontaneously across a cell membrane, it is called ‘passive transport’. A process in the opposite direction, one requiring an input of energy, is called ‘active transport’. Electrophoresis and ion migration through K＋ channels are also considered as case studies.
Electron transfer
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter demonstrates how electron transfer rates can be expressed in terms of Gibbs activation energies. Many biological processes depend on the transfer of electrons between electron donors and acceptors. In some instances, the electron donors and acceptors are free to diffuse in the aqueous solutions of the cell or in the fluid bilayers that make up the membranes, and electron transfer takes place when the donor and acceptor meet. However, in many other instances electron donors and acceptors exist as redox centres within protein molecules and electron transfer from donor to acceptor occurs without a diffusional encounter being necessary. Thus, this chapter introduces Marcus theory, an adaptation of transition-state theory, which is widely used to account for the rates of electron transfer. It also discusses protein electron transfer processes and examines electron transfer in photosystem I as a case study.
Atomic orbitals
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter takes a look at the atomic orbital, which is a one-electron wavefunction describing the spatial distribution of an electron in an atom. Atomic orbitals are used throughout chemistry in discussions of the electronic structure of atoms in general and in discussions of molecular electronic structure. This chapter extends the discussion of atomic structure to include the effect of nuclear charge by considering one-electron ions with higher atomic numbers. It shows how hydrogenic atoms are important because the Schrödinger equation can be solved for them. Furthermore, the concepts learned from a study of hydrogenic atoms can be used to describe the structures of many-electron atoms and of molecules too. To that end the chapter takes a look at the energy levels of hydrogenic atoms as well as the wavefunctions of hydrogenic atoms.
Valence Bond Theory
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter explains valence bond (VB) theory. In VB theory, a bond is regarded as forming when an electron in an atomic orbital on one atom pairs its spin with that of an electron in an atomic orbital on another atom. To understand why this pairing leads to bonding, the chapter examines the wavefunction for the two electrons that form the bond. It begins by discussing diatomic molecules, as the bonding in these molecules determines their physical and chemical properties and hence their biological function. The chapter then extends the ideas introduced so far to accommodate molecules containing more than two atoms — the polyatomic molecules.
Molecular orbital theory: diatomic molecules
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter introduces molecular orbital (MB) theory using diatomic molecules. In molecular orbital theory, electrons are treated as spreading throughout the entire molecule. The diatomic molecules treated here include the vitally important dioxygen molecule, O2; the potentially poisonous carbon monoxide molecule, CO; and the biochemically active nitric oxide molecule, NO. In each case, a knowledge of their electronic structure helps to explain their biochemical activity. Moreover, although MO theory treats an entire polyatomic molecule as a whole, with the electrons binding all the atoms together, it is possible to consider a diatomic fragment of the molecule, such as an NH fragment of an amino acid, and to explore how the electrons in it are distributed.
Macromolecular structure
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter discusses the absence of structure: the shape a macromolecule would adopt if there were no organizing forces at work. As the shapes adopted by biological macromolecules are crucial to their function, the chapter reveals how intramolecular non-covalent interactions can lead to folding into specific shapes. To begin, the chapter considers random coils, in which the polymer can adopt any of the conformations that are consistent with its configuration while avoiding the steric repulsion that arises when atoms occupy the same region of space. Each polymer molecule in a random coil state in a sample might be in a different conformation, so the sample must be described as a statistical distribution over those conformations. Afterward, the chapter follows case studies based on three topics: oligosaccharides and polysaccharides, nucleic acids, and proteins.
General features of spectroscopy
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter explores the common features of spectroscopic techniques. It begins with an account of the variety of experimental procedures and then goes on to describe how the intensity of absorption and emission is reported. The molecular feature that is central to understanding intensity is a quantity called the ‘transition dipole moment’, and an analysis of this quantum mechanical property is the basis of selection rules that govern whether a transition can be observed in a spectrum. Additionally, special techniques for examining molecules attached to surfaces allow the study of macromolecular interactions. A case study on biosensor analysis is also presented.
Electron paramagnetic resonance
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter explores electron paramagnetic resonance. This technique is used to study species with unpaired electrons and to infer structural and motional information. This chapter demonstrates how an electron spin gives rise to a magnetic moment. The energy of an unpaired electron in a magnetic field depends on its orientation, and transitions between states occur when a resonance condition is fulfilled. Here, electron spin energy levels come into resonance with a microwave field at applied magnetic fields that depend on the local environment and magnetic interactions with nuclei. Linewidth data can then be interpreted in terms of the motion of molecules and the local behaviour of molecules tethered to macromolecules.
Scattering by individual molecules
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter explores the information that is obtained from electromagnetic radiation scattered by individual molecules. This scattering a result of the interaction between the electric field vector of the radiation and the electrons in the molecule. Careful analysis of the angular distribution of intensities can be interpreted in terms of the molar mass of the macromolecules responsible for the scattering. Their size and shape can be assessed by decreasing the wavelength of the radiation and using X-rays instead of visible light. Neutron scattering also provides information, but as it is a result of nuclear forces, isotopic substitution can add to the information that can be obtained.