bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteins with partners
Authors: Lesk Arthur M.
Published: September 2023

This chapter focuses on protein–protein interfaces, which may modulate transcriptional regulation. The interfaces can be characterized by the following: the overall amount of surface buried, the chemical composition of the buried surfaces, the shape and charge complementarity of occluding surfaces, and specific interactions, such as hydrogen bonds. The chapter then considers the common role of aggregation of proteins in several diseases, including sickle-cell anaemia, amyloidoses, Huntington's, Parkinson's, and Alzheimer's diseases, and prion diseases such as ‘mad cow disease’. It also looks at the immune system and virus structures. Finally, the chapter outlines the basic principles of viral capsid assembly, before examining protein–DNA complexes.
Molecular tools for molecular ecologists
Authors: Rowe Graham , Sweet Michael , Beebee Trevor J. C.
Published: September 2023

This chapter explores the molecular tools used in studying molecular ecology. It explains genetic manipulation in terms of molecular ecology. The chapter explains the process of protein and DNA extraction from tissue samples. It also lists the non-PCR-based tools for studying genetic variations such as restriction fragment length polymorphism (RFLP). Moreover, the chapter discusses PCR-based molecular markers which may or may not require sequence information by referencing microsatellite loci and randomly amplified polymorphic DNA (RAPD) as respective examples. It notes the measurement of gene expression using DNA microarrays. This has become an increasingly common approach among molecular ecologists. The chapter looks into next generation sequencing and the marker revolution. It highlights the importance of understanding genetic manipulation and cloning.
Population genetics
Authors: Rowe Graham , Sweet Michael , Beebee Trevor J. C.
Published: September 2023

This chapter focuses on the field of evolutionary biology in relation to changing distributions and frequencies of alleles within populations. This is called population genetics. The chapter looks into genetic diversity in natural populations and population size. The chapter highlights the importance of population bottlenecks. This is considered as a radical reduction in population size accompanied by the loss of genetic diversity. The chapter cites population structure and marker selection as important in the study of population subdivisions. Metapopulation is defined as the population of subpopulations with numerous genetic interconnectivities. The chapter also looks into the genetic estimation of gene flow and migration rate while looking into the identification of immigrant species. Additionally, it expounds on the molecular markers in terms of population genetics.
Algebra V
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter assesses the process of rearranging simple equations, starting with a focus on the importance of the equals sign. The equals sign lies at the heart of all our mathematics: an equation is only complete when it contains an equals sign to relate the expressions on either side of the equation. An equation is balanced when the variables and numbers on the left of the equals sign have the same overall value as the collection of variables and numbers written to its right. Thus, we can change the magnitude of the variables and numbers on the left-hand side of an equation provided we do exactly the same to the right-hand side. The chapter then looks at the process of rearranging equations that have one operator; rearranging equations that have many operators, using the BODMAS scheme; and rearranging equations with negative coefficients.
Integration I
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter focuses on the process of integration, which performs the opposite function to differentiation. We integrate a variety of simple polynomial functions by rule. The chapter then looks at the process of calculating the constant of integration. We say an integral is definite if we do know the value of the constant of integration. Meanwhile, we say an integral is indefinite if we do not know the value of the constant of integration. The simplest method of determining a value for the constant of integration c requires us to know the gradient of a line and a single point through which the line passes. Finally, the chapter considers the process of integrating functions other than simple powers.
Complex numbers
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter highlights complex numbers, which refer to numbers comprising both real and imaginary numbers. Some complex numbers can be easily simplified. If the imaginary part is expressed as the square root of a negative number, we merely take the root of the number. Sometimes a number comprises both real components and the square root of a negative number. In such cases, we can often leave the real component and perform algebra on the imaginary component. Ultimately, complex numbers may be added and subtracted like any other algebraic sum or difference. Multiplying complex numbers is trickier than adding or subtracting because we need to keep separate the real and imaginary components. The chapter then looks at the complex conjugate, complex fractions, and graphical representations of complex numbers. It also considers complex numbers with exponentials, de Moivre's theorem, and the Fourier transform operation.
Vectors
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter discusses scalars and vectors. A scalar quantity has magnitude but no direction, while vectors have both magnitude and direction. A vector can be expressed in terms of plane polar coordinates, as a magnitude and a direction. We obtain the magnitude of a vector in Cartesian space using Pythagoras' theorem and the coefficients of the unit vectors. The chapter then looks at the scalar multiplication of vectors, as well as the process of adding and subtracting vectors. It explains how vectors are good at describing the result of relative motion, when one object is moving with respect to a reference object. Finally, the chapter considers the process of multiplying vectors as a cross product and as a dot product, before focusing on vector derivatives.
Statistics III
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter explores variance and significance testing. We determine both standard deviation and variance using the mean of a data set. Standard deviation measures the extent to which the data in a population or sample set differ from the mean. It is most useful when it helps us quantify our confidence in a statistical conclusion. Meanwhile, variance measures the way the distribution within a population or within a sample set of data varies about its mean. The chapter then looks at nominal variables, the concept of null hypotheses, and degrees of freedom. It also considers the different types of t-test: one-sample, two-sample, and paired t-test methods.
What is histopathology?
Authors: Muskett David , Orchard Guy , Warren Anne
Published: September 2023

This chapter provides an overview of histopathology, which is a mix of cell biology, biochemistry, chemistry, and genetics. All organs in every human being show the same general histology, and possibly more importantly, each pathology of the same type has a characteristic morphology and pattern. It is the manual visual interpretation of these things that forms the basis of histopathology. The chapter describes the role of histopathology in the diagnosis of disease. It then looks at the different types of biopsy submitted to the histopathology laboratory; outlines the specimen journey through the laboratory; and considers the special staining techniques that can be used to aid diagnosis. The chapter also discusses the concept of consent, the principles of the Human Tissue Act 2004, and the laboratory management systems that support an effective histopathology service.
Data recording and histopathological dissection
Authors: McTaggert Vanda , Pritchard Sue , Warren Anne
Published: September 2023

This chapter discusses appropriate data recording and histopathological dissection procedures. It is essential that identification checks are performed, to an agreed standard, throughout the analytic stage, so that the right report is generated for the right patient. The biomedical scientist (BMS) is key in ensuring this is completed. In addition, dissection techniques must be of the highest standard to ensure that the tissue sampled allows all the histological questions being asked by the requesting clinician to be answered. The chapter then looks at the process of accepting specimens for histopathological examination, working safely in the dissecting room, and gathering clinical data relevant to specimen dissection. It also outlines the basics of dissection and the macroscopic report, and considers common organ systems, head and neck pathology, and gynaecological cases.
Routine processing, embedding and staining
Authors: Muskett David
Published: September 2023

This chapter examines routine processing, embedding, and staining. The aim of tissue processing is to prepare tissue in a supporting medium ready to be cut into thin sections, in order to observe individual cells under the microscope. The tissue blocks prepared during specimen dissection are immersed in a number of different chemical solutions. These solutions act to prepare the tissue for mixing with an embedding medium, in most cases paraffin wax, although resin is sometimes used for hard tissue. Tissues are generally processed together in an overnight batch, but this may result in poor processing of fatty tissue and particularly hard tissue. The chapter then discusses microtomy, cryotechniques and cryotomy, and haematoxylin and eosin staining.
Stains in action
Authors: Muskett David , Orchard Guy
Published: September 2023

This chapter evaluates tissue staining. Fixed and processed tissue lacks contrast, and appears largely colourless despite containing numerous individual entities. Routine staining is most commonly carried out using the haematoxylin and eosin method. There are circumstances where the initial stain will not reveal sufficient information and subsequent demonstration methods are required. Various coloured dyes and stains can be used to emphasize the different structures present. These stains have evolved over many years, and in the modern diagnostic histopathology laboratory there are dozens of methods available to colour many entities. This gives contrasting appearances. Most of these methods rely on chemical principles whereby structures of a specific chemical nature can be stained selectively with the appropriate dyes. Often, two or more dyes can be used to provide a vivid contrast between the various structures within the tissue. The chapter looks at liver, native renal, muscle, and nerve biopsies.
Artefacts
Authors: Orchard Guy , Hodgson Chantell , Nation Brian
Published: September 2023

This chapter focuses on key artefacts in histological procedures. Artefacts in histopathological studies can be commonplace and have a profound impact on the outcome of any investigations. Pre-analytical artefacts are largely due to the processes and procedures undertaken prior to specimen receipt in the histopathology laboratory. They relate to the need to ensure that Good Clinical Practice (more precisely Good Surgical Practice) is followed while removing tissue samples from patients, to reduce their impact on viable tissue harvesting. Meanwhile, post-analytical artefacts are produced as a result of laboratory procedures and techniques, and there is greater emphasis on appreciating their impact because quality control procedures will need to define what they represent and facilitate the introduction of measures to reduce their incidence.
Immunocytochemical techniques
Authors: Ibrahim Merdol , Orchard Guy
Published: September 2023

This chapter addresses immunocytochemical techniques and their role in diagnostic histopathology. Immunocytochemistry (ICC) is used as a second string of investigations following conventional staining techniques. The role of the primary investigations is to demonstrate the morphological appearance of the cell and tissue architecture. This enables identification of the disease process, and in a substantial number of cases is adequate to formulate a final diagnosis. However, the demonstration of morphological detail alone may not enable a diagnosis to be made in all cases, and in such instances an assessment of the cell marker (antigen) expression on the cell membrane, cytoplasm, or nucleus is required. This provides selective information that can be used to define certain cell types. This is the role of ICC, which, in some instances, is closely allied to molecular diagnostics. The chapter then details the process of tissue preparation and antigen retrieval.
Molecular diagnostics: techniques and applications
Authors: O'Sullivan Brendan , Taniere Philippe
Published: September 2023

This chapter studies molecular diagnostics, which is the use of widely varied techniques and platforms to profile variation in a broad array of biomolecules, supporting medical decisions regarding the diagnosis of disease, patient prognosis, and prediction of response to treatments and interventions. The chapter begins by outlining the essential theory and concepts of DNA replication and translation. It then looks at the polymerase chain reaction, before explaining the basic principles, organic or semi-synthetic, which underlie the broad range of techniques utilized in the molecular pathology laboratory. The chapter also considers molecular diagnostic processing and testing. Finally, it discusses nucleic acid extraction and explores the different PCR analysis methods.
Light microscopy and digital pathology
Authors: Orchard Guy
Published: September 2023

This chapter examines light microscopy and digital pathology. The principle behind the light microscope is to provide a magnified image of the sample of interest such that what is happening to the samples can be seen at a scale which the eyes alone could not perceive. It is not enough, however, simply to provide a large image of a specimen, as a simple magnifying lens would. Biomedical scientists are typically interested in quite small and fine detailed structures so it is important that the microscopic image contains sufficient resolution of fine detail. The chapter then looks at the compound microscope, phase contrast microscope, polarization microscope, darkfield microscope, fluorescence microscope, and confocal microscopy.
Electron microscopy
Authors: Furness David N
Published: September 2023

This chapter evaluates electron microscopy, which allows higher magnification than other types of microscopy and is responsible for the discovery and detailed description of most subcellular organelles. There are two kinds of electron microscopes (EMs): the transmission EM and the scanning EM. The main difference between these two types of microscope is that TEM is used to look at sections of samples, or naturally very thin/small samples, while SEM is used to image the surface and so can handle bulky samples of a size that is only limited by the microscope sample chamber size, although typically, samples are only a few millimetres across. The chapter then outlines the specific preparatory requirements for samples requiring electron microscopy. It also considers the application of transmission and scanning electron microscopy in the field of biomedical science and provides examples of their use in pathological evaluation.
Mortuary practice
Authors: Gall Ishbel
Published: September 2023

This chapter focuses on the functions which may be fulfilled by a mortuary and post-mortem facility. These include receipt and storage of the deceased; investigation of the cause and/or circumstances of death by performing a post-mortem examination of the deceased; demonstration of post-mortem findings to clinical staff and to allow teaching; and viewing and/or identification of a body, if requested or required. The mortuary delivers the last point of care for pathology and can be the final stage of the patient care pathway. The chapter then outlines the naturally occurring processes which occur after death, including rigor mortis and decomposition. It looks at the work of the Human Tissue Authority (HTA) and how it impacts on the mortuary. The chapter also differentiates between consented, or authorized, post-mortem examinations and those instructed by legal process.
Essentials of laboratory management
Authors: Alexander Sue , Fernando Patricia
Published: September 2023

This chapter assesses the essentials of laboratory management. Good laboratory management is a difficult concept to define absolutely, being made up of many different component parts, but it is essential to the smooth running of a modern histopathology laboratory. The chapter considers how all aspects of work involved in laboratory management interact within a clinical governance framework in histopathology. It also looks at quality management systems and risk management. In addition to defined standards for laboratories undertaking histological investigations on human tissue samples, there are also national laws governing the use of tissue samples, and compliance with such laws and regulations is required, being assessed in a similar way to laboratory standards. The chapter then studies the Human Tissue Act 2004.
Polar Regions
Authors: Kaiser Michel J. , Attrill Martin J. , Jennings Simon , Thomas David N. , Barnes David K. A. , Brierley Andrew S. , Graham Nicholas A. J. , Hiddink Jan Geert , Howell Kerry L. , Kaartokallio Hermanni
Published: September 2023

This chapter takes a look at the polar oceans and seas. Organisms living in Arctic and Antarctic waters are adapted to low temperatures, long periods in the year of poor or entirely absent light, and an ecosystem dominated by the seasonal formation, consolidation, and subsequent melt of frozen seawater. These areas are now receiving much attention due to a rapidly changing landscape and seasonal dynamics attributable to global climate change. The effects of global climate change are likely to have profound influences on these regions, especially in the Arctic. However, an understanding of their ecology, and therefore the potential threats of climate change, is still rudimentary due largely to the hostile working conditions. Like other extreme environments, the metabolic and physiological adaptations that enable life to go on are a potential source for novel biotechnological applications, and polar organisms, in particular microorganisms, are also potential proxies for life on extraterrestrial systems.
Fisheries
Authors: Kaiser Michel J. , Attrill Martin J. , Jennings Simon , Thomas David N. , Barnes David K. A. , Brierley Andrew S. , Graham Nicholas A. J. , Hiddink Jan Geert , Howell Kerry L. , Kaartokallio Hermanni
Published: September 2023

This chapter deals with fishing. Fisheries are a key contributor to global food security and economic activity, but without good management fisheries may be subsidized, unproductive, wasteful, cause excessive environmental damage, and ignite conflicts between otherwise friendly nations. The chapter contends that scientific understanding of fish populations and their management has to be translated into effective management for fisheries to realize their potential benefits to fishers and society. In past decades, the main objective of fishery management was to maximize catches without compromising future catches. For many biological, social, and economic reasons, this objective was difficult to meet. Some fisheries collapsed while others threatened species and habitats of conservation concern that were not their intended targets. In the last two decades, some countries and regional management organizations have shown that it is possible to institute effective management and reverse overfishing. But, in many places, managers still face many challenges.
Aquaculture
Authors: Kaiser Michel J. , Attrill Martin J. , Jennings Simon , Thomas David N. , Barnes David K. A. , Brierley Andrew S. , Graham Nicholas A. J. , Hiddink Jan Geert , Howell Kerry L. , Kaartokallio Hermanni
Published: September 2023

This chapter introduces the historical development of aquaculture, insight into the variety of techniques used to rear a range of different organisms, the technology employed to increase productivity, and the environmental and biological consequences of aquaculture in marine ecosystems. As in any food production system, aquaculture creates its own environmental problems. It has led to disease outbreaks, over-harvesting of forage fishes to generate fish-meal, and genetic dilution of wild stocks from farm escapees, and it has caused ecological problems in areas where local carrying capacity has been exceeded. In addition, aquaculture has its own emerging issues that have extended beyond simply a consideration of biological or environmental science. As aquaculture involves the rearing of organisms in an artificial environment, there are potential welfare issues that are of concern to wider society, and concerns about labour conditions (modern slavery) are now much higher on the societal agenda.
Applied Ecology
Authors: Goodenough Anne E. , Hart Adam G.
Published: September 2023

Applied Ecology shows how an understanding of ecological theory can be used to address the most important issues facing ecologists today. It emphasizes the use of ecological tools and approaches in applied contexts and consists of four parts. Part 1 provides an overview of the subjects covered in this text and introduces applied ecology. Part 2 covers monitoring and looks at ecological surveying, monitoring, and ecological indicators. The next part is about managing and examines ecological impact assessment, remediation ecology, landscape ecology and management, non-native species management, and pest management. The final part is about conserving and includes the principles of conservation, in situ conservation, ex situ conservation, and reintroduction and rewilding.
Introducing Applied Ecology
Authors: Goodenough Anne E. , Hart Adam G.
Published: September 2023

This chapter provides a summary of applied ecology. It explains the series of topics included in ecology, applied ecology as a science, and its fundamentals. The chapter delves into the history behind applied ecology and clarifies the themes of applied ecology. The chapter notes how applied ecology operates within a changing and complex economic, political, social, and globalized landscape. It considers real-world applications, which are the focus of this book, but emphasizes that these applications are underpinned by theory. Additionally, the chapter delivers a summary of the title's chapters and their respective sub-chapters, which are grouped into sections on monitoring, managing, and conserving.
Fundamentals of Ecology
Authors: Goodenough Anne E. , Hart Adam G.
Published: September 2023

This chapter focuses on the fundamentals of ecology. Organisms interact in various ways regardless of relationship, pattern, space, and time. The chapter looks at various ecological relationships such as mutualism, competition, decomposition, predation, parasitism, competition, and commensalism. The chapter examines the concepts of an animal's niche, habitat, and geographical range which are informed by requirements and limitations. It briefly considers the role humans play in the context of ecology. Moreover, the chapter discusses life history theory in relation to r-strategists and k-strategists. The chapter also highlights the importance of evolution in ecology and ecological succession. It introduces some early ecologists like Ernst Haeckel, Eugen Warming, and Charles Sutherland Elton.
Pest Management
Authors: Goodenough Anne E. , Hart Adam G.
Published: September 2023

This chapter discusses pest management. It highlights that numerous insect species are considered pests. The chapter explores the concept behind pest management by noting the threshold value of harm called the Economic Injury Level. Additionally, it explains how the physical, chemical, and biological management of pests is becoming more sophisticated in line with technological advances. The chapter notes the central issues with pest management, including the possible resurgence of pests, the increase of secondary pests, and the ecological impact of pests. It introduces the Integrated Pest Management approach. Then, the chapter presents an interview with applied ecologist Luciano A. Moreira.
Reintroduction and Rewilding
Authors: Goodenough Anne E. , Hart Adam G.
Published: September 2023

This chapter explains the practice of reintroduction and rewilding. It discusses the process of reintroduction, which can be achieved through restoration, translocation, and captive breeding based on species-focused, site-focused, or human-focused motivations. Moreover, the chapter looks at regulatory frameworks and policies for reintroduction, such as those of the Convention on Biological Diversity and the IUCN’s Species Survival Commission, as well as the Reintroduction Specialist Group's comprehensive guidelines. The chapter highlights the significance of post-release monitoring in relation to reintroduction. In addition, the chapter explores rewilding, which prioritizes habitats and landscapes, and notes the challenges of bringing species back to the wild. It includes an interview with applied ecologist Lynne MacTavish.
Physical change
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter describes physical change, in which one form of a substance changes into another form of the same substance. The conversion of one phase of a substance to another phase is called a phase transition. Most phase transitions are accompanied by a change of enthalpy because the rearrangement of atoms or molecules usually requires or releases energy. The chapter then looks at vaporization, fusion, condensation, freezing, sublimation, and vapour deposition. Some enthalpy changes often needed in chemistry are those accompanying changes to individual atoms and molecules. Among the most important is the standard enthalpy of ionization, the standard molar enthalpy change accompanying the removal of an electron from a gas-phase atom (or ion).
The thermodynamics of transition
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter loos at the thermodynamics of phase transitions. The Gibbs energy of a system, particularly a single substance that might form the system, is defined as G = H − TS, with H its enthalpy, T its temperature, and S its entropy. It is at centre stage in almost all the applications of thermodynamics to chemistry and in particular of how physical and chemical processes depend on pressure and temperature. At equilibrium, the molar Gibbs energies of the phases are equal. The molar Gibbs energy increases with pressure and is most sensitive when the molar volume is large. Meanwhile, the molar Gibbs energy decreases with temperature and is most sensitive when the molar entropy is large. Although the temperature-dependence of the Gibbs energy is expressed in terms of the entropy, it can also be expressed in terms of the enthalpy. The chapter then looks at the Gibbs–Helmholtz equation.
Phase diagrams of mixtures
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter details the phase diagrams of mixtures. The equilibria between phases (at constant pressure) are represented by lines on a temperature–composition diagram. The chapter begins by looking at the phase diagram of a binary mixture of two volatile liquids. This kind of system is important for understanding fractional distillation, which is a widely used technique in industry and the laboratory. The chapter then considers liquid–liquid phase diagrams, as well as liquid–solid phase diagrams. It differentiates between an azeotrope mixture and a eutectic mixture, and explains the lever rule and the technique of zone refining. Finally, the chapter examines the Nernst distribution law, which states that, in an ideal system, the ratio of mole fractions in the two phases is independent of the total amount of solute.
The equilibrium constant
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter assesses the equilibrium constant, which expresses the composition of an equilibrium mixture as a ratio of products of activities. It is a succinct summary of the equilibrium composition of a reaction mixture, but special techniques have to be applied in order to extract individual concentrations of the reactants and products. The chapter then explains how to set up and use an equilibrium table that does the task systematically. An equilibrium table is a table with columns headed by the species and, in successive rows, the changes in composition needed to reach equilibrium. Ultimately, the equilibrium constant of a gas-phase reaction may be expressed as a ratio of products of pressures or, after the appropriate conversion, concentrations.
Polyprotic acids
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter explores polyprotic acids. A polyprotic acid is a molecular compound that can donate more than one proton. It is best considered to be a molecular species that can give rise to a series of Brønsted acids as it donates a succession of protons. The chapter begins by looking at the process of successive deprotonation. Enzymes are polyprotic acids, for they possess many protons that can be donated to a substrate molecule or to the surrounding aqueous medium of the cell. For them, successive acidity constants vary much less because the molecules are so large that the loss of a proton from one part of the molecule has little effect on the ease with which another some distance away may be lost. The chapter then considers speciation, which is the specification of the fractional composition of ions in a solution.
Empirical chemical kinetics
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter evaluates how the first step in the investigation of the rate and mechanism of a reaction is the determination of the overall stoichiometry of the reaction and the identification of any side reactions. The next step is to determine how the concentrations of the reactants and products change with time after the reaction has been initiated. Because the rates at which reactants are consumed and products are formed change in the course of a reaction, it is necessary to consider the instantaneous rate of the reaction, its rate at a specific instant. The chapter then defines the unique rate. Ultimately, the rates of chemical reactions are measured by using techniques that monitor the concentrations of species present in the reaction mixture. Techniques of chemical kinetics include spectrophotometry, real-time and quenching procedures, flow and stopped-flow techniques, and flash photolysis.
The temperature dependence of reaction rates
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter assesses how the rates of most chemical reactions increase as the temperature is raised. This variation is expressed by the ‘Arrhenius equation’, which expresses the rate constant as a function of temperature. Not only can this law be used to predict the effect of temperature, but it is also used to infer details about the molecular processes taking place during a reaction and to build models of the processes. In collision theory, it is supposed that the rate of a gas-phase reaction is proportional to the collision frequency, a steric factor, and the fraction of collisions that occur with at least the kinetic energy along their lines of centres. In transition-state theory, it is supposed that an activated complex is in equilibrium with the reactants, and that the rate at which that complex forms products depends on the rate at which it passes through a transition state.
Reaction mechanisms
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter describes reaction mechanisms. Many reactions occur in a series of steps called elementary reactions, each of which involves only one or two molecules or ions. The molecularity of an elementary reaction is the number of molecules coming together to react. The chapter then looks at the formulation of rate laws. In a pre-equilibrium, it is assumed that an intermediate establishes a rapid equilibrium with the reactants and the subsequent formation of products is slow. In the steady-state approximation, it is assumed that the concentrations of all reaction intermediates remain constant and small throughout the reaction. The chapter also considers the rate-determining step, which is the slowest step in a reaction mechanism that controls the rate of the overall reaction. Provided a reaction has not reached equilibrium, the products of competing reactions are controlled by kinetics. Finally, the chapter discusses the Lindemann mechanism of ‘unimolecular’ reactions.
Hydrogenic atoms
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter examines the hydrogenic atom, which is a one-electron atom or ion of general atomic number Z. It provides a set of concepts which are used to describe the structures of atoms and of molecules. It analyzes the experimental information from a study of the spectrum of atomic hydrogen and describes the results of solving the Schrödinger equation. It also considers the importance of wavefunctions to the atomic orbitals of hydrogenic atoms. The chapter talks about the atomic orbitals which are labelled by quantum numbers that specify the energy and angular momentum of an electron in a hydrogenic atom. It shows the production of energetically excited atoms when an electric discharge is passed through a gas or vapour or when an element is exposed to a hot flame.
Atomic spectroscopy
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter considers atomic spectroscopy as an important way of determining the energies of electrons in atoms and reviews the spectra of hydrogenic atoms and many-electron atoms. It highlights the concept of selection rules which is used to predict which spectroscopic transitions can be observed. It also analyzes the spectra of many-electron atoms which are more complicated than those of hydrogen as they are influenced by the Coulombic and magnetic interactions of electrons. The chapter describes the term symbols and shows how these are based on the various contributions to the total angular momentum of the electrons. It details how spectroscopic measurements confirm the theoretical prediction that the energy levels of atoms correlate with the contributions to the total angular momentum of their electrons.
Valence bond theory
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter discusses the procedure for writing wavefunction for a shared electron pair and it gives an account for the structures of a wide variety of molecules. It explains how the valence bond theory (VB theory) introduces the concepts of σ bonds, π bonds, promotion, and hybridization. It also points out how a bond forms 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. The chapter analyzes the covalence-shell electron pair repulsion (VSEPR) model, in which it is supposed that the shape of a molecule is determined by the repulsions between electron pairs in the valence shell. It extends the general concepts of the VB theory with arguments grounded in quantum theory.
Nuclear magnetic resonance
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter gives an account of the principles that govern spectroscopic transitions between spin states of nuclei in molecules. It describes simple experimental arrangements for the detection of these transitions in nuclear magnetic resonance (NMR) spectroscopy. It shows how NMR spectroscopy is used widely in chemistry and medicine. It also discusses resonant absorption which occurs when the separation of the energy levels of spins in a magnetic field matches the energy of incident photons. The chapter highlights the application of resonance which depends on the fact that many nuclei possess spin angular momentum. It highlights nuclear spin quantum number, I, of a nucleus is either a non-negative integer or half-integer.
Bonding in solids
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter talks about X-ray diffraction which is related to the structures of metallic, ionic, and molecular solids. It reviews some typical results and their rationalization in terms of atomic and ionic radii and discusses the electronic structure of metallic and ionic solids. It also demonstrates how atoms and molecules aggregate into metallic, ionic, molecular, and covalently bonded solids. The chapter analyzes the different characteristic types of bonding that result in several types of solids with characteristic physical properties. It explains the coordination number of an atom in a metal, which is the number of its nearest neighbours, noting elemental metals that have close-packed structures with coordination number 12.
Research, the law, and you
Authors: Holmes Debbie , Moody Peter , Dine Diana , Trueman Laurence
Published: September 2023

This chapter examines UK law primarily as it relates to undergraduate bioscience research. In most respects, at present UK law is similar across England, Northern Ireland, Scotland, and Wales, with the exception of the laws of trespass. The chapter examines the law as it relates to health and safety, access, wild species, domesticated animal species, and humans. In the UK, the body of law is derived from two sources: international law and national law. Furthermore, research in the UK should be guided primarily by the two basic principles behind an ethical basis for research: ‘to do no harm’ (non-maleficence) and ‘to do good’ (beneficence). The chapter also covers intellectual property rights.
What to do with raw data
Authors: Holmes Debbie , Moody Peter , Dine Diana , Trueman Laurence
Published: September 2023

This chapter considers how to record measurements when planning experiments and summarizing them for presentation. It starts by explaining the terms that are used to describe the data, the scales they are measured on, and the types of distributions seen in the data. This allows us then to decide whether the data are normally distributed or not and to calculate the correct summary statistics. The types of data covered in the chapter are qualitative, quantitative, discrete, continuous, and rankable. Qualitative data are observations that are descriptive and non-numerical. Quantitative data are observations that are numerical. Discrete observations are measured on a discontinuous scale or a variable that falls into a series of distinct categories and where the number of categories is limited. Continuous observations do not fall into a series of distinct categories and may take any value in the scale of measurement. Finally, rankable observations consist of named categories or values that have a consistent order to them.
An introduction to hypothesis testing
Authors: Holmes Debbie , Moody Peter , Dine Diana , Trueman Laurence
Published: September 2023

This chapter considers the general principles behind hypothesis testing. There are six steps to follow in all hypothesis testing. The first is to confirm which distribution is the best one to use. Next, the chapter shows how to select and correctly phrase the hypotheses to be tested and determine which is/are the correct statistical test(s) to use. Afterwards, the calculated value of the test statistic must be worked out. The critical value of the test statistic is then found. The chapter also takes a look at whether or not to reject the null hypothesis depending on the rule relating to the critical and calculated test statistics. Finally, the chapter considers how to decide what the outcome of the statistical test means in terms of the biology of the system.
Which statistical test should I choose?
Authors: Holmes Debbie , Moody Peter , Dine Diana , Trueman Laurence
Published: September 2023

This chapter shows how to choose the correct statistical test, illustrating this with examples and additional explanations of terms to make it easier to understand the process. It also shows how to review the analysis of data in published research so that it can be evaluated and so that the conclusions that have been drawn have an appropriate basis. Here, the chapter outlines three occasions during which we must decide on the correct statistical test. The first is designing an experiment. Next is analysing data from an experiment designed by someone else. Finally, there is establishing the merits of research that has been designed and evaluated by someone else.
Hypothesis testing: Do my data fit an expected ratio?
Authors: Holmes Debbie , Moody Peter , Dine Diana , Trueman Laurence
Published: September 2023

This chapter considers statistical tests and experimental designs that will be suitable for testing the hypothesis, ‘Do my data fit an expected ratio?’ The statistical test most often used to test this hypothesis is the chi-squared goodness-of-fit test. The chapter explains more about this type of hypothesis, how to carry out the necessary calculations, and how to resolve some of the problems that may be encountered. The statistics tests covered in the chapter are: chi-squared goodness-of-fit test: one sample. It then explores how to check whether the data have a normal distribution using the chi-squared goodness-of-fit test. Finally, the chapter takes a look at replication in a goodness-of-fit test.
Hypothesis testing: Do my samples come from the same population? Parametric data
Authors: Holmes Debbie , Moody Peter , Dine Diana , Trueman Laurence
Published: September 2023

This chapter talks about how we may analyse parametric data to test the hypothesis that two or more samples come from the same statistical population. These data are usually presented in tables or summary histograms rather than a scatter plot, and the treatment variables are usually measured on an ordinal and/or nominal scale, or occasionally measured on an interval scale and arranged into discrete categories. Other (dependent) variables are measured on an interval scale. All these tests use the underlying mathematical relationships that come from the data having a normal distribution. The tests outlined in the chapter cover a wide range of experimental designs with one or more treatment variables, with or without replicates. Particular design features are covered in the relevant sections; however, whether observations are matched or unmatched is a central point common to all these tests.
Hypothesis testing: Do my samples come from the same population? Non-parametric data
Authors: Holmes Debbie , Moody Peter , Dine Diana , Trueman Laurence
Published: September 2023

This chapter discusses how to test the hypothesis that samples come from the same statistical population using non-parametric tests. It includes the tests used most often by undergraduates and which mirror those covered in the previous chapter for testing the same hypothesis with parametric data. There are a number of key principles that need to be understood in relation to the use and interpretation of these tests, including how to rank the data, absolute values, matched data, and the interaction between treatment variables. These points are covered when they first become relevant to the statistics tests being considered. Additionally, these tests are ‘distribution free’ and the data therefore do not have to be distributed normally.
Foundations
Authors: Cook Michael , Cranwell Philippa
Published: September 2023

This chapter provides an overview of organic chemistry. Organic chemistry involves the study of molecules containing carbon, which make up the majority of biological matter. Due to the ability of carbon to bond so that it forms long chains, the complexity of organic molecules can be very challenging. The chapter then explains the drawing and naming of organic structures, before looking at orbital overlap and bonding and orbital hybridization. It also considers double bond equivalents. When we are trying to determine the structure of a molecule from its molecular formula, it is useful to know the number of π-bonds and cyclic structures in the molecule. This knowledge can be attained by calculation of the double bond equivalents. Finally, the chapter examines polarity, aromaticity, resonance, and tautomerism..
Nucleophilic substitution
Authors: Cook Michael , Cranwell Philippa
Published: September 2023

This chapter examines nucleophilic substitution. It begins by defining electrophiles and nucleophiles. An electrophile is a neutral or positively charged species with an empty orbital (or an energetically accessible anti-bonding orbital) which can accept electrons. Lewis acids can also be considered electrophiles as they have an empty orbital that can accept an electron pair. Meanwhile, a nucleophile contains a pair of electrons that can be used to form a new chemical bond. Nucleophiles thus act as electron donors. The chapter then looks at Lewis acids/bases.. The chapter then looks at Lewis acids/bases. It also considers SN1 and SN2, which are two classes of reaction that describe the nucleophilic substitution, or replacement, of one functional group at a saturated carbon centre by another. Finally, the chapter studies the impact of pK
a on leaving group ability.
Human Blood Group Antigens
Authors: Avent Neil D.
Published: September 2023

This chapter focuses on how blood groups represent some of the best examples of the clinical implications of human polymorphism. It traces the existence of blood-group antigens and antisera. During the second half of the twentieth century, serology revealed all clinically significant blood groups. The chapter then explains the new molecular techniques that permitted the identification of protein species involved in blood-group antigen expression by the small-scale purification (immunoprecipitation) of those involved. It also looks at the completion of the first membrane protein to be sequenced, glycophorin A (GPA), which happened in 1975. Towards the end, the chapter explores the significant blood-group active genes, then considers what constitutes a polymorphic trait.
Haemolytic Disease of the Fetus and Newborn
Authors: Avent Neil D.
Published: September 2023

This chapter examines the pathophysiology of haemolytic diseases of the fetus and newborn (HDFN). Here it considers fetal and neonatal anaemia and alloimmunization events. It seeks to understand blood-group incompatibilities that cause HDFN, including partial D antigens. It discusses the current clinical management of HDFN. The chapter also details the immunology of maternal alloimmunization to paternally inherited fetal antigens, feto-maternal IgG trafficking, the biochemistry of bilirubin detoxification, and clinical interventions and assessment by ultrasound. Near the end, the chapter shows the proposed mechanisms of action of prophylactic anti-D, and cellular assays to predict the severity of the disease. It then demonstrates the implementation of fetal blood-group genotyping in the management of HDFN.