bluuebunny/crossref_metadata_2025 huggingface dataset:
Rotation
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter focuses on the motion first on a circle and then on the surface of a sphere. It discusses the imposition of certain constraints on the wavefunction which shows how the energy and angular momentum of a rotating particle are quantized. It also examines the energy and the angular momentum of a rotating object which are quantized. The chapter reviews quantum mechanics and shows what they reveal about rotational motion. The chapter also considers a particle of mass m moving in a circular path of radius r in the xy-plane. It highlights translational motion which focuses on linear momentum, p and analogous angular momentum, J if rotational motion is considered.
General features of molecular spectroscopy
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter provides a description of features of the instrumentation used to monitor the absorption, emission, and scattering of radiation spanning a wide range of frequencies. It discusses the theory of absorption and emission of radiation, leading to the factors that determine the intensities and widths of spectral lines. It also reviews experimental and theoretical features of all types of spectra to interpret data from a wide range of varieties of molecular spectroscopy. The chapter explores different arrangements of light sources, wavelength analysers, and detectors that make the study of absorption, emission, and scattering of electromagnetic radiation by molecules in gaseous, liquid, and solid samples possible. It also points out how molecular spectroscopy is used to analyse materials and monitor changing concentrations in kinetic studies.
Rotational spectroscopy
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter derives expressions for the rotational energy levels of diatomic and polyatomic molecules. It shows how to interpret rotational spectra, in which only the rotational state of a molecule changes. It also emphasizes how rotational spectroscopy provides very precise details of bond lengths and bond angles of molecules in the gas phase. The chapter looks at transitions between rotational levels that contribute to vibrational and electronic spectra and are used in the investigation of gas-phase reactions, such as those taking place in the atmosphere. It explains how the analysis of rotational spectra yields the bond lengths and bond angles of molecules in the gas phase.
Mesophases and disperse systems
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter explores colloids and micelles, which are assemblies with some of the typical properties of molecules and with their own characteristic features. It analyzes aggregates of small and large molecules that form the basis of many applications and are abundant in biological cells. It also discusses colloids, micelles, and biological membranes that form spontaneously by self-assembly of molecules or macromolecules and are held together by molecular interactions. The chapter describes a mesophase, which is a bulk phase that is intermediate in character between a solid and a liquid. It mentions colloidal particles that are thermodynamically unstable but kinetically non-labile and liquid crystals that are classified as smectic, nematic, or cholesteric.
Planning your experiment
Authors: Holmes Debbie , Moody Peter , Dine Diana , Trueman Laurence
Published: September 2023

This chapter goes through the process of planning experiments. The best way to learn about the design of investigations is to look at what other people have done and make a similar attempt. The chapter shows how to understand the strengths and weaknesses of an experimental design and how to identify the ways in which the design might be improved. It also provides information about the process of designing experiments and the things we would need to consider. To that end, the chapter considers how to critically review published experimental designs. The first step in this process is to identify the aim and objectives and then to consider the strengths and weaknesses of the work. Next, the chapter explores the process of designing experiments using the decision web.
Reporting your research
Authors: Holmes Debbie , Moody Peter , Dine Diana , Trueman Laurence
Published: September 2023

This chapter goes through the most common approaches taken to communicating findings to research. This includes: writing a report, presenting a poster, and giving a presentation. These all have similar elements: Title, Introduction, Methods, Results, and Discussion. The chapter thus explains what each section is for, approaches to take when writing each section, common errors, and issues specific to each form of communication. It first provides a guide to the general format common in scientific papers and reports. The chapter then demonstrates how, in a research poster, the written content and the visual tools used in the presentation are of equal importance. Finally, using oral presentation to discuss results is covered.
Atomic structure
Authors: Almond Matthew , Spillman Mark , Page Elizabeth
Published: September 2023

This chapter discusses topics which are related to atomic structure, starting with electromagnetic waves and matter. Chemists frequently make use of spectroscopic techniques to study materials. Such techniques rely on the interaction between electromagnetic waves and matter. As well as its speed, an electromagnetic wave is also described by its wavelength and its frequency. For mostly historical reasons, spectroscopists also frequently make use of another related quantity known as the wavenumber. The chapter then considers Albert Einstein's explanation of the photoelectric effect, which is observed when electromagnetic radiation of a sufficiently high energy strikes a metal surface. It also looks at hydrogenic emission spectra and the Rydberg equation; quantum numbers and atomic orbitals; and multi-electron atoms and the periodic table.
Molecular orbitals and structure
Authors: Almond Matthew , Spillman Mark , Page Elizabeth
Published: September 2023

This chapter examines molecular orbitals, which are single-electron wavefunctions that describe the behaviour of electrons in molecules. Molecular orbital (MO) theory relies on two important approximations: the orbital approximation and the linear combination of atomic orbitals. The orbital approximation is the assumption that the overall wavefunction for an atom containing N-electrons can be approximated by the product of N single-electron atomic orbitals. Extending this idea to molecules leads to the assumption that the overall wavefunction for an N electron molecule can be approximated by the product of N single-electron molecular orbitals. Wavefunctions have wave characteristics and therefore, atomic orbitals on one atom can interfere with those on another atom. The interference can be constructive (addition) or destructive (subtraction). We can therefore use an approach called the linear combination of atomic orbitals (LCAO) to build up molecular orbitals via addition and subtraction of atomic orbitals.
Aromatic chemistry
Authors: Cook Michael , Cranwell Philippa
Published: September 2023

This chapter explores aromatic chemistry. It begins by looking at electrophilic aromatic substitution (SEAr), where a functional group on an aromatic ring, usually a proton, is replaced by an electrophile. In order to undergo reaction with the electrophile, the aromatic ring must be electron-rich. This is because the mechanism requires the cloud of electrons on the benzene ring to attack the electrophile; if the ring were electron-deficient, it would not be able to do this as readily. The mechanism proceeds via a carbocation intermediate, also known as the Wheland intermediate. The chapter then considers nucleophilic aromatic substitution (SNAr), where a group on an aromatic ring is replaced by a nucleophile. It also discusses azo coupling, which is when an aromatic diazonium-containing compound is joined to another aromatic compound.
Introduction to Basic Immunology and Techniques
Authors: Avent Neil D.
Published: September 2023

This chapter describes the laboratory and scientific aspects of the transfusion of human blood and products or components made from blood, and the transplantation of tissues and stem cells. It examines the historical background to the science of transfusion and transplantation. The chapter also outlines the various components of the immune system and the functioning of the humoral immune system. The chapter then switches topics to describe the agglutination of human red cells by serum of other humans, which is a difference within a species, rather than between species. It then presents two other major developments that enabled advances to be made in transfusion practice. The first is the use of plastic bags for the collection of blood, instead of glass bottles. The second major advance was the introduction of monoclonal antibody technology.
Compatibility Testing and Adverse Effects
Authors: Needs Malcolm
Published: September 2023

This chapter assesses the process of compatibility testing and how it applies to each type of blood component. It describes the various crossmatch methods used in laboratories to determine compatibility, and explains when and why each crossmatch method either may or may not be used. The chapter also outlines the various national guidelines regarding pre-transfusion compatibility testing, then details the role the laboratory has in the investigation of an adverse reaction. Next, the chapter distinguishes between the UK Serious Hazards of Transfusion (SHOT) reporting scheme and the incident reporting requirements of the Medicines and Healthcare products Regulatory Agency (MHRA). It cites a number of UK regulations, guidelines, and recommendations.
Human Leucocyte Antigens (HLA) and Their Clinical Significance
Authors: Avent Neil D.
Published: September 2023

This chapter reviews the human leucocyte antigens, the genes of which are found within the major histocompatibility complex (MHC), and how the detection and matching of the genes and gene products has contributed to the success of transplantation and the study of human disease. It begins by defining the Human Leucocyte Antigens (HLA) system. The chapter explores the role of the HLA system in transplantation and transfusion, then shows the principles of matching for haemopoietic stem cell transplantation, solid organ transplantation, and platelet transfusion. The chapter also studies the methods and technology for HLA typing and antibody testing used in the HLA laboratory. Finally, the chapter investigates the key immunological pathways targeted by immunosuppression, then looks at the hurdles to overcome in xenotransplantation.
Mutation
Authors: Bromham Lindell
Published: September 2023

This chapter discusses mutation, which is any heritable change to the genome that will be passed on when the genome is copied. Mutation is essential for evolution: without it, all genomes would be identical. Yet, because mutations are inherited, we can also expect the genomes of individuals to be similar to those of close relatives. As such, by comparing DNA sequences, we can distinguish individuals, identify family groups, and study the heritability of traits across generations. The development of new and faster ways of revealing the mutations that an individual carries has wide-ranging implications for both research and wider society. The chapter then looks at single nucleotide polymorphisms (SNPs) and the estimation of the mutation rate.
Species
Authors: Bromham Lindell
Published: September 2023

This chapter describes the origin of species. Genetically isolated populations that cannot exchange alleles with other populations accumulate a distinct set of substitutions. When genomes from different daughter populations have accumulated sufficient distinct substitutions that they cannot be combined together to produce healthy hybrids, due to genomic incompatibility or adaptation to different niches, we can say they have become distinct species. Taxonomy aims to identify and name these distinct species, while also recognizing that all populations form a hierarchy of relatedness. This provides a natural basis for classification and allows prediction of similarities, because relatives are likely to be more similar in many different traits, due to their shared ancestry. DNA sequence data is increasingly being used to identify species, and to place these species within a broader systematic framework that reflects patterns of descent with modification.
Nerve cells and their connections
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter examines the nervous system. The nervous system is adapted to provide rapid and discrete signalling over long distances. It is divided into the central nervous system (CNS) comprising the brain and spinal cord, and the peripheral nervous system comprising the peripheral nerves, the enteric nervous system, and autonomic nervous system. The chapter describes the two main types of cells that make up the nervous system: the nerve cells or neurons and the satellite cells. The chapter clarifies that the satellite cells in the brain and spinal cord are called glial cells or neuroglia, while elsewhere they have different names, such as Schwann cells, Müller cells, or pituicytes. The neurons are the fast-signalling elements of the nervous system.
Introduction to the nervous system
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter focuses on the nervous system. This includes motor control and the basis of sensation. It outlines the organization of the nervous system and the nature of its constituent cells. The nervous system may be divided into five main parts: the brain, the spinal cord, peripheral nerves, the autonomic nervous system, and the enteric nervous system. The chapter discusses how the brain and spinal cord constitute the central nervous system (CNS), while the peripheral nerves, autonomic nervous system, and enteric nervous system make up the peripheral nervous system. The autonomic nervous system is the part of the nervous system that is concerned with the innervation of blood vessels and the internal organs, which includes the autonomic ganglia that run parallel to the spinal column and their associated nerves.
The eye and visual pathways
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter describes light as a component of the electromagnetic spectrum, wherein the human eye responds to radiation with wavelengths between about 380 nm to 750 nm. The chapter talks about particles that carry radiation called light. These particles are known as photons. They have no mass or electric charge but carry a very small amount of energy that depends on the wavelength of light. Although the eye is able to respond to light of intensities over 15 orders of magnitude, the range of light intensities that are normally encountered in daily life is somewhat smaller. The chapter looks at different phases of vision in bright, low-level light, and dark conditions. These conditions are classified as photopic, mesopic, and scotopic. During the day, photopic vision is dominant, but at night, especially in the absence of artificial light, the ability to see depends entirely on scotopic vision.
The vestibular system and the sense of balance
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter highlights the important role the sense of balance plays in the maintenance of normal posture and in stabilizing the retinal image, particularly during running and walking. It refers to people with impaired vestibular function. These people often have difficulty in walking over irregular or compliant surfaces, particularly when they are deprived of visual cues. Such people also have difficulty with their vision during walking, as the visual world appears to move up and down rather than remaining stable as it does for normal individuals. The chapter explores the basic structure and function of the vestibular system and some common vestibular disorders. The organ of balance is the vestibular portion of the inner ear, which consists of two chambers, the utricle and saccule, and three semicircular canals.
The chemical senses—smell and taste
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter considers chemical senses, olfaction, and gustation. It argues that these are amongst the most basic responses of higher animals to their environment. It details how olfaction and gustation play a distinct role in survival: the sense of smell allows for the assessment of foods or whether a foodstuff is rotten and unfit to eat, while the sense of taste plays a vital role once food is in the mouth. This is especially important both in the selection of nutritious foods and in the avoidance of poisons. The chapter discusses the classification of different odours before describing the cellular basis of the sense of smell. It examines the physiology of taste receptors and the central pathways involved in taste sensations.
The cerebral cortex, sleep, and circadian rhythms
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter describes the cerebral hemispheres as the largest and most obvious structures of the human brain, receiving information from the primary senses and control coordinated motor activity. It shows how the main somatosensory and motor pathways are crossed, so that the left hemisphere receives information from, and controls the motor activity of the right side of the body, while the right hemisphere is concerned with the left side. It is commonly recognized that people prefer to use one hand rather than another and most people prefer to use their right hand for writing, holding a knife or tennis racquet, and so on. The chapter emphasizes how the two halves of the brain are not equal with respect to the information to which they pay attention or with respect to the activities they control. It mentions Paul Broca and Marc Dax from the nineteenth century, who described an association between the loss of speech and paralysis of the right side of the body in patients who had suffered a stroke.
Introduction to the respiratory system
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter analyses the energy needed by animals for normal activities. This is mainly derived from the oxidative breakdown of foodstuffs, particularly that of carbohydrates and fats. It discusses the process called internal or cellular respiration, wherein the mitochondria oxidize carbohydrates and fatty acids generate adenosine triphosphate (ATP). The oxygen needed for this energy metabolism is ultimately derived from the atmosphere by the process of external respiration, which also serves to eliminate the carbon dioxide produced by the cells. The chapter cites the key process of external respiration, which is gas exchange between the air deep in the lungs and the blood that perfuses them. In addition to their role in gas exchange, the lungs have a variety of non-respiratory functions such as their role in trapping blood-borne particles.
Alveolar ventilation and blood gas exchange
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter examines the main function of the respiratory system, which is to provide the cells of the body with oxygen for the generation of metabolic energy and to remove the carbon dioxide produced by oxidative metabolism. To do so, it must have a means of transporting these two gases to and from the tissues and exchanging them with the atmospheric air. It focuses on the gas exchange in the alveoli and the matching of blood flow to the availability of oxygen. The chapter details the transport of oxygen and carbon dioxide by the blood. Broadly, the respiratory system can be considered to consist of two parts: the conducting airways and the area of gas exchange.
The physiology of high altitude and diving
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter describes the physiology of the cardiovascular and respiratory systems under the stresses imposed by changes to ambient pressure. It refers to the physiological adaptations which occur when a person experiences the reduced atmospheric pressure of high altitudes. It also looks at the respiratory problems associated with high ambient atmospheric pressures, such as those experienced by divers. The chapter clarifies how atmospheric pressure decreases with altitude and how the partial pressure of oxygen in the inspired air falls progressively with increasing altitude as the fraction of oxygen in the air does not change. The hypoxia of altitude can be divided into acute hypoxia, which is experienced by subjects who have been exposed to high altitude for a few minutes or hours, and chronic hypoxia, which is experienced by people living for long periods at high altitude or by mountaineers who have become acclimatized to high altitude.
The gastrointestinal tract
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter discusses the principal function of the gastrointestinal (GI) system. It highlights how the GI system converts foods eaten into simple molecules that can be absorbed into the bloodstream and utilized by the cells of the body for energy and to build and repair body tissues. The structures that carry out these tasks may be divided into those that form the alimentary canal itself and the accessory organs that contribute to mechanical digestion or to chemical digestion through the secretion of various fluids and enzymes. The chapter provides a detailed explanation of the roles played by the different parts of the GI system in the processes of ingestion, digestion, absorption, and elimination of indigestible remains. It covers the complex nervous and hormonal mechanisms that regulate motility and secretory activity.
Fundamentals of neurobiology
Authors: Zupanc Günther K. H.
Published: September 2023

This chapter introduces the fundamentals of neurobiology, specifically the concepts and methodologies that are of immediate relevance to behavioral neurobiology. It discusses the cellular and subcellular composition of nervous systems – comparing cell theory and reticular theory. The discussion covers the Golgi method, an histological staining technique invented by Camillo Golgi, as well as the work of Spanish neurohistologist Santiago Ramón y Cajal who further improved the staining technique and applied it to many parts of the nervous system, providing strong evidence in support of cell theory. Furthermore, the chapter explains the salient features of neurons and nervous systems, the axons ensheathment by myelin, and the physiology and ionic basis of the electrical properties of neurons. It describes synapses, the specialized contact zones in the nervous system where a neuron communicates with another cell. The chapter also gives a glimpse of some neurobiological approaches in neuroethology.
The study of animal behavior and its neural basis: A brief history
Authors: Zupanc Günther K. H.
Published: September 2023

This chapter takes a closer look at the historical development of the study of animal behavior and neuroethology. It begins by discussing how anthropocentric approaches – the view that places humans as the most important element in the centre of the universe and interprets the world exclusively in terms of human values and experience – compromised the study of animal behavior. The chapter reviews the approach employed by Aristotle, considered the father of natural history and founder of zoology, in studying animals. It also introduces the mind-body dualism, a philosophical concept that holds perception, emotion, thoughts, and other mental phenomena as supernatural and not the result of brain activity. The chapter progresses to discuss evolutionary theory and comparative approaches in the study of animal behavior. It also explains how Konrad Lorenz and Niko Tinbergen founded the discipline of ethology, and the emergence of neuroethology at the end of the twentieth century.
Orienting movements
Authors: Zupanc Günther K. H.
Published: September 2023

This chapter examines how animals continuously collect and process relevant stimuli from the environment and translate them into proper behavioral action. It looks at the diversity of orienting movements in animals and summarizes the rules defining how to classify and name these movements. The discussion introduces concepts such as primary and secondary orientations of animals, as well as taxis and kinesis. The chapter then describes in more detail the cellular and neural mechanisms governing spatial orientation. Furthermore, it shows some model systems such as the taxis behavior in animal-like unicellular protist Paramecium species which exhibits chemotaxis, phobotaxis, and galvanotaxis, among others. The chapter also describes another model system, the geotaxis in vertebrates – a taxis behavior that involves the orientation of the body relative to gravity.
Neuromodulation: The accommodation of motivational changes in behavior
Authors: Zupanc Günther K. H.
Published: September 2023

This chapter discusses neural mechanisms that mediate motivational changes in the behavior of animals. It tackles the two major neural mechanisms that mediate motivational changes in behavior: structural reorganization of neural networks and biochemical switching of neural networks. The chapter considers some well-studied model systems to illustrate underlying principles. It explains dendritic plasticity by examining the seasonal changes in chirping behavior of weakly electric knifefish. It also discusses the seasonal variation in dendritic morphology of motoneurons in white-footed mice. Furthermore, it explains axonal or synaptic plasticity as a mechanism for accommodating variability in reproductive behavior during the estrous cycle of female cats. Then it reviews the modulation of the stomatogastric ganglion and the modulation of crayfish aggressive behavior to explain biochemical switching.
Sources of Lead Compounds
Authors: Rostron Chris
Published: September 2023

This chapter identifies the many and varied sources of lead compounds that have been exploited and those that continue to be used by academic researchers and the pharmaceutical industry. A lead compound is one that exhibits a desired pharmacological property which can then be developed further to optimize its biological activity. It provides a starting point for further structural modifications in order to achieve greater potency, greater selectivity, and more appropriate pharmacokinetic parameters. Identification of a lead compound is an important feature of the drug design process. But from where do we obtain these lead compounds? The chapter then looks at natural and synthetic sources of lead compounds and explains the concept of serendipity in terms of drug discovery. It also considers the use of in vitro tests and in vivo tests to determine as much information about the biological activity of the lead compounds.
Clinical Research and Its Regulation
Authors: Rostron Chris
Published: September 2023

This chapter focuses on clinical research and its regulation. Clinical trials have a very long history but it is only since the 1940s that the ethical considerations of such trials began to become important. However, the current integrated regulatory framework, known as the International Conference on Harmonisation (ICH), was not developed until 1990. This framework is administered by various regulatory bodies worldwide with the aim of harmonizing the application of guidelines and requirements for new product registration. The chapter states that clinical trials are required to take place in a number of steps, referred to as the phases of clinical trials, all of which should be conducted according to the principles of good clinical practice (GCP).
Design and Management of Clinical Trials
Authors: Rostron Chris
Published: September 2023

This chapter assesses the design and management of clinical trials. The objective of the trial should be clearly set out, as this will influence all aspects of the trial, such as target population,patient selection, the nature of the disorder and treatment duration. In order to ensure comparability between test and control groups of subjects, a process of randomization is utilized. Meanwhile, to eliminate any bias in the conduct of the clinical trial, a process of blinding is utilized. There are a number of standard designs for clinical trials, each of which may be utilized in order to address the objective of the trial. Because clinical trials involve volunteers or patients, there are ethical issues that must be addressed. The chapter also highlights that a key aspect of clinical data management is that it utilizes good data management practice (GDMP).
Stratospheric chemistry—ozone
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter deals with the chemistry of ozone in the stratosphere, analysing how ozone is distributed within the atmosphere and the concerns about decreasing amounts of stratospheric ozone. It talks about the oxygen-only synthesis and decomposition chemistry of ozone, including the catalytic cycles of destruction involving both natural and anthropogenic origins. It also covers the properties, nomenclature, impacts, and replacements of chlorofluorocarbons (CFCs) and halons. The chapter presents the rate of ozone destruction reactions through kinetic calculations and illustrates the process of ozone thinning or ‘ozone hole’ formation at the poles. It examines important aspects of stratospheric chemistry, such as gas molecules in the stratosphere that absorb some of the solar radiation and moderate what is transmitted to the Earth's surface.
Atmospheric aerosols
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter concentrates on understanding the role played by atmospheric aerosols in the global environmental chemistry context. It explains the nature of aerosols and their environmental significance and identifies their sources, both natural and anthropogenic. It then goes on to investigate the condensation chemistry processes for the formation of aerosols before considering their concentrations, lifetimes, and other properties. It also examines control technologies that are used to minimize industrial emissions of particulates. The chapter defines an aerosol as a suspension of particles in a gas and explains that an atmospheric aerosol consists of particles that remain aloft in the air. It distinguishes particles in an aerosol from smaller gas molecules or molecular clusters by their ability to cause incoherent scattering of visible light and interfere with light transmission.
Gases in water
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter explores how gases distribute themselves between air and water and how the properties of water change accordingly. It cites Henry's law for simple gases, such as oxygen or nitrogen, that do not react with water and considers the specific case of carbon dioxide, which is a gas that reacts with water and creates a more complex equilibrium system. It also demonstrates how to define alkalinity and acid neutralization capacity and their relation to environmental issues. The chapter refers to gases and other volatile compounds whose vapours may be present at low concentration in the atmosphere. It provides a quantitative description of the distribution of gases between air and water, which depends on the substance's vapour pressure, solubility, and ability to react with water and other components in the hydrosphere.
Metals and semi-metals in the hydrosphere
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter describes the nature, occurrence, and behaviour of dissolved metals and semi-metals found in various aquatic systems and their influence within the environment. It discusses the types of metals and semi-metals that occur in water and explains how various classification schemes are used to explain the complexation behaviour of metals, including an environmental classification. It also examines how chemical speciation influences the bioavailability of metals and semi-metals. The chapter discusses the elements calcium, copper, and mercury as examples for understanding the environmental chemical behaviour of different classes of metals. It mentions the arsenic contamination of surface and groundwater that occurs in many other countries.
Mapping, Sequencing, Annotation, and Databases
Authors: Lesk Arthur M.
Published: September 2023

This chapter focuses on the history of classical genomics, genes, types of genetic maps, and principles of DNA sequencing. It expounds on genetic maps and linkage as some gene traits are different but their alleles are co-inherited. It mentions the automation of DNA sequencing and explains the different processes of sequencing available. Maps vary from linkage, banding patterns, DNA cleavage fragments, and DNA sequences. After sequencing and annotation, the chapter discusses the databanks in molecular biology. It emphasizes the need for logical structure in these as their power resides in the links they contain. The chapter also tackles computer programming in genomics, explicating computational molecular biology as the internet provides free available tools and data.
Genomics and Anthropology: Human Evolution, Migration, and Domestication of Plants and Animals
Authors: Lesk Arthur M.
Published: September 2023

This chapter acknowledges that genomics, archaeology, and languages merged to explain important transitions throughout human history. It considers the evidence for the origin of modern humans in Southern and Eastern Africa. It explicates how the sequencing of mitochondrial and nuclear genomes establishes links between modern humans and our early European relatives, which are known as Neanderthals and Denisovans. It explores how DNA sequencing informs the tracing of patterns of human migration. The chapter highlights the domestication of animals and plants as an experiment in directed genomes. It states the phenotypic qualities required for domestication and discusses the genome changes associated with animal domestication, using dogs, horses, rice, and corn as prime examples. It also mentions the genome effects that domestications have had on human civilization.
Transcriptomics
Authors: Lesk Arthur M.
Published: September 2023

This chapter focuses on transcriptomes. A transcriptome is the inventory of the RNA molecules in a cell. The chapter differentiates between proteomes and genomes. It explains the relationship between microarray technology and RNAseq methods, including the gene expression table and how it is derived from experiments using these methods. It clarifies the types of applications for which microarrays are suitable. The chapter points out that transcriptomics could be used in the study of changing gene expression patterns in different physiological states and to work out the genes and proteins responsible for specific features of a phenotype. It notes the general features of the correlation of gene expression patterns with development in Drosophila melanogaster. The chapter also considers that transcriptomics are being used to study the molecular biology of higher mental processes in mammals, such as learning and the evolution of human language abilities.
Systems Biology
Authors: Lesk Arthur M.
Published: September 2023

This chapter focuses on systems biology as an integrative approach to all the 'omics disciplines. It notes the static and dynamic aspects of biological networks, expounding the structure, dynamics, and evolution of metabolic networks and regulatory networks. It mentions the stability, adaptability, and robustness of living systems as well. The chapter also explores different ways of experimentally determining protein–protein and protein–nucleic acid interactions. It explains the basic features of the lytic-lysogenic switch in bacteriophage λ and the regulatory network of Escherichia coli. Finally, it talks about how transcriptomics are being used to reveal the different time courses of expression of various genes during the yeast diauxic shift.
Quantum Chemical Methods
Authors: Harvey Jeremy
Published: September 2023

This chapter examines quantum chemical methods. The remarkable success of quantum chemical methods in contemporary chemical research is due to the availability of powerful computers, of course, but also to the development of accurate methods and of efficient algorithms that implement these methods. Due to its product form, the Hartree–Fock wavefunction neglects correlations in the positions of electrons, but correlated methods exist that can yield improved results. Particular noteworthy methods include configuration interaction methods. As well as ab initio methods, semiempirical methods and density functional theory are extremely useful methods for solving the Schrödinger equation. Quantum chemical methods yield energies that can be combined to obtain reaction energies, and these can be predicted very accurately using some methods. Quantum chemistry can also be used to characterize many molecular properties. As well as calculations on isolated molecules, computations of wavefunctions and energies for periodic crystalline systems are possible.
Molecular Mechanics Methods
Authors: Harvey Jeremy
Published: September 2023

This chapter evaluates molecular mechanics methods. In this approach, a known chemical bonding pattern is assumed and used to define preferred bond lengths and angles, and thereby an energy expression that takes into account distortions away from these ideal values. For a given bonding environment, the type of energy terms needed, and the numerical parameters within the energy expression, are transferable from one system to another. Hence, general forcefields can be constructed with quite general applicability. The chapter describes how the energy terms and parameters are chosen, based on input from experiment and quantum chemistry. Molecular mechanics can be applied to large systems due to its efficiency, allowing calculations on liquids, solutions, and solids. This frequently makes use of periodically repeating models and the chapter looks at special measures needed to treat such models. Finally, it discusses the type of software used for molecular mechanics.
Atomic Structure
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter looks at the atomic structure and shows that atoms are bonded together to form compounds. The chapter atoms, nucleus, electron, proton, and neutron by referring to the nuclear model. A mass spectrometer can be used to measure the masses of atoms. Electronic structures are often called electronic configurations. The Schrödinger equation can be used to explain arising subshells in the configuration and the electron density. The electron density is defined as the probability of finding a particular electron. The chapter also shows how the current numbering system of the periodic table is based on the Schrödinger equation. The chapter then tackles the ionization energy. This refers to the minimum energy required to remove an electron from an isolated gas atom.
Moles
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter explores different types of formulae in chemistry: empirical formula and molecular formula. It defines empirical formula as the simplest whole-number ratio of atoms of each element in a compound. Molecular formula can be defined as the whole-number multiple of the empirical formula. The chapter also explains the value of the Avogadro constant, which is the number of atoms per mole. It notes the strategies for solving mass-to-mass calculations, ideal gas models, molar concentration, and molar volume. Molar mass is defined as the mass per mole of a substance. A solution is mostly expressed through mass concentration. This specifies the mass of the solute dissolved per cubic decimetre of the solution.
Trends Across the Periodic Table
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter explores trends across the periodic table. The physical trends across the periodic table include metal, non-metal, metalloids, and electrical conductivity. The chemical trends across the periodic table involve the oxidation state as elements shift drastically due to their reaction to oxygen. Phosphorus, sulfur, and chloride for a variety of oxides. The chapter also tackles the melting points, ionization energies, and atomic radii across periods 2 and 3 of the periodic table. The melting point of a metallic element is dependent on the strength of the metallic bonding and the attraction between metal ions and a delocalized sea of electrons.
Hydrocarbons: Alkenes
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter focuses on alkenes, which are known to be unsaturated hydrocarbons with a carbon-carbon double bond. Ethene is known to be the simplest alkene, this is closely followed by propane. Alkenes undergo electrophilic addition reactions. This involves the addition of hydrogen halides, acidified water, and halogens. The chapter explains the Markovnikov's rule wherein the alkene and adduct are unsymmetrical. This is something which two isomers could form. Markovnikov's rule refers to the more stable carbocation forms carrying a positive charge with three bonds. The chapter also explicates the addition of a neutral molecule to ethene which is largely similar to the electrophilic addition of molecules under acidic conditions.
Alcohols
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter focuses on alcohols (ROH) which have at least one hydroxyl group bonded to a carbon atom. Alcohols are known to undergo two reactions similar to the reactions of halogenoalkanes. Additionally, esters are formed through an alcohol's reaction to carboxylic acids. Alcohols also undergo oxidation reactions. The chapter explores the main manufacturing processes for ethanol which are fermentation and the direct hydration of ethene. It also considers the nucleophilic substitution and oxidation reactions of alcohols. The elimination reactions coincide with alcohol being dehydrated through heating with acid. However, conditions depend on the specific alcohol involved in the process as some of the alcohols could produce more than a single product.
Aldehydes and Ketones
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter describes aldehydes and ketones. Aldehydes have one alkyl group and one hydrogen atom attached to the carbonyl carbon. Ketones have two alkyl groups and resist oxidation. Both aldehydes and ketones contain the carbonyl group which has a carbon atom doubly bonded to an oxygen atom. Fehling's solution and Tollens' reagent can also help determine the differences between aldehydes and ketones. Oxidation can also help the reduction of aldehydes and ketones to primary and secondary alcohols respectively. The chapter also explains nucleophilic addition, condensation reactions, and alpha carbon reaction of aldehydes and ketones.
Carboxylic Acids and Their Derivatives
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter discusses carboxylic acids and their derivatives. It notes RCOOH as the general formula for carboxylic acids. Thus, the weak acids neutralize alkalis and react with carbonates. Additionally, acyl chlorides typically react with water, alcohols, ammonia, and amines. In esters, the presence of a concentrated sulfuric acid catalyst forms an equilibrium mixture as the option of leaving the tetrahedral intermediate becomes available. On the other hand, acylation reactions are triggered when an acyl group replaces a hydrogen atom in the nucleophile. The chapter also covers the nucleophilic additional-elimination reactions of acid derivatives. It lists the general formula of esters and acyl chlorides as well.
Polymers
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter focuses on the polymer, which is the resulting very large molecule following the reactions of monomers. Polymers, then, are classified as either addition polymers or condensation polymers. As well as polymers, the addition polymerization of alkenes involves the formation of a large molecule by combining a large number of alkene monomers. The chapter also identifies ethene as the monomer of polyethene. Condensation polymers are generated through the reaction of varying factors such as polyesters, polyamides, dicarboxylic acid, diamines and diols. Chain polymerization can help form polyethene, while step polymerization aid in generating condensation polymers like polyurethanes, polyesters and polyamides.
Nitrogen metabolism: nucleotide metabolism
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter talks about nucleotides. These are synthesized de novo. Purine nucleotides are synthesized by a salvage pathway via ribotidation of free bases released by the degradation of nucleotides. The chapter reviews the de novo synthesis of purine nucleotides, wherein the purine ring that is assembled by a series of steps in which the intermediates are already joined to ribose-5-phosphate. 5-Phosphoribosyl-1-pyrophosphate (PRPP) is the universal ribotidation agent. The product of the synthesis pathway is inosine phosphate (IMP), which is converted to form both GMP and AMP. The chapter analyzes the pathway which involves two additions of formyl groups and reactions that depend on the coenzyme tetrahydrofolate (FH4). Dividing cells require deoxynucleotides and so are sensitive to deficiencies in the synthesis pathway.
Mechanisms of metabolic control and their applications to metabolic integration
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter highlights metabolic pathways that must be regulated to avoid futile substrate cycling. It determines how enzyme activities may be controlled by changing the amount of enzyme or by changing the rate of catalysis of enzymes. Control points in metabolic pathways usually occur at irreversible steps in which the forward and backward reactions can be separately controlled. The chapter cites allosteric control, which is a powerful concept essential for cells to exist. Allosteric enzymes are multisub-unit proteins which contain allosteric sites to which molecules attach and affect the activity. The chapter notes the effect of substrate concentration on reaction rates which is sigmoidal rather than hyperbolic.
Methods in protein investigation
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter examines the relatively simple protein purification procedures which can be applied on a large scale and are used as preliminary purification steps. The chapter looks at differential centrifugation which sediments organelles on the basis of mass. These can be discarded or collected depending on the location of the protein of interest. Purification methods for soluble proteins include selective precipitation by high concentrations of ammonium sulphate. The chapter looks at specific separations that can be achieved by column chromatography, such as molecules that are separated as they run through column packings. Separations are variously based on molecular exclusion, ion exchange, or specific molecular affinities.