bluuebunny/crossref_metadata_2025 huggingface dataset:
Tests of difference: two related samples
Authors: Hawkins Dawn
Published: September 2023

This chapter describes tests of difference on two samples of related data, in particular the parametric paired t-test and the nonparametric Wilcoxon signed-rank test. Both these tests are used to assess whether a difference between two samples of related data is due to chance alone, or to chance plus something of potential biological interest. The data from the dependent variable must be measured at least at the ordinal level for a Wilcoxon signed-rank test and at the scale level for a paired t-test. Any level of measurement will work for the independent variable, provided that only two categories are defined. The chapter offers guidance on what sample sizes to use when planning to collect data for use in these tests, demonstrates how to perform each test by hand and with SPSS using real data sets, and illustrates how to identify and report the key results of both tests.
Tests of difference: more than two samples
Authors: Hawkins Dawn
Published: September 2023

This chapter explores tests of differences on two or more samples of unrelated data, particularly the parametric one-way Anova and the nonparametric Kruskal—Wallis test. Neither test works if the data in the samples are measured at a nominal level, but the Kruskal—Wallis test can cope with ordinal data. Both tests work with scale data. The independent variable can technically be measured at any level, provided it can be used to distinguish a small number of categories. The chapter then offers guidance on what sample sizes to use when planning to collect data for use in these tests, demonstrates how to perform each test by hand and with SPSS using real data sets, and illustrates how to identify and report the key results of both tests. It also differentiates between model I and model II Anovas.
Connecting phenotypes with DNA sequences
Authors: Meneely Philip
Published: September 2023

This chapter shows how we can connect mutant phenotypes to the corresponding DNA sequence after the mutations had been identified and classified. The process is colloquially known as cloning the gene. The chapter looks at complementation tests and sequence analysis which are often conducted to confirm the causative gene of the phenotype. The chapter presents the processes that have helped identify the causative genes for some rare genetic human conditions. The chapter also looks at the process of a typical gene-cloning strategy which includes mapping a mutant phenotype or looking at genes transcribed in a pattern. It explains how the DNA sequence corresponding to a mutant or variant phenotype can now be identified directly, by sequencing the genomes or the exons of affected individuals.
Genome editing
Authors: Meneely Philip
Published: September 2023

This chapter looks into genome editing, which is currently a system of analysis for most eukaryotes as a result of the widespread adoption of the technique known as CRISPR-Cas9. The chapter discusses the genome editing process: searching the genome for the location of the desired edit, interrupting the DNA sequence at the specific location, and editing the function of a gene or site using double-stranded break repair mechanisms. It describes how the CRISPR array provides the search and find function when using the CRISPR-Cas9 technique, while Cas9 nuclease provides the interrupt and double-stranded break function. It also discusses how editing the targeted double-stranded break depends on the two processes by which cells repair other double-stranded breaks: homology- directed repair and non-homologous end joining (NHEJ).
Gene interactions
Authors: Meneely Philip
Published: September 2023

This chapter focuses on gene interactions, whereby many different genes and their polypeptide products work together to carry out a biological process. Genetic approaches like suppression and synthetic enhancement find functionally related genes by examining changes to the mutant phenotypes that occur in double mutants. Genetic interactions find both direct and indirect interactions, so they are especially useful for obtaining a broad picture of the activities of the genes in the biological process; however, they usually do not provide many details about the specific roles. The chapter explains how information about the specific roles of the proteins is found using molecular approaches such as yeast two-hybrid screens or co-immunoprecipitation, the latter being considered the standard for proving that the proteins are part of the same complex in vivo.
Presenting data in graphical form
Authors: Blann Andrew D.
Published: September 2023

This chapter provides a background on the most common formats in which data can be presented visually, and how such data can be interpreted. It looks at methods of presenting both categorical and continuously variable data and reviews software packages that can produce excellent figures suitable for presentation and publication, limiting the requirement for hand-drawn artistic skills. It also explains how to interpret numerical data when they are presented graphically in the form of a normal and non-normal distribution, scatterplot, histogram, pie chart, dot plot and box plot and whisker plot, line plot, and graph. The chapter clarifies that continuously variable data with a normal distribution is represented by a bell-shaped curve, while data with a non-normal distribution is skewed to the left or to the right. It mentions data with a categorical distribution that is presented as a histogram.
Communication
Authors: Blann Andrew D.
Published: September 2023

This chapter describes communication in the context of biomedical science practice ranging from the everyday interactions between colleagues regarding clinical matters to the dissemination of the results of research. It outlines how to communicate effectively with various colleagues, such as presenting the findings of studies internally or externally as abstracts to learned societies, writing formal documents, and preparing data for publication in a journal. It also describes the key aspects of the layout of a PowerPoint presentation, the major sections of a written communication, the significant elements of an abstract, and the leading features of a research paper. The chapter promotes the correct passage of information, which is crucial for the safe and efficient working of a routine laboratory and is a key part of good laboratory practice. It emphasizes how failing to communicate in a clinical setting endangers life or can lead to poor experimental or process results.
Cancer Fundamentals
Authors: Divan Aysha , Royds Janice A.
Published: September 2023

This chapter provides an overview of the fundamentals of cancer. Normal cells evolve to become cancer cells by acquiring successive mutations in primarily two classes of genes: the proto-oncogenes and the tumour suppressor genes. Mutations that specifically drive cancer development and disease progression are called driver mutations; the rest are termed passenger mutations and their role in carcinogenesis is less clear. Large-scale cancer genome studies have provided deep insight into the mutational profile of the cancer genome, and are presently informing not only basic research but also the clinical management of cancer patients. The chapter then looks at cancer stem cells, which have the capacity to self-renew and differentiate into cell types that recreate the cellular heterogeneity of the tumour from which they derive. Viruses are also associated with the development of some cancers as are certain bacteria.
Soils
Authors: Hudson Paul F. , Houben Peter , Bosker Thijs
Published: September 2023

This chapter focuses on the impacts of agriculture on soil, which is a vital natural resource for food production and provides a range of ecosystem services. About 95% of the world's food production comes from the soil while the remaining 5% comes from glass greenhouses and fisheries. The chapter describes the basic components of soil and the soil ecosystem services: provisioning, supporting, regulating, and cultural services. The discussion emphasizes that about a third of global soil resources already have been degraded by human activities, mostly due to modern agricultural practices. The chapter also tackles the key causes of soil degradation: water and wind erosion, pollution, and salinization. Furthermore, the chapter reviews how to examine a soil horizon and explores hydroponic agriculture – the growing of crops outside the soil.
Food Security
Authors: Niles Meredith T. , Brown Molly E.
Published: September 2023

This chapter discusses the concepts of food security and its connection to sustainability. It looks at where food is produced, by whom it is produced, and how humans then move and use this food around the planet. The chapter first defines the expanding concept of food security, which has begun with narrower concerns of providing enough food and, more recently, encompassing social and cultural issues. The chapter also introduces the four pillars of food security: availability, access, utilization, and stability. Then the discussion explores urban agriculture as well as the use of satellite information and Internet-connected devices to improve farm management.
Governance
Authors: Breeman Gerard , Ehrhardt David
Published: September 2023

This chapter explores the politics and policymaking processes involved in the problem of food governance. The discussion emphasizes that governance is both a problem-solving process and a political process in which stakeholders use power to try to promote their own interests. It considers food governance as a wicked problem, complicated by technical complexity, multiple stakeholders, boundary conflicts, and the need for constant adaptation. The chapter outlines the policy cycle in which stakeholders negotiate and compete to promote their interests, then it looks at the goals these stakeholders have in influencing government policy and other institutions and how these shape food systems. Next, it illustrates the difficulties in governing food systems to make them more sustainable.
A pantheon of pathogens 2: Parasites, prions, and cultures
Authors: Fullick William
Published: September 2023

This chapter examines parasites, prions, and cultures. Parasites take many different forms—some are multicellular and very large in size, others microscopic and difficult to detect. When parasites infect us, they always have some effect on us—usually, but not always, causing an infectious disease. Meanwhile, prions are misshapen proteins which can induce similar misfolding in other proteins throughout the body. They cause progressive, degenerative, and irreversible neurological symptoms, and are very hard to detect and diagnose. The chapter then looks at different laboratory techniques for growing or identifying different types of pathogen, which are vital for diagnosis of disease and the selection of the appropriate treatment. It also considers the concept of biosecurity, the term used for a set of precautions that aim to prevent the introduction and spread of harmful organisms.
Thermodynamics of Chemical Processes
Authors: Price Gareth
Published: September 2023

Thermodynamics of Chemical Processes describes the basic principles which govern reactivity and phase equilibria in chemical systems and contains a number of worked examples and problems. The first chapter considers preamble energy in chemical systems. The second chapter covers enthalpy and thermochemistry. The next chapter is about entropy in chemistry. There follows a chapter on free energy and equilibrium. The last chapter is about phase changes and solutions.
Photosynthesis, oxygen, and the evolution of life
Authors: Murphy Denis , Cardona Tanai
Published: September 2023

This chapter discusses photosynthesis, which involves the use of solar energy to convert simple inorganic substrates into complex carbon-based compounds. It surveys the basic processes involved in the various types of photosynthesis found in bacteria and eukaryotes and the pivotal role played by photosynthesis in the evolution of life on Earth. It also considers the broader significance of photosynthesis in terms of the many important roles that it plays in both the biosphere and the geosphere. The chapter shows how photosynthetic oxygen generated by cyanobacteria led to a global oxygen increase during the GOE1 about 2.4 Ga. It describes the evolution of photosynthetic eukaryotes, which gradually diversified and eventually overtook cyanobacteria as the major oxygen producers.
Introduction to microbiology
Authors: Ford Michael
Published: September 2023

This introductory chapter provides an overview of microbiology and its importance in the detection and prevention of infection. All living things, including microorganisms, are placed into a system of classification. This system highlights characteristics that are common among certain groups, while giving order to the huge variety of microorganisms that exist on our planet. This science of classifying living things is known as taxonomy. The chapter then looks at the anatomy of bacterial cells, considering flagella, fimbriae, and pili. It also explains the principles of bacterial growth, which is a complex process and important in the diagnosis of bacterial disease. This growth allows the organism to reach a critical mass so that the laboratory scientist can examine the bacteria and use the information to determine the cause of an infection. Finally, the chapter considers sterilization and disinfection, as well as bacterial colony recognition.
Culture media
Authors: Perry John
Published: September 2023

This chapter discusses the basic ingredients of culture media and the different types of media available. A bacterial culture medium must provide all of the nutritional requirements for the bacterial species it is expected to recover. In practice, culture media used by diagnostic laboratories are not defined as they contain extracts of complex biological materials of which the exact composition is unknown. The reasons for this are convenience and the fact that bacteria generally grow better on complex, undefined media. Some common constituents of complex culture media include water, protein derivatives, yeast extract, gelling agents, buffers, blood and serum, charcoal, and other additives for fastidious bacteria and anaerobes. The chapter then explores selective, differential, and enrichment media and what they are used for. It also explains chromogenic media, antimicrobial susceptibility testing, and the principles and pitfalls of culture media preparation.
Examination of cerebrospinal fluid and fluids from sterile sites
Authors: Law Derek
Published: September 2023

This chapter describes the examination of cerebrospinal fluid and fluids from sterile sites, including synovial, pleural, ascitic, pericardial, and peritoneal dialysis fluids. The meninges constitute a system of membranes that envelope and protect the central nervous system (brain and spinal column). Inflammation of the meninges is known as meningitis, which can be caused by bacteria, viruses, or fungi and is an extremely serious condition owing to the proximity of the infection and inflammation to the brain and spinal cord. In a patient with suspected meningitis, it is necessary to obtain a sample of cerebrospinal fluid for analysis by lumbar puncture. The chapter then looks at the procedure for handling the samples safely, as well as the role of cell counts in processing and diagnosis. It also considers the different culture methods for fluids and the common pathogens isolated from the different fluids.
Interactions Among Species
Authors: Gilbert Francis , Gilbert Hilary
Published: September 2023

This chapter evaluates interactions among species. Most species interactions in ecology are between insects and plants. Selection for defence against herbivores has led plants to evolve toxins, while selection for the ability to use a toxic diet has led herbivores to evolve counter-measures, such as P450 detoxification enzymes. This coevolutionary process is a major source of evolutionary change. Meanwhile, top predators can have disproportionate effects (a 'trophic cascade') on the species below them in the food web of their community. The eradication of wolves by humans in Yellowstone National Park had the unintended consequence of preventing tree regeneration. The chapter also looks at indirect interactions via intermediate species. Conservation needs to pay attention to the variety of ways in which such indirect interactions work.
What Processes Create Ecological Communities?
Authors: Gilbert Francis , Gilbert Hilary
Published: September 2023

This chapter focuses on four processes at work in ecological communities. These are selective forces (competition, predation, and coevolution) that modify the characteristics of populations and species, and/or determine their presence in a community; ecological drift, i.e. random chance that affects small populations in particular, that might lead to extinction or immigration events; speciation; and dispersal. On the large scale, the relative importance of these processes is not the same as on the small scale. The species richness of local communities depends on large-scale species richness via the processes of dispersal, and abiotic and biotic filtering. The chapter then considers the idea of the 'balance of Nature'.
Study and Communication Skills for the Chemical Sciences
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

Study and Communication Skills for the Chemical Sciences shows how to develop the study and communication skills that are central to succeeding in studying university-level chemistry. It shows the reader how to make the most of lectures, tutorials, workshops, group work, and practical work. The book also offers guidance on working with different sources of information, choosing the correct writing style, and completing writing assignments, including practical and project reports. Other topics covered include communicating to a non-scientific audience, avoiding plagiarism, using feedback, preparing and delivering presentations, and creating academic posters. Finally, the text looks at how to get the most out of revision and exams and provides advice on developing skills for a future career.
Making the most of practical work
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

This chapter considers practical work as the defining feature of an education in the sciences, noting that the knowledge base in all areas of chemistry is underpinned by careful experimentation and observation. It explores the aims of all types of practical work, which are to develop skills as a scientist and also to deepen knowledge and understanding of the subject. It also focuses on laboratory-based practical work and recognizes many practical activities that may not take place in a laboratory. The chapter includes some examples that help contextualize its key points, including an undergraduate investigation of the hardness of tap water by analysing the concentrations of calcium and magnesium ions by a complexometric titration. It outlines preparations for a laboratory class and how to carry out the experimental work.
Working with different information sources
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

This chapter focuses on working with different sources of information, such as using Google or another internet search engine in order to access information. It points out that information accessed through the internet is not necessarily reliable and could have been posted there by anyone. But it also stresses that internet searches can lead to types of sources with a high degree of reliability, such as research journals. The chapter emphasizes reading as an essential part of being a student at university, explaining that students were said to go to university to ‘read’ for a degree in previous generations. It explains that students spent most of their working time reading up on the subject they were studying, even in subjects like chemistry that have a strong emphasis on practical work. Even now, reading is still a very important part of studying.
Using feedback
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

This chapter discusses the importance of feedback and how to use it effectively. It emphasizes how a student can make use of feedback to improve, even if it is really limited and the student only has basic marks. The chapter also provides guidance for making the most of feedback, which applies for both printed copies of work handed in and online submissions, such as those made via the institution’s online learning environment. The chapter explains that feedback provides a clear indication of how well a student is progressing in their work in relation to the standards established by the university. It clarifies that the marks gotten for a piece of work also constitute a form of feedback as they give an overall indication of how well a student is doing.
Creating academic posters
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

This chapter describes poster presentations, which are a common format for presenting academic work and are a regular feature at academic conferences. It explains the purpose of academic posters and suggests key steps for creating them effectively. It also discusses the context for academic posters. The chapter stresses how poster presentations are often used to allow many people to present their research at once as not everyone at a conference will be able to present their research orally. It points out that a poster presentation is more limited than an oral presentation in terms of the amount of information that can be communicated, emphasizing that posters should be designed to summarize the most important elements and promote discussion.
Developing and articulating your skills
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

This chapter reflects on and recognizes the transferable skills that a student develops during their degree. It cites Peter Hawkins’s book The Art of Building Windmills, which implies that to be employed is to be at risk, but to be employable is to be secure. It also highlights the importance of being employable in order to increase the chances of being employed whatever the circumstances. The chapter explains that being employable is about the skills and qualities that can be developed beyond the subject knowledge of the degree. It talks about the importance of engaging early with employability, reflecting on the development of skills, articulating skills, and gaining experiences that will enhance transferable skills.
Organometallic chemistry
Authors: Aspinall Helen C.
Published: September 2023

This chapter focuses on the organometallic chemistry of the f-elements, which is very different from that of the d-transition metals. This is mainly due to the predominantly ionic nature of the bonding and the lack of two-electron redox chemistry for the f-elements. The chapter begins with examples of homoleptic σ-bonded alkyls and aryls and then moves on to homoleptic π-bonded complexes, some of which display 'non-classical' oxidation states. The π-bonded organometallics have been the subject of numerous experimental and theoretical investigations aimed at understanding the bonding, and particularly the possibility of f-orbital contributions. The chapter also looks at some of the unique reactions of σ-bonded organometallics for heteroleptic complexes in which the reactivity of the σ-bonded alkyl/aryl is moderated by the presence of stabilizing ancillary ligands. Finally, it presents some examples of organo-f-element catalysed reactions.
Plant Biosecurity
Authors: Lane Charles
Published: September 2023

This chapter discusses how plant diseases affect food and ornamental crops and have devastating impacts on whole ecosystems, pointing out that if a single plant or tree is wiped out by disease, the whole ecosystem is undermined. It explains how the threat of plant diseases spreading across the globe has become more real and more pressing as international travel has become easy and relatively cheap. It also highlights biosecurity which involves a set of precautions that aim to prevent the introduction and spread of harmful organisms. The chapter outlines four key areas associated with biosecurity: trade pathways; international regulations; risk assessment; and introduction, spread, and detection of harmful organisms. It analyses the term 'biosecurity', which means preventing the introduction and spread of harmful organisms, whether in plants, or in animals.
Chemistry3
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

Chemistry
3 covers organic, inorganic, and physical chemistry to provide balanced coverage of the fundamentals of chemistry. Chemistry is widely considered to be the central science: it encompasses concepts on which all other branches of science are developed. Yet for many, gaining a firm grounding in chemistry is a real challenge. The text tackles head-on two issues pervading chemistry education: mathematical skills, and the ability to see the subject as a single, unified discipline. Topics covered include molecules (diatomic and polyatomic), acids and bases, gases, and molecular spectroscopy and characterization. There are also chapters looking at energy and thermochemistry, entropy, Gibbs energy, chemical equilibrium, and electrochemistry. The latter half of the book covers phase equilibrium and solutions, isomerism and stereochemistry, organic reaction mechanisms, and halogenoalkanes. Next, the text moves on to alkenes and alkynes, benzene and other aromatic compounds, aldehydes and ketones, carboxylic acids and derivatives, and hydrogen. Finally, the last three chapters cover s-, p-, and d-Block chemistry.
The language of organic chemistry
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter introduces organic chemistry, which concentrates on the study of compounds that contain carbon. The carbon atom shares electrons with other carbon atoms as well as atoms of many other elements and it can bond together to form chains, rings, and branches. The chapter highlights the common names for a number of well-known organic solvents and reagents that have been accepted into the IUPAC system and classifies carbon atoms as primary, secondary, tertiary, or quaternary. The chapter shows that all carbonyl compounds contain the C=O group, while aldehydes (RCHO), ketones (RCOR), and carboxylic acids (RCO2H) are named from the parent alkane. The important organic functional groups and organic compounds identified using IUPAC nomenclature are also covered.
Reaction kinetics
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter emphasizes the importance of studying reaction kinetics which has an importance in many branches of chemistry. Reaction kinetics can provide fundamental information about the interactions and energy changes that take place at a molecular level during an elementary reaction. The chapter highlights what is meant by the rate of a reaction, including how to write a differential equation for the rate in terms of the consumption of a reactant or formation of a product and the rate equation for an elementary reaction from the stoichiometric chemical equation. It analyses the mechanism of a complex reaction that involves a series of elementary reactions and shows that the rate equation must be determined experimentally. It also explains how kinetic studies can be used as evidence for reaction mechanisms and why some reactions show zero order kinetics.
Molecular characterization
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter discusses mass spectrometry (MS), infrared (IR) spectroscopy, and, particularly, nuclear magnetic resonance (NMR) spectroscopy, concentrating on how chemists analyse the different types of spectra. It illustrates how the techniques can be used together to determine unknown chemical structures. The chapter reviews how the molecular ion gives the relative molecular mass of a molecule and how high-resolution mass spectrometers can determine the molecular formula of a molecule. It identifies and predicts characteristic fragmentation patterns of molecular ions from compounds containing groups, such as alkyl, halogenoalkyl, ether, amine, and carbonyl. It also highlights the factors that influence the position of absorption bands in an IR spectrum and factors that affect the position of a resonance signal in a 1H NMR spectrum and in a 13C NMR spectrum.
Energy and thermochemistry
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter focuses on the branch of chemistry known as thermodynamics, which deals with energy in chemistry. This important and powerful topic is based around some simple laws and equations that allow chemists to understand and predict the behaviour of substances and their reactions. The chapter gives examples of the different ways that energy can be transferred in chemical systems and explains what is meant by the terms system and surroundings. It determines the difference between isolated, open, and closed systems and the difference between heat capacity, specific heat capacity, and molar heat capacity, including how to carry out calculations using these properties. It also defines enthalpy change and illustrates how to calculate changes of enthalpy during phase changes and chemical reactions.
Electrochemistry
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter looks at electrochemistry, which helps explain the rusting of iron and lies behind some important biochemical processes, such as the transmission of nerve impulses. Modern life would be impossible without electrochemistry as much of the energy that powers mobile existence comes from batteries. The chapter defines conductivity and molar conductivity for a solution of an electrolyte and elaborates how the molar conductivity of a strong electrolyte depends on concentration. It details how to calculate the limiting molar conductivity of a strong electrolyte from the individual ionic conductivities of the cations and anions present. The understanding that an electrochemical cell is made up of two half cells and that reduction occurs at the cathode and oxidation at the anode are also explored.
Organic reaction mechanisms
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter provides the key tools needed to understand and write mechanisms for the reactions of organic molecules and gives an overview of the characteristic reaction mechanisms of common functional groups. A set of guidelines for drawing reaction mechanisms, classifying organic reactions, and determining the different types of selectivity in organic reactions are included. The chapter demonstrates how to use double-headed and single-headed arrows to represent the movement of electrons in polar and radical reactions, respectively. It discusses hyperconjugation, inductive effects, and mesomeric effects that affect the stability of ions and neutral organic molecules and shows the inductive and mesomeric effects of some functional groups. It also compares the relative strengths of nucleophiles and electrophiles.
Benzene and other aromatic compounds
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter considers benzene as one of the most fascinating organic molecules. Six carbon atoms in benzene are linked in a planar hexagon and, as each carbon atom is bonded to only one hydrogen atom, benzene is an unsaturated hydrocarbon. The chapter determines what aromatic, antiaromatic, and nonaromatic compounds are and give examples of each. It identifies reagents and reaction mechanisms to explain how benzene undergoes halogenation, nitration, sulfonation, Friedel–Crafts alkylation, and Friedel–Crafts acylation. It also talks about how the electronic and steric effects of substituents on benzene rings influence the rates and regioselectivities of electrophilic substitution reactions and how substituents on benzene rings can be converted into other substituents by redox reactions or by forming diazonium ions.
Chemical change
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter considers chemical change. Studying the enthalpies of chemical reactions is one of the foundations of biochemical thermodynamics and therefore crucial to the discussion of energy deployment in organisms. As such, the chapter takes a look at how reaction enthalpies may be constructed from enthalpies of formation. The fact that enthalpy is a state function implies that the required reaction enthalpy can be constructed from the reaction enthalpies of known reactions. The chapter goes on to describe the standard enthalpies of formation as well as the application of computational chemistry. Finally, the chapter demonstrates the variation of reaction enthalpy with temperature.
The thermodynamic description of aqueous solutions
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter turns to the thermodynamic description of aqueous solutions. In order to assess the energy requirements of a particular process, it is necessary to develop a framework for assessing the thermodynamic stability of the components in a solution. As a first step, this chapter considers only homogeneous mixtures, or solutions, in which the composition is uniform throughout. The component in smaller abundance is called the ‘solute’ and that in larger abundance is the ‘solvent’. Most of the chapter focuses on aqueous solutions, as these are of great importance in biochemistry, but the concepts transfer with little change to more general systems. Except in one case, the chapter focuses on non-electrolyte solutions, where the solute is not present as ions, for example a solution of glucose in water.
Ligand binding equilibria
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter examines ligand binding equilibria. Most macromolecules interact with a range of other, often smaller, molecules, which are referred to as ‘ligands’. The strength of these interactions is often modulated to suit the needs of the cell: sometimes they are strong, sometimes weak, and sometimes non-existent. The chapter first considers ligand binding to a single site, before proceeding to ligand binding to multiple sites. Next, cooperative binding is discussed. Finally, the chapter explores a further complication — avidity, or when both the ligand and the macromolecule may be polydentate, in the sense that a single binding event may involve several sites.
Ion transport across membranes
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter presents a thermodynamic discussion of the transport of ions, and thus electrical charge, across membranes. Here, the concept of activity plays an important role, and this chapter begins by explaining how the activities of ions may be estimated. It goes on to explore a model of how ions distribute themselves differently on either side of a semipermeable membrane and give rise to a potential difference there. Substantial concentration differences are maintained both passively and actively, the latter by a variety of ion pumps driven by ATP. These pumps include the structures that permit action potentials to flow along neurons and thus enable one to think and respond to stimuli.
The quantum mechanics of motion
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter pays particular attention to the quantum mechanics of motion. It is not possible to explain the structures and properties of atoms and molecules, where the role of electrons is central, without using quantum mechanics. Many of the processes of biochemistry involve the transfer of electrons and protons from a donor to an acceptor, and this migration can be understood only in terms of quantum theory. Here, the chapter introduces three fundamental types of motion — translation, rotation, and vibration — along with their characteristic quantum mechanical behaviours. It shows how various unexpected properties emerge, such as the ability of particles to penetrate into classically forbidden regions, the quantization of energy and angular momentum, and the existence of energy that cannot be removed from the system.
Molecular orbital theory: polyatomic molecules
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter extends MB theory to polyatomic molecules. Here, all the atoms contribute atomic orbitals to the construction of molecular orbitals. There are two special cases. One consists of molecules with conjugated chains of carbon atoms. Although the Hückel theory used to treat these molecules is very primitive, it generates orbitals and energy levels in a simple way and in fact underlies more sophisticated calculations. The other case consists of d-metal complexes where their high symmetry can be used to establish their spectroscopic and magnetic properties. Modern computational techniques for calculating molecular structure bring together all these features and provide deep insight into the properties of molecules of almost any complexity, with striking graphical displays.
Computer-aided simulation
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter considers computer-aided simulations via molecular forcefields, molecular mechanics and molecular dynamics, and quantitative structure–activity relationships. Computational techniques have become a major component of biochemistry and molecular biology, not only for the calculation of electronic structure but also for the prediction of molecular conformation, motion, and function. Computer simulations provide insight into the structures and dynamics of macromolecules, including their binding properties. To establish the shape of a macromolecule, the chapter shows how the forces operating within the molecule are established and then calculates their consequences. Another approach is to establish correlations between electron density distributions and biological, specifically pharmacological, activity.
Ultraviolet and visible spectroscopy
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter turns to ultraviolet and visible spectroscopy. The spectroscopic techniques which use electromagnetic radiation in the visible and ultraviolet region explore transitions in which the distribution of electrons changes. However, when electrons are excited from one molecular orbital to another, the molecule bursts into vibration and the absorption in biochemically interesting media are spread over many wavelengths. The general features of absorption in this region of the electromagnetic spectrum can be discussed in terms of groups of atoms with characteristic absorption and the transitions of d-electrons in metalloproteins. Techniques have been developed that use another feature of radiation, the possibility that it is polarized.
Nuclear magnetic resonance
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter takes a look at nuclear magnetic resonance. One of the most powerful and widely used spectroscopic techniques makes use of the resonant absorption of radiofrequency radiation by magnetic nuclei exposed to strong magnetic fields. The precise frequencies at which resonant absorption occurs depend on the local magnetic fields generated by the applied field and by interactions with other nearby magnetic nuclei. The application of the technique is greatly extended by observing how nuclei respond to a series of pulses of radiofrequency radiation. Here, detailed information about the structures of molecules in their native environment and their motion can be obtained.
Electrophoresis
Authors: Wang Qiuyu , Ahmed Nessar , Smith Chris
Published: September 2023

This chapter discusses electrophoresis, which is the movement of charged molecules or ions in an electric field. Ions that differ in their charge and/or mass will move at different rates such that if they have a common starting point they will separate over time as some will move faster than others. As a result, the components of a mixture will be separated. Thus, electrophoresis is a separation technique. However, it can also be adapted to provide analytical data, such as the size of molecules. Electrophoresis has many applications in the biomedical sciences: in separating proteins and nucleic acids, in assessing purity of biological samples, and in estimating the sizes of molecules. The chapter then describes the uses of the major types of electrophoretic separation techniques. It also explains the underlying principles of isoelectric focusing, before considering the uses of pulsed field and two-dimensional gel electrophoresis.
Hormones and disease: What happens when things go wrong?
Authors: Hinson Joy , Raven Peter
Published: September 2023

This chapter discusses hormones and disease. All of the diseases associated with hormones result from either too much hormone activity or too little. Too much hormone activity is usually the result of a disorder in the gland that produces the hormone, often due to uncontrolled growth of the gland. Meanwhile, too little hormone activity can be a fault in hormone production or it can be a problem with hormone action, where the hormone receptor does not work properly. Endocrine disease can have many causes, including autoimmune disease, defects in the receptor, enzyme defects, and hormone resistance syndromes. Some forms of cancer are also dependent on hormones and can be treated by blocking either production or action of the hormone.
Binding of neutral guests
Authors: Beer Paul D. , Barendt Timothy A. , Lim Jason Y. C.
Published: September 2023

This chapter examines the binding of neutral guest molecules. Primarily, due to their uncharged nature, the interactions between neutral guests and host molecules are comparatively a lot weaker than the dominant electrostatic forces of ions. Instead, receptors designed to bind neutral molecules have to rely on hydrogen bonding, π–π interactions, Lewis acid interactions, and the hydrophobic effect to a much greater extent. Selectivity by dedicated host molecules is now dictated to an even greater extent by the fundamental principles of complementarity and preorganization. In addition, binding by 'physical incarceration/imprisonment' of neutral molecules within the cavities of larger host molecules now plays a much bigger and prominent role than that for ions. The chapter then considers how macroscopic crystalline solid host molecules, such as metal–organic frameworks (MOFs), can be exploited and engineered for binding of neutral guest molecules both in solution and in the gaseous phase.
The cancer genome: mutations versus repair
Authors: Pecorino Lauren
Published: September 2023

This chapter looks at the structures of genes and describes the mutations that occur during carcinogenesis. It argues that changes in the nucleotide sequence of DNA — called mutations — are crucial for acquiring the hallmarks of cancer and have been labeled an enabling characteristic. The chapter then investigates how, on the one hand, mutations in DNA occur as a consequence of exposure to carcinogens and, on the other hand, examine the DNA repair systems that are in place to maintain the integrity of the genome and suppress tumorigenesis. The chapter then shifts to define the genetic information, coded within DNA, and the role of the accumulation of mutations. Ultimately, the chapter concludes with a discussion of conventional chemotherapies and a new class of drugs that target DNA repair pathways. It also studies the recent findings from advances in sequencing technology and imaging.
Reprogrammed metabolism and diet
Authors: Pecorino Lauren
Published: September 2023

This chapter highlights the role of diet in cancer prevention and causation. It explores our understanding that some food constituents exert their cancer-relevant effects by their ability to regulate gene expression: a paradigm of how environmental factors work together with genes, rather than the concept of environment versus genes. The chapter also describes the new therapeutic approaches that exploit our knowledge of reprogrammed metabolism and the molecular mechanisms of food constituents. The chapter then shifts to demonstrate the preventative factors of diet and causative factors of diet. It also investigates the link between nutrients, cancer, and hormone action. Next, the chapter addresses the drug strategies that target metabolic pathways. It also considers “enhanced” foods and dietary supplements for chemoprevention.
Symmetry and Structure
Authors: Jenkins Stephen J.
Published: September 2023

Introduction

Having established a firm thermodynamic foundation in Chapter 1, we may now build our understanding of surface symmetry and surface structure upon a secure footing. In liquids, this amounts to little more than acknowledging the possibility of a density gradient in the...
Compounds of the s- and p-block elements
Authors: Norman Nicholas C.
Published: September 2023

This chapter focuses on acids and bases. The broadest definition of acids and bases is the Lewis definition. In this scheme, a Lewis acid is an electron-pair acceptor while a Lewis base is an electron-pair donor. Meanwhile, the Brønsted–Lowry concept is probably the second most commonly employed description of acids and bases, although in aqueous solution it is by far the most widely used. In this scheme, an acid is defined as a proton donor and a base as a proton acceptor. It is important to note that the concept of Lewis acidity and basicity incorporates the Brønsted–Lowry approach as a special case. The chapter then looks at element oxides and hydroxides, as well as the Lewis acidity of the heavier p-block elements. It also considers hard and soft acids and bases.
Acids and bases
Authors: Norman Nicholas C.
Published: September 2023

This chapter assesses periodic trends in relation to structure, looking at electron counting rules including the octet rule. The octet rule was first formulated by Gilbert Lewis and Irving Langmuir in the early twentieth century. Octet refers to 8, of course, and this is an important number especially for the s- and p-block elements. The importance of the number 8 arises since, for these elements, we have one valence s and three valence p orbitals which, when involved in covalent bonding, will result in four bonding orbitals and four antibonding orbitals (or a reduced number corresponding to the number of lone pairs or non-bonding orbitals). Eight electrons will therefore fill the bonding/non-bonding orbitals completely. The chapter then considers the valence shell electron-pair repulsion (VSEPR) theory; the trivalent compounds of Group 15; and the Zintl principle.