bluuebunny/crossref_metadata_2025 huggingface dataset:
Coordination complexes of the d-block metals
Authors: Almond Matthew , Spillman Mark , Page Elizabeth
Published: September 2023

This chapter assesses the coordination complexes of the d-block metals. The d-block elements are distinguished by having electrons in d orbitals. There are five d orbitals and it is important to be able to draw these orbitals and be able to label them according to their shape and orientation. The chapter begins by looking at electronic configurations of the d-block metals and their ions, before explaining the determination of oxidation states of d-block metal complexes and their electronic configurations. It then considers the coordination number and the coordination geometry in coordination complexes. The chapter also studies isomerism in coordination complexes, studying structural isomerism and stereoisomerism. Finally, it explores crystal-field theory, which is an electrostatic bonding model that assumes that metal ions in coordination complexes are surrounded by ligands that act as negative point charges.
Elimination reactions
Authors: Cook Michael , Cranwell Philippa
Published: September 2023

This chapter evaluates elimination reactions. In elimination reactions, a base (nucleophile) removes a hydrogen nucleus (proton), which results in the formation of an alkene with loss of a leaving group. This process can occur by three mechanisms: E2, E1, and E1cB. The mechanism of elimination is dependent on factors including the solvent, the nature of the nucleophile, and the nature of the eliminating species. Elimination reactions often compete with substitution reactions. Bulky nucleophiles, strong bases, and high temperatures favour elimination over substitution, as does increasing the concentration of base. The chapter looks at the major products of elimination reactions, but in practice some of these experiments would yield several impurities, including substitution products.
Carbonyl chemistry
Authors: Cook Michael , Cranwell Philippa
Published: September 2023

This chapter studies carbonyl chemistry. In its simplest form, the carbonyl group is a carbon to oxygen double bond. A neutral carbon atom must have four bonds, therefore the nature of the other substituents at the central carbon atom will dictate what type of carbonyl group it is and also its reactivity profile. The chapter then looks at reactions with nucleophiles and with reducing agents. There are a range of methods to reduce a carbonyl group, but the simplest ones usually provide a source of hydride that acts as a nucleophile and adds to the central carbon atom. The chapter also considers carboxylic acids, acyl chlorides, esters, and amides.
Human Platelet Antigens (HPA) and Human Neutrophil Antigens (HNA) and Their Clinical Significance
Authors: Lucas Geoff
Published: September 2023

This chapter describes the nomenclature of human platelet antigens (HPA) and human neutrophil antigens (HNA). It presents the common principles involved in the immunohaematology of red cells and the immunohaematology of platelets and granulocytes. The chapter then outlines the most important HPA and HNA. It explores the principles, techniques, and problems in detecting HPA and HNA and associated antibodies. The chapter also investigates the clinical management and problems associated with the management of neonatal alloimmune thrombocytopenia (NAIT) cases. It discusses the role of platelet transfusion in other platelet immune disorders, and the processes of immune destruction affecting platelets. Finally, the chapter reports the other types of clinical interventions that are used to manage the range of clinical conditions associated with HPA and HNA antibodies.
Muscle
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter looks at one of the distinguishing characteristics of most multicellular animals, which is their ability to use coordinated movement to explore their environment. It emphasizes how this movement is achieved by the use of muscles, which consist of cells or myocytes that can change their length by a specific contractile process. In vertebrates, including man, three types of muscle can be identified on the basis of their structure and function: skeletal muscle, cardiac muscle, and smooth muscle. The chapter clarifies that skeletal muscle is the muscle directly attached to the bones of the skeleton, and its role is both to maintain posture and to move the limbs by contracting in a coordinated way. Cardiac muscle is the muscle of the heart, while smooth muscle is the muscle that lines the blood vessels and the hollow organs of the body.
The ear and auditory pathways
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter looks at higher animals, including primates, that use sound to detect danger, raise the alarm, claim territory, and attract a mate. Humans have developed the ability to communicate via sounds to a high degree than other higher animals by using speech and language. Interpreting these sounds is vital to human existence, so it is hardly surprising to find that large areas of the human brain are devoted to decoding what is heard. The chapter is concerned with the processes involved in the detection of sounds and with the nervous pathways that enable the process of hearing. It concludes with a brief discussion of the causes of deafness.
Introduction to the endocrine system
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter talks about complex multicellular organisms which require coordinating systems that can regulate and integrate the functions of different cell types. Two coordinating systems have evolved: the nervous system and the endocrine system. It details how the endocrine system uses chemical signalling to regulate the activity of particular cell populations. The chapter looks at chemical agents known as hormones, which are produced by cells within endocrine tissues and travel in the bloodstream to other cells upon which they exert a regulatory effect. Therefore, a hormone is usually defined as a blood-borne chemical messenger, and endocrinology is defined as the study of the endocrine glands, their hormones, and their target tissues.
The properties of blood
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter describes blood as a vital vehicle of communication between the tissues of multicellular organisms. It covers the numerous functions of the blood, such as carrying oxygen from the lungs to the other body tissues and carbon dioxide from the tissues to the lungs. Blood consists of a fluid called plasma in which are suspended the red cells or erythrocytes, white cells or leukocytes, and platelets or thrombocytes. The chapter demonstrates the nature of the suspension by centrifuging a sample of whole blood in a test-tube at ≈2000 × g for 5–10 minutes. After such treatment, the heavier red cells are packed at the bottom of the tube while the plasma is seen above them as a clear pale-yellow fluid.
Defence against infection: the immune system
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter discusses how animals inevitably come into contact with other organisms as they move through their environment to feed and reproduce. It describes some of the organisms that may attempt to invade the body and may live in harmony with the host. When this is of benefit to both the host and the other organism, it is known as mutualism, while it is called commensalism if the association is neither beneficial nor harmful. The chapter analyses the relationship known as parasitism when the presence of the invading organism compromises the health of the host. It highlights the various ways in which the body defends itself against infectious diseases that are caused by bacteria, fungi, viruses, protozoa, and worms of various kinds.
The microcirculation and lymphatic system
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter highlights the chief function of circulation, which is the exchange of fluid, nutrients, and metabolites between the blood and tissues. It details how blood flows from the arterioles to the venules via the capillaries, which are the main exchange vessels. In the course of tissue exchange, a small volume of fluid passes from the capillaries to the interstitial space. The chapter outlines the basic organization of the lymphatic system and its role in the regulation of the volume of the interstitial fluid. The arterioles that branch directly from the arteries are known as primary arterioles, and they are extensively innervated by sympathetic nerve fibres.
Energy balance and the control of metabolic rate
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter looks at energy balance and metabolic rate and the various factors that influence them. The scale of the chemical reactions of the body can be gauged by considering the fact that an average human being uses about 360 litres of oxygen each day to burn several hundred grams of carbohydrates and fats and generate about 7500 kJ of heat. The chapter details the chemical processes of the body which are responsible for generating the heat which make up the metabolism of the body. This may be divided into two categories: anabolic and catabolic. The chapter then discusses anabolic metabolism, which involves the synthesis of complex molecules from simpler ones. Catabolic metabolism involves the breaking down of large, complex molecules to smaller, simpler ones.
Large-scale navigation: Migration and homing
Authors: Zupanc Günther K. H.
Published: September 2023

This chapter focuses on long-distance migrations of animals, introducing some key concepts of these phenomena. It discusses different modes of migration and briefly reviews previous experiments on the genetic control of migratory behavior. The chapter also explains homing, or the ability of an animal to specifically return to the place it considers home. Then it takes a closer look at the general methods used to study animal migration, including the use of tags, radar, and microtransmitters, and satellite-based radiotelemetry. Moreover, the chapter provides a detailed discussion of the behavioral, sensory, and neural mechanisms involved in orientation during migration and homing, using representatives of two particularly well-studied animal groups — birds and fish.
Organic matter in water
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter talks about the occurrence and nature of dissolved organic matter (OM) found in various aquatic systems. It also looks at its influence on environmental processes. The chapter investigates the origins and occurrence of organic matter in water and environmental functions that are related to organic matter, including the properties and interactions of humic material. It also refers to the most analytical methods for measuring OM in water that determine the carbon content, which is an essential element that is present in the aqueous environment as a component of inorganic species in the carbonate family. The chapter highlights the distinction between organic and inorganic forms when measuring the carbon content. It demonstrates various ways of classifying OM in water that determine the relations between the various chemical types of OM and the natural or anthropogenic origins of particular compounds.
Water pollution and water treatment chemistry
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter focuses on the meaning of water pollution and water treatment for the protection of water resources. In a first step, it defines what is meant by pollution in this context. It considers definitions based on purity, on naturalness, and a utilitarian definition and highlights their limitations. The chapter then reviews the desired chemical characteristics of various types of water and corresponding water quality guidelines before outlining wastewater treatment processes with emphasis on secondary and tertiary technologies. The chapter covers the chemistry of water treatment processes as wastewater which is discharged from urban centres is one of the principal contributors to water pollution.
The future Earth
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter reviews environmental chemistry by summarizing the beginning and early stages of the Earth's natural history. It highlights the interactions and cycles of the inorganic and living components of the Earth which have been acting together to make the planet what it is. It also emphasizes that environmental chemistry begins with a knowledge of the natural processes that have taken place and are ongoing now. The chapter highlights the processes within the atmosphere, the hydrosphere, the geosphere, and the biosphere, as well as the processes that move across boundaries, linking all parts of the environment together. It emphasizes that while the impact that modern humans exert on the environment through industry and agriculture is massive, the nature of the environmental footprint of humans varies across geographies.
The Human Genome Project: Achievements and Applications
Authors: Lesk Arthur M.
Published: September 2023

This chapter discusses the Human Genome Project, including its history and links to various organizations. The chapter acknowledges that technological advancement has turned genome sequencing into a high-throughput data-generation engine and anticipates that pharmacogenomics, or personalized medicine, will continue to grow. It explains that identifying the genetic substrate underlying diseases can become crucial in clinical treatment as gene editing using CRISPR/Cas technology could be used to repair defective genes of human embryos. The chapter considers how humans differ from other species and from one another, and looks into DNA and the application of genomics in the context of personal identification and parental determination. The chapter also mentions the ethical, legal, and social issues linked to genomics and the Human Genome Project.
Introduction and Background
Authors: Lesk Arthur M.
Published: September 2023

This chapter introduces genomics by identifying genomes, genes, their roles, scope, history, and organization. It aims to recognize the contributions to any individuals phenotype from their genome sequence, life history, and epigenetic factors. It explains major genome projects and the current library of genome information, which include high-throughput sequencing, de novo sequencing, resequencing, and exome sequencing. It also relates genes and minds to the study of neurogenomics. The chapter furthermore introduces proteomics and the mechanism of protein evolution in relation to natural selection. It argues that modern genomics merged biological data, computer science, and statistics in an effort to archive high amounts of data.
Metabolomics
Authors: Lesk Arthur M.
Published: September 2023

This chapter expounds on metabolomics, which is focused on metabolites, that is, molecules undergoing a transformation in a biological system. The chapter notes that the metabolic networks of any organism correspond to graphs with metabolites as nodes and linking reactions as edges. It highlights the defining principles of the Enzyme Commission and the Gene Ontology Consortium classifications of the functions of biological molecules. It mentions the significance of accurate enzyme function annotations in databases of metabolic networks. The chapter also considers the ways in which metabolic pathways differ between species. It points out the physicochemical basis of enzymatic catalysis and the quantities needed to characterize enzyme kineticsinformation needed to consider modelling flows through metabolic networks. It also talks about the difficulties in modelling the metabolic networks' traffic patterns.
Comparative Genomics
Authors: Lesk Arthur M.
Published: September 2023

This chapter analyses the three major divisions of living things (archaea, bacteria, and eukaryotes) based on the sequences of 16S rRNA genes. It notes the prevalence of historical gene transfer among prokaryotes. Historical gene transfer is not consistent with the hierarchical Linnaean classification scheme. The chapter discusses the general distribution of genome sizes and gene numbers while determining the characteristics of different types of genome organization in viruses, prokaryotes, and eukaryotes. The chapter notes the impact of gene duplication on genome evolution and considers the mechanism of genome change at the levels of individual bases, genes, chromosome segments, and whole genomes. It differentiates homologue, orthologue, and paralogue as well. The chapter also expounds on the human genome and the idea of a model organism in the study of human diseases.
Computational Chemistry
Authors: Harvey Jeremy
Published: September 2023

Computational Chemistry begins with an introduction to computation and the use of computers in chemistry. Next it turns to quantum chemistry and quantum chemical methods. The chapter that follows examines molecular mechanical methods. There follows a chapter on geometry optimization. The next couple of chapters look at dynamics and rate constants and equilibria. The last main chapter is about hybrid and multi-scale methods.
Thermochemistry
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter focuses on thermochemistry. It starts with enthalpy change which is the heat added to a system at constant pressure. The reaction is considered endothermic if heat is taken, while it would be exothermic if heat is given out. As the chapter shows, a calorimeter can be used to measure enthalpy changes. According to Hess's law, the standard enthalpy change for a reaction is independent of the route taken from reactants to products. Atomization enthalpy, on the other hand, is the standard enthalpy change accompanying the formation of a gaseous atom from either a solid or a gas containing molecule. Finally, the chapter explains bond enthalpy, solution enthalpy, and hydration enthalpy as well.
Kinetics
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter discusses rates of reactions in kinetics. The rate of reaction is based on the rate of change of concentration per unit time. The activation energy for a reaction is the minimum energy necessary for a collision to lead to a successful reaction. The rate of reaction, then, depends on the concentration of the reactants, temperature, presence of a catalyst, and state of subdivision. The Maxwell–Boltzmann distribution pins the number of molecules in a gas with given energy against energy. On the other hand, the Arrhenius equation measures the activation energy on how the rate constant depends on the temperature.
Halogenoalkanes
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter explains the concept of halogenoalkanes which have carbon-halogen bonds which are significantly polar. However, the carbon atom is partially positively charged and susceptible to a nucleophilic attack. The chapter explains that carbon-halogen bond enthalpy determines the relative rate of reaction. The three common nucleophilic substitution reactions of halogenoalkanes involve sodium hydroxide, potassium cyanide, and ammonia. Elimination is the second vital characteristic type of reaction of halogenoalkanes as it produces an alkene. The hydroxide ion is acting as the base of the compound rather than a nucleophile. Elimination is favoured over substitution where we see nucleophiles with strong bases, bulky nucleophiles, and high temperatures.
The basic molecular themes of life
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter talks about living cells. These obey the laws of physics and chemistry. Energy is derived in cells from the breaking down of food molecules and released in a form that can drive chemical and physical work. The chapter considers adenosine triphosphate (ATP) as the universal energy currency in life. Energy from food breakdown is used to synthesize ATP from adenosine diphosphate (ADP) and phosphate. ATP breakdown can then be coupled to carry out biochemical work. The chapter analyses biological molecules which are based on the carbon atom bonded mainly to hydrogen, oxygen, nitrogen, and other carbon atoms. Noncovalent bonds are weak in comparison with covalent bonds but important in allowing interactions between molecules.
Energy considerations in biochemistrya
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter looks at energy which changes during chemical reactions. Looking at this energy provides a reliable guide to the biochemistry of cells. The chapter describes free energy change (ΔG) as the most useful value as it expresses the amount of energy change in a reaction available to perform useful work. The ΔG value can be used to determine the equilibrium constant of a reaction. It also shows whether the reaction is likely to be reversible in cells. The chapter mentions free energy made available from food breakdown. This energy is used to synthesize adenosine triphosphate (ATP), the universal energy carrier of life. Catabolism or breakdown of food molecules drives anabolism or synthesis of molecules with ATP being the energy-carrying go-between.
Enzymes
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter defines an enzyme as a catalyst which brings about a specific reaction by increasing the rate of reaction while remaining unchanged in the process. Also, the enzyme here cannot affect the equilibrium of a reaction. The chapter points out that an enzyme is a protein that binds substrates and lowers the activation energy of the reaction it catalyses, as the active site binding the substrate is perfectly complementary to the transition state. An enzyme aligns substrates and provides a catalytic site, which is a small region of the protein that contains chemical groupings essential for the catalysis. The chapter discusses enzyme kinetics. This explores enzymes by measuring reaction rates and the Michaelis-Menten equation which explains the kinetics of many enzyme-catalysed reactions in terms of the substrate binding to the enzyme and the enzyme-substrate complex breaking down to liberate products. An enzyme displaying Michaelis-Menten kinetics gives a hyperbolic curve. This happens when the initial reaction velocity is plotted against increasing substrate concentration.
Muscle contraction, the cytoskeleton, and molecular motors
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter focuses on muscle contraction and molecular motors which depend on conformational changes in proteins. It describes skeletal muscle cells, which have multiple myofibrils running through their length and are divided into sarcomeres, the contractile units. The sarcomeres have at each end a strong Z disc, and projecting from these are thin filaments made of the fibrous protein actin pointing to the centre of the sarcomere. The chapter reviews how the thin filaments form a hexagonal “cage”, the inside of which is a thick filament, a bundle of hundreds of myosin molecules arranged in a bipolar fashion. Myosins are rod-like molecules, each a dimer arranged as a coiled-coil and terminating in a pair of globular heads.
General principles of nutrition
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter shows that nutrition is the science of food and the substances contained in it. The chapter notes that the main components of diet are macronutrients, which provide the bulk of the diet, and micronutrients, which include essential vitamins and minerals. The chapter explains that protein is needed to supply essential amino acids and fat is needed to supply essential fatty acids and provide sufficient energy in the diet. Most diets provide 10-15% of the energy in the form of protein and the remainder is made up of carbohydrate and fat. The chapter talks about the consumption of saturated fat, which is one of the risk factors for cardiovascular disease and some cancers, whereas consumption of polyunsaturated fat is considered healthy. A high consumption of sucrose can lead to dental caries.
The storage fuels: mechanisms of transport, storage, and mobilization of carbohydrate and fat
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter shows how glucose is stored as glycogen by the action of the enzyme glycogen synthase after a meal. It details the activation of the glucose as uridine diphosphoglucose (UDPG) and then polymerization into glycogen by glycogen synthase. Glycogen is degraded in times of need by glycogen phosphorylase and supplies the cells with an energy source. The chapter clarifies the important function of glycogen phosphatase in the liver, which is to liberate free glucose into the bloodstream and maintain sufficient levels for the use, primarily, of brain and erythrocytes. Other sugars absorbed from the intestine are converted into glucose or its derivatives and are also stored as glycogen.
Glycolysis, the TCA cycle, and the electron transport system
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter looks at glycolysis, which is stage 1 in the complete oxidation of glucose or glucosyl units of glycogen. It splits the lysis of the C6 glucose molecule into the two C3 molecules of pyruvate. The chapter looks at how glycolysis produces a net gain of only two adenosine triphosphate (ATP) molecules and prepares the glucose for the next stage, the tricarboxylic acid (TCA) cycle. Since nicotinamide adenine dinucleotide (NAD+) is limited in amount it must be reoxidized via the mitochondrion or glycolysis would halt. The chapter points out that the TCA cycle is stage 2 of the oxidation of glucose. Pyruvate is transported into the mitochondrial matrix where it is converted by pyruvate dehydrogenase into acetyl-CoA, which enters the TCA cycle.
Synthesis of glucose (gluconeogenesis)
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter highlights the importance of the liver to synthesize glucose through the pathway of gluconeogenesis and release it into the bloodstream. It details what happens when the liver's glycogen stores are exhausted. The essential supplies of glucose to the brain come from glucose synthesized in the liver during fasting or after 24 hours of food deprivation. The substrate for gluconeogenesis is pyruvate but any compound convertible to pyruvate or an intermediate of the tricarboxylic acid (TCA) cycle can be gluconeogenic. The chapter analyses the main sources of glucose in starvation, which are alanine and glutamine. These are derived from muscle protein catabolism and transported in the blood to the liver. The muscle protein degradation is caused by the high glucagon/insulin ratio and the stress hormone cortisol, which is liberated during starvation.
DNA synthesis, repair, and recombination
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter considers DNA synthesis as semiconservative as it is catalysed by DNA polymerases, which require the four deoxyribonucleoside triphosphates, a template or parental strand to copy, and a primer. The chapter refers to the primer of prokaryotes which is synthesized by the primase enzyme and is a short RNA copy of part of the parental strand. Synthesis starts at a site of origin on the chromosome where strand separation occurs. The chapter notes that E. coli has a single site of origin while eukaryotic chromosomes have hundreds. The chapter clarifies how a helicase separates parental strands that produces supercoiling ahead of it, noting that supercoils are removed by topoisomerases. The problem of maintaining the 5′→3′ direction of synthesis of both strands is solved by continuous synthesis of the leading strand and discontinuous synthesis of the lagging strand.
Control of gene expression
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter explains how gene expression can be regulated at each stage of protein synthesis, but the majority of regulation is of transcription. The chapter covers E. coli , wherein groups of genes called operons often occur and are transcribed together, forming polycistronic messengers. In the lac operon, comprising three genes, a repressor protein effects control by blocking an operator region at the initiation site of transcription. The chapter considers the repressor as an allosteric protein that detaches and allows transcription of genes required to form enzymes needed to utilize the sugar in the presence of lactose. Transcription factors (TFs) are the keys to eukaryotic gene-control.
The cell cycle, cell division, cell death, and cancer
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter looks at the eukaryotic cell cycle. This is divided into several phases: the first gap phase (G1), the DNA synthesis phase (S), the second gap phase (G2), and the mitotic or cell division phase (M). The chapter reviews progression through the phases. This depends on the synthesis of cyclin proteins specific for different phases. At the end of each phase the cyclins are destroyed by proteolysis. The cyclins are required to activate different cyclin-dependent protein kinases (Cdks) and determine which substrates a given kinase works on in each phase of the cycle. The chapter refers to the cyclin synthesis in G1, stating that it requires the receipt by the cell of a mitogenic signal from a growth factor or cytokine. After entering M phase, a further check is made to establish that all of the chromosomes are correctly placed on the mitotic spindle.
The immune system
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter focuses on the immune system of animals. This immune system protects against pathogenic invaders, wherein there is an innate immune response in which phagocytes engulf invading pathogens. The chapter explores the adaptive immune response. This responds to macromolecules, mainly proteins and complex polysaccharides, but not to small foreign molecules unless attached to large ones. Foreign macromolecules are indicative of an invader and are called antigens because antibodies are generated in response to them. The chapter includes two arms of the adaptive immune response: the humoral in which antibodies prevent pathogens in the blood and tissue fluids from entering cells and aid their removal from the body, and cell-mediated immunity in which cytotoxic T cells destroy infected cells. Cells of the immune system, known as lymphocytes, recirculate through the blood and lymphoid tissues to the sites of potential infection.
The ideal monatomic gas: the translational partition function
Authors: Maczek Andrew , Meijer Anthony
Published: September 2023

This chapter focuses on the ideal monatomic gas, which is linked with the translational partition function. It notes how quantum restrictions place limits on the actual kinetic energies that are found. Therefore, it is necessary to establish values for the allowed kinetic energies to determine the partition function for such a system. The chapter discusses the translational partition function in relation to a particle in a one-dimensional box, in three dimensions, and with continuum approximation. It lists the logarithm equation of the ideal monatomic gas for thermodynamic functions and entropy. The chapter refers to the Sackur–Tetrode equation. Moreover, statistical thermodynamics allows for the calculation of theoretical values of entropies for monatomic gases. These are used for comparison with experiments.
The Importance of Pharmaceutical Chemistry
Authors: Barber Jill , Rostron Chris
Published: September 2023

This chapter discusses the pharmacy, which is about how drugs are made, how to get them into the body, and how they work, their metabolism, their side-effects, and their interactions with other drugs. At the heart of the discipline of pharmacy is chemistry, because drugs are, of course, chemicals. The chapter provides an overview of the importance of pharmaceutical chemistry. It describes every living organism as a test tube, carrying out huge numbers of chemical reactions. Every drug is made using chemical reactions, some of these are in a laboratory, and every drug needs to be made up into a formulation, such as a tablet, or a cream, or an injectable solution.
RNA processing
Authors: Craig Nancy L , Green Rachel , Greider Carol , Storz Gisela , Wolberger Cynthia , Cohen-Fix Orna
Published: September 2023

This chapter explores RNA processing events, which are points for regulation and quality control, and are sources of diversity. Many RNA processing reactions are directed by RNA components. Transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) are processed out of longer precursor transcripts, and the nucleotides are post-transcriptionally modified. Meanwhile, the maturation of eukaryotic messenger RNAs (mRNAs) requires the addition of a 5' cap and a poly(A) tail—processes that are closely tied to transcription, splicing, transport out of the nucleus, and ultimately translation. The chapter then explains RNA splicing, RNA editing, and RNA degradation. RNA splicing allows the generation of great diversity in RNA products and can be catalysed by the RNA itself (self-splicing) or by a large protein and RNA-containing complex called the spliceosome. The chapter also looks at RNA-binding domains in proteins.
Translation
Authors: Craig Nancy L , Green Rachel , Greider Carol , Storz Gisela , Wolberger Cynthia , Cohen-Fix Orna
Published: September 2023

This chapter focuses on translation, the process by which a polypeptide chain is synthesized according to the instructions in an mRNA template molecule; it is the final step in the flow of genetic information from DNA to protein. tRNAs are bifunctional molecules that decipher the genetic information through Watson–Crick pairing interactions with the mRNA, bringing the activated amino acid along for peptide bond formation. The chapter then considers aminoacyl-tRNA synthetases and the structure of the ribosome. Aminoacyl-tRNA synthetases are responsible for the first event in decoding as they determine which of the 40 or so tRNAs in the cell get attached to which amino acids. Meanwhile, the ribosome is the macromolecular ribonucleoprotein machine that coordinates the process of translation through events in two distinct subunits, one primarily responsible for decoding and the other for making peptide bonds. Translation can be divided into multiple stages: initiation, elongation, termination, and ribosome recycling.
Repair of DNA double-strand breaks and homologous recombination
Authors: Craig Nancy L , Green Rachel , Greider Carol , Storz Gisela , Wolberger Cynthia , Cohen-Fix Orna
Published: September 2023

This chapter examines the repair of DNA double-strand breaks and homologous recombination. DNA double-strand breaks are particularly dangerous lesions—failure to repair them can lead to chromosome fragmentation and cell death. There are two major strategies for double-strand break repair: non-homologous end joining (NHEJ) and homology-directed repair. NHEJ rejoins the ends across a double-strand break in the absence of a DNA template. It is often mutagenic because of nucleolytic processing of the ends prior to joining. Meanwhile, homology-directed DNA synthesis can repair double-strand breaks by synthesizing new DNA across the break. The chapter then explains homologous recombination, which is the reciprocal exchange of large segments of DNA between homologous duplexes. Homologous recombination occurs during meiosis to generate gametes and occurs between the bacterial chromosome and exogenous DNA that enter the cell by conjugation or transformation, or in viruses.
Genomics and genetic variation
Authors: Craig Nancy L , Green Rachel , Greider Carol , Storz Gisela , Wolberger Cynthia , Cohen-Fix Orna
Published: September 2023

This chapter focuses on genomics and genetic variation. The field of genomics studies both the similarities and differences between the genomes of living organisms. The chapter therefore has two key themes: the evolutionary conservation of genomes on the one hand and the variation that leads to differences between individuals and species on the other. Selection and genetic drift work on genetic variation to shape natural populations. Evolutionary differences between species involve changes in size of genomes, the structure of genomes, and the number of genes, as well as the sequence of genes. The chapter then considers human genomics. Our rapidly expanding knowledge of the sequence and haplotype structure of the human genome allows us to trace our history, as well as to identify genes associated with many different traits and important diseases, but also carries with it the responsibility to use the information wisely.
Introduction to electrochemistry
Authors: Browne Wesley R.
Published: September 2023

This chapter introduces the concept of electrochemistry. Electrochemistry is the movement of charge, ions in a liquid or solid solution, and electrons from a solid to a species in solution. Next, the chapter looks into oxidation, reduction, and polarization. It explores the basic concepts in electrical circuits such as alternating current, direct current, Ohm's law and resistivity, impedance, EMF, voltage, and capacitance. The chapter shows how current is carried in any of several ways around a circuit in electrochemistry. The chapter also highlights the significance of voltage, work, and Gibbs energy. It presents the symbols and equations needed to achieve desired electrochemical measurements.
Heterogeneous electron transfer and the Tafel equation
Authors: Browne Wesley R.
Published: September 2023

This chapter discusses heterogeneous electron transfer and the Tafel equation. It notes the phenomenon of heterogeneous electron transfer. This happens when electrons move from electrode to solution by tunnelling from the atoms on the electrode surface to a species in solution through reduction and oxidation. The chapter references the Tafel equation, then cites equilibrium potential as the potential at which the forward and reverse electron transfer rates are equal and the net current flow is zero. The chapter also presents the overpotential, which is linked to Gibbs energy change. In addition, the chapter mentions the Galvani potential, Volta potential, and surface potential. It looks into the kinetics of electrochemical reactions as well as the symmetry factor.
Kinetics: what affects the speed of a reaction?
Authors: Crowe Jonathan , Bradshaw Tony
Published: September 2023

This chapter discusses chemical kinetics, looking at the factors that control the rate of a chemical reaction. The rate of a chemical reaction is the speed of change in concentration of reactants or products per unit time as the reaction proceeds. One can determine the rate of a reaction by measuring the concentrations of reactants or products at different times during the course of a reaction, and plotting on a graph the change of concentration with time. Every reaction has an energy threshold called the activation energy that must be reached before the reaction can occur. The chapter then considers catalysis and enzymes, and their impact upon the activation energy and reaction kinetics, before explaining enzyme kinetics and enzyme inhibition and the ways in which these can be described.
Why are study and communication skills important?
Authors: Stuart Johnson , Jon Scott
Published: September 2023

This chapter argues that good study and communication skills are vital for doing well at university and in future employment. Undergraduate study is different from pre-university study in a number of important ways. The skills a student has already gained up to this point will be useful, but there is still a need to develop and adapt them for new contexts. Managing time well, thinking critically, and being committed to self-development underpin the other skills that will be explored in the subsequent chapters. These, together with appropriate experience and the ability to articulate strengths to potential employers, are what will help a student to succeed not just in their studies, but also in their working life beyond university.
Using feedback
Authors: Stuart Johnson , Jon Scott
Published: September 2023

This chapter discusses the processes of using feedback. Ideally, feedback should serve three key functions: to provide a clear indication of progress in relation to the standards established by the university; to give guidance for improving when preparing the next piece of work; and to flag up areas where the student is doing well. However, feedback comes in a variety of forms. As the chapter shows, there is a range of different feedback types available. The student must be able to recognize these forms of feedback so as not to miss valuable learning opportunities. Finally, the chapter considers how the student can benefit from the provided feedback. It argues that feedback must be engaged with as an active process.
Making the most of lectures
Authors: Stuart Johnson , Jon Scott
Published: September 2023

This chapter discusses pointers for getting the most benefit out of lectures. There is much that can be done to improve the ability to listen and make notes; this includes activities which can be accomplished before, during, and after lectures. As this chapter shows, the first step is to be prepared by getting to know the course structure and doing pre-lecture reading. It then takes a look at how the student can create a system for storing notes (either paper-based or on a laptop/tablet), listen for structure, and learn how to emphasise listening and understanding by keeping notes brief. Indeed, this chapter considers note-taking to be an active process, though it also provides advice on what to do if a point is missed during the lecture. Finally, the chapter considers how to actively review notes after the lecture.
Writing practical and project reports
Authors: Stuart Johnson , Jon Scott
Published: September 2023

This chapter considers how to prepare practical work and high-quality reports. A number of fundamental aspects of data presentation are also discussed, albeit in limited detail. The chapter demonstrates that it is always good practice not just to focus on the scientific content, but also to evaluate the way in which the science is presented. Although the focus of the chapter is on laboratory-based practical classes and project work, much of the material is also directly relevant to fieldwork. To help create some context, the text uses as its examples an undergraduate investigation into the jumping ability of the locust. From there, the chapter follows the timeline of the stages of the practical class from initial preparation to completing the report.
The changing shapes of organic molecules
Authors: Robinson Michael J.T.
Published: September 2023

This chapter looks at how molecules can change shape, with emphasis on changing torsion angles. It focuses on the different shapes of molecules which result from changes in torsion angles. These are
conformations
. The chapter then argues that torsion angles in molecules are inextricably bound up with energy differences and rates of interconversion of the different shapes of molecules. The chapter then shifts to highlight ethane as a very simple example of conformations. Ultimately, the chapter demonstrates one of the important experimental methods for small molecules in the gas phase: rotation spectra and electron diffraction. The remainder of the chapter further examines the carbocyclic compounds.
Problems: hints and answers
Authors: Robinson Michael J.T.
Published: September 2023

Chapter 2

1. (a) Cs; (b) C∝v,; (c) D2h; (d) D2d; (e) D2; (f) S4; (g) Dn; (h) Sn;...
Magnetochemistry
Authors: Orchard A. F.
Published: September 2023

Magnetochemistry provides an introduction to this area of study, which is the study of the magnetic properties of materials. Magnetochemistry is of central importance in the study of transition-metal complexes, providing information on the chemical bonding in these molecules. This text provides an introductory survey of the magnetic properties of chemical compounds with a particular focus, later in the book, on paramagnets. It also illustrates the applications of both susceptibility measurements and EPR spectra in the characterization of electronic structures. The uses of ordered materials in magnetics technology are highlighted throughout.
Introduction
Authors: Perkins John
Published: September 2023

This chapter defines radical, which designates some polyatomic fragment of a molecule that remains unchanged during one or more chemical transformations. The chapter also cites ethyl as a modern example of an organic radical that is unaltered throughout the sequence of changes. It reviews some of the earliest evidence that electrically neutral carbon-centered radicals may be considered important intermediates in organic chemistry. It also talks about the gas-phase chlorination of methane which was interpreted in the early 1930s in terms of a radical mechanism. The chapter describes molecular entities containing an unpaired electron, such as metal ions and alkali-metal atoms. These would not normally be regarded as radicals. It analyzes halogenation reactions, which are among the most familiar of simple radical-mediated processes.
Energetics, kinetics, and mechanism
Authors: Perkins John
Published: September 2023

This chapter reviews some basic aspects of the energetics and kinetics of radical processes and the factors that determine them. It examines the decomposition of a dilute solution of a diacyl peroxide in an unreactive, non-polar medium, such as benzene. It also provides a kinetic analysis of the use of peroxide to initiate a chain reaction in which an alkene is polymerized, and demonstrates how slow propagations may compete with diffusion-controlled termination. The chapter discusses the modest stabilization found with alkyl-substituted methyl radicals that can be attributed in part to hyperconjugation, which is revealed both by theory and by spectroscopic data. The chapter finally explains that stabilization is a thermodynamic property that arise from electron delocalization.
Autoxidation - a case study
Authors: Perkins John
Published: September 2023

This chapter deals with the aspects of autoxidation, complexities that are important with particular substrates. It also looks at the ramifications of autoxidation in biological systems. The chapter outlines the chain-propagating steps for autoxidation, which include the abstraction of hydrogen from substrate. It also mentions the durability of commercial products in the case of hydrocarbons, such as might be enhanced by the minimization of the number of relatively weak tertiary C-H bonds in the molecular structure. The chapter details how initial hydrogen abstraction forms a stabilized pentadienyl radical which that combines with oxygen at a terminal carbon. It looks at the resulting peroxyl radical that abstracts hydrogen from a second skipped diene and gives a hydroperoxide.