bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbiological Testing of Blood Donations
Authors: Hyland Catherine , Barbara John , Mohabir Lionel
Published: September 2023

This chapter discusses viral, bacterial, and parasitic agents which are transfusion-transmissible infections (TTIs) and are of major concern for blood safety. It starts with defining the biology and life cycle for viral pathogens after they have infected the human host. The chapter then explains the aetiology (i.e. how the disease condition is caused) for transfusion transmitted viral infections such as hepatitis B (HBV), hepatitis C (HCV), and human immunodeficiency virus (HIV). It also outlines the principle and key steps for a chemiluminescent immunoassay, an enzyme linked immunosorbent sandwich assay (ELISA), and nucleic acid tests (NAT). Next, the chapter investigates the algorithms for microbiology testing and donor re-instatement, then considers the emerging issues for blood safety, insect- and animal-borne pathogens (malaria), and management strategies for the future.
Immune-Mediated Red Cell Destruction
Authors: Needs Malcolm
Published: September 2023

This chapter shows how and why red blood cells (RBCs) are destroyed in the body, in vivo, by antibodies. It first describes the difference between intravascular and extravascular haemolysis. The chapter then defines the role of antibodies and complement in red cell destruction. It outlines the clinical significance of red cell antibodies and the use of the direct antiglobulin test (DAT). The chapter then shifts to detail the causes of haemolytic transfusion reactions, and the types of autoimmune haemolytic anaemias and the problems associated with finding compatible blood. Finally, the chapter examines how red antibodies can cause hyperacute rejection in solid organ transplant. It also considers the phenomenon of passenger lymphocyte syndrome.
Haematopoietic Stem Cell Transplantation and Stem Cell Plasticity
Authors: Morse Ruth , Kabrah Saeed
Published: September 2023

This chapter focuses on the biology of haematopoietic stem cells (HSC) transplants. It first defines the term “stem cells” (SC), and notes that the initial all-encompassing SC is represented by the “totipotent” SC which has the capacity to produce all the tissues of an embryo. The chapter also argues that the most well-known and utilized SCs are those of the bone marrow (BM), which early in the twentieth century were shown to develop into a range of different blood cell types including those of the myeloid lineage and lymphoid lineages. The chapter then moves to explain the various sources and methods of stem cell collection. It explores the clinical and laboratory requirement involved in stem cell transplantation. The chapter concludes by discussing the plasticity of haematopoietic stem cells and how this may be exploited for personalized medicine.
Tissue Banking
Authors: Lomas Richard , Avent Neil D. , Salih Vehid
Published: September 2023

This chapter illustrates how tissue grafts are used clinically, and examines the process by which tissue grafts are collected and treated to improve their clinical efficacy, make them safer, and render them suitable for long-term storage. It also shows how donors are selected and screened, and how consent is obtained. The chapter then outlines how tissues are procured from living and deceased donors, how the collected tissue is processed, how that tissue is preserved, and how tissues are stored and distributed. Near the end, the chapter talks about the requirements of the UK Human Tissue Act. It then investigates how regenerative medicine may impact on tissue transplantation.
Quality Issues
Authors: Jones Joan
Published: September 2023

This chapter reviews how blood transfusion and transplantation departments can satisfy the various standards and regulations that govern these disciplines, and guarantee the quality of the services they provide. It illustrates how a department can prove it is maintaining these standards to the regulatory bodies and demonstrate that it is improving the quality of the service. The chapter also addresses quality assurance, quality assessment, quality management systems, and how the principles of good manufacturing practice (GMP) are an integral part of maintaining the system. It then details the GMP Standards required by the Medicines and Healthcare products Regulatory Agency (MHRA) to conform with the Blood Safety and Quality Regulations (BSQR). Ultimately, the chapter analyses the haemovigilance and the current systems in place within the UK.
DNA
Authors: Bromham Lindell
Published: September 2023

This chapter traces the history of the discovery of the genomic information system, illustrating the important principles of heredity. Life relies upon the continuity of genetic information coded in DNA and copied from generation to generation. The DNA found in every living cell contains the genetic information needed to construct the organism, as well as providing biologists with a wealth of information about evolutionary past and processes. While Charles Darwin clearly illustrated the role of heredity in the process of evolution by descent with modification, he did not know how information about an organism's form or behaviour was transmitted to its offspring. The material basis of heredity was not uncovered until Rosalind Franklin's images of the DNA helix allowed James Watson and Francis Crick to uncover how complementary base pairing provided a means to copy information endlessly down the generations. The chapter then considers the process of DNA extraction.
Rates
Authors: Bromham Lindell
Published: September 2023

This chapter discusses the rate of evolutionary change. Genomes constantly accumulate changes, but the rate of change can vary between lineages. Anything that increases the number of mutations, such as copying the DNA more often or being exposed to more mutagens, could increase the rate of molecular evolution. Similarly, anything that influences the number of mutations that go to fixation, such as population size and patterns of selection, can also affect rates of molecular evolution. The upshot of this is that many species characteristics, such as physiology, life history, ecology and habitat, can influence the average rate of molecular evolution. We can study the kind of species traits that influence the rate of genomic change by comparing estimates of substitution rate, using statistical analyses that allow for the patterns of descent created by the evolutionary process.
Human Physiology
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

Human Physiology provides clear explanations of the principles that govern the body’s physiological processes and shows how these can be applied. It is made up of eleven sections. Section 1 is about basic concepts. The second section covers the organization and basic functions of cells. The third section looks at the excitable tissues, nerve, and muscle. The fourth section goes into detail about the nervous system and special senses. The section which follows is about the endocrine system and it includes details on the pituitary gland, hypothalamus, the thyroid and parathyroid glands, the adrenal gland, and the endocrine pancreas. The text also looks at blood and the immune system, before turning to the cardiovascular and respiratory systems. There follows a section of the regulation of the internal environment. Towards the end the text turns to the gastrointestinal system. Finally, the text looks at reproduction and growth.
The chemical constitution of the body
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter describes the human body as consisting largely of four elements: oxygen, carbon, hydrogen, and nitrogen. It shows that about 70 percent of the lean body tissues is water, while the remaining 30 percent made up of organic material (i.e. molecules and minerals). The principal organic constituents of mammalian cells are the carbohydrates, fats, proteins, and nucleic acids, which are built from smaller molecules belonging to four classes of chemical compounds: sugars, fatty acids, amino acids, and nucleotides respectively. The chapter outlines the principal minerals found in tissues: calcium, phosphorus, potassium, and sodium. It gives an approximate indication of the chemical composition of the body for a young adult male, noting that there is individual variation and that the proportions of the various constituents vary between tissues and change during development.
Introducing cells and tissues
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter explains that cells are the building blocks of the body. There are many different types according to characteristic size and shape. The chapter explains that some cells can be very large, for example the cells of skeletal muscle. These may extend for up to 30 cm along the length of a large muscle. Other cells are very small. The red cells of the blood are small biconcave discs with diameters in the region of 7 μm. The chapter emphasizes that the skeletal muscle fibres and red cells represent some of the striking variations in cell morphology, noting that all cells have certain characteristics which can be evident during differentiation. The structure of a typical mammalian cell is bounded by a cell membrane called the plasma membrane or plasmalemma, which is a continuous sheet that separates the watery phase inside the cell from that outside the cell.
The transport functions of the plasma membrane
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter looks at the plasma membrane, wherein the region outside the cell or the extracellular compartment is separated from the inside of the cell or intracellular compartment. It shows how the physical separation allows each cell to regulate its internal composition independently of other cells. Chemical analysis has shown that the composition of the intracellular fluid is very different to that of the extracellular fluid, noting that it is rich in potassium ions but relatively poor in both sodium ions and chloride ions. The chapter highlights the mechanisms responsible for establishing and maintaining the difference in ionic composition between the intracellular and the extracellular compartments. The chapter outlines the ways in which cells utilize ionic gradients to perform their essential physiological roles and the mechanisms by which proteins and other large molecules cross the cell membrane.
Principles of cell signalling
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter talks about individual cells which carry out specific physiological roles, such as secretion or contraction. It examines how cells receive and transmit signals of various kinds in order to coordinate their activities. As the plasma membrane forms a barrier between the signalling components within the cell and the extracellular environment, the cells have evolved various signalling methods to get around this. The chapter highlights the generation of diffusible chemical signals, the expression of receptors in the plasma membrane that are able to convey the external signals across the plasma membrane, direct contact between the plasma membrane proteins of adjacent cells, direct cytoplasmic contact via gap junctions, and the use of signals generated by a cell itself at particular stages of development. Diffusible chemical signals allow cells to communicate at a distance, while direct contact between cells is particularly important in cell–cell recognition.
The physiology of motor systems
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter explores the capacity to perform the precise movements needed for complex manipulations and speech, emphasizing that coordinated purposeful movement is a fundamental aspect of human existence. The chapter points out that the simplest form of motor act controlled by the nervous system is called reflex. This is a rapidly executed, automatic, and stereotyped response to a given stimulus. The chapter discusses how most reflexes involve extensive coordination between groups of muscles and is achieved by interconnections between various groups of central neurons. The neurons forming the pathway taken by the nerve impulses responsible for a reflex make up a reflex arc.
Emotion, learning, and memory
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter explores how the brain assesses aspects of the world which cause humans to adjust their behaviour to assist survival. Moreover, human beings are social creatures who enjoy the company of their fellows, with whom they communicate using the complicated processes of speech. It points out that people require a certain level of self-awareness, this is called consciousness, to achieve all these behaviours. The chapter considers underlying physiological processes which raise many questions, such as what consciousness is, how is a representation of the external world formed, and how memories trigger emotions. It discusses the neural processes that underlie the phenomena of emotion, learning, and memory.
The pituitary gland and hypothalamus
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter reviews the nervous and endocrine systems. These are both concerned with communication within the body. It explains how nerves communicate through rapid, specific electrical signals, whereas the endocrine system uses hormones as chemical signals to regulate physiological processes. Nevertheless, the nervous and endocrine systems are closely linked via the control that the hypothalamus exerts over the pituitary gland. The chapter explores the hypothalamo-pituitary system and provides a brief description of the principal hormones of the anterior and posterior lobes of the pituitary gland. The actions of the individual hormones deal with their target glands through hormonal control of the thyroid and parathyroid glands.
The thyroid and parathyroid glands
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter focuses on the principal hormones secreted by the thyroid and the parathyroid glands. It looks at the thyroid gland which secretes two iodine-containing hormones, thyroxine (T4) and tri-iodothyronine (T3). These exert a wide variety of actions throughout the body. These glands are chiefly concerned with the regulation of metabolism and the promotion of normal growth and development. The chapter refers to a third hormone known as calcitonin, which is secreted by cells scattered throughout the gland and is considered a peptide hormone that plays a role in the regulation of plasma calcium levels. Lying embedded within the thyroid gland are several small glands known as the parathyroid glands that secrete a polypeptide hormone called parathyroid hormone (PTH).
The endocrine pancreas and the regulation of plasma glucose
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter examines the cells of the body which have continuous access to glucose to carry out their normal metabolism, the major fuel used to produce cellular energy. It also looks at certain tissues, notably the central nervous system, the retina, and the germinal epithelium. These rely almost entirely on glucose metabolism for the generation of adenosine triphosphate (ATP). The nervous system alone requires around 110 g of glucose each day to meet its metabolic needs. The chapter discusses the concentration gradient for glucose between the blood and the extracellular environment of the brain cells that is maintained. Blood glucose levels are normally maintained between 70 and 125 mg glucose dl-1 blood despite wide fluctuations in dietary intake and regulation takes place continuously over a timescale of minutes.
The heart
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter concentrates on the heart. The heart lies in the mediastinum of the thoracic cavity beneath a tough membrane called the fibrous pericardium. The chapter describes the fibrous pericardium. This is attached to the central tendon of the diaphragm and to the outer coats of the aorta and venae cavae. The heart itself is covered by a pair of thin membranes, the serous pericardium. These enclose a narrow, fluid-filled space called the pericardial sac. The chapter demonstrates how the pericardium restricts the movement of the diaphragm and prevents overfilling of the heart. The overall shape of the heart is approximately that of a blunt cone which has its base around the midline and its apex facing obliquely downward towards the left side of the chest.
The circulation
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter examines the detailed physiology of systemic circulation. It deals with the relationship between pressure and flow in circulation and looks at the factors that regulate blood flow through particular tissue beds. It also discusses hypertension, and the specific features of several regional circulations, namely that of the heart, the skin, the skeletal muscles, and the brain. The chapter reviews specific adaptations of the blood supply to the respiratory, renal, and gastrointestinal systems. The flow of blood through any part of the circulation is driven by the difference in pressure between the arteries that supply the region in question and the veins that drain it.
Introduction to the respiratory system
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter analyses breathing. This is associated with changes in the volume of the chest. It details how the chest is expanded and air enters the lungs during inspiration, while the volume of the chest decreases and air is expelled from the lungs during expiration. This movement of air into and out of the lungs is known as ventilation and the volume of air entering and leaving the lungs each minute is called the minute volume, which is the product of the air taken in each breath and the number of breaths taken each minute. The chapter looks at the mechanisms responsible for the changes in the dimensions of the chest and the factors governing the flow of air in the airways. The volume of air that moves in and out of the chest during breathing can be measured with the aid of a spirometer.
The control of respiration
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter considers breathing as an automatic, rhythmical process that is constantly adjusted to meet the everyday requirements of life, such as exercise and speech. It addresses three important questions: Where does this rhythmical activity originate? How is it generated? How is the rate and depth of respiration controlled? The chapter talks about the basic respiratory rhythm, which is maintained even if all the afferent nerves are cut. The chapter explains how the basic rhythm of respiration continues, even if the brainstem of an anaesthetized animal is completely cut through above the pons. Cutting the spinal cord below the outflow of the phrenic nerve leads to paralysis of the intercostal muscles but not of the diaphragm.
Pulmonary defence mechanisms and common disorders of the respiratory system
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter explains that the respiratory minute volume of 6 l min-1 results in the intake of over 8500 litres of air each day. Even if the concentration of particles were to be only 0.001 per cent, this would include 85 ml of particulate matter. The chapter points out how the respiratory system needs to remove the inert material and inactivate the infectious and allergenic agents. The chapter mentions the three curved bony plates within the nasal cavity, which is the nasal conchae or turbinates which are covered with respiratory epithelium. These disturb the smooth flow of air and make it turbulent by forcing it into narrow passages where it is warmed and moistened.
The renal system
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter discusses how human beings, like all animals, feed on other organisms both to provide energy and to provide themselves with the resources required for growth and reproduction. This lifestyle inevitably leads to the intake of variable quantities of essential body constituents to the production of metabolic waste products. It details how the body needs to maintain a close control over the composition of body fluids, which is the principal role carried out by the kidneys. The chapter refers to how body fluids are maintained by the composition of the blood and how the kidneys effectively regulate the composition of the extracellular fluid. In doing so, the kidneys excrete the excess water, salts, and metabolic waste products.
Fluid and electrolyte balance
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter describes water as the principal constituent of the human body and is essential for life. In healthy individuals, the volume and osmolality of the tissue fluids are maintained within closely defined limits. This process is mainly concerned with the mechanisms that regulate the quantity of water that is present in the body and maintain its distribution between the different body compartments. The chapter cites some common disorders of electrolyte balance and the detailed mechanisms by which the osmolality of the body fluids is regulated. Broadly speaking, body water is distributed between the intracellular fluid or ICF and the extracellular fluid or ECF.
The liver and gall bladder
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter explores the major functions of the liver and gall bladder, including the common causes of different types of jaundice and the consequences of liver failure. The liver plays a crucial role in energy metabolism as it stores glucose as glycogen, converts amino acids to glucose, and metabolizes fatty acids. The chapter discusses how the liver regulates plasma cholesterol levels. The chapter details how the liver secretes a number of peptide hormones, including the insulin-like growth factors IGF-1 and IGF-2, hepcidin, and thrombopoietin. The liver also acts as a store of a number of vitamins including vitamin A, vitamin D, and vitamin B12.
Fertilization, pregnancy, and lactation
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter concentrates on the events surrounding fertilization, pregnancy, and parturition. It discusses the physiological changes that take place in the body of a pregnant woman during gestation and the physiology of lactation. Fertilization of an ovum requires that sperm are deposited high in the vagina of a woman close to the time of ovulation. Fertilization, except by artificial insemination, is achieved through the act of sexual intercourse. The chapter details how the penis of the male must become erect. Then the ejaculation of seminal fluid must occur within the vagina for successful fertilization to take place. The sexual response in both males and females can be divided into four main phases: excitement, plateau, orgasm, and resolution.
Fetal and neonatal physiology
Authors: Pocock Gillian , Richards Christopher D. , Richards David A.
Published: September 2023

This chapter describes a fetus. A fetus totally dependent upon the placenta for gas exchange, nutrition, and waste disposal while it remains within the uterus of its mother. The chapter notes physiological changes that take place at, or soon after, birth. This enables a baby to make a successful transition from its intrauterine existence to a semi-independent air-breathing life. While the changes in the cardiovascular and pulmonary systems that occur around the time of birth are of paramount importance to its survival, a number of other organs must also adapt at birth to the different requirements of extra-uterine life. The chapter highlights changes in the adrenal glands, kidneys, thermoregulatory tissues, and gastrointestinal tract. It examines important aspects of the physiology of the fetus and newborn and provides a simple account of the differentiation of the male and female reproductive systems.
Active orientation and localization
Authors: Zupanc Günther K. H.
Published: September 2023

This chapter looks at the active orientation mechanisms developed by some animals. The chapter focuses on echolocation, a mechanism to negotiate an animal's surroundings based on the emission of sound, its reflection by objects located within the emission beam, and the analysis of the returning echo. Echolocation has been found in bats, toothed whales, and oilbirds. The chapter revisits the beginning of echolocation research at the end of the eighteenth century when several scientists conducted a series of experiments on how bats orient in the dark. It describes the two major categories of sounds produced by bats: frequency-modulated (FM) signals which are used to estimate the distance of the bat from an object, and constant-frequency (CF) signals which are well suited for the so-called Doppler shift analysis. Lastly, the chapter discusses the adaptations developed by some insects to counteract bat echolocation.
Neuronal processing of sensory information
Authors: Zupanc Günther K. H.
Published: September 2023

This chapter looks at how organisms distinguish behaviorally relevant information from behaviorally irrelevant background noise, and how recognition of such behaviorally important information is achieved at the neural level. It uses two particularly well-examined model systems to provide effective illustrations: the recognition of prey and predators in the toad and the directional localization of sound in the barn owl. Before delving into the details of those models, the chapter first reviews some ethological concepts that are crucial in understanding how the sensory organs and the brain process behaviorally relevant sensory stimuli. It explains the concept of Umwelt, the part of the environment which is perceived after sensory and central filtering. It also sheds light on sign stimulus or the component of the environment that triggers a specific behavior. Furthermore, the chapter discusses the law of heterogeneous summation and the Gestalt principle.
Computer-aided Drug Design
Authors: Rostron Chris
Published: September 2023

This chapter describes computer-aided drug design. In the early days of drug design, success often relied on a significant element of luck. As the drug design process developed, medicinal chemists were able to produce guidelines which made the process much less dependent on luck, allowing a more informed choice with respect to which molecules to synthesize. During the latter part of the twentieth century, the increase in the power of computers led to the realization that they could prove extremely useful in aiding the drug design process. This resulted in the development of a new tool to be used in drug design, namely computer-aided drug design. The chapter notes that the use of computers in aiding drug design takes a number of forms, such as the storage and prediction of data (cheminformatics); quantitative structure-activity relationships (QSAR); computer modelling of molecular properties; drug-receptor interactions; and receptor mapping.
Toxicity Testing
Authors: Rostron Chris
Published: September 2023

This chapter reviews toxicity testing. The testing of the toxicity profile of a potential drug candidate is a vital component of drug development. Toxicological studies are usually carried out at the same time as other aspects of drug development as, if any significant toxicity problems are detected, further development of the drug can be stopped, saving valuable time and expense for the pharmaceutical company. The chapter then outlines the types of tests which may be involved in toxicity testing, including carcinogenicity testing, mutagenicity testing, teratogenicity testing, immunotoxicity testing, and safety pharmacology testing. It also differentiates between acute and chronic toxicity testing, before explaining in vitro toxicity testing. Not all toxicity tests are required in each circumstance and so toxicity testing is subject to a variety of regulations and guidelines.
Solubility and Drug Development
Authors: Rostron Chris
Published: September 2023

This chapter discusses the importance of solubility in drug development. The solubility of a potential drug molecule is a critical physicochemical property. In order to assist in the design of a suitable formulation, use can be made of solubility classification systems which employ specific criteria. There are numerous factors which affect the solubility, such as temperature, the nature of the solute and solvent, pH and the dissociation constants if the drug is ionizable, and salt formation. All these previous aspects relate largely to aqueous solubility, but equally important is the lipid solubility of a drug as represented by partition coefficient and log P. Whereas the processes of solubility and dissociation are equilibrium situations, the process of dissolution is a kinetic situation, i.e. it occurs at a particular rate, and the measurement of the dissolution rate is another important preformulation parameter.
Drug Stability
Authors: Rostron Chris
Published: September 2023

This chapter evaluates drug stability, which is a vital aspect of drug development. The types of stability that will need to be examined are physical stability and chemical stability. In particular, at an early stage, it is important to determine the mechanism of any instability, the reaction kinetics involved in any instability, and the factors that can influence such reactions. The submission of a new drug product is required to present the results of any stability studies undertaken and the range of these is specified by the International Conference on Harmonisation (ICH) regulations. During preformulation studies, the most important stability studies to be carried out is stress testing in order to identify degradation pathways and mechanisms. The results from the stress testing can then be used to inform the design of longer-term and accelerated stability testing and determination of shelf life.
Environmental chemistry
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter defines the universe as consisting of a system and its surroundings, where the system is the portion of the universe that is under direct investigation while the surroundings comprise everything beyond the system. To illustrate, it applies this concept of the universe in considering an industrial chemical process, such as the production of the wood preservative pentachlorophenol (PCP). In this context, what happens in the factory is the system whereas the impact of the industrial process outside the factory would concern the surroundings. The chapter also examines mechanisms by which chemicals, such as dioxins, enter a living organism, the biochemical transformations they undergo, their molecular mode of action, and their elimination. The chapter explains that what goes on in the surroundings outside a system is the subject matter of environmental chemistry. It provides the chemical basis for understanding the surroundings, or the global environment.
The Earth’s atmosphere
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter focuses on the fundamental concepts needed to understand chemical processes that occur in the atmosphere. It describes the physical nature of the atmosphere, its structure and composition, and the important role played by solar radiation in defining these features. The chapter also outlines basic concepts to describe important chemical processes related to ozone, smog, acid precipitation chemistry, atmospheric aerosols, urban and indoor air, and global climate. The chapter reviews fundamental physical chemistry properties of gases. It introduces gas-phase reactions along with related thermodynamic and kinetic calculations, including photochemical reactions as the extremely important category of free radical reactions.
The chemistry of global climate
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter examines the ways in which global climate is influenced by the composition and chemistry of the atmosphere. It discusses the composition of the atmosphere and investigates the energy balance of incoming solar radiation and outgoing infrared or black-body radiation from the Earth. It also identifies greenhouse gases and their infrared radiation absorption properties and examines the radiative influence of aerosols. The chapter introduces the concepts of radiative forcing (RF) and the global warming potential (GWP) index for measuring the present and long-term impact of greenhouse gases. It provides an overview of energy resources, the relationships between carbon-based fuels and carbon dioxide emissions, and mitigation strategies.
Toxic organic chemicals
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter focuses on organic chemicals, both synthetic pesticides and industrial by-products, particularly those that are toxic or can generate other adverse effects within the environment. It investigates the nature and environmental properties of toxic organic chemicals by first defining what is meant by the terms ‘biocide’ and ‘xenobiotic compound’. It then explores the nature of the chemistry and stability, redox properties, and photoactivity of toxic organic chemicals. The chapter reviews the means by which the transport of organic chemicals in the environment occurs, primarily in soil and water systems. It looks at the concepts of leachability and a simple function that predicts the potential of organic chemicals for harm.
Genomes of Prokaryotes and Viruses
Authors: Lesk Arthur M.
Published: September 2023

This chapter identifies archaea, bacteria, and eukarya as the three major divisions of cellular life. It expounds on the idea of prokaryotes causing diseases, being simple, and representing the earliest form of life. It shows how molecular adaptation is dependent on genomes, structures, temperatures, and ocean depths. It considers how archaea, bacteria, and eukarya adapt, transfer, and multiply. Some prokaryote genomes contain insertion sequences whose mobile genetic elements are similar to eukaryotic transposons. It explores the developments of metagenomics and metaproteomics, that is, the applications of methods from the laboratory to natural ecosystems. It explains the issue of bacterial pathogenicity and the significance of developing antibiotic resistance. It explicates the evolution of viruses and the genomics behind developing vaccines, using influenza as an example.
Genomes of Eukaryotes
Authors: Lesk Arthur M.
Published: September 2023

This chapter focuses on differentiating eukaryotic cells from prokaryotic cells while citing the origins, evolution, and phylogenetic relationships of eukaryotes. It considers the relationships between the major types of eukaryotes. It notes that fungi and yeasts are among the simplest eukaryotes, which have served as model organisms in molecular biology laboratories, agriculture, and cooking. It explores the features and evolution of higher plants, with a focus on Arabidopsis thaliana, which is widely known as the fruit fly of botany. Animals are regarded as distantly related to humans due to the evolutionary path of mammals. The chapter looks at the genomes of numerous animals, such as sea squirt, platypus, chickens, pufferfish, and dogs. It mentions palaeosequencing, which is the ability to recover and sequence DNA from extinct organisms.
The Impact of Genome Sequences on Human Health and Disease
Authors: Lesk Arthur M.
Published: September 2023

This chapter looks into the human microbiome and its role in health and disease. It notes the broad categories of causes of diseases and the sources of diseases caused by abnormalities. It considers the role of genetics in diseases such as phenylketonuria, Alzheimer's disease, cystic fibrosis, and cancer. It cites the variability of phenotypic responses to mutations, defining penetrance as the fraction of people who carry the allele for a condition and manifest it. The chapter explores the methods and results of genome-wide association studies (GWAS). It also considers the role of genomics in the aetiology, diagnosis, and treatment of cancer as well. Cancer is a disease of genome instability, and cancer genome sequencing has led to great advancements in cancer diagnosis, prognosis, and therapy by identifying particular mutations that are associated with different types of cancer. The chapter finishes with the conclusion that personalized medicine has become an effective reality after the illumination of disease by various genome sequence-based investigations.
Proteomics
Authors: Lesk Arthur M.
Published: September 2023

This chapter discusses the fundamental chemical structure of proteins, including protein conformation, mainchain, sidechains, and common post-translational modifications. It clarifies the differences between primary, secondary, tertiary, and quaternary structures. It clarifies the use and technique of polyacrylamide gel electrophoresis and mass spectrometry. It notes the power of experimental methods such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo electron microscopy for protein structure determination. The chapter looks at the principles of classifications of protein folding patterns. It notes the invisibility of numerous properties of proteins in genome sequences. It considers diseases of protein aggregation, citing the difficulties and possibilities of protein structure prediction and structural genomics projects. Finally, it considers the generation of useful artificial proteins, both by directed evolution and by a priori design.
Computation and Computers in Chemistry
Authors: Harvey Jeremy
Published: September 2023

This chapter provides an overview of computation and computers in chemistry. Devising an experiment or analysing its results usually involves some calculation or other. A more fundamental role for computation is to work out the details of the prediction of a particular chemical theory. Very often, this requires so many calculations that they cannot be done by hand or with a calculator—a computer is needed instead. In modern chemical research, computation is used for such diverse aims as studying the diffusion of molecules through a membrane, for exploring the motions of one part of a protein with respect to the others, for predicting the features in an electronic absorption spectrum, or for trying to understand the mechanism of a chemical reaction. This book explores how the corresponding methods work and introduces the computational techniques used to carry out such calculations.
Geometry Optimization
Authors: Harvey Jeremy
Published: September 2023

This chapter details the features of potential energy surfaces, with a focus on energy minima and saddlepoints or transition states. It also describes methods to explore potential energy surfaces in a systematic way through geometry optimization. Efficient optimization methods are based on calculation of the potential energy, its first derivative with respect to the positions of the atoms (the gradient), and the second derivative (the Hessian matrix). Geometry optimization is frequently used in quantum chemical studies; predicted molecular structures usually agree very well with experiments. The curvature of the potential energy surface around the optimum structure can be used to predict vibrational frequencies. As well as minima, optimization can also be used to locate transition states and reaction paths.
Biochemistry and Molecular Biology
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

Biochemistry and Molecular Biology is made up of six parts. Part 1 covers the basic concepts of life. Part 2 is about the structure and function of proteins and membranes. The third part looks at metabolism and nutrition. The fourth part of the book covers information storage and utilization. The fifth part looks at cells and tissues. Finally, the sixth part is about protective mechanisms against disease such as blood clotting, xenobiotic metabolism, reactive oxygen, and the immune system.
Cells and viruses
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter offers a broad survey of the structures and properties of cells and viruses, providing a biological background for the more detailed mechanisms of cell biology, biochemistry, and molecular biology. It explains that cells are the units of living systems, wherein each cell is surrounded by a lipid membrane and has a DNA genome. The two main classes of cellular organism are prokaryotes and eukaryotes, including archaea that are a third class of organism that can live in unusual environments. The chapter examines the large numbers of ribosomes in both prokaryotic and eukaryotic cells, which are large complex structures of RNA and proteins found in the cytosol. The cytoplasm of eukaryotic cells can be defined as the content of the cell excluding the nucleus, while the cytosol refers to the soluble constituents of the cytoplasm from which membrane-bounded organelles have been removed.
Nitrogen metabolism: amino acid metabolism
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter refers to amino acids which are supplied in the diet from protein hydrolysis in the gut. This includes proteins in the body that are constantly degraded and resynthesized. The chapter clarifies how the body can synthesize about ten of the amino acids. The rest must be obtained from the diet, but all 20 are needed for protein synthesis. Amino acids are also used to synthesize a wide variety of other molecules. The chapter discusses amino acids in excess of immediate requirements and shows that these are deaminated as the amino nitrogen is mainly converted into urea in mammals and excreted. The carbon-hydrogen skeletons are oxidized to release energy or converted into fat or glycogen according to the metabolic controls operating at the time and the particular amino acid.
Raising electrons of water back up the energy scale: photosynthesis
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter explains how photosynthesis occurs in plant cell chloroplasts, noting that the part that is dependent on light is the splitting of water to generate NADPH. It describes chlorophyll, which is a green pigment that receives light energy and is present in the membrane of organelles called thylakoids. When activated by photons, chlorophyll molecules donate electrons to chains of electron carriers arranged in two photosystems: PSI and PSII. The chapter talks about the loss of the electrons by chlorophyll. This makes it a very powerful oxidizing agent, capable of accepting electrons from water in the water-splitting centre. Adenosine triphosphate (ATP) is generated by the chemiosmotic mechanism during the passage of electrons from one photosystem to the other.
Gene transcription
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter discusses how a gene is expressed by one strand of DNA, a template strand. It is then copied into single-stranded RNA and protein-coding genes, wherein the mRNA is translated to form protein. The chapter refers to transcription and notes that this is catalysed by RNA polymerase using ATP, CTP, GTP, and UTP as building blocks. Prokaryotes have a single RNA polymerase, while eukaryotes have three: Pol I, Pol II, and Pol III. The chapter explains Pol II and shows that it transcribes protein-coding genes to make mRNA, while Pol I transcribes a large rRNA precursor, and Pol III transcribes small RNAs. The coding region of a prokaryotic gene is a continuous stretch of DNA, so that the primary transcript is a messenger RNA (mRNA) and can be translated immediately, while in eukaryotes the primary transcript.
Protein sorting and delivery
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter discusses proteins which are synthesized on cytosolic ribosomes but function in different cellular locations. These are targeted to their destinations by a number of mechanisms. The chapter mentions GTP-binding proteins with slow GTPase activity. These are important in many protein transport processes, acting as molecular switches. The proteins undergo allosteric changes when GTP replaces GDP or bound GTP is hydrolysed. The chapter examines proteins destined for the lumen of the rough ER. These traverse the ER membrane as they are synthesized. The chapter then looks at the peptide signal sequence which is first synthesized on free cytosolic ribosomes. A signal-recognition particle (SRP) docks the ribosome to a translocon site in the ER membrane.
Cell signalling
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter discusses the receptors of cells which receive signals from other cells. This is limited in scope in unicellular organisms, such as yeast and bacteria. However, in animal cells, such as mammalian ones, the number of signals needed to coordinate their activities is large. The chapter clarifies how signals control the most fundamental aspects of gene-control, cell survival, programmed cell death, and cell division. Cancer usually involves the malfunction of signalling pathways. The chapter analyzes signals that are variously proteins, peptides, steroids, and other lipid-related molecules, and nitric oxide. The signalling molecules bind to specific receptors of target cells and activate signalling pathways, which result in gene-control events in the nucleus and more direct effects on metabolism.
Atomic structure
Authors: Weller Mark , Rourke Jonathan , Overton Tina , Armstrong Fraser
Published: September 2023

This chapter provides foundations for an explanation of the trends in the physical and chemical properties of all inorganic compounds. The chapter begins with a discussion on the origin of matter in the solar system and then considers the development of understanding of atomic structure and the behaviour of electrons in atoms. It reviews the structures and properties of atoms, acknowledging that these are crucial in understanding the behaviour of molecules and solids. The chapter also qualitatively introduces quantum theory and uses the results to rationalize properties such as atomic radii, ionization energy, electron affinity, and electronegativity.
Physical techniques in inorganic chemistry
Authors: Weller Mark , Rourke Jonathan , Overton Tina , Armstrong Fraser
Published: September 2023

This chapter introduces the most important physical techniques that are used to investigate the atomic and electronic structures of inorganic compounds and to study their reactions. It explains the two diffraction methods: X-ray and neutron diffraction. Then it looks at absorption and emission spectroscopies, covering ultraviolet-visible spectroscopy, fluorescence spectroscopy, as well as infrared and Raman spectroscopy. The chapter also describes nuclear magnetic resonance, electron paramagnetic resonance, and Mössbauer spectroscopy. Furthermore, it discusses ionization-based techniques: photoelectron spectroscopy, X-ray absorption spectroscopy, and mass spectrometry. The chapter explains atomic absorption spectroscopy, CHN analysis, X-ray fluorescence elemental analysis, and thermal analysis. Next, it tackles magnetometry and magnetic susceptibility, as well as electrochemical techniques, before looking at scanning probe microscopy and electron microscopy.