bluuebunny/crossref_metadata_2025 huggingface dataset:
Glycosylation and disease
Authors: Taylor Maureen E. , Drickamer Kurt
Published: September 2023

This chapter reviews the relationship between glycobiology and disease. Demonstrating that changes in glycosylation have a direct role in the aetiology of disease continues to be a challenge. Examples show that genetic diseases associated with mutations in glycan biosynthesis pathways and recognition systems can provide important insights into the processes mediated by glycans and their receptors. However, in many cases the changes brought about by such mutations can be subtle and unexpected. The analysis of the molecular basis for von Willebrand disease demonstrates how the role of glycosylation in the disease may only become evident when an appropriate genetic linkage is established. Large numbers of polymorphisms associated with disease and disease susceptibility are now being mapped. Our improving ability to identify genes that encode proteins that function in biosynthesis, transport, degradation, and recognition of glycoconjugates will undoubtedly facilitate the establishment of further links between glycans and disease processes.
Introduction
Authors: Barnes Geoffrey , Gentle Ian
Published: September 2023

This chapter provides a background on surfaces or interfaces, which are regions of finite thickness wherein two homogeneous bulk phases meet and change properties when there is movement from one bulk phase to the other. It highlights a phenomenon at a molecular level in which the thickness of the interfacial region is significant and definitely non-zero. It also emphasizes the importance of the properties of the interfacial region when one of the phases is dispersed as very small particles in the other phase due to the dramatic increase in surface area. The chapter cites examples of the disperse phase and the continuous phase, which include colloids, emulsions, aerosols, and some natural and synthetic polymers. It classifies interfaces based on the nature of the bulk phases that lie on either side of the interface.
The liquid–solid interface: adsorption; colloids
Authors: Barnes Geoffrey , Gentle Ian
Published: September 2023

This chapter discusses the removal of unwanted impurities from a liquid by passage through a column of a solid adsorbent. It explores the separation of different solutes by column chromatography, high performance liquid chromatography, and paper chromatography, which are all examples of the adsorption of solutes at the liquid-solid interface. It also analyses the sols as examples of solid-liquid interfaces, which are dispersions of solid colloidal particles in a liquid. The chapter demonstrates how clay minerals interact readily with water and dissolved ions, and some of them swell, generating considerable expansion pressures. It talks about clay minerals when mixed with water, which have important industrial applications, such as for making bricks and tiles, pottery and ceramics, and drilling muds.
Biological interfaces
Authors: Barnes Geoffrey , Gentle Ian
Published: September 2023

This chapter look at interfaces in biological systems, plants, and animals wherein the bulk phases are separated by a thin film known as a membrane. It describes cell membranes as some of the most important examples, without which many of the complex biological reactions that take place in cells could not occur. It also highlights the two important functions of the cell membrane: one is to contain the ingredients necessary for the cell to function and the other is to interact with the environment by allowing unwanted materials to leave the cell and needed materials to enter. The chapter mentions the fluid lining of the lung that contains material without which breathing would be impossible. It details how aerosols often enter the lungs, sometimes as contaminants of the air or deliberately for the introduction of medications into the lungs or the blood stream.
Thermodynamics and the Second Law
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter assesses how the approach to chemical equilibrium is governed by the Second Law of Thermodynamics, which involves the physical property known as entropy. These ideas arise within the physical theory generally known as thermodynamics. Thermodynamics is a theory which describes the behaviour of bulk matter; quantum mechanics, in contrast, focuses on the behaviour of individual atoms and molecules. Of course, it is certainly the case that the behaviour of a mole of hydrogen molecules must be intimately connected to the properties of a single hydrogen molecule, and this connection can be made in a precise way using statistical thermodynamics. However, the principles of thermodynamics are not dependent on an understanding of the microscopic behaviour of atoms and molecules. The chapter also looks at spontaneous processes and the Gibbs energy.
Bonding between the elements
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter describes what happens when different elements combine. The sizes of the orbitals involved and the number of valence electrons is important when considering the bonding in the elements, but when different elements combine there is the added complication that their orbital energies will be different. This leads to the possibilities of polar bonds and compounds in which electrons have essentially been transferred from one element to another, i.e. ionic compounds. Depending on the energy separation of the orbitals involved, the bonding can vary on a spectrum from purely covalent to ionic. Trying to predict the structure that a particular compound will adopt is very difficult. However, there are a few general concepts which can be applied to at least give some indication as to the likely structure. The concept of the radius ratio can help one to understand the different structures adopted by ionic solids.
What is macroevolution? What is macroecology?
Authors: Bromham Lindell , Cardillo Marcel
Published: September 2023

This chapter starts by defining macroevolution and macroecology. Macroevolution focuses on changing patterns of biological diversity across time, space, and lineages. Meanwhile, macroecology concerns broad-scale patterns in the abundance and distribution of species. Evolution and ecology are central to the study of biology, and the key to understanding the world around us. Not surprisingly, evolution and ecology are taking an increasingly prominent role in biological education. The chapter then provides a brief, selective account that highlights some key ideas relevant to contemporary research in macroevolution and macroecology. These include Jean-Baptiste Lamarck's evolutionary theory; the role of fossils in revealing the history of the living world; uniformitarianism; evolution by natural selection; and Darwinism. The chapter also considers the challenge of testing hypotheses in macroevolution. Testing claims about the natural world lies at the heart of a scientific investigation, but there are many possible ways to conduct a scientific test.
Why are there so many kinds of beetles?
Authors: Bromham Lindell , Cardillo Marcel
Published: September 2023

This chapter studies beetle diversity. Beetles are the largest order of animals on earth; their diversity eclipses other insect orders, even their nearest relatives. Why are beetles, of all groups, so diverse? Is there something about their biology or ecology that has promoted diversification, do they have a longer evolutionary history than other groups, or is the great diversity of beetles simply the outcome of random diversification processes? By investigating some of the proposed explanations for the great diversity of beetles, we can get to grips with the basic logic of setting up comparative analyses to discover why diversity is so unevenly distributed among clades. Exploring beetle diversity is also a good way to become familiar with the ways that evidence from phylogenetics, biogeography, and palaeontology can be used to describe patterns and test hypotheses for variation in diversity.
The wavefunction
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Postulate I: the wavefunction 42

Brief illustration 5.1: The wavefunction 43

Postulate II: the Born interpretation 43

Probabilities and probability densities 43

Example 5.1: Interpreting a wavefunction 44

Normalization 44

Example 5.2: Normalizing a wavefunction 45

Constraints on the...
Tunnelling
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The rectangular potential energy barrier 80

Brief illustration 10.1: Transmission probabilities for a rectangular barrier 83

The Eckart potential energy barrier 83

Brief illustration 10.2: Transmission probabilities for an Eckart barrier 84

The double-well potential 85

Brief illustration 10.3: The inversion...
Rotational motion in three dimensions
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

A particle on a sphere 111

The wavefunctions 112

Brief illustration 14.1: The angular nodes of the spherical harmonics 114

The energies 114

Example 14.1: Using the rotational energy levels 115

Angular momentum 115

The angular momentum operators 115...
Hydrogenic atomic orbitals
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Shells and subshells 160

Brief illustration 18.1: The number of orbitals in a shell 161

s Orbitals 161

Example 18.1: Calculating the mean radius of an s orbital 162

p Orbitals 163

Brief illustration 18.2: The 2px orbital 165...
Self-consistent fields
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The central challenge 238

Brief illustration 27.1: The hamiltonian 239

The Hartree–Fock formalism 239

Brief illustration 27.2: A many-electron wavefunction 240

Brief illustration 27.3: The Hartree–Fock equations 241

The Roothaan equations 242

Example 27.1: Setting up the Roothaan equations 242

Example...
The analysis of molecular shape
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Symmetry operations and symmetry elements 275

Brief illustration 31.1: Symmetry elements 276

The symmetry classification of molecules 276

Brief illustration 31.2: Symmetry classification 277

The groups C1, Ci, and Cs 278

Brief illustration 31.3: C...
Group theory
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The elements of group theory 283

Example 32.1: Showing that symmetry operations form a group 284

Brief illustration 32.1: Classes 284

Matrix representations 285

Representatives of operations 285

Brief illustration 32.2: Representatives 285

The representation of a group 285

Brief...
Electric properties of molecules
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Electric dipole moments 303

Brief illustration 34.1: Symmetry and the polarity of molecules 304

Brief illustration 34.2: Molecular dipole moments 304

Example 34.1: Calculating a molecular dipole moment 305

Polarizabilities 306

Brief illustration 34.3: The induced dipole moment 306

Checklist of concepts...
Bonding in solids
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Metallic solids 343

Close packing 343

Example 38.1: Calculating a packing fraction 344

Electronic structure of metals 345

Brief illustration 38.1: Energy levels in a band 346

Ionic solids 347

Structure 347

Brief illustration 38.2: The radius ratio 348...
Decay of excited states
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Fluorescence and phosphorescence 433

Brief illustration 46.1: Fluorescence and phosphorescence of organic molecules 435

Dissociation and predissociation 436

Brief illustration 46.2: The effect of predissociation on an electronic spectrum 436

Laser action 436

Population inversion 437

Brief illustration 46.3: Simple...
Pulse techniques in NMR
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The magnetization vector 476

The effect of the radiofrequency field 477

Brief illustration 49.1: Radiofrequency pulses 478

Time- and frequency-domain signals 478

Brief illustration 49.2: Fourier analysis 479

Spin relaxation 479

Brief illustration 49.3: Inhomogeneous broadening 481

The nuclear...
Entropy changes for specific processes
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Isothermal expansion of a perfect gas 615

Brief illustration 62.1: The entropy change accompanying expansion 616

Phase transitions 616

Brief illustration 62.2: Trouton’s rule 617

Entropy changes on heating 617

Example 62.1: Calculating an entropy change 618

Checklist of concepts 619...
Unimolecular reactions
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The Lindemann–Hinshelwood mechanism 876

Example 91.1: Analysing the Lindemann–Hinshelwood mechanism 877

The RRK model 877

Brief illustration 91.1: The RRK model 879

Checklist of concepts 880

Checklist of equations 880

Why do you need to know this material?

The analysis of...
Photochemistry
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Photochemical processes 889

Brief illustration 93.1: The nature of the excited state 890

The primary quantum yield 891

Example 93.1: Calculating a primary quantum yield 891

Mechanism of decay of excited singlet states 892

Brief illustration 93.2: The fluorescence rate constant...
Chromatography
Authors: Campbell Iain D.
Published: September 2023

Introduction

Chromatography refers to a broad range of methods that separate and analyze mixtures of molecules. The components to be separated are distributed between two phases: a stationary phase and a mobile phase which percolates through the stationary phase. Chromatography literally...
Introduction to absorption and emission spectra
Authors: Campbell Iain D.
Published: September 2023

Introduction

The development and application of spectroscopy has had an enormous influence on our understanding of the world; from microscopic atomic structure (nm) to the macroscopic (light year scale!) universe. William Wollaston discovered the existence of dark lines in the solar spectrum in 1801. A...
Electron paramagnetic resonance
Authors: Campbell Iain D.
Published: September 2023

Introduction

Electron paramagnetic resonance (EPR) was first observed by Yevgeny Zavoisky in 1944. Also known as electron spin resonance (ESR), the method detects unpaired electrons. Unpaired electrons are relatively rare in biological systems but they occur in important processes—for example, free radicals in photosynthesis. EPR...
Microscopy
Authors: Campbell Iain D.
Published: September 2023

Introduction

The main purpose of a microscope is to magnify an object and to resolve as much detail as possible in the resulting image. Magnification alone does not necessarily produce a more detailed picture as other factors are also important, such...
Electrical circuits
Authors: Campbell Iain D.
Published: September 2023

The aim of this tutorial is to introduce some basic ideas and nomenclature for electrical circuits. These concepts are helpful for understanding aspects of
Chapters 3.4
and
3.6.

Some of the nomenclature used in this field is illustrated in Figure T4A; this...
Fourier series, Fourier transforms, and convolution
Authors: Campbell Iain D.
Published: September 2023

The aim of this tutorial is to introduce some mathematical concepts that are essential for understanding many parts of this book. The Fourier transform is very important for understanding material in Sections 4, 5, 6, and 7.

In 1807, Joseph Fourier introduced the idea...
How is the Immune System Activated?
Authors: Cunningham Anne C.
Published: September 2023

This chapter discusses how the immune system is activated. The recognition of pathogens depends on receptors. Receptor binding results in signals being sent to the nucleus via the generation of second messengers which lead to new gene transcription and cellular activation. The majority of white blood cells belong to the innate immune system and they possess many receptors which can recognize elements associated with pathogens. They are pattern recognition receptors (PRRs) which bind to various pathogen-associated molecular patterns (PAMPs). Meanwhile, only lymphocytes (T and B) are responsible for adaptive immune responses and they possess only one type of receptor (either the T cell antigen receptor TCR or B cell antigen receptor BCR). TCR and BCR are randomly rearranged receptors, and each lymphocyte expresses a unique antigen receptor (with a different amino acid sequence at the antigen binding domain).
Enzymes
Authors: Cox Lynne S. , Harris David A. , Pears Catherine J.
Published: September 2023

This chapter focuses on enzymes, which are highly specific biological catalysts. Most are proteins, though some RNAs can act enzymatically. The chapter then looks at enzyme kinetics, enzyme inhibition, enzyme mechanisms, and enzyme regulation. An enzyme inhibitor is a substance that binds to an enzyme and interferes with its activity; inhibition may be reversible or irreversible. Most enzymes carry out relatively simple chemical transformations. Complex transformations involve a number of simple steps which together constitute a biochemical pathway. A subset of amino acid side chains of the enzyme frequently acts as acid/base catalysts or nucleophiles, and/or hydrogen bond to the transition state to stabilize it. Certain cofactors (such as metal ions or vitamin derivatives) confer additional chemical versatility on enzyme active sites. Finally, the chapter considers some multienzyme complexes.
Metabolism of structural components
Authors: Cox Lynne S. , Harris David A. , Pears Catherine J.
Published: September 2023

This chapter studies the metabolism of structural components, including nucleotides, structural lipids, glycoproteins, and vitamins. Nucleotides can be synthesized de novo, or via salvage pathways that recycle pre-existing components such as RNA to make new nucleotides. Dietary nucleotides are broken down and products used for energy generation, with excretion of the nitrogenous components. Structural lipids can also be broken down to generate energy, though they do not constitute major catabolites under normal conditions. Meanwhile, glycosylation occurs in the endoplasmic reticulum (ER) and in the Golgi body. Vitamins also serve various critical roles in metabolism; indeed, they are essential components of the diet. Dietary deficiency can lead to fatal disease.
Introduction to Training for High Performance
Authors: MacDougall Duncan , Sale Digby
Published: September 2023

This chapter discusses the quality of an athlete's performance as the result of a complex blend of many factors that determines the athlete's potential to excel, is his or herwith a major factor being genetic endowment. It mentions body size, cardiovascular traits, proportions of muscle-fiber types, and gross motor coordination as factors that are genetically predetermined. It also emphasizes the most important factor affecting athletic performance, which is the amount and suitability of the training that precedes the competition. The chapter defines training as the stimulation of biological adaptations that result in an improvement in performance in a given task. It focuses on determining the most effective stimulus to exploit the body's ability to adapt to potentially harmful stimuli in order to effect biological changes that will improve performance.
Neuromuscular Bases for Performance
Authors: MacDougall Duncan , Sale Digby
Published: September 2023

This chapter explains how the nervous system controls muscle contraction as reflected in the activation of motor units. It focuses on exercise-induced fatigue and its effects on neural and muscle function and considers factors such as muscle size and muscle temperature that affect strength, power, and speed performance. It also mentions the motor unit, which is the common pathway for muscle control wherein several parts of the brain and spinal reflexes control the force of muscle contraction. The chapter talks about motoneurons, which consists of a neuronal cell body situated in the ventral horn of the spinal cord or within nuclei of the brain stem. It refers to dendrites that extend from the soma and a motor axon that extends from the soma, which is part of a motor nerve serving a muscle.
Other Considerations
Authors: MacDougall Duncan , Sale Digby
Published: September 2023

This chapter looks at blood glucose, which is the primary energy source for cells in the brain and the central nervous system and the only energy source for red blood cells. It details how an hour of heavy continuous exercise training, competing in a team sport, or a 30-second sprint-training intervals can reduce muscle glycogen concentration by more than 60%. It also examines carbohydrates that are converted by digestive enzymes to the six-carbon sugar, glucose, before they enter the glycolytic pathway or be stored as glycogen. The chapter talks about nutritionists that have derived a numerical scale known as the glycemic index (GI), a numerical scale developed by nutritionists which rates various foods by how quickly and to what extent they increase blood glucose. It refers to international competitions wherein athletes must travel by air across a number of time zones to participate.
Liver
Authors: Rayner Anne , Quaglia Alberto
Published: September 2023

This chapter studies the cells and microscopic structures found within the liver. The liver is a large, solid organ situated in the upper right quadrant of the abdomen, below and partly behind the lower rib cage, separated from the thoracic cavity by the diaphragm. At the microscopical level, the liver parenchyma consists of a main epithelial cell population (hepatocytes) arranged in cords (hepatic plates) in close contact with a network of capillary-like vascular structures (sinusoids) containing a mixture of oxygenated arterial blood and venous blood carrying nutrients from the gastrointestinal tract. Other cell components include biliary epithelial cells lining the biliary tree ducts, endothelial cells lining the sinusoids, stellate cells involved in vitamin storage and fibrogenesis, and lymphocytes and macrophages providing an immunological barrier against circulating antigens. The chapter then looks at the main types of pathology affecting the liver and biliary tract.
Characterisation of inorganic compounds: example problems with multiple techniques
Authors: Weller Mark T. , Young Nigel A.
Published: September 2023

This chapter presents a series of problems, with worked answers, that exemplify the application of multiple techniques to the characterization of inorganic compounds and demonstrates how these are used to identify reaction products and unknowns. Each of the previous chapters covered a specific technique, or group of related techniques, and provided problems associated with that analytical method. Here the problems require the application of a combination of instrumental methods to elucidate the composition and structure of a compound. Indeed, the determination of the structure of a molecular, main-group compound often needs information from several techniques, such as mass spectrometry, multinuclear nuclear magnetic resonance (NMR), and infrared (IR) spectroscopy. Many of the more challenging example problems are taken from inorganic chemistry journals to show how characterization methods are employed in the research laboratory.
X-ray and photoelectron spectroscopy, electron microscopy, and energy dispersive analysis of X-rays
Authors: Weller Mark T. , Young Nigel A.
Published: September 2023

This chapter addresses X-ray and photoelectron spectroscopy, electron microscopy, and energy dispersive analysis of X-rays. Photoelectron spectroscopy (PES) employs electromagnetic radiation to excite electrons from a compound. The analysis of the kinetic energy distribution of the emitted photoelectrons provides information on the composition and electronic energy levels of the sample. The technique is often subdivided according to the energy of the exciting radiation. X-ray photoelectron spectroscopy (XPS) uses soft X-rays which excite and, therefore, provide information on core electron energy levels. Meanwhile, ultraviolet photoelectron spectroscopy (UPS) employs vacuum ultraviolet (UV) radiation which excites and allows the study of outer or valence electrons; it is mainly used to study bonding electrons in molecular compounds and the band structures of solids. The chapter also looks at electron spectroscopy for chemical analysis (ESCA), scanning electron microscopy (SEM), and transmission electron microscopy (TEM).
Pre-life and early life forms; extremophiles
Authors: Rehder Dieter
Published: September 2023

This chapter explores the chemistry that made life possible on Earth. It probes the question of how life evolved by looking at primordial scenarios for the development of the first cells and their adaptation to an alleged inhospitable environment. In doing so, the chapter tackles the Miller–Urey and Wächtershäuser scenarios. It also describes clay organisms or phyllosilicates that breathe by absorbing and releasing water. Furthermore, it looks at bacterial and archaean species, as well as some eukaryan algae that have adapted to extreme situations and are therefore referred to as extremophiles. This includes extremes in temperature, pressure, pH, salt and toxic metal concentrations, resistance towards UV and γ radiation and carbon sources.
Metal– and metalloid–carbon bonds
Authors: Rehder Dieter
Published: September 2023

This chapter discusses the role of the transition metal-carbon bond in the activation of substrates such as carbon oxide, carbon dioxide, nitrogen, methane, alkenes, and alkynes, focusing in part on selected examples of metalloenzymes. It looks at the processing of organometal and -metalloid compounds in biogeochemical cycles. The chapter also explores the special role of adenosyl- and methyl-cobalamin (vitamin B12), the latter in the frame of the broad range of physiologically important methyl transfer reactions. Furthermore, it briefly sets out the physiological implications of the selenium-carbon bond. Lastly, the chapter addresses the biogeochemical making and breaking of the metal and -metalloid carbon bond in poisoning by, and detoxification of, mercury, lead, and arsenic.
The diversity of animals and their interactions with natural environments
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter begins by setting out the scope of environmental animal physiology before discussing the range of environments and the challenges they pose for the animals that occupy them. Environmental animal psychology provides mechanistic explanations that help predict the impacts of environmental change on the most vulnerable species. Terrestrial and aquatic biomes are characterized by the abiotic conditions and the communities of organisms present. Two similar schemes are used to classify terrestrial biomes, ecoregions, and habitats based on their climate: hydric (wet), mesic (moist), and xeric (very dry); and humid, semi-humid, semi-arid, and arid. Meanwhile, aquatic habitats contain dissolved oxygen and nutrients that feed the plants and algae, which themselves provide food and oxygen for animals. The chapter then looks at how animals are related to each other, studying phylogeny, species, genus, and genetic drift, before considering animal diversity.
Water Balance of Land Animals
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter assesses the major routes for water loss from land animals and the evolutionary adaptations that limit these water losses. Evaporative water loss (EWL) is driven by the difference in partial pressures of water vapour in the solution from which evaporation occurs and in the air surrounding an animal. Burrowing reduces EWL of some animals when there is a higher water vapour pressure of air in the burrow than at the surface. Condensation of evaporative water in the cooled nasal cavities and respiratory turbinates of vertebrates retrieves water vapour from expired air, and is a well-developed adaptation of mammals living in arid environments. The chapter then looks at discontinuous ventilation and heterothermy. Animals balance water losses by acquiring preformed water in food items; generating water during metabolism; and/or water uptake from the environment.
Kidneys and excretion
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter addresses the role of kidneys for excretion of waste in animals. It begins by looking at how animals produce the primary urine by secretion or ultrafiltration. The size and electrical charge of solutes determines their ultrafiltration by the vertebrate glomerulus via an extracellular route across the capillary endothelium, basement membrane and slit diaphragms in the capillary epithelium. The chapter then looks at effective filtration pressure and colloid osmotic pressure, before considering single nephron glomerular filtration rates (SNGFRs) and glomerular filtration rate (GFR). It also studies autoregulation of kidney GFR and renal blood flows, which occurs in mammals and birds. Finally, the chapter examines kidney tubules and their functions, invertebrate nephridia, and nitrogenous excretion.
Temperature and the principles of heat exchange
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter describes the effects of temperature on biological functions to explain why all animals need to control their body temperature to a greater or lesser extent. The rate of a chemical reaction is directly proportional to the concentration of the reactant molecules and the proportionality constant is called the rate constant. As temperature rises, the rate constant increases and so the rate of reaction increases. This relationship can be represented by an Arrhenius plot. In many biological processes there is a breakpoint in an Arrhenius plot at which the rate of reaction slows as temperature continues to increase. If temperature is too high, or too low, animals die, but these lethal temperatures vary between species and between individuals of a species. The chapter then looks at processes of heat exchange and strategies of thermoregulation in animals.
Temperature regulation in ectotherms
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter explores temperature regulation in ectotherms. Almost all invertebrates, all amphibians, most fish, and most reptiles are ectotherms. Ectotherms influence their body temperatures by behavioural thermoregulation. The simplest form of behavioural thermoregulation is thermal selection according to the preferred body temperatures of aquatic animals. Meanwhile, terrestrial ectotherms adjust their rate of heat uptake and heat loss by shuttle behaviour. The chapter then looks at albedo, melanism, and thermal hysteresis. Some animals cope with cold conditions by entering a resting phase called diapause or hibernation. The chapter also considers the implications of temperature change for tissue functioning of ectotherms. According to the oxygen- and capacity-limited thermal tolerance (OCLTT) hypothesis, the capacity for oxygen uptake and transport is the major determinant of thermal tolerance of aquatic ectotherms.
The respiratory gases, gas exchange and transport
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter identifies the general characteristics of the respiratory gases and the principles underlying the processes involved in respiratory gas-exchange. When it was originally formed, about 4.5 billion years ago, the atmosphere of the Earth contained no oxygen. The subsequent changes in the concentration of oxygen in the atmosphere coincided with major changes in the evolution of organisms. The relationship between pressure, volume and temperature of gases is described by the combined gas law. Each gas in the atmosphere, including water vapour, exerts its own pressure, known as its partial pressure. The partial pressures of all the gases in the atmosphere contribute to total atmospheric pressure. The chapter then considers the transport of respiratory gases between an animal and its environment, looking at passive diffusion and forced convection.
Muscles and animal movement
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter assesses muscular systems and animal locomotion. Animal movement and behaviour in the environment is powered by the pulling force produced by contracting muscles. The contractile apparatus in all muscles consists of myofibrils made up of myosin-containing and actin-containing filaments. Contraction of voluntary muscles is under the direct control of the nervous system. The chapter then looks at excitation–contraction coupling, which refers to the sequence of events that starts with excitation at the sarcolemma and finishes with force production by the contractile apparatus. It also considers cardiac myocytes and smooth muscle fibres. Ultimately, the mechanical power generated by muscles is proportional to the muscle volume (mass) and depends on how fast muscles shorten when carrying loads.
Integration of the respiratory and circulatory systems
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter studies the integration of the respiratory and circulatory systems in animals. The activity of the respiratory pumps is produced within the central nervous system by a network of oscillating neurons: a central rhythm (pattern) generator. Meanwhile, the rhythmic activity of the circulatory pumps (hearts) is produced in most groups of animals by myogenic pacemakers. The control of the pumps and the diameters of peripheral blood vessels in many circulatory systems rely on sensory information from chemoreceptors and mechanoreceptors. The chapter then looks at the generation of respiratory rhythm and control of the respiratory system, before considering the generation of the cardiac rhythm and control of the cardiovascular system. It also examines the location of terminations of the respiratory and cardiovascular sense organs in the central nervous system.
Complement
Authors: Hall Angela , Scott Chris , Buckland Matthew
Published: September 2023

This chapter discusses the concept of complement, which is a vital part of the immune system. It lists ways to initiate complement activation: classical, lectin, and alternative pathways. The chapter notes the results of complement activation such as opsonization of targets, clearance of antigen-antibody complexes, inflammation, phagocyte recruitment, and formation of the membrane attack complex which can result in cell lysis. It adds how the deficiency in complement components might lead to infection susceptibility such as hereditary angioedema. The chapter explains the concentration of complement components and their functions, and shows how these could be assessed through laboratory tests. Moreover, it recognizes that most complement components, receptors, and regulators are polymorphic, some of which have several different allotypes.
Autoimmune rheumatological disease
Authors: Hall Angela , Scott Chris , Buckland Matthew
Published: September 2023

This chapter looks into rheumatic diseases. It looks at systemic lupus erythematosus (SLE) which is a multisystem disease affecting various organs in the body. The chapter recognizes that auto-antibodies are useful tools in the diagnosis and management of autoimmune rheumatic diseases. It presents the American College of Rheumatology's eleven diagnostic criteria. The chapter clarifies that the SLE's aetiology and auto-antibodies' role in pathogenesis remains unclear. In addition, it explores the antibodies in SLE, rheumatoid arthritis, scleroderma, Sjogren's syndrome, antiphospholid syndrome, polymyositis, and dermatomyositis. The chapter discusses auto-antibodies and anti-nuclear antibodies as well.
Autoimmune liver diseases
Authors: Hall Angela , Scott Chris , Buckland Matthew
Published: September 2023

This chapter focuses on autoimmune liver diseases like autoimmune hepatitis (AIH), autoimmune sclerosing cholangitis (ASC), and primary biliary cirrhosis (PBC). Then, it looks at AIH, ASC, and PBC. It explains incidence, serology, and histopathology. The chapter also looks into the anti-smooth muscle antibody (SMA), anti-nuclear antibodies (ANA), anti-liver kidney microsomal antibody (LKM), anti-liver cytosol (LC 1), anti-soluble liver antigen (SLA). In addition, it explains that ASC has a disease characterized by inflammation of intra- and extrahepatic bile duct and hepatitis. PBC is the result of the destruction of the small intrahepatic bile ducts' epithelia. The chapter notes immunosuppression as a major therapeutic action. However, a therapeutic modality is required to manage bile acids when the biliary tree is involved.
Human immunodeficiency virus (HIV)
Authors: Hall Angela , Scott Chris , Buckland Matthew
Published: September 2023

This chapter examines the human immunodeficiency virus (HIV). It recognizes HIV-1 as the most common cause of immunodeficiency. This remains a major problem in the world. The chapter highlights HIV's lack of cure, but it continues to be slow growing with the help of antiretroviral therapy. It notes HIV diagnosis depends on the detection of antibodies and/or viral proteins which is usually conducted with enzyme-linked immunosorbent assay (ELISA). In addition, the chapter explains how the prognosis is worse for people with high viral loads and CD4 counts. It points out that failure to control the adverse immune system effects may suggest failed treatment or poor patient compliance.
Pathways are the key to signalling
Authors: Hancock John T.
Published: September 2023

This chapter highlights how signalling components are grouped together in pathways. It looks at the barriers to be crossed and distances to be travelled in situations where signalling is required. The chapter contends that the relay of the message in biological signalling usually involves many components and many mechanisms, which is illustrated by some simple examples. Clearly, there are many other examples that could have been used, but these well-characterized examples have been chosen because they illustrate pertinent points that can be used to understand more complicated pathways. Finally, the chapter considers computer modelling and a systems biology approach in terms of the complexity of pathways in the future.
Protein phosphorylation, kinases and phosphatases
Authors: Hancock John T.
Published: September 2023

This chapter addresses the mechanisms used to carry out protein alteration. Signalling, as the chapter argues, often involves the alteration of the activity of a protein, seen as either an increase or a decrease. Such alterations of a protein's function are often, although not always, brought about by the addition or removal of a phosphate group: phosphorylation and dephosphorylation. The chapter emphasizes that phosphorylation is a central and extremely important theme of cell signalling. It mentions that phosphorylation is not restricted to proteins and their modifications. Many other compounds can be phosphorylated too. The chapter then looks at other major classes of kinases: serine/threonine kinases, tyrosine kinases, and mitogen-activated protein kinases. The chapter considers ‘protein kinases’ and ‘protein phosphatases’ before exploring how proteins undergo covalent modifications—noting the ubiquitin–proteasome system.
Cyclic nucleotides, cyclases and G proteins
Authors: Hancock John T.
Published: September 2023

This chapter demonstrates the alteration of a class of molecules called cyclic nucleotides. Cyclic nucleotides, in particular cAMP and cGMP, are central signalling molecules in many transduction pathways. The chapter emphasizes that alteration of the concentration of other molecules is one of the most common ways for the signal to be propagated in a cell. It then explores the mechanisms involved in control of the cyclic nucleotides production. The chapter also investigates how cAMP is produced from ATP by enzymes known as adenylyl cyclases. It defines adenylyl cyclase as a single polypeptide integral to the plasma membrane before discussing its interaction with heterotrimeric G proteins, particularly Gs and Gi, which are stimulatory and inhibitory, respectively. Towards the end, the chapter considers guanylyl cyclase and its two forms: one soluble and one membrane bound. It also looks at cyclic nucleotide signalling and the functions of monomeric G proteins.
Inositol phosphate metabolism and roles of membrane lipids
Authors: Hancock John T.
Published: September 2023

This chapter describes the breakdown of lipids in the plasma membrane and the subsequent formation of messenger molecules that can transmit the signal(s) into the cell. It looks at the importance of the formation of new phosphorylated inositol lipids by phosphatidylinositol 3-kinase in many transduction events. The chapter also examines the inositol phosphates and highlights the inositol trisphosphate (InsP3) which may be the precursor of both higher and lower inositol phosphates, that is, it can be phosphorylated or dephosphorylated to create new metabolites, each of which may have a signalling role within the cell. Finally, the chapter analyses the role of diacylglycerol. Diacylglycerol (DAG) is known to act as an activator of protein kinase C. The chapter also reviews other lipid metabolism and several inositol phosphates which are thought to have defined signalling functions.
Intracellular calcium ions: control of their concentrations and roles in signalling
Authors: Hancock John T.
Published: September 2023

This chapter explicates other mechanisms involved in the movement of calcium ions. It stresses that the calcium ions themselves control a myriad of functions in cells and that their action is often mediated by a protein known as calmodulin. The chapter argues that the movement of calcium ions is central to cell signalling events. The chapter then shifts to a discussion of the plasma membrane and its role in calcium ion concentration maintenance. It also considers the presence of oscillations and waves moving through cells. Next, the chapter looks at one of the main active second messengers, sphingosine-1-phosphate (S1P), and investigates other small signalling molecules which can be used by cells to mobilize calcium ions to increase intracellular calcium: cyclic ADP-ribose (cADPr), and examines the nicotinate adenine-dinucleotide phosphate (NAADP+), a deaminated derivative of NADP+.
Life, death and apoptosis
Authors: Hancock John T.
Published: September 2023

This chapter gives a brief insight into some of the signalling mechanisms involved in the process of apoptosis. It explicates the process called programmed cell death (PCD), often referred to as apoptosis, which leads to the death of the cell. The processes are initiated with the recognition of extracellular signals or intracellular damage, which leads to cascades of events involving specific interactions and results in a response, in this case the death of the cell involved. The chapter highlights that it is not only the survival, adaptation, and normal functioning of the cell that are under the control of cell signalling events, but also that, ultimately, death of the cell may be brought about by cell signalling cascades. Lastly, the chapter considers the two signalling pathways leading to apoptosis—the intrinsic and extrinsic pathways—and investigates the role of caspases during apoptosis.
Cell signalling: importance, complexity and the future
Authors: Hancock John T.
Published: September 2023

This chapter recalls the mechanisms used by cells to control their activities. It introduces many recurring themes in cell signalling, showing that there is a steady state condition of signalling components. The chapter argues that the most important aspects of cell signalling are that there needs to be a change and that this change needs to be recognized to elicit a response. The chapter also looks at the uniqueness of the signals used and the specific perception of the signals. The chapter considers moonlighting proteins, drug discovery, and cell signalling manipulation. Finally, it examines the future of cell signalling research.
Introduction
Authors: Kay Ian , Evans Gethin
Published: September 2023

This chapter considers underlying molecular and cellular elements and the link between structure and function in physiology to provide an understanding of the structures within the body. It discusses the body in terms of the hierarchical nature of organization from the molecular level through to the organismal level. It also highlights the elemental composition of the vast majority of the body which is formed from carbon, oxygen, hydrogen, oxygenydrogen, carbon, and nitrogen. The chapter analyzes an individual's body weight in terms of body composition, which is accounted for by water and is found in a variety of compartments. Given that water accounts for most of an individual’s body weight, the chapter looks in depth at the forms this water takes. It explains that the water within the body has a variety of solutes dissolved in it that. These form extracellular fluid and intracellular fluid, each of which has a unique composition.
The nervous system
Authors: Kay Ian , Evans Gethin
Published: September 2023

This chapter talks about the fundamental role of the nervous system, which is control and coordination. It describes neurons as the functional elements of the nervous system. Neurons are supported by a second group of cells called glial cells, whose role purpose is to support neurons and ensure that they function effectively. It also reviews neural control. This is characterized by its electrical mediation, its rapidity, and its duration of response. The chapter discusses neurons as being characterized by a large resting membrane potential, the polarity of which is reversed during an action potential. It demonstrates how neurons communicate with each other by the release of chemical compounds called neurotransmitters.
Gastrointestinal physiology
Authors: Kay Ian , Evans Gethin
Published: September 2023

This chapter highlights reproduction, which is the process of producing offspring from parents wherein the genetic material from each of the parents is transmitted to the offspring. It refers to genetic fusion that occurs when a male sperm cell fertilizes a female ovum or egg cell. It also details how the fertilized egg undergoes a series of phenomenal changes over the nine months following fertilization. This results in the birth of an offspring. The chapter describes the male gamete formation as a continuous process, while a female gamete production is a cyclical process and only occurs for about 30 to 35 years in females. It covers fertilization, which completes the meiotic division of ova and results in the formation of a zygote, ultimately dividing and growing to produce a fetus.
Organometallic Compounds of Main Group Elements
Authors: Bochmann Manfred
Published: September 2023

This chapter discusses the main group of organometallic compounds which contain metal–carbon σ-bonds generated by orbital overlap along the M–C axis. It reviews the possibility of interaction of the metal with the π-electron systems of unsaturated organic compounds, in particular, when the unsaturated moiety carries a negative charge. The chapter also looks at one important aspect that governs the reactivity of organometallic species: the polarity of the Mδ+ Cδ-bond. It explicates the nature of bond polarity, then studies the concept of electronegativity and ‘group electronegativity’. Towards the end, the chapter turns to the reactivity of main group metal alkyls. It also considers ionic organometallics and lithium ions.